A detailed kinetic mechanism including methanol and nitrogen pollutants relevant to the gas-phase combustion and pyrolysis of biomass-derived fuels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coda Zabetta, Edgardo; Hupa, Mikko

2008-01-15

A detailed chemical kinetic mechanism for the simulation of the gas-phase combustion and pyrolysis of biomass-derived fuels was compiled by assembling selected reaction subsets from existing mechanisms (parents). The mechanism, here referred to as ''AaA,'' includes reaction subsets for the oxidation of hydrogen (H{sub 2}), carbon monoxide (CO), light hydrocarbons (C{sub 1} and C{sub 2}), and methanol (CH{sub 3}OH). The mechanism also takes into account reaction subsets of nitrogen pollutants, including the reactions relevant to staged combustion, reburning, and selective noncatalytic reduction (SNCR). The AaA mechanism was validated against suitable experimental data from the literature. Overall, the AaA mechanism gavemore » more accurate predictions than three other mechanisms of reference, although the reference mechanisms performed better occasionally. The predictions from AaA were also found to be consistent with the predictions of its parent mechanisms within most of their range of validity, thus transferring the validity of the parents to the inheriting mechanism (AaA). In parametric studies the AaA mechanism predicted that the effect of methanol on combustion and pollutants is often similar to that of light hydrocarbons, but it also showed that there are important exceptions, thus suggesting that methanol should be taken into account when simulating biomass combustion. To our knowledge, the AaA mechanism is currently the only mechanism that accounts for the chemistry of methanol and nitrogen relevant to the gas-phase combustion and pyrolysis of biomass-derived fuels. (author)« less

Chemical kinetic modeling of propene oxidation at low and intermediate temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilk, R.D.; Cernansky, N.P.; Pitz, W.J.

1986-01-13

A detailed chemical kinetic mechanism for propene oxidation is developed and used to model reactions in a static reactor at temperatures of 590 to 740/sup 0/K, equivalence ratios of 0.8 to 2.0, and a pressure of 600 torr. Modeling of hydrocarbon oxidation in this temperature range is important for the validation of detailed models to be used for performing calculations related to automotive engine knock. The model predicted induction periods and species concentrations for all the species measured experimentally in a static reactor by Wilk, Cernansky, and Cohen. The detailed model predicted a temperature region of approximately constant induction periodmore » which corresponded very closely to the region of negative temperature coefficient behavior found in the experiment. Overall, the calculated concentrations of acetaldehyde, ethene, and methane were somewhat low compared to the experimental measurements, and the calculated concentrations of formaldehyde and methanol were high. The characteristic s-shape of the fuel concentration history was well predicted. The importance of OH+C/sub 3/H/sub 6/ and related rections in determining product distributions and the importance of consumption reactions for allyl radicals was demonstrated by the modeling calculations. 18 refs., 4 figs., 1 tab.« less

CFD analysis of municipal solid waste combustion using detailed chemical kinetic modelling.

PubMed

Frank, Alex; Castaldi, Marco J

2014-08-01

Nitrogen oxides (NO x ) emissions from the combustion of municipal solid waste (MSW) in waste-to-energy (WtE) facilities are receiving renewed attention to reduce their output further. While NO x emissions are currently 60% below allowed limits, further reductions will decrease the air pollution control (APC) system burden and reduce consumption of NH3. This work combines the incorporation of the GRI 3.0 mechanism as a detailed chemical kinetic model (DCKM) into a custom three-dimensional (3D) computational fluid dynamics (CFD) model fully to understand the NO x chemistry in the above-bed burnout zones. Specifically, thermal, prompt and fuel NO formation mechanisms were evaluated for the system and a parametric study was utilized to determine the effect of varying fuel nitrogen conversion intermediates between HCN, NH3 and NO directly. Simulation results indicate that the fuel nitrogen mechanism accounts for 92% of the total NO produced in the system with thermal and prompt mechanisms accounting for the remaining 8%. Results also show a 5% variation in final NO concentration between HCN and NH3 inlet conditions, demonstrating that the fuel nitrogen intermediate assumed is not significant. Furthermore, the conversion ratio of fuel nitrogen to NO was 0.33, revealing that the majority of fuel nitrogen forms N2. © The Author(s) 2014.

Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.

PubMed

Kooshkbaghi, Mahdi; Frouzakis, Christos E; Boulouchos, Konstantinos; Karlin, Iliya V

2016-05-26

The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique for chemical kinetics based on entropy maximization under constraints built by the slowest eigenvectors at equilibrium. The method is revisited here and discussed and validated through the Michaelis-Menten kinetic scheme, and the quality of the reduction is related to the temporal evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mechanisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air in adiabatic constant pressure reactors. The system states computed using SQEM are compared with those obtained by direct integration of the detailed mechanism, and good agreement between the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is found to provide a more accurate description.

Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models

PubMed Central

Battin-Leclerc, Frédérique; Blurock, Edward; Bounaceur, Roda; Fournet, René; Glaude, Pierre-Alexandre; Herbinet, Olivier; Sirjean, Baptiste; Warth, V.

2013-01-01

In the context of limiting the environmental impact of transportation, this paper reviews new directions which are being followed in the development of more predictive and more accurate detailed chemical kinetic models for the combustion of fuels. In the first part, the performance of current models, especially in terms of the prediction of pollutant formation, is evaluated. In the next parts, recent methods and ways to improve these models are described. An emphasis is given on the development of detailed models based on elementary reactions, on the production of the related thermochemical and kinetic parameters, and on the experimental techniques available to produce the data necessary to evaluate model predictions under well defined conditions. PMID:21597604

Detailed and reduced chemical-kinetic descriptions for hydrocarbon combustion

NASA Astrophysics Data System (ADS)

Petrova, Maria V.

Numerical and theoretical studies of autoignition processes of fuels such as propane are in need of realistic simplified chemical-kinetic descriptions that retain the essential features of the detailed descriptions. These descriptions should be computationally feasible and cost-effective. Such descriptions are useful for investigating ignition processes that occur, for example, in homogeneous-charge compression-ignition engines, for studying the structures and dynamics of detonations and in fields such as multi-dimensional Computational Fluid Dynamics (CFD). Reduced chemistry has previously been developed successfully for a number of other hydrocarbon fuels, however, propane has not been considered in this manner. This work focuses on the fuels of propane, as well propene, allene and propyne, for several reasons. The ignition properties of propane resemble those of other higher hydrocarbons but are different from those of the lower hydrocarbons (e.g. ethylene and acetylene). Propane, therefore, may be the smallest hydrocarbon that is representative of higher hydrocarbons in ignition and detonation processes. Since the overall activation energy and ignition times for propane are similar to those of other higher hydrocarbons, including liquid fuels that are suitable for many applications, propane has been used as a model fuel for several numerical and experimental studies. The reason for studying elementary chemistry of propene and C3H4 (allene or propyne) is that during the combustion process, propane breaks down to propene and C3H4 before proceeding to products. Similarly, propene combustion includes C3H4 chemistry. In studying propane combustion, it is therefore necessary to understand the underlying combustion chemistry of propene as well as C3H 4. The first part of this thesis focuses on obtaining and testing a detailed chemical-kinetic description for autoignition of propane, propene and C 3H4, by comparing predictions obtained with this detailed mechanism against numerous experimental data available from shock-tube studies and flame-speed measurements. To keep the detailed mechanism small, attention is restricted to pressures below about 100 atm, temperatures above about 1000 K and equivalence ratios less than about 3. Based on this detailed chemistry description, short (or skeletal) mechanisms are then obtained for each of the three fuels by eliminating reactions that are unimportant for the autoignition process under conditions presented above. This was achieved by utilizing tools such as sensitivity and reaction pathway analyses. Two distinct methodologies were then used in order to obtain a reduced mechanism for autoignition from the short mechanisms. A Systematic Reduction approach is first taken that involves introducing steady-state approximations to as many species as analytically possible. To avoid resorting to numerical methods, the analysis for obtaining ignition times for heptane, presented by Peters and co-workers is followed in order to obtain a rough estimate for an expression of propane ignition time. The results from this expression are then compared to the ignition times obtained computationally with the detailed mechanism. The second method is an Empirical Approach in which chemistry is not derived formally, but rather postulated empirically on the basis of experimental, computational and theoretical observations. As a result, generalized reduced mechanisms are proposed for autoignition of propane, propene and C3H 4. Expressions for ignition times obtained via this empirical approach are compared to the computational results obtained from the detailed mechanism.

Solid State Kinetic Parameters and Chemical Mechanism of the Dehydration of CoCl2.6H2O.

ERIC Educational Resources Information Center

Ribas, Joan; And Others

1988-01-01

Presents an experimental example illustrating the most common methods for the determination of kinetic parameters. Discusses the different theories and equations to be applied and the mechanism derived from the kinetic results. (CW)

Atom-efficient regioselective 1,2-dearomatization of functionalized pyridines by an earth-abundant organolanthanide catalyst

NASA Astrophysics Data System (ADS)

Dudnik, Alexander S.; Weidner, Victoria L.; Motta, Alessandro; Delferro, Massimiliano; Marks, Tobin J.

2014-12-01

Developing earth-abundant, non-platinum metal catalysts for high-value chemical transformations is a critical challenge to contemporary chemical synthesis. Dearomatization of pyridine derivatives is an important transformation to access a wide range of valuable nitrogenous natural products, pharmaceuticals and materials. Here, we report an efficient 1,2-regioselective organolanthanide-catalysed pyridine dearomatization process using pinacolborane, which is compatible with a broad range of pyridines and functional groups and employs equimolar reagent stoichiometry. Regarding the mechanism, derivation of the rate law from NMR spectroscopic and kinetic measurements suggests first order in catalyst concentration, fractional order in pyridine concentration and inverse first order in pinacolborane concentration, with C=N insertion into the La-H bond as turnover-determining. An energetic span analysis affords a more detailed understanding of experimental activity trends and the unusual kinetic behaviour, and proposes the catalyst ‘resting’ state and potential deactivation pathways.

Development of Comprehensive Reduced Kinetic Models for Supersonic Reacting Shear Layer Simulations

NASA Technical Reports Server (NTRS)

Zambon, A. C.; Chelliah, H. K.; Drummond, J. P.

2006-01-01

Large-scale simulations of multi-dimensional unsteady turbulent reacting flows with detailed chemistry and transport can be computationally extremely intensive even on distributed computing architectures. With the development of suitable reduced chemical kinetic models, the number of scalar variables to be integrated can be decreased, leading to a significant reduction in the computational time required for the simulation with limited loss of accuracy in the results. A general MATLAB-based automated mechanism reduction procedure is presented to reduce any complex starting mechanism (detailed or skeletal) with minimal human intervention. Based on the application of the quasi steady-state (QSS) approximation for certain chemical species and on the elimination of the fast reaction rates in the mechanism, several comprehensive reduced models, capable of handling different fuels such as C2H4, CH4 and H2, have been developed and thoroughly tested for several combustion problems (ignition, propagation and extinction) and physical conditions (reactant compositions, temperatures, and pressures). A key feature of the present reduction procedure is the explicit solution of the concentrations of the QSS species, needed for the evaluation of the elementary reaction rates. In contrast, previous approaches relied on an implicit solution due to the strong coupling between QSS species, requiring computationally expensive inner iterations. A novel algorithm, based on the definition of a QSS species coupling matrix, is presented to (i) introduce appropriate truncations to the QSS algebraic relations and (ii) identify the optimal sequence for the explicit solution of the concentration of the QSS species. With the automatic generation of the relevant source code, the resulting reduced models can be readily implemented into numerical codes.

Interactions of Hydrazine and Blowby Gases

NASA Technical Reports Server (NTRS)

Meagher, Nancy E.

2003-01-01

The interactions between hydrazine and blowby gases from pyrovalves was explored in this research project. Investigating the decomposition chemistry of hydrazine through detailed chemical kinetic modeling is a project started last summer while participating in the Summer Faculty Fellowship program. During the 1999-2000 academic year, the chemical kinetic mechanism for hydrazine decomposition developed while a SFF at NASA's White Sands Test Facility was further revised and validated against the limited experimental data in the literature. This mechanism was then used in assessing the effects of blowby gas species on hydrazine decomposition. The combustion products introduced into the fuel line by pyrovalve actuation consist primarily of hydrogen gas. Hydrogen is also a product of the decomposition of hydrazine. Additional gaseous chemical species are introduced into the fuel, as well as metals and metal salts that deposit onto the walls of the fuel line. The deposition process is undoubtedly very rapid, and exothermic. Therefore, the major focus of this summer's work was examining the effects of hydrogen presence on hydrazine decomposition, with some representative calculations including the remaining gaseous species found to exist in blowby gases. Since hydrogen is a product of hydrazine decomposition, all reactions necessary to evaluate its effect on hydrazine decomposition chemistry were in the original mechanism developed. However, the mechanism needed to be considerably expanded to include the reactions of the other gaseous blowby species with hydrazine, all the intermediate species formed in its decomposition, and each other. The expanded mechanism consists of 70 species interacting via a network of 452 reactions. Calculations with molecular hydrogen introduced into hydrazine gas in an inert bath gas indicate that H2 presence as an initial reactant in substantial amounts can dramatically impact the decomposition process for hydrazine. The other gaseous blowby species (CO, CO2, H2O, CH4, O2, and N2) were found to have little effect compared to the inclusion of hydrogen itself as an initial reagent. This result is undoubtedly due, in part, to the fact that the blowby gas used in these calculations consisted of 94.6% H2. A more rigorous examination of the behavior of the full detailed mechanism under a variety of conditions was not performed.

Experimental and computational study of methane counterflow diffusion flames perturbed by trace amounts of either jet fuel or a 6-component surrogate under non-sooting conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bufferand, H.; Tosatto, L.; La Mantia, B.

2009-08-15

The chemical structure of a methane counterflow diffusion flame and of the same flame doped with 1000 ppm (molar) of either jet fuel or a 6-component jet fuel surrogate was analyzed experimentally, by gas sampling via quartz microprobes and subsequent GC/MS analysis, and computationally using a semi-detailed kinetic mechanism for the surrogate blend. Conditions were chosen to ensure that all three flames were non-sooting, with identical temperature profiles and stoichiometric mixture fraction, through a judicious selection of feed stream composition and strain rate. The experimental dataset provides a glimpse of the pyrolysis and oxidation behavior of jet fuel in amore » diffusion flame. The jet fuel initial oxidation is consistent with anticipated chemical kinetic behavior, based on thermal decomposition of large alkanes to smaller and smaller fragments and the survival of ring-stabilized aromatics at higher temperatures. The 6-component surrogate captures the same trend correctly, but the agreement is not quantitative with respect to some of the aromatics such as benzene and toluene. Various alkanes, alkenes and aromatics among the jet fuel components are either only qualitatively characterized or could not be identified, because of the presence of many isomers and overlapping spectra in the chromatogram, leaving 80% of the carbon from the jet fuel unaccounted for in the early pyrolysis history of the parent fuel. Computationally, the one-dimensional code adopted a semi-detailed kinetic mechanism for the surrogate blend that is based on an existing hierarchically constructed kinetic model for alkanes and simple aromatics, extended to account for the presence of tetralin and methylcyclohexane as reference fuels. The computational results are in reasonably good agreement with the experimental ones for the surrogate behavior, with the greatest discrepancy in the concentrations of aromatics and ethylene. (author)« less

Mechanism of Phosphine Dissociation on the Si(001) Surface

NASA Astrophysics Data System (ADS)

Warschkow, Oliver; Schofield, Steven R.; Smith, Phil V.

2005-03-01

The continued down-scaling of electronic devices to the atomic scale increasingly requires an atomic-level understanding of the elementary processes of semiconductor doping. We present a combined experimental and theoretical investigation into the dissociation mechanism of phosphine (PH3) on the Si(001) surface. As reported by us elsewhere in this conference, a number of prominent intermediate species of PH3 dissociation observed in STM experiments have been structurally characterized as PH2+H, PH+2H and P+3H species respectively. In this poster we present detailed quantum chemical calculations of these and other short-lived intermediates as well as the transition (kinetic) barriers between them. This leads us to formulate a step-by-step mechanism for the complete dissociation of PH3 on the Si(001) surface.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D.

Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamicmore » computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.« less

First-principles chemical kinetic modeling of methyl trans-3-hexenoate epoxidation by HO 2

DOE PAGES

Cagnina, S.; Nicolle, Andre; de Bruin, T.; ...

2017-02-16

The design of innovative combustion processes relies on a comprehensive understanding of biodiesel oxidation kinetics. The present study aims at unraveling the reaction mechanism involved in the epoxidation of a realistic biodiesel surrogate, methyl trans-3-hexenoate, by hydroperoxy radicals using a bottom-up theoretical kinetics methodology. The obtained rate constants are in good agreement with experimental data for alkene epoxidation by HO 2. The impact of temperature and pressure on epoxidation pathways involving H-bonded and non-H-bonded conformers was assessed. As a result, the obtained rate constant was finally implemented into a state-of-the-art detailed combustion mechanism, resulting in fairly good agreement with enginemore » experiments.« less

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

PubMed

Harris, Michael E; Piccirilli, Joseph A; York, Darrin M

2015-11-01

The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

CLEPS 1.0: A new protocol for cloud aqueous phase oxidation of VOC mechanisms

NASA Astrophysics Data System (ADS)

Mouchel-Vallon, Camille; Deguillaume, Laurent; Monod, Anne; Perroux, Hélène; Rose, Clémence; Ghigo, Giovanni; Long, Yoann; Leriche, Maud; Aumont, Bernard; Patryl, Luc; Armand, Patrick; Chaumerliac, Nadine

2017-03-01

A new detailed aqueous phase mechanism named the Cloud Explicit Physico-chemical Scheme (CLEPS 1.0) is proposed to describe the oxidation of water soluble organic compounds resulting from isoprene oxidation. It is based on structure activity relationships (SARs) which provide global rate constants together with branching ratios for HOṡ abstraction and addition on atmospheric organic compounds. The GROMHE SAR allows the evaluation of Henry's law constants for undocumented organic compounds. This new aqueous phase mechanism is coupled with the MCM v3.3.1 gas phase mechanism through a mass transfer scheme between gas phase and aqueous phase. The resulting multiphase mechanism has then been implemented in a model based on the Dynamically Simple Model for Atmospheric Chemical Complexity (DSMACC) using the Kinetic PreProcessor (KPP) that can serve to analyze data from cloud chamber experiments and field campaigns. The simulation of permanent cloud under low-NOx conditions describes the formation of oxidized monoacids and diacids in the aqueous phase as well as a significant influence on the gas phase chemistry and composition and shows that the aqueous phase reactivity leads to an efficient fragmentation and functionalization of organic compounds.

KINETIC MODELING OF COUNTERFLOW DIFFUSION FLAMES OF BUTADIENE. (R828193)

EPA Science Inventory

A comprehensive, semi-detailed kinetic scheme was used to simulate the chemical structures of counterflow diffusion and fuel-rich premixed 1,3-butadiene flames, to better understand the formation of polycyclic aromatic hydrocarbons (PAH). The results showed that model predicti...

Aromatic ring generation as a dust precursor in acetylene discharges

NASA Astrophysics Data System (ADS)

De Bleecker, Kathleen; Bogaerts, Annemie; Goedheer, Wim

2006-04-01

Production of aromatic hydrocarbon compounds as an intermediate step for particle formation in low-pressure acetylene discharges is investigated via a kinetic approach. The detailed chemical reaction mechanism contains 140 reactions among 55 species. The cyclic hydrocarbon chemistry is mainly based on studies of polycyclic aromatic hydrocarbon formation in cosmic environments. The model explicitly includes organic chain, cyclic molecules, radicals, and ions up to a size of 12 carbon atoms. The calculated density profiles show that the aromatic formation yields are quite significant, suggesting that aromatic compounds play a role in the underlying mechanisms of particle formation in hydrocarbon plasmas.

High temperature chemical kinetic study of the H2-CO-CO2-NO reaction system

NASA Technical Reports Server (NTRS)

Jachimowski, C. J.

1975-01-01

An experimental study of the kinetics of the H2-CO-CO2-NO reaction system was made behind incident shock waves at temperatures of 2460 and 2950 K. The overall rate of the reaction was measured by monitoring radiation from the CO + O yields CO2 + h upoilon reaction. Correlation of these data with a detailed reaction mechanism showed that the high-temperature rate of the reaction N + OH yields NO + H can be described by the low-temperature (320 K) rate coefficient. Catalytic dissociation of molecular hydrogen was an important reaction under the tests conditions.

How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome

PubMed Central

Noel, Jeffrey K.; Whitford, Paul C.

2016-01-01

It has long been recognized that the thermodynamics of mRNA–tRNA base pairing is insufficient to explain the high fidelity and efficiency of aminoacyl-tRNA (aa-tRNA) selection by the ribosome. To rationalize this apparent inconsistency, Hopfield proposed that the ribosome may improve accuracy by utilizing a multi-step kinetic proofreading mechanism. While biochemical, structural and single-molecule studies have provided a detailed characterization of aa-tRNA selection, there is a limited understanding of how the physical–chemical properties of the ribosome enable proofreading. To this end, we probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading. PMID:27796304

Physical and Chemical Processes in Flames

DTIC Science & Technology

2010-02-15

Results: Use of comprehensively validated reduced chemical kinetic mechanism allows realistic description of methane oxidation chemistry with NOx ...PERFORMING ORGANIZATION REPORT NUMBER Department of Mechanical and Aerospace Engineering Princeton University Princeton, NJ 08544... mechanism reduction; skeletal mechanism ; CO/H2 oxidation; ethylene oxidation; heptane oxidation; directed relation graph; high-pressure combustion

Development of a detailed chemical mechanism (MCMv3.1) for the atmospheric oxidation of aromatic hydrocarbons

NASA Astrophysics Data System (ADS)

Bloss, C.; Wagner, V.; Jenkin, M. E.; Volkamer, R.; Bloss, W. J.; Lee, J. D.; Heard, D. E.; Wirtz, K.; Martin-Reviejo, M.; Rea, G.; Wenger, J. C.; Pilling, M. J.

2005-03-01

The Master Chemical Mechanism has been updated from MCMv3 to MCMv3.1 in order to take into account recent improvements in the understanding of aromatic photo-oxidation. Newly available kinetic and product data from the literature have been incorporated into the mechanism. In particular, the degradation mechanisms for hydroxyarenes have been revised following the observation of high yields of ring-retained products, and product studies of aromatic oxidation under relatively low NOx conditions have provided new information on the branching ratios to first generation products. Experiments have been carried out at the European Photoreactor (EUPHORE) to investigate key subsets of the toluene system. These results have been used to test our understanding of toluene oxidation, and, where possible, refine the degradation mechanisms. The evaluation of MCMv3 and MCMv3.1 using data on benzene, toluene, p-xylene and 1,3,5-trimethylbenzene photosmog systems is described in a companion paper, and significant model shortcomings are identified. Ideas for additional modifications to the mechanisms, and for future experiments to further our knowledge of the details of aromatic photo-oxidation are discussed.

The role of cool-flame chemistry in quasi-steady combustion and extinction of n-heptane droplets

NASA Astrophysics Data System (ADS)

Paczko, Guenter; Peters, Norbert; Seshadri, Kalyanasundaram; Williams, Forman Arthur

2014-09-01

Experiments on the combustion of large n-heptane droplets, performed by the National Aeronautics and Space Administration in the International Space Station, revealed a second stage of continued quasi-steady burning, supported by low-temperature chemistry, that follows radiative extinction of the first stage of burning, which is supported by normal hot-flame chemistry. The second stage of combustion experienced diffusive extinction, after which a large vapour cloud was observed to form around the droplet. In the present work, a 770-step reduced chemical-kinetic mechanism and a new 62-step skeletal chemical-kinetic mechanism, developed as an extension of an earlier 56-step mechanism, are employed to calculate the droplet burning rates, flame structures, and extinction diameters for this cool-flame regime. The calculations are performed for quasi-steady burning with the mixture fraction as the independent variable, which is then related to the physical variables of droplet combustion. The predictions with the new mechanism, which agree well with measured autoignition times, reveal that, in decreasing order of abundance, H2O, CO, H2O2, CH2O, and C2H4 are the principal reaction products during the low-temperature stage and that, during this stage, there is substantial leakage of n-heptane and O2 through the flame, and very little production of CO2 with no soot in the mechanism. The fuel leakage has been suggested to be the source of the observed vapour cloud that forms after flame extinction. While the new skeletal chemical-kinetic mechanism facilitates understanding of the chemical kinetics and predicts ignition times well, its predicted droplet diameters at extinction are appreciably larger than observed experimentally, but predictions with the 770-step reduced chemical-kinetic mechanism are in reasonably good agreement with experiment. The computations show how the key ketohydroperoxide compounds control the diffusion-flame structure and its extinction.

Development of a detailed chemical mechanism (MCMv3.1) for the atmospheric oxidation of aromatic hydrocarbons

NASA Astrophysics Data System (ADS)

Bloss, C.; Wagner, V.; Jenkin, M. E.; Volkamer, R.; Bloss, W. J.; Lee, J. D.; Heard, D. E.; Wirtz, K.; Martin-Reviejo, M.; Rea, G.; Wenger, J. C.; Pilling, M. J.

2004-09-01

The Master Chemical Mechanism has been updated from MCMv3 to MCMv3.1 in order to take into account recent improvements in the understanding of aromatic photo-oxidation. Newly available kinetic and product data from the literature has been incorporated into the mechanism. In particular, the degradation mechanisms for hydroxyarenes have been revised following the observation of high yields of ring-retained products, and product studies of aromatic oxidation under relatively low NOx conditions have provided new information on the branching ratios to first generation products. Experiments have been carried out at the European Photoreactor (EUPHORE) to investigate key subsets of the toluene system. These results have been used to test our understanding of toluene oxidation, and where possible, refine the degradation mechanisms. The evaluation of MCMv3 and MCMv3.1 using data on benzene, toluene, p-xylene and 1,3,5-trimethylbenzene photosmog systems is described in a companion paper, and significant model shortcomings are identified. Ideas for additional modifications to the mechanisms, and for future experiments to further our knowledge of the details of aromatic photo-oxidation are discussed.

Investigation of Iso-octane Ignition and Validation of a Multizone Modeling Method in an Ignition Quality Tester

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osecky, Eric M.; Bogin, Gregory E.; Villano, Stephanie M.

An ignition quality tester was used to characterize the autoignition delay times of iso-octane. The experimental data were characterized between temperatures of 653 and 996 K, pressures of 1.0 and 1.5 MPa, and global equivalence ratios of 0.7 and 1.05. A clear negative temperature coefficient behavior was seen at both pressures in the experimental data. These data were used to characterize the effectiveness of three modeling methods: a single-zone homogeneous batch reactor, a multizone engine model, and a three-dimensional computational fluid dynamics (CFD) model. A detailed 874 species iso-octane ignition mechanism (Mehl, M.; Curran, H. J.; Pitz, W. J.; Westbrook,more » C. K.Chemical kinetic modeling of component mixtures relevant to gasoline. Proceedings of the European Combustion Meeting; Vienna, Austria, April 14-17, 2009) was reduced to 89 species for use in these models, and the predictions of the reduced mechanism were consistent with ignition delay times predicted by the detailed chemical mechanism across a broad range of temperatures, pressures, and equivalence ratios. The CFD model was also run without chemistry to characterize the extent of mixing of fuel and air in the chamber. The calculations predicted that the main part of the combustion chamber was fairly well-mixed at longer times (> ~30 ms), suggesting that the simpler models might be applicable in this quasi-homogeneous region. The multizone predictions, where the combustion chamber was divided into 20 zones of temperature and equivalence ratio, were quite close to the coupled CFD-kinetics results, but the calculation time was ~11 times faster than the coupled CFD-kinetics model. Although the coupled CFD-kinetics model captured the observed negative temperature coefficient behavior and pressure dependence, discrepancies remain between the predictions and the observed ignition time delays, suggesting improvements are still needed in the kinetic mechanism and/or the CFD model. This approach suggests a combined modeling approach, wherein the CFD calculations (without chemistry) can be used to examine the sensitivity of various model inputs to in-cylinder temperature and equivalence ratios. In conclusion, these values can be used as inputs to the multizone model to examine the impact on ignition delay. Additionally, the speed of the multizone model also makes it feasible to quickly test more detailed kinetic mechanisms for comparison to experimental data and sensitivity analysis.« less

MECHANISMS OF NITROUS OXIDE FORMATION IN COAL FLAMES

EPA Science Inventory

The paper gives results of a study, using both detailed kinetic modeling and plug-flow simulator experiments, to investigate an unknown mechanism by which N2O is formed in coal flames. This mechanism has considerable importance in determining the influence of common and advanced ...

Investigation of Iso-octane Ignition and Validation of a Multizone Modeling Method in an Ignition Quality Tester

DOE PAGES

Osecky, Eric M.; Bogin, Gregory E.; Villano, Stephanie M.; ...

2016-08-18

An ignition quality tester was used to characterize the autoignition delay times of iso-octane. The experimental data were characterized between temperatures of 653 and 996 K, pressures of 1.0 and 1.5 MPa, and global equivalence ratios of 0.7 and 1.05. A clear negative temperature coefficient behavior was seen at both pressures in the experimental data. These data were used to characterize the effectiveness of three modeling methods: a single-zone homogeneous batch reactor, a multizone engine model, and a three-dimensional computational fluid dynamics (CFD) model. A detailed 874 species iso-octane ignition mechanism (Mehl, M.; Curran, H. J.; Pitz, W. J.; Westbrook,more » C. K.Chemical kinetic modeling of component mixtures relevant to gasoline. Proceedings of the European Combustion Meeting; Vienna, Austria, April 14-17, 2009) was reduced to 89 species for use in these models, and the predictions of the reduced mechanism were consistent with ignition delay times predicted by the detailed chemical mechanism across a broad range of temperatures, pressures, and equivalence ratios. The CFD model was also run without chemistry to characterize the extent of mixing of fuel and air in the chamber. The calculations predicted that the main part of the combustion chamber was fairly well-mixed at longer times (> ~30 ms), suggesting that the simpler models might be applicable in this quasi-homogeneous region. The multizone predictions, where the combustion chamber was divided into 20 zones of temperature and equivalence ratio, were quite close to the coupled CFD-kinetics results, but the calculation time was ~11 times faster than the coupled CFD-kinetics model. Although the coupled CFD-kinetics model captured the observed negative temperature coefficient behavior and pressure dependence, discrepancies remain between the predictions and the observed ignition time delays, suggesting improvements are still needed in the kinetic mechanism and/or the CFD model. This approach suggests a combined modeling approach, wherein the CFD calculations (without chemistry) can be used to examine the sensitivity of various model inputs to in-cylinder temperature and equivalence ratios. In conclusion, these values can be used as inputs to the multizone model to examine the impact on ignition delay. Additionally, the speed of the multizone model also makes it feasible to quickly test more detailed kinetic mechanisms for comparison to experimental data and sensitivity analysis.« less

An extensible framework for capturing solvent effects in computer generated kinetic models.

PubMed

Jalan, Amrit; West, Richard H; Green, William H

2013-03-14

Detailed kinetic models provide useful mechanistic insight into a chemical system. Manual construction of such models is laborious and error-prone, which has led to the development of automated methods for exploring chemical pathways. These methods rely on fast, high-throughput estimation of species thermochemistry and kinetic parameters. In this paper, we present a methodology for extending automatic mechanism generation to solution phase systems which requires estimation of solvent effects on reaction rates and equilibria. The linear solvation energy relationship (LSER) method of Abraham and co-workers is combined with Mintz correlations to estimate ΔG(solv)°(T) in over 30 solvents using solute descriptors estimated from group additivity. Simple corrections are found to be adequate for the treatment of radical sites, as suggested by comparison with known experimental data. The performance of scaled particle theory expressions for enthalpic-entropic decomposition of ΔG(solv)°(T) is also presented along with the associated computational issues. Similar high-throughput methods for solvent effects on free-radical kinetics are only available for a handful of reactions due to lack of reliable experimental data, and continuum dielectric calculations offer an alternative method for their estimation. For illustration, we model liquid phase oxidation of tetralin in different solvents computing the solvent dependence for ROO• + ROO• and ROO• + solvent reactions using polarizable continuum quantum chemistry methods. The resulting kinetic models show an increase in oxidation rate with solvent polarity, consistent with experiment. Further work needed to make this approach more generally useful is outlined.

An experimental and kinetic modeling study on dimethyl carbonate (DMC) pyrolysis and combustion

DOE PAGES

Sun, Wenyu; Yang, Bin; Hansen, Nils; ...

2015-12-08

Because of the absence of C–C bonds and the large oxygen content in its molecular structure, dimethyl carbonate (DMC) is a promising oxygenated additive or substitute for hydrocarbon fuels. In order to understand its chemical oxidation and combustion kinetics, flow reactor pyrolysis at different pressures (40, 200 and 1040 mbar) and low-pressure laminar premixed flames with different equivalence ratios (1.0 and 1.5) were investigated. Mole fraction profiles of many reaction intermediates and products were obtained within estimated experimental uncertainties. From theoretical calculations and estimations, a detailed kinetic model for DMC pyrolysis and high-temperature combustion consisting of 257 species and 1563more » reactions was developed. The performance of the kinetic model was then analyzed using detailed chemical composition information, primarily from the present measurements. In addition, it was examined against the chemical structure of an opposed-flow diffusion flame, relying on global combustion properties such as the ignition delay times and laminar burning velocities. Furthermore, these extended comparisons yielded overall satisfactory agreement, demonstrating the applicability of the present model over a wide range of high-temperature conditions.« less

Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach

PubMed Central

Kim, Young C.; Hummer, Gerhard

2011-01-01

Cytochrome c oxidase (CcO) is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, CcO translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in CcO. Basic principles of the CcO proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the ative-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for CcO provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. PMID:21946020

Kinetic modeling of methyl butanoate in shock tube.

PubMed

Huynh, Lam K; Lin, Kuang C; Violi, Angela

2008-12-25

An increased necessity for energy independence and heightened concern about the effects of rising carbon dioxide levels have intensified the search for renewable fuels that could reduce our current consumption of petrol and diesel. One such fuel is biodiesel, which consists of the methyl esters of fatty acids. Methyl butanoate (MB) contains the essential chemical structure of the long-chain fatty acids and a shorter, but similar, alkyl chain. This paper reports on a detailed kinetic mechanism for MB that is assembled using theoretical approaches. Thirteen pathways that include fuel decomposition, isomerization, and propagation steps were computed using ab initio calculations [J. Org. Chem. 2008, 73, 94]. Rate constants from first principles for important reactions in CO(2) formation, namely CH(3)OCO=CH(3) + CO(2) (R1) and CH(3)OCO=CH(3)O + CO (R2) reactions, are computed at high levels of theory and implemented in the mechanism. Using the G3B3 potential energy surface together with the B3LYP/6-31G(d) gradient, Hessian and geometries, the rate constants for reactions R1 and R2 are calculated using the Rice-Ramsperger-Kassel-Marcus theory with corrections from treatments for tunneling, hindered rotation, and variational effects. The calculated rate constants of reaction R1 differ from the data present in the literature by at most 20%, while those of reaction R2 are about a factor of 4 lower than the available values. The new kinetic model derived from ab initio simulations is combined with the kinetic mechanism presented by Fisher et al. [Proc. Combust. Inst. 2000, 28, 1579] together with the addition of the newly found six-centered unimolecular elimination reaction that yields ethylene and methyl acetate, MB = C(2)H(4) + CH(3)COOCH(3). This latter pathway requires the inclusion of the CH(3)COOCH(3) decomposition model suggested by Westbrook et al. [Proc. Combust. Inst. 2008, accepted]. The newly composed kinetic mechanism for MB is used to study the CO(2) formation during the pyrolysis of MB as well as to investigate the autoignition of MB in a shock tube reactor at different temperatures and pressures. The computed results agree very well with experimental data present in the literature. Sensitivity and flux (rate-of-production) analyses are carried out for the CO(2) formation with the new MB mechanism, together with available reaction mechanisms, to assess the importance of various kinetic pathways for each regime. With the new mechanism, the flux analyses for the formation of C(2)H species, one of the most important species for ignition delay time, are also presented at different conditions. In addition to giving a better chemical insight of the pyrolysis/oxidation of MB, the results suggest ways to improve the mechanism's capability to predict CO(2) formation and ignition delay times in pyrolysis and oxidation conditions.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Combustion modeling of RDX, HMX and GAP with detailed kinetics

NASA Astrophysics Data System (ADS)

Davidson, Jeffrey Edward

A one-dimensional, steady-state numerical model of the combustion of homogeneous solid propellant has been developed. The combustion processes is modeled in three regions: solid, two-phase (liquid and gas) and gas. Conservation of energy and mass equations are solved in the two-phase and gas regions and the eigenvalue of the system (the mass burning rate) is converged by matching the heat flux at the interface of these two regions. The chemical reactions of the system are modeled using a global kinetic mechanism in the two-phase region and an elementary kinetic mechanism in the gas region. The model has been applied to RDX, HMX and GAP. There is very reasonable agreement between experimental data and model predictions for burning rate, temperature sensitivity, surface temperature, adiabatic flame temperature, species concentration profiles and melt-layer thickness. Many of the similarities and differences in the combustion of RDX and HMX are explained from sensitivity analysis results. The combustion characteristics of RDX and HMX are similar because of their similar chemistry. Differences in combustion characteristics arise due to differences in melting temperature, vapor pressure and initial decomposition steps. A reduced mechanism consisting of 18 species and 39 reactions was developed from the Melius-Yetter RDX mechanism (45 species, 232 reactions). This reduced mechanism reproduces most of the predictions of the full mechanism but is 7.5 times faster. Because of lack of concrete thermophysical property data for GAP, the modeling results are preliminary but indicate what type of experimental data is necessary before GAP can be modeled with more certainty.

ACCURACY AND COST CONSIDERATIONS IN CHOOSING A CHEMICAL MECHANISM FOR OPERATIONAL USE IN AQ MODELS

EPA Science Inventory

There are several contemporary chemical kinetic mechanisms available for use in tropospheric air quality simulation models, with varying degrees of condensation of the chemical reaction pathways. Likewise, there are several different numerical solution methods available to use w...

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

DOE PAGES

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

2016-02-24

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 involvingmore » 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.« less

Numerical investigation of spray ignition of a multi-component fuel surrogate

NASA Astrophysics Data System (ADS)

Backer, Lara; Narayanaswamy, Krithika; Pepiot, Perrine

2014-11-01

Simulating turbulent spray ignition, an important process in engine combustion, is challenging, since it combines the complexity of multi-scale, multiphase turbulent flow modeling with the need for an accurate description of chemical kinetics. In this work, we use direct numerical simulation to investigate the role of the evaporation model on the ignition characteristics of a multi-component fuel surrogate, injected as droplets in a turbulent environment. The fuel is represented as a mixture of several components, each one being representative of a different chemical class. A reduced kinetic scheme for the mixture is extracted from a well-validated detailed chemical mechanism, and integrated into the multiphase turbulent reactive flow solver NGA. Comparisons are made between a single-component evaporation model, in which the evaporating gas has the same composition as the liquid droplet, and a multi-component model, where component segregation does occur. In particular, the corresponding production of radical species, which are characteristic of the ignition of individual fuel components, is thoroughly analyzed.

Modelling non-equilibrium secondary organic aerosol formation and evaporation with the aerosol dynamics, gas- and particle-phase chemistry kinetic multilayer model ADCHAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roldin, P.; Eriksson, A. C.; Nordin, E. Z.

2014-08-11

We have developed the novel Aerosol Dynamics, gas- and particle- phase chemistry model for laboratory CHAMber studies (ADCHAM). The model combines the detailed gas phase Master Chemical Mechanism version 3.2, an aerosol dynamics and particle phase chemistry module (which considers acid catalysed oligomerization, heterogeneous oxidation reactions in the particle phase and non-ideal interactions between organic compounds, water and inorganic ions) and a kinetic multilayer module for diffusion limited transport of compounds between the gas phase, particle surface and particle bulk phase. In this article we describe and use ADCHAM to study: 1) the mass transfer limited uptake of ammonia (NH3)more » and formation of organic salts between ammonium (NH4+) and carboxylic acids (RCOOH), 2) the slow and almost particle size independent evaporation of α-pinene secondary organic aerosol (SOA) particles, and 3) the influence of chamber wall effects on the observed SOA formation in smog chambers.« less

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.

Detailed Kinetic Mechanism of the Combustion of Homogeneous Gaseous Mixtures with Participation of Oxygen-containing Oxidants

NASA Astrophysics Data System (ADS)

Baevich, V. Ya

1987-05-01

The kinetic mechanisms of the oxidation and combustion of hydrogen, methane, methyl alcohol, acetylene, ethylene, ethane, and methylamine, using oxygen as well as hydrogen peroxide and nitric acid as oxidants, are discussed. The calculated and experimental data obtained under static conditions, in a flow, during flame propagation, and in shock tubes are compared. The bibliography includes 184 references.

Chemical kinetic modeling of propane oxidation behind shock waves

NASA Technical Reports Server (NTRS)

Mclain, A. G.; Jachimowski, C. J.

1977-01-01

The stoichiometric combustion of propane behind incident shock waves was studied experimentally and analytically over a temperature range from 1700 K to 2600 K and a pressure range from 1.2 to 1.9 atm. Measurements of the concentrations of carbon monoxide (CO) and carbon dioxide (CO2) and the product of the oxygen atom and carbon dioxide concentrations (O)(CO) were made after passage of the incident shock wave. A kinetic mechanism was developed which, when used in a computer program for a flowing, reacting gas behind an incident shock wave predicted experimentally measured results quite well. Ignition delay times from the literature were also predicted quite well. The kinetic mechanism consisted of 59 individual kinetic steps.

Reduction and Uncertainty Analysis of Chemical Mechanisms Based on Local and Global Sensitivities

NASA Astrophysics Data System (ADS)

Esposito, Gaetano

Numerical simulations of critical reacting flow phenomena in hypersonic propulsion devices require accurate representation of finite-rate chemical kinetics. The chemical kinetic models available for hydrocarbon fuel combustion are rather large, involving hundreds of species and thousands of reactions. As a consequence, they cannot be used in multi-dimensional computational fluid dynamic calculations in the foreseeable future due to the prohibitive computational cost. In addition to the computational difficulties, it is also known that some fundamental chemical kinetic parameters of detailed models have significant level of uncertainty due to limited experimental data available and to poor understanding of interactions among kinetic parameters. In the present investigation, local and global sensitivity analysis techniques are employed to develop a systematic approach of reducing and analyzing detailed chemical kinetic models. Unlike previous studies in which skeletal model reduction was based on the separate analysis of simple cases, in this work a novel strategy based on Principal Component Analysis of local sensitivity values is presented. This new approach is capable of simultaneously taking into account all the relevant canonical combustion configurations over different composition, temperature and pressure conditions. Moreover, the procedure developed in this work represents the first documented inclusion of non-premixed extinction phenomena, which is of great relevance in hypersonic combustors, in an automated reduction algorithm. The application of the skeletal reduction to a detailed kinetic model consisting of 111 species in 784 reactions is demonstrated. The resulting reduced skeletal model of 37--38 species showed that the global ignition/propagation/extinction phenomena of ethylene-air mixtures can be predicted within an accuracy of 2% of the full detailed model. The problems of both understanding non-linear interactions between kinetic parameters and identifying sources of uncertainty affecting relevant reaction pathways are usually addressed by resorting to Global Sensitivity Analysis (GSA) techniques. In particular, the most sensitive reactions controlling combustion phenomena are first identified using the Morris Method and then analyzed under the Random Sampling -- High Dimensional Model Representation (RS-HDMR) framework. The HDMR decomposition shows that 10% of the variance seen in the extinction strain rate of non-premixed flames is due to second-order effects between parameters, whereas the maximum concentration of acetylene, a key soot precursor, is affected by mostly only first-order contributions. Moreover, the analysis of the global sensitivity indices demonstrates that improving the accuracy of the reaction rates including the vinyl radical, C2H3, can drastically reduce the uncertainty of predicting targeted flame properties. Finally, the back-propagation of the experimental uncertainty of the extinction strain rate to the parameter space is also performed. This exercise, achieved by recycling the numerical solutions of the RS-HDMR, shows that some regions of the parameter space have a high probability of reproducing the experimental value of the extinction strain rate between its own uncertainty bounds. Therefore this study demonstrates that the uncertainty analysis of bulk flame properties can effectively provide information on relevant chemical reactions.

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

PubMed Central

Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

2007-01-01

Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. PMID:17919319

Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

PubMed

Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

2016-07-14

We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

Molecular mechanisms of protein aggregation from global fitting of kinetic models.

PubMed

Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J

2016-02-01

The elucidation of the molecular mechanisms by which soluble proteins convert into their amyloid forms is a fundamental prerequisite for understanding and controlling disorders that are linked to protein aggregation, such as Alzheimer's and Parkinson's diseases. However, because of the complexity associated with aggregation reaction networks, the analysis of kinetic data of protein aggregation to obtain the underlying mechanisms represents a complex task. Here we describe a framework, using quantitative kinetic assays and global fitting, to determine and to verify a molecular mechanism for aggregation reactions that is compatible with experimental kinetic data. We implement this approach in a web-based software, AmyloFit. Our procedure starts from the results of kinetic experiments that measure the concentration of aggregate mass as a function of time. We illustrate the approach with results from the aggregation of the β-amyloid (Aβ) peptides measured using thioflavin T, but the method is suitable for data from any similar kinetic experiment measuring the accumulation of aggregate mass as a function of time; the input data are in the form of a tab-separated text file. We also outline general experimental strategies and practical considerations for obtaining kinetic data of sufficient quality to draw detailed mechanistic conclusions, and the procedure starts with instructions for extensive data quality control. For the core part of the analysis, we provide an online platform (http://www.amylofit.ch.cam.ac.uk) that enables robust global analysis of kinetic data without the need for extensive programming or detailed mathematical knowledge. The software automates repetitive tasks and guides users through the key steps of kinetic analysis: determination of constraints to be placed on the aggregation mechanism based on the concentration dependence of the aggregation reaction, choosing from several fundamental models describing assembly into linear aggregates and fitting the chosen models using an advanced minimization algorithm to yield the reaction orders and rate constants. Finally, we outline how to use this approach to investigate which targets potential inhibitors of amyloid formation bind to and where in the reaction mechanism they act. The protocol, from processing data to determining mechanisms, can be completed in <1 d.

A Combined Kinetic and Volatility Basis Set Approach to Model Secondary Organic Aerosol from Toluene and Diesel Exhaust/Meat Cooking Mixtures

NASA Astrophysics Data System (ADS)

Parikh, H. M.; Carlton, A. G.; Zhang, H.; Kamens, R.; Vizuete, W.

2011-12-01

Secondary organic aerosol (SOA) is simulated for 6 outdoor smog chamber experiments using a SOA model based on a kinetic chemical mechanism in conjunction with a volatility basis set (VBS) approach. The experiments include toluene, a non-SOA-forming hydrocarbon mixture, diesel exhaust or meat cooking emissions and NOx, and are performed under varying conditions of relative humidity. SOA formation from toluene is modeled using a condensed kinetic aromatic mechanism that includes partitioning of lumped semi-volatile products in particle organic-phase and incorporates particle aqueous-phase chemistry to describe uptake of glyoxal and methylglyoxal. Modeling using the kinetic mechanism alone, along with primary organic aerosol (POA) from diesel exhaust (DE) /meat cooking (MC) fails to simulate the rapid SOA formation at the beginning hours of the experiments. Inclusion of a VBS approach with the kinetic mechanism to characterize the emissions and chemistry of complex mixture of intermediate volatility organic compounds (IVOCs) from DE/MC, substantially improves SOA predictions when compared with observed data. The VBS model includes photochemical aging of IVOCs and evaporation of POA after dilution. The relative contribution of SOA mass from DE/MC is as high as 95% in the morning, but substantially decreases after mid-afternoon. For high humidity experiments, aqueous-phase SOA fraction dominates the total SOA mass at the end of the day (approximately 50%). In summary, the combined kinetic and VBS approach provides a new and improved framework to semi-explicitly model SOA from VOC precursors in conjunction with a VBS approach that can be used on complex emission mixtures comprised with hundreds of individual chemical species.

Remarks on the chemical Fokker-Planck and Langevin equations: Nonphysical currents at equilibrium.

PubMed

Ceccato, Alessandro; Frezzato, Diego

2018-02-14

The chemical Langevin equation and the associated chemical Fokker-Planck equation are well-known continuous approximations of the discrete stochastic evolution of reaction networks. In this work, we show that these approximations suffer from a physical inconsistency, namely, the presence of nonphysical probability currents at the thermal equilibrium even for closed and fully detailed-balanced kinetic schemes. An illustration is given for a model case.

Direct Numerical Simulations of Autoignition in Stratified Dimethyl-ether (DME)/Air Turbulent Mixtures

DOE PAGES

Bansal, Gaurav; Mascarenhas, Ajith; Chen, Jacqueline H.

2014-10-01

In our paper, two- and three-dimensional direct numerical simulations (DNS) of autoignition phenomena in stratified dimethyl-ether (DME)/air turbulent mixtures are performed. A reduced DME oxidation mechanism, which was obtained using rigorous mathematical reduction and stiffness removal procedure from a detailed DME mechanism with 55 species, is used in the present DNS. The reduced DME mechanism consists of 30 chemical species. This study investigates the fundamental aspects of turbulence-mixing-autoignition interaction occurring in homogeneous charge compression ignition (HCCI) engine environments. A homogeneous isotropic turbulence spectrum is used to initialize the velocity field in the domain. Moreover, the computational configuration corresponds to amore » constant volume combustion vessel with inert mass source terms added to the governing equations to mimic the pressure rise due to piston motion, as present in practical engines. DME autoignition is found to be a complex three-staged process; each stage corresponds to a distinct chemical kinetic pathway. The distinct role of turbulence and reaction in generating scalar gradients and hence promoting molecular transport processes are investigated. Then, by applying numerical diagnostic techniques, the different heat release modes present in the igniting mixture are identified. In particular, the contribution of homogeneous autoignition, spontaneous ignition front propagation, and premixed deflagration towards the total heat release are quantified.« less

Deducing Reaction Mechanism: A Guide for Students, Researchers, and Instructors

ERIC Educational Resources Information Center

Meek, Simon J.; Pitman, Catherine L.; Miller, Alexander J. M.

2016-01-01

An introductory guide to deducing the mechanism of chemical reactions is presented. Following a typical workflow for probing reaction mechanism, the guide introduces a wide range of kinetic and mechanistic tools. In addition to serving as a broad introduction to mechanistic analysis for students and researchers, the guide has also been used by…

Kinetic mechanism for modeling of electrochemical reactions.

PubMed

Cervenka, Petr; Hrdlička, Jiří; Přibyl, Michal; Snita, Dalimil

2012-04-01

We propose a kinetic mechanism of electrochemical interactions. We assume fast formation and recombination of electron donors D- and acceptors A+ on electrode surfaces. These mediators are continuously formed in the electrode matter by thermal fluctuations. The mediators D- and A+, chemically equivalent to the electrode metal, enter electrochemical interactions on the electrode surfaces. Electrochemical dynamics and current-voltage characteristics of a selected electrochemical system are studied. Our results are in good qualitative agreement with those given by the classical Butler-Volmer kinetics. The proposed model can be used to study fast electrochemical processes in microsystems and nanosystems that are often out of the thermal equilibrium. Moreover, the kinetic mechanism operates only with the surface concentrations of chemical reactants and local electric potentials, which facilitates the study of electrochemical systems with indefinable bulk.

Study on reaction mechanism by analysis of kinetic energy spectra of light particles and formation of final products

NASA Astrophysics Data System (ADS)

Giardina, G.; Mandaglio, G.; Nasirov, A. K.; Anastasi, A.; Curciarello, F.; Fazio, G.

2018-05-01

The sensitivity of reaction mechanism in the formation of compound nucleus (CN) by the analysis of kinetic energy spectra of light particles and of reaction products are shown. The dependence of the P CN fusion probability of reactants and W sur survival probability of CN against fission at its deexcitation on the mass and charge symmetries in the entrance channel of heavy-ion collisions, as well as on the neutron numbers is discussed. The possibility of conducting a complex program of investigations of the complete fusion by reliable ways depends on the detailed and refined methods of experimental and theoretical analyses.

Formation of polycyclic aromatic hydrocarbons in circumstellar envelopes

NASA Technical Reports Server (NTRS)

Frenklach, Michael; Feigelson, Eric D.

1989-01-01

Production of polycyclic aromatic hydrocarbons in carbon-rich circumstellar envelopes was investigated using a kinetic approach. A detailed chemical reaction mechanism of gas-phase PAH formation and growth, containing approximately 100 reactions of 40 species, was numerically solved under the physical conditions expected in cool stellar winds. The chemistry is based on studies of soot production in hydrocarbon pyrolysis and combustion. Several first-ring and second-ring cyclization processes were considered. A linear lumping algorithm was used to describe PAH growth beyond the second aromatic ring. PAH production using this mechanism was examined with respect to a grid of idealized constant velocity stellar winds as well as several published astrophysical models. The basic result is that the onset of PAH production in the interstellar envelopes is predicted to occur within the temperature interval of 1100 to 900 K. The absolute amounts of the PAHs formed, however, are very sensitive to a number of parameters, both chemical and astrophysical, whose values are not accurately known. Astrophysically meaningful quantities of PAHs require particularly dense and slow stellar winds and high initial acetylene abundance. It is suggested that most of the PAHs may be produced in a relatively small fraction of carbon-rich red giants.

Detailed chemical analysis of regional-scale air pollution in western Portugal using an adapted version of MCM v3.1.

PubMed

Pinho, P G; Lemos, L T; Pio, C A; Evtyugina, M G; Nunes, T V; Jenkin, M E

2009-03-01

A version of the Master Chemical Mechanism (MCM) v3.1, refined on the basis of recent chamber evaluations, has been incorporated into a Photochemical Trajectory Model (PTM) and applied to the simulation of boundary layer photochemistry in the Portuguese west coast region. Comparison of modelled concentrations of ozone and a number of other species (NO(x) and selected hydrocarbons and organic oxygenates) was carried out, using data from three connected sites on two case study days when well-defined sea breeze conditions were established. The ozone concentrations obtained through the application of the PTM are a good approximation to the measured values, the average difference being ca. 15%, indicating that the model was acceptable for evaluation of the details of the chemical processing. The detailed chemistry is examined, allowing conclusions to be drawn concerning chemical interferences in the measurements of NO(2), and in relation to the sensitivity of ozone formation to changes in ambient temperature. Three important, and comparable, contributions to the temperature sensitivity are identified and quantified, namely (i) an effect of increasing biogenic emissions with temperature; (ii) an effect of increasing ambient water vapour concentration with temperature, and its influence on radical production; and (iii) an increase in VOC oxidation chain lengths resulting from the temperature-dependence of the kinetic parameters, particularly in relation to the stability of PAN and its higher analogues. The sensitivity of the simulations to the refinements implemented into MCM v3.1 are also presented and discussed.

Experimental Study and Mathematical Modeling of Self-Sustained Kinetic Oscillations in Catalytic Oxidation of Methane over Nickel.

PubMed

Lashina, Elena A; Kaichev, Vasily V; Saraev, Andrey A; Vinokurov, Zakhar S; Chumakova, Nataliya A; Chumakov, Gennadii A; Bukhtiyarov, Valerii I

2017-09-21

The self-sustained kinetic oscillations in the oxidation of CH 4 over Ni foil have been studied at atmospheric pressure using an X-ray diffraction technique and mass spectrometry. It has been shown that the regular oscillations appear under oxygen-deficient conditions; CO, CO 2 , H 2 , and H 2 O are detected as the products. According to in situ X-ray diffraction measurements, nickel periodically oxidizes to NiO initiating the reaction-rate oscillations. To describe the oscillations, we have proposed a five-stage mechanism of the partial oxidation of methane over Ni and a corresponding three-variable kinetic model. The mechanism considers catalytic methane decomposition, dissociative adsorption of oxygen, transformation of chemisorbed oxygen to surface nickel oxide, and reaction of adsorbed carbon and oxygen species to form CO. Analysis of the kinetic model indicates that the competition of two processes, i.e., the oxidation and the carbonization of the catalyst surface, is the driving force of the self-sustained oscillations in the oxidation of methane. We have compared this mechanism with the detailed 18-stage mechanism described previously by Lashina et al. (Kinetics and Catalysis 2012, 53, 374-383). It has been shown that both kinetic mechanisms coupled with a continuous stirred-tank reactor model describe well the oscillatory behavior in the oxidation of methane under non-isothermal conditions.

Bisubstrate inhibition: Theory and application to N-acetyltransferases.

PubMed

Yu, Michael; Magalhães, Maria L B; Cook, Paul F; Blanchard, John S

2006-12-12

Bisubstrate inhibitors represent a potentially powerful group of compounds that have found significant therapeutic utility. Although these compounds have been synthesized and tested against a number of enzymes that catalyze sequential bireactant reactions, the detailed theory for predicting the expected patterns of inhibition against the two substrates for various bireactant kinetic mechanisms has, heretofore, not been presented. We have derived the rate equations for all likely sequential bireactant mechanisms and provide two examples in which bisubstrate inhibitors allow the kinetic mechanism to be determined. Bisubstrate inhibitor kinetics is a powerful diagnostic for the determination of kinetic mechanisms.

Kinetic mechanism of molecular energy transfer and chemical reactions in low-temperature air-fuel plasmas.

PubMed

Adamovich, Igor V; Li, Ting; Lempert, Walter R

2015-08-13

This work describes the kinetic mechanism of coupled molecular energy transfer and chemical reactions in low-temperature air, H2-air and hydrocarbon-air plasmas sustained by nanosecond pulse discharges (single-pulse or repetitive pulse burst). The model incorporates electron impact processes, state-specific N(2) vibrational energy transfer, reactions of excited electronic species of N(2), O(2), N and O, and 'conventional' chemical reactions (Konnov mechanism). Effects of diffusion and conduction heat transfer, energy coupled to the cathode layer and gasdynamic compression/expansion are incorporated as quasi-zero-dimensional corrections. The model is exercised using a combination of freeware (Bolsig+) and commercial software (ChemKin-Pro). The model predictions are validated using time-resolved measurements of temperature and N(2) vibrational level populations in nanosecond pulse discharges in air in plane-to-plane and sphere-to-sphere geometry; temperature and OH number density after nanosecond pulse burst discharges in lean H(2)-air, CH(4)-air and C(2)H(4)-air mixtures; and temperature after the nanosecond pulse discharge burst during plasma-assisted ignition of lean H2-mixtures, showing good agreement with the data. The model predictions for OH number density in lean C(3)H(8)-air mixtures differ from the experimental results, over-predicting its absolute value and failing to predict transient OH rise and decay after the discharge burst. The agreement with the data for C(3)H(8)-air is improved considerably if a different conventional hydrocarbon chemistry reaction set (LLNL methane-n-butane flame mechanism) is used. The results of mechanism validation demonstrate its applicability for analysis of plasma chemical oxidation and ignition of low-temperature H(2)-air, CH(4)-air and C(2)H(4)-air mixtures using nanosecond pulse discharges. Kinetic modelling of low-temperature plasma excited propane-air mixtures demonstrates the need for development of a more accurate 'conventional' chemistry mechanism. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The Reduction in the Rate of Hydrolysis of Diphenylbromomethane by the Common-Ion Effect

ERIC Educational Resources Information Center

Cameron-Holford, Richard; Ratneswaren, Tarini; Hughes, D. E. Peter

2010-01-01

Kinetic study on the hydrolysis of diphenylbromomethane does not provide clear-cut evidence for the mechanism of the reaction. The reduction in the rate of the reaction by added bromide ions suggested that the reaction took place by a S[subscript N]1 mechanism. A more detailed study of this common-ion effect, using conductivity to measure the rate…

A STUDY OF GAS-PHASE MERCURY SPECIATION USING DETAILED CHEMICAL KINETICS

EPA Science Inventory

Mercury (Hg) speciation in combustion-generated flue gas is modeled using a detailed chemical mechanism consisting of 60 reactions and 21 species. This speciation model accounts for chlorination and oxidation of key flue-gas components, including elemental mercury. Results indica...

ESR Analysis of Polymer Photo-Oxidation

NASA Technical Reports Server (NTRS)

Kim, Soon Sam; Liang, Ranty Hing; Tsay, Fun-Dow; Gupta, Amitave

1987-01-01

Electron-spin resonance identifies polymer-degradation reactions and their kinetics. New technique enables derivation of kinetic model of specific chemical reactions involved in degradation of particular polymer. Detailed information provided by new method enables prediction of aging characteristics long before manifestation of macroscopic mechanical properties.

An analytical study of the hydrogen-air reaction mechanism with application to scramjet combustion

NASA Technical Reports Server (NTRS)

Jachimowski, Casimir J.

1988-01-01

A chemical kinetic mechanism for the combustion of hydrogen has been assembled and optimized by comparing the observed behavior as determined in shock tube and flame studies with that predicted by the mechanism. The reactions contained in the mechanism reflect the current state of knowledge of the chemistry of the hydrogen/air system, and the assigned rate coefficients are consistent with accepted values. It was determined that the mechanism is capable of satisfactorily reproducing the experimental results for a range of conditions relevant to scramjet combustion. Calculations made with the reaction mechanism for representative scramjet combustor conditions at Mach 8, 16, and 25 showed that chemical kinetic effects can be important and that combustor models which use nonequilibrium chemistry should be used in preference to models that assume equilibrium chemistry. For the conditions examined the results also showed the importance of including the HO2 chemistry in the mechanism. For Mach numbers less than 16, the studies suggest that an ignition source will most likely be required to overcome slow ignition chemistry. At Mach 25, the initial temperature and pressure was high enough that ignition was rapid and the presence of an ignition source did not significantly affect reaction rates.

Bridging from Replication to Translation with a Thermal, Autonomous Replicator Made from Transfer RNA

NASA Astrophysics Data System (ADS)

Braun, Dieter; Möller, Friederike M.; Krammer, Hubert

2013-03-01

Central to the understanding of living systems is the interplay between DNA/RNA and proteins. Known as Eigen paradox, proteins require genetic information while proteins are needed for the replication of genes. RNA world scenarios focus on a base by base replication disconnected from translation. Here we used strategies from DNA machines to demonstrate a tight connection between a basic replication mechanism and translation. A pool of hairpin molecules replicate a two-letter code. The replication is thermally driven: the energy and negative entropy to drive replication is initially stored in metastable hairpins by kinetic cooling. Both are released by a highly specific and exponential replication reaction that is solely implemented by base hybridization. The duplication time is 30s. The reaction is monitored by fluorescence and described by a detailed kinetic model. The RNA hairpins usetransfer RNA sequences and the replication is driven by the simple disequilibrium setting of a thermal gradient The experiments propose a physical rather than a chemical scenario for the autonomous replication of protein encoding information. Supported by the NanoSystems Initiative Munich and ERC.

Superactivity of MOF-808 toward Peptide Bond Hydrolysis.

PubMed

Ly, Hong Giang T; Fu, Guangxia; Kondinski, Aleksandar; Bueken, Bart; De Vos, Dirk; Parac-Vogt, Tatjana N

2018-05-03

MOF-808, a Zr(IV)-based metal-organic framework, has been proven to be a very effective heterogeneous catalyst for the hydrolysis of the peptide bond in a wide range of peptides and in hen egg white lysozyme protein. The kinetic experiments with a series of Gly-X dipeptides with varying nature of amino acid side chain have shown that MOF-808 exhibits selectivity depending on the size and chemical nature of the X side chain. Dipeptides with smaller or hydrophilic residues were hydrolyzed faster than those with bulky and hydrophobic residues that lack electron rich functionalities which could engage in favorable intermolecular interactions with the btc linkers. Detailed kinetic studies performed by 1 H NMR spectroscopy revealed that the rate of glycylglycine (Gly-Gly) hydrolysis at pD 7.4 and 60 °C was 2.69 × 10 -4 s -1 ( t 1/2 = 0.72 h), which is more than 4 orders of magnitude faster compared to the uncatalyzed reaction. Importantly, MOF-808 can be recycled several times without significantly compromising the catalytic activity. A detailed quantum-chemical study combined with experimental data allowed to unravel the role of the {Zr 6 O 8 } core of MOF-808 in accelerating Gly-Gly hydrolysis. A mechanism for the hydrolysis of Gly-Gly by MOF-808 is proposed in which Gly-Gly binds to two Zr(IV) centers of the {Zr 6 O 8 } core via the oxygen atom of the amide group and the N-terminus. The activity of MOF-808 was also demonstrated toward the hydrolysis of hen egg white lysozyme, a protein consisting of 129 amino acids. Selective fragmentation of the protein was observed with 55% yield after 25 h under physiological pH.

High-temperature oxidation chemistry of n-butanol--experiments in low-pressure premixed flames and detailed kinetic modeling.

PubMed

Hansen, N; Harper, M R; Green, W H

2011-12-07

An automated reaction mechanism generator is used to develop a predictive, comprehensive reaction mechanism for the high-temperature oxidation chemistry of n-butanol. This new kinetic model is an advancement of an earlier model, which had been extensively tested against earlier experimental data (Harper et al., Combust. Flame, 2011, 158, 16-41). In this study, the model's predictive capabilities are improved by targeting isomer-resolved quantitative mole fraction profiles of flame species in low-pressure flames. To this end, a total of three burner-stabilized premixed flames are isomer-selectively analyzed by flame-sampling molecular-beam time-of-flight mass spectrometry using photoionization by tunable vacuum-ultraviolet synchrotron radiation. For most species, the newly developed chemical kinetic model is capable of accurately reproducing the experimental trends in these flames. The results clearly indicate that n-butanol is mainly consumed by H-atom abstraction with H, O, and OH, forming predominantly the α-C(4)H(9)O radical (CH(3)CH(2)CH(2)˙CHOH). Fission of C-C bonds in n-butanol is only predicted to be significant in a similar, but hotter flame studied by Oßwald et al. (Combust. Flame, 2011, 158, 2-15). The water-elimination reaction to 1-butene is found to be of no importance under the premixed conditions studied here. The initially formed isomeric C(4)H(9)O radicals are predicted to further oxidize by reacting with H and O(2) or to decompose to smaller fragments via β-scission. Enols are detected experimentally, with their importance being overpredicted by the model.

Linear prediction and single-channel recording.

PubMed

Carter, A A; Oswald, R E

1995-08-01

The measurement of individual single-channel events arising from the gating of ion channels provides a detailed data set from which the kinetic mechanism of a channel can be deduced. In many cases, the pattern of dwells in the open and closed states is very complex, and the kinetic mechanism and parameters are not easily determined. Assuming a Markov model for channel kinetics, the probability density function for open and closed time dwells should consist of a sum of decaying exponentials. One method of approaching the kinetic analysis of such a system is to determine the number of exponentials and the corresponding parameters which comprise the open and closed dwell time distributions. These can then be compared to the relaxations predicted from the kinetic model to determine, where possible, the kinetic constants. We report here the use of a linear technique, linear prediction/singular value decomposition, to determine the number of exponentials and the exponential parameters. Using simulated distributions and comparing with standard maximum-likelihood analysis, the singular value decomposition techniques provide advantages in some situations and are a useful adjunct to other single-channel analysis techniques.

General theory of the multistage geminate reactions of the isolated pairs of reactants. II. Detailed balance and universal asymptotes of kinetics.

PubMed

Kipriyanov, Alexey A; Doktorov, Alexander B

2014-10-14

The analysis of general (matrix) kinetic equations for the mean survival probabilities of any of the species in a sample (or mean concentrations) has been made for a wide class of the multistage geminate reactions of the isolated pairs. These kinetic equations (obtained in the frame of the kinetic approach based on the concept of "effective" particles in Paper I) take into account various possible elementary reactions (stages of a multistage reaction) excluding monomolecular, but including physical and chemical processes of the change in internal quantum states carried out with the isolated pairs of reactants (or isolated reactants). The general basic principles of total and detailed balance have been established. The behavior of the reacting system has been considered on macroscopic time scales, and the universal long-term kinetics has been determined.

Shock tube study of the fuel structure effects on the chemical kinetic mechanisms responsible for soot formation, part 2

NASA Technical Reports Server (NTRS)

Frenklach, M.; Clary, D. W.; Ramachandra, M. K.

1985-01-01

Soot formation in oxidation of allene, 1,3-butadiene, vinylacetylene and chlorobenzene and in pyrolysis of ethylene, vinylacetylene, 1-butene, chlorobenzene, acetylen-hydrogen, benzene-acetylene, benzene-butadiene and chlorobenzene-acetylene argon-diluted mixtures was studied behind reflected shock waves. The results are rationalized within the framework of the conceptual models. It is shown that vinylacetylene is much less sooty than allene, which indicates that conjugation by itself is not a sufficient factor for determining the sooting tendency of a molecule. Structural reactivity in the context of the chemical kinetics is the dominant factor in soot formation. Detailed chemical kinetic modeling of soot formation in pyrolysis of acetylene is reported. The main mass growth was found to proceed through a single dominant route composed of conventional radical reactions. The practically irreversible formation reactions of the fused polycyclic aromatics and the overshoot by hydrogen atom over its equilibrium concentration are the g-driving kinetic forces for soot formation.

Verification of kinetic schemes of hydrogen ignition and combustion in air

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Fedorova, N. N.; Vankova, O. S.; Tropin, D. A.

2018-03-01

Three chemical kinetic models for hydrogen combustion in oxygen and three gas-dynamic models for reactive mixture flow behind the initiating SW front were analyzed. The calculated results were compared with experimental data on the dependences of the ignition delay on the temperature and the dilution of the mixture with argon or nitrogen. Based on detailed kinetic mechanisms of nonequilibrium chemical transformations, a mathematical technique for describing the ignition and combustion of hydrogen in air was developed using the ANSYS Fluent code. The problem of ignition of a hydrogen jet fed coaxially into supersonic flow was solved numerically. The calculations were carried out using the Favre-averaged Navier-Stokes equations for a multi-species gas taking into account chemical reactions combined with the k-ω SST turbulence model. The problem was solved in several steps. In the first step, verification of the calculated and experimental data for the three kinetic schemes was performed without considering the conicity of the flow. In the second step, parametric calculations were performed to determine the influence of the conicity of the flow on the mixing and ignition of hydrogen in air using a kinetic scheme consisting of 38 reactions. Three conical supersonic nozzles for a Mach number M = 2 with different expansion angles β = 4°, 4.5°, and 5° were considered.

Investigation of detailed kinetic scheme performance on modelling of turbulent non-premixed sooting flames

NASA Astrophysics Data System (ADS)

Yunardi, Y.; Darmadi, D.; Hisbullah, H.; Fairweather, M.

2011-12-01

This paper presents the results of an application of a first-order conditional moment closure (CMC) approach coupled with a semi-empirical soot model to investigate the effect of various detailed combustion chemistry schemes on soot formation and destruction in turbulent non-premixed flames. A two-equation soot model representing soot particle nucleation, growth, coagulation and oxidation, was incorporated into the CMC model. The turbulent flow-field of both flames is described using the Favre-averaged fluid-flow equations, applying a standard k-ɛ turbulence model. A number of five reaction kinetic mechanisms having 50-100 species and 200-1000 elementary reactions called ABF, Miller-Bowman, GRI-Mech3.0, Warnatz, and Qin were employed to study the effect of combustion chemistry schemes on soot predictions. The results showed that of various kinetic schemes being studied, each yields similar accuracy in temperature prediction when compared with experimental data. With respect to soot prediction, the kinetic scheme containing benzene elementary reactions tends to result in a better prediction on soot concentrations in comparison to those contain no benzene elementary reactions. Among five kinetic mechanisms being studied, the Qin combustion scheme mechanism turned to yield the best prediction on both flame temperature and soot levels.

Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vitello, P; Fried, L E; Pudliner, B

2003-07-14

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values, called the ''cache'' is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamicmore » calculations, CHEETAH uses MPI communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.« less

BioMOL: a computer-assisted biological modeling tool for complex chemical mixtures and biological processes at the molecular level.

PubMed Central

Klein, Michael T; Hou, Gang; Quann, Richard J; Wei, Wei; Liao, Kai H; Yang, Raymond S H; Campain, Julie A; Mazurek, Monica A; Broadbelt, Linda J

2002-01-01

A chemical engineering approach for the rigorous construction, solution, and optimization of detailed kinetic models for biological processes is described. This modeling capability addresses the required technical components of detailed kinetic modeling, namely, the modeling of reactant structure and composition, the building of the reaction network, the organization of model parameters, the solution of the kinetic model, and the optimization of the model. Even though this modeling approach has enjoyed successful application in the petroleum industry, its application to biomedical research has just begun. We propose to expand the horizons on classic pharmacokinetics and physiologically based pharmacokinetics (PBPK), where human or animal bodies were often described by a few compartments, by integrating PBPK with reaction network modeling described in this article. If one draws a parallel between an oil refinery, where the application of this modeling approach has been very successful, and a human body, the individual processing units in the oil refinery may be considered equivalent to the vital organs of the human body. Even though the cell or organ may be much more complicated, the complex biochemical reaction networks in each organ may be similarly modeled and linked in much the same way as the modeling of the entire oil refinery through linkage of the individual processing units. The integrated chemical engineering software package described in this article, BioMOL, denotes the biological application of molecular-oriented lumping. BioMOL can build a detailed model in 1-1,000 CPU sec using standard desktop hardware. The models solve and optimize using standard and widely available hardware and software and can be presented in the context of a user-friendly interface. We believe this is an engineering tool with great promise in its application to complex biological reaction networks. PMID:12634134

Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

NASA Astrophysics Data System (ADS)

Vitello, Peter; Fried, Laurence E.; Pudliner, Brian; McAbee, Tom

2004-07-01

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamic calculations, CHEETAH uses parallel communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH coupled to an ALE hydrocode. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.

The intensity of knock in an internal combustion engine: An experimental and modeling study

NASA Astrophysics Data System (ADS)

Cowart, J. S.; Haghooie, M.; Newman, C. E.; Davis, G. C.; Pitz, W. J.; Westbrook, C. K.

1992-09-01

Experimental data have been obtained that characterize knock occurrence times and knock intensities in a spark ignition engine operating on indolene and 91 primary reference fuel, as spark timing and inlet temperature were varied. Individual, in-cylinder pressure histories measured under knocking conditions were conditioned and averaged to obtain representative pressure traces. These averaged pressure histories were used as input to a reduced and detailed chemical kinetic model. The time derivative of CO concentration and temperature were correlated with the measured knock intensity and percent cycles knocking. The goal was to evaluate the potential of using homogeneous, chemical kinetic models as predictive tools for knock intensity.

Evaluation of modeled cloud chemistry mechanism against laboratory irradiation experiments: The HxOy/iron/carboxylic acid chemical system

NASA Astrophysics Data System (ADS)

Long, Yoann; Charbouillot, Tiffany; Brigante, Marcello; Mailhot, Gilles; Delort, Anne-Marie; Chaumerliac, Nadine; Deguillaume, Laurent

2013-10-01

Currently, cloud chemistry models are including more detailed and explicit multiphase mechanisms based on laboratory experiments that determine such values as kinetic constants, stability constants of complexes and hydration constants. However, these models are still subject to many uncertainties related to the aqueous chemical mechanism they used. Particularly, the role of oxidants such as iron and hydrogen peroxide in the oxidative capacity of the cloud aqueous phase has typically never been validated against laboratory experimental data. To fill this gap, we adapted the M2C2 model (Model of Multiphase Cloud Chemistry) to simulate irradiation experiments on synthetic aqueous solutions under controlled conditions (e.g., pH, temperature, light intensity) and for actual cloud water samples. Various chemical compounds that purportedly contribute to the oxidative budget in cloud water (i.e., iron, oxidants, such as hydrogen peroxide: H2O2) were considered. Organic compounds (oxalic, formic and acetic acids) were taken into account as target species because they have the potential to form iron complexes and are good indicators of the oxidative capacity of the cloud aqueous phase via their oxidation in this medium. The range of concentrations for all of the chemical compounds evaluated was representative of in situ measurements. Numerical outputs were compared with experimental data that consisted of a time evolution of the concentrations of the target species. The chemical mechanism in the model describing the “oxidative engine” of the HxOy/iron (HxOy = H2O2, HO2rad /O2rad - and HOrad ) chemical system was consistent with laboratory measurements. Thus, the degradation of the carboxylic acids evaluated was closely reproduced by the model. However, photolysis of the Fe(C2O4)+ complex needs to be considered in cloud chemistry models for polluted conditions (i.e., acidic pH) to correctly reproduce oxalic acid degradation. We also show that iron and formic acid lead to a stable complex whose photoreactivity has currently not been investigated. The updated aqueous chemical mechanism was compared with data from irradiation experiments using natural cloud water. The new reactions considered in the model (i.e., iron complex formation with oxalic and formic acids) correctly reproduced the experimental observations.

A detailed kinetic modeling study of toluene oxidation in a premixed laminar flame

PubMed Central

Tian, Zhenyu; Pitz, William J.; Fournet, René; Glaude, Pierre-Alexander; Battin-Leclerc, Frédérique

2013-01-01

An improved chemical kinetic model for the toluene oxidation based on experimental data obtained in a premixed laminar low-pressure flame with vacuum ultraviolet (VUV) photoionization and molecular beam mass spectrometry (MBMS) techniques has been proposed. The present mechanism consists of 273 species up to chrysene and 1740 reactions. The rate constants of reactions of toluene decomposition, reaction with oxygen, ipso-additions and metatheses with abstraction of phenylic H-atom are updated; new pathways of C4 + C2 species giving benzene and fulvene are added. Based on the experimental observations, combustion intermediates such as fulvenallene, naphtol, methylnaphthalene, acenaphthylene, 2-ethynylnaphthalene, phenanthrene, anthracene, 1-methylphenanthrene, pyrene and chrysene are involved in the present mechanism. The final toluene model leads to an overall satisfactory agreement between the experimentally observed and predicted mole fraction profiles for the major products and most combustion intermediates. The toluene depletion is governed by metathese giving benzyl radicals, ipso-addition forming benzene and metatheses leading to C6H4CH3 radicals. A sensitivity analysis indicates that the unimolecular decomposition via the cleavage of a methyl C-H bond has a strong inhibiting effect, while decomposition via C-C bond breaking, ipso-addition of H-atom to toluene, decomposition of benzyl radicals and reactions related to C6H4CH3 radicals have promoting effect for the consumption of toluene. Moreover, flow rate analysis is performed to illustrate the formation pathways of mono- and polycyclic aromatics. PMID:23762016

Theoretical Basis for Estimated Test Times and Conditions for Drop Tower and Space-Based Droplet Burning Experiments With Methanol and N-Heptane

NASA Technical Reports Server (NTRS)

Marchese, Anthony J.; Dryer, Fredrick L.; Choi, Mun Y.

1994-01-01

In order to develop an extensive envelope of test conditions for NASA's space-based Droplet Combustion Experiment (DCE) as well those droplet experiments which can be performed using a drop tower, the transient vaporization and combustion of methanol and n-heptane droplets were simulated using a recently developed fully time-dependent, spherically symmetric droplet combustion model. The transient vaporization of methanol and n-heptane was modeled to characterize the instantaneous gas phase composition surrounding the droplet prior to the introduction of an ignition source. The results for methanol/air showed that the entire gas phase surrounding a 2 mm methanol droplet deployed in zero-g .quickly falls outside the lean flammability limit. The gas phase surrounding an identically-sized n-heptane droplet, on the other hand, remains flammable. The combustion of methanol was then modeled considering a detailed gas phase chemical kinetic mechanism (168 steps, 26 species) and the effect of the dissolution of flame-generated water into the liquid droplet. These results were used to determine the critical ignition diameter required to achieve quasi-steady droplet combustion in a given oxidizing environment. For droplet diameters greater than the critical ignition diameter, the model predicted a finite diameter at which the flame would extinguish. These extinction diameters were found to vary significantly with initial droplet diameter. This phenomenon appears to be unique to the transient heat transfer, mass transfer and chemical kinetics of the system and thus has not been reported elsewhere to date. The extinction diameter was also shown to vary significantly with the liquid phase Lewis number since the amount of water present in the droplet at extinction is largely governed by the rate at which water is transported into the droplet via mass diffusion. Finally, the numerical results for n-heptane combustion were obtained using both 2 step and 96 step semi-emperical chemical kinetic mechanisms. Neither mechanism exhibited the variation of extinction diameter with initial diameter.

Modelling the effect of ascorbic acid, sodium metabisulphite and sodium chloride on the kinetic responses of lactic acid bacteria and yeasts in table olive storage using a specifically implemented Quasi-chemical primary model.

PubMed

Echevarria, R; Bautista-Gallego, J; Arroyo-López, F N; Garrido-Fernández, A

2010-04-15

The goal of this work was to apply the Quasi-chemical primary model (a system of four ordinary differential equations that derives from a hypothetical four-step chemical mechanism involving an antagonistic metabolite) in the study of the evolution of yeast and lactic acid bacteria populations during the storage of Manzanilla-Aloreña table olives subjected to different mixtures of ascorbic acid, sodium metabisulphite and NaCl. Firstly, the Quasi-chemical model was applied to microbial count data to estimate the growth-decay biological parameters. The model accurately described the evolution of both populations during storage, providing detailed information on the microbial behaviour. Secondly, these parameters were used as responses and analysed according to a mixture design experiment (secondary model). The contour lines of the corresponding response surfaces clearly disclosed the relationships between growth and environmental conditions, showing the stimulating and inhibitory effect of ascorbic acid and sodium metabisulphite, respectively, on both populations of microorganisms. This work opens new possibilities for the potential use of the Quasi-chemical primary model in the study of table olive fermentations. (c) 2010 Elsevier B.V. All rights reserved.

Kinetic method for the large-scale analysis of the binding mechanism of histone deacetylase inhibitors.

PubMed

Meyners, Christian; Baud, Matthias G J; Fuchter, Matthew J; Meyer-Almes, Franz-Josef

2014-09-01

Performing kinetic studies on protein ligand interactions provides important information on complex formation and dissociation. Beside kinetic parameters such as association rates and residence times, kinetic experiments also reveal insights into reaction mechanisms. Exploiting intrinsic tryptophan fluorescence a parallelized high-throughput Förster resonance energy transfer (FRET)-based reporter displacement assay with very low protein consumption was developed to enable the large-scale kinetic characterization of the binding of ligands to recombinant human histone deacetylases (HDACs) and a bacterial histone deacetylase-like amidohydrolase (HDAH) from Bordetella/Alcaligenes. For the binding of trichostatin A (TSA), suberoylanilide hydroxamic acid (SAHA), and two other SAHA derivatives to HDAH, two different modes of action, simple one-step binding and a two-step mechanism comprising initial binding and induced fit, were verified. In contrast to HDAH, all compounds bound to human HDAC1, HDAC6, and HDAC8 through a two-step mechanism. A quantitative view on the inhibitor-HDAC systems revealed two types of interaction, fast binding and slow dissociation. We provide arguments for the thesis that the relationship between quantitative kinetic and mechanistic information and chemical structures of compounds will serve as a valuable tool for drug optimization. Copyright © 2014 Elsevier Inc. All rights reserved.

AROMATIC AND POLYCYCLIC AROMATIC HYDROCARBON FORMATION IN A LAMINAR PREMIXED N-BUTANE FLAME. (R825412)

EPA Science Inventory

Abstract

Experimental and detailed chemical kinetic modeling work has been performed to investigate aromatic and polycyclic aromatic hydrocarbon (PAH) formation pathways in a premixed, rich, sooting, n-butane_¯oxygen_¯argon burner s...

Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process.

PubMed

Anandakrishnan, Ramu; Zhang, Zining; Donovan-Maiye, Rory; Zuckerman, Daniel M

2016-10-04

The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using numerical and theoretical means. When the alternative models are optimized subject to fundamental thermodynamic constraints, they fail to match the kinetic ability of the rotary mechanism over a wide range of conditions, particularly under low-energy conditions. We used a physically interpretable, closed-form solution for the steady-state rate for an arbitrary chemical cycle, which clarifies kinetic effects of complex free-energy landscapes. Our analysis also yields insights into the debated "kinetic equivalence" of ATP synthesis driven by transmembrane pH and potential difference. Overall, our study suggests that the complexity of the F-ATPase may have resulted from positive selection for its kinetic advantage.

A comprehensive model to determine the effects of temperature and species fluctuations on reaction rates in turbulent reaction flows

NASA Technical Reports Server (NTRS)

Magnotti, F.; Diskin, G.; Matulaitis, J.; Chinitz, W.

1984-01-01

The use of silane (SiH4) as an effective ignitor and flame stabilizing pilot fuel is well documented. A reliable chemical kinetic mechanism for prediction of its behavior at the conditions encountered in the combustor of a SCRAMJET engine was calculated. The effects of hydrogen addition on hydrocarbon ignition and flame stabilization as a means for reduction of lengthy ignition delays and reaction times were studied. The ranges of applicability of chemical kinetic models of hydrogen-air combustors were also investigated. The CHARNAL computer code was applied to the turbulent reaction rate modeling.

Jet-A reaction mechanism study for combustion application

NASA Technical Reports Server (NTRS)

Lee, Chi-Ming; Kundu, Krishna; Acosta, Waldo

1991-01-01

Simplified chemical kinetic reaction mechanisms for the combustion of Jet A fuel was studied. Initially, 40 reacting species and 118 elementary chemical reactions were chosen based on a literature review. Through a sensitivity analysis with the use of LSENS General Kinetics and Sensitivity Analysis Code, 16 species and 21 elementary chemical reactions were determined from this study. This mechanism is first justified by comparison of calculated ignition delay time with the available shock tube data, then it is validated by comparison of calculated emissions from the plug flow reactor code with in-house flame tube data.

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

PubMed

Doktorov, Alexander B

2015-08-21

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

Controlling the position of a stabilized detonation wave in a supersonic gas mixture flow in a plane channel

NASA Astrophysics Data System (ADS)

Levin, V. A.; Zhuravskaya, T. A.

2017-03-01

Stabilization of a detonation wave in a stoichiometric hydrogen-air mixture flowing at a supersonic velocity into a plane symmetric channel with constriction has been studied in the framework of a detailed kinetic mechanism of the chemical interaction. Conditions ensuring the formation of a thrust-producing f low with a stabilized detonation wave in the channel are determined. The inf luence of the inf low Mach number, dustiness of the combustible gas mixture supplied to the channel, and output cross-section size on the position of a stabilized detonation wave in the f low has been analyzed with a view to increasing the efficiency of detonation combustion of the gas mixture. It is established that thrust-producing flow with a stabilized detonation wave can be formed in the channel without any energy consumption.

Recent progress on the development of anisotropic gold nanoparticles: Design strategies and growth mechanism.

PubMed

Jones, Stacy; Pramanik, Avijit; Sweet, Carrie; Keyes, Anthony; Begum, Salma; Vangra, Aruna; Yu, Hongtal; Fu, Peter P; Ray, Paresh Chandra

2017-01-02

This review summarizes recent advances on design strategies for shape-controlled anisotropic gold nanoparticles. Detailed chemical mechanism has been discussed to understand the anisotropic growth. The effect of various chemical parameters and surface facets for the formation of different shaped anisotropic nanoparticles have been addressed.

The carbon dioxide chaperon efficiency for the reaction H + O2 + M yields HO2 + M from ignition delay times behind reflected shock waves

NASA Technical Reports Server (NTRS)

Brabbs, Theodore A.; Robertson, Thomas F.

1987-01-01

Ignition delay times for stoichiometric hydrogen-oxygen in argon with and without carbon dioxide were measured behind reflected shock waves. A 20-reaction kinetic mechanism models the measured hydrogen-oxygen delay times over the temperature range 950 to 1300 K. The chaperon efficiency for carbon dioxide determined for the hydrogen-oxygen carbon dioxide mixture was 7.0. This value is in agreement with literature values but much less than a recent value obtained from flow tube experiments. Delay times measured behind a reflected shock wave were about 20% longer than those measured behind incident shock waves. The kinetic mechanism successfully modeled the high-pressure data of Skinner and the hydrogen-air data of Stack. It is suggested that the lowest temperature points for the hydrogen-air data of Slack are unreliable and that the 0.27-atm data may illustrate a case where vibrational relaxation of nitrogen is important. The reaction pathway HO2 yields H2O2 yields OH yields H was required to model the high-pressure data of Skinner. The successful modeling of the stoichiometric hydrogen-air data demonstrates the appropriateness of deriving kinetic models from data for gas mixtures highly diluted with argon. The technique of reducing a detailed kinetic mechanism to only the important reactions for a limited range of experimental data may render the mechanism useless for other test conditions.

Some Considerations on the Fundamentals of Chemical Kinetics: Steady State, Quasi-Equilibrium, and Transition State Theory

ERIC Educational Resources Information Center

Perez-Benito, Joaquin F.

2017-01-01

The elementary reaction sequence A ? I ? Products is the simplest mechanism for which the steady-state and quasi-equilibrium kinetic approximations can be applied. The exact integrated solutions for this chemical system allow inferring the conditions that must fulfill the rate constants for the different approximations to hold. A graphical…

Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielsen, Jens; D’Avezac, Mayeul; Hetherington, James

2013-12-14

Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. Moremore » recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.« less

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity.

PubMed

Garratt, Shaun A; Hughes, Russell P; Kovacik, Ivan; Ward, Antony J; Willemsen, Stefan; Zhang, Donghui

2005-11-09

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.

Temperature and Pressure Dependences of the Reactions of Fe+ with Methyl Halides CH3X (X = Cl, Br, I): Experiments and Kinetic Modeling Results.

PubMed

Ard, Shaun G; Shuman, Nicholas S; Martinez, Oscar; Keyes, Nicholas R; Viggiano, Albert A; Guo, Hua; Troe, Jürgen

2017-06-01

The pressure and temperature dependences of the reactions of Fe + with methyl halides CH 3 X (X = Cl, Br, I) in He were measured in a selected ion flow tube over the ranges 0.4 to 1.2 Torr and 300-600 K. FeX + was observed for all three halides and FeCH 3 + was observed for the CH 3 I reaction. FeCH 3 X + adducts (for all X) were detected in all reactions. The results were interpreted assuming two-state reactivity with spin-inversions between sextet and quartet potentials. Kinetic modeling allowed for a quantitative representation of the experiments and for extrapolation to conditions outside the experimentally accessible range. The modeling required quantum-chemical calculations of molecular parameters and detailed accounting of angular momentum effects. The results show that the FeX + products come via an insertion mechanism, while the FeCH 3 + can be produced from either insertion or S N 2 mechanisms, but the latter we conclude is unlikely at thermal energies. A statistical modeling cannot reproduce the competition between the bimolecular pathways in the CH 3 I reaction, indicating that some more direct process must be important.

Temperature and H2O sensing in laminar premixed flames using mid-infrared heterodyne phase-sensitive dispersion spectroscopy

NASA Astrophysics Data System (ADS)

Ma, Liuhao; Wang, Zhen; Cheong, Kin-Pang; Ning, Hongbo; Ren, Wei

2018-06-01

We report the first demonstration of heterodyne phase-sensitive dispersion spectroscopy (HPSDS) for the simultaneous temperature and H2O concentration measurements in combustion environments. Two continuous-wave distributed-feedback quantum cascade lasers (DFB-QCLs) at 5.27 and 10.53 µm were used to exploit the strong H2O transitions (1897.52 and 949.53 cm-1) at high temperatures. The injection current of each QCL was modulated at sub-GHz or GHz to generate the three-tone radiation and the dispersion signal was detected by the radio-frequency down-conversion heterodyning. The peak-to-peak ratio of the two H2O dispersion spectra exhibits a monotonic relationship with temperature over the temperature range of 1000-3000 K, indicating the capability of performing two-line thermometry using laser dispersion spectroscopy. We measured the temperatures of CH4/air flames at different equivalence ratios ( Φ = 0.8-1.2), yielding a good agreement with the corresponding thermocouple measurements. In addition, one-dimensional kinetic modeling coupled with a detailed chemical kinetic mechanism (GRI 3.0) was conducted to compare with the measured H2O concentrations using HPSDS. Finally, we demonstrated HPSDS is immune to optical power fluctuations by measuring the dispersion spectra at varied incident laser powers.

A computational investigation of diesel and biodiesel combustion and NOx formation in a light-duty compression ignition engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zihan; Srinivasan, Kalyan K.; Krishnan, Sundar R.

Diesel and biodiesel combustion in a multi-cylinder light duty diesel engine were simulated during a closed cycle (from IVC to EVO), using a commercial computational fluid dynamics (CFD) code, CONVERGE, coupled with detailed chemical kinetics. The computational domain was constructed based on engine geometry and compression ratio measurements. A skeletal n-heptane-based diesel mechanism developed by researchers at Chalmers University of Technology and a reduced biodiesel mechanism derived and validated by Luo and co-workers were applied to model the combustion chemistry. The biodiesel mechanism contains 89 species and 364 reactions and uses methyl decanoate, methyl-9- decenoate, and n-heptane as the surrogatemore » fuel mixture. The Kelvin-Helmholtz and Rayleigh-Taylor (KH-RT) spray breakup model for diesel and biodiesel was calibrated to account for the differences in physical properties of the fuels which result in variations in atomization and spray development characteristics. The simulations were able to capture the experimentally observed pressure and apparent heat release rate trends for both the fuels over a range of engine loads (BMEPs from 2.5 to 10 bar) and fuel injection timings (from 0° BTDC to 10° BTDC), thus validating the overall modeling approach as well as the chemical kinetic models of diesel and biodiesel surrogates. Moreover, quantitative NOx predictions for diesel combustion and qualitative NOx predictions for biodiesel combustion were obtained with the CFD simulations and the in-cylinder temperature trends were correlated to the NOx trends.« less

Cooperative mechanism of RNA packaging motor.

PubMed

Lísal, Jirí; Tuma, Roman

2005-06-17

P4 is a hexameric ATPase that serves as the RNA packaging motor in double-stranded RNA bacteriophages from the Cystoviridae family. P4 shares sequence and structural similarities with hexameric helicases. A structure-based mechanism for mechano-chemical coupling has recently been proposed for P4 from bacteriophage phi12. However, coordination of ATP hydrolysis among the subunits and coupling with RNA translocation remains elusive. Here we present detailed kinetic study of nucleotide binding, hydrolysis, and product release by phi12 P4 in the presence of different RNA and DNA substrates. Whereas binding affinities for ATP and ADP are not affected by RNA binding, the hydrolysis step is accelerated and the apparent cooperativity is increased. No nucleotide binding cooperativity is observed. We propose a stochastic-sequential cooperativity model to describe the coordination of ATP hydrolysis within the hexamer. In this model the apparent cooperativity is a result of hydrolysis stimulation by ATP and RNA binding to neighboring subunits rather than cooperative nucleotide binding. The translocation step appears coupled to hydrolysis, which is coordinated among three neighboring subunits. Simultaneous interaction of neighboring subunits with RNA makes the otherwise random hydrolysis sequential and processive.

Structural and silver/vanadium ratio effects on silver vanadium phosphorous oxide solution formation kinetics: impact on battery electrochemistry.

PubMed

Bock, David C; Takeuchi, Kenneth J; Marschilok, Amy C; Takeuchi, Esther S

2015-01-21

The detailed understanding of non-faradaic parasitic reactions which diminish battery calendar life is essential to the development of effective batteries for use in long life applications. The dissolution of cathode materials including manganese, cobalt and vanadium oxides in battery systems has been identified as a battery failure mechanism, yet detailed dissolution studies including kinetic analysis are absent from the literature. The results presented here provide a framework for the quantitative and kinetic analyses of the dissolution of cathode materials which will aid the broader community in more fully understanding this battery failure mechanism. In this study, the dissolution of silver vanadium oxide, representing the primary battery powering implantable cardioverter defibrillators (ICD), is compared with the dissolution of silver vanadium phosphorous oxide (Ag(w)VxPyOz) materials which were targeted as alternatives to minimize solubility. This study contains the first kinetic analyses of silver and vanadium solution formation from Ag0.48VOPO4·1.9H2O and Ag2VP2O8, in a non-aqueous battery electrolyte. The kinetic results are compared with those of Ag2VO2PO4 and Ag2V4O11 to probe the relationships among crystal structure, stoichiometry, and solubility. For vanadium, significant dissolution was observed for Ag2V4O11 as well as for the phosphate oxide Ag0.49VOPO4·1.9H2O, which may involve structural water or the existence of multiple vanadium oxidation states. Notably, the materials from the SVPO family with the lowest vanadium solubility are Ag2VO2PO4 and Ag2VP2O8. The low concentrations and solution rates coupled with their electrochemical performance make these materials interesting alternatives to Ag2V4O11 for the ICD application.

Mechanistic and kinetic investigation on OH-initiated oxidation of tetrabromobisphenol A.

PubMed

He, Maoxia; Li, Xin; Zhang, Shiqing; Sun, Jianfei; Cao, Haijie; Wang, Wenxing

2016-06-01

Detailed mechanism of the OH-initiated transformation of tetrabromobisphenol A (TBBPA) has been investigated by quantum chemical methods in this paper. Abstraction reactions of hydrogen atoms from the OH groups and CH3 groups of TBBPA are the dominant pathways of the initial reactions. The produced phenolic-type radical and alkyl-type radical may transfer to 4,4'-(ethene-1,1-diyl)bis(2,6-dibromophenol), 4-acetyl-2,6-dibromophenol and 2,6-dibromobenzoquinone at high temperature. In water, major products are 2,6-dibromo-p-hydroquinone, 4-isopropylene-2,6-dibromophenol and 4-(2-hydroxyisopropyl)-2,6-dibromophenol resulting from the addition reactions. Total rate constants of the initial reaction are 1.02 × 10(-12) cm(3) molecule(-1) s(-1) in gas phase and 1.93 × 10(-12) cm(3) molecule(-1) s(-1) in water at 298 K. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modeling complex chemical effects in turbulent nonpremixed combustion

NASA Technical Reports Server (NTRS)

Smith, Nigel S. A.

1995-01-01

Virtually all of the energy derived from the consumption of combustibles occurs in systems which utilize turbulent fluid motion. Since combustion is largely related to the mixing of fluids and mixing processes are orders of magnitude more rapid when enhanced by turbulent motion, efficiency criteria dictate that chemically powered devices necessarily involve fluid turbulence. Where combustion occurs concurrently with mixing at an interface between two reactive fluid bodies, this mode of combustion is called nonpremixed combustion. This is distinct from premixed combustion where flame-fronts propagate into a homogeneous mixture of reactants. These two modes are limiting cases in the range of temporal lag between mixing of reactants and the onset of reaction. Nonpremixed combustion occurs where this lag tends to zero, while premixed combustion occurs where this lag tends to infinity. Many combustion processes are hybrids of these two extremes with finite non-zero lag times. Turbulent nonpremixed combustion is important from a practical standpoint because it occurs in gas fired boilers, furnaces, waste incinerators, diesel engines, gas turbine combustors, and afterburners etc. To a large extent, past development of these practical systems involved an empirical methodology. Presently, efficiency standards and emission regulations are being further tightened (Correa 1993), and empiricism has had to give way to more fundamental research in order to understand and effectively model practical combustion processes (Pope 1991). A key element in effective modeling of turbulent combustion is making use of a sufficiently detailed chemical kinetic mechanism. The prediction of pollutant emission such as oxides of nitrogen (NO(x)) and sulphur (SO(x)) unburned hydrocarbons, and particulates demands the use of detailed chemical mechanisms. It is essential that practical models for turbulent nonpremixed combustion are capable of handling large numbers of 'stiff' chemical species equations.

The Tropospheric Lifetimes of Halocarbons and Their Reactions with OH Radicals: an Assessment Based on the Concentration of CO-14

NASA Technical Reports Server (NTRS)

Derwent, Richard G.; Volz-Thomas, Andreas

1990-01-01

Chemical reaction with hydroxyl radicals formed in the troposphere from ozone photolysis in the presence of methane, carbon monoxide and nitrogen oxides provides an important removal mechanism for halocarbons containing C-H and C = C double bonds. The isotropic distribution in atmospheric carbon monoxide was used to quantify the tropospheric hydroxyl radical distribution. Here, this methodology is reevaluated in the light of recent chemical kinetic data evaluations and new understandings gained in the life cycles of methane and carbon monoxide. None of these changes has forced a significant revision in the CO-14 approach. However, it is somewhat more clearly apparent how important basic chemical kinetic data are to the accurate establishment of the tropospheric hydroxyl radical distribution.

Saponification reaction system: a detailed mass transfer coefficient determination.

PubMed

Pečar, Darja; Goršek, Andreja

2015-01-01

The saponification of an aromatic ester with an aqueous sodium hydroxide was studied within a heterogeneous reaction medium in order to determine the overall kinetics of the selected system. The extended thermo-kinetic model was developed compared to the previously used simple one. The reaction rate within a heterogeneous liquid-liquid system incorporates a chemical kinetics term as well as mass transfer between both phases. Chemical rate constant was obtained from experiments within a homogeneous medium, whilst the mass-transfer coefficient was determined separately. The measured thermal profiles were then the bases for determining the overall reaction-rate. This study presents the development of an extended kinetic model for considering mass transfer regarding the saponification of ethyl benzoate with sodium hydroxide within a heterogeneous reaction medium. The time-dependences are presented for the mass transfer coefficient and the interfacial areas at different heterogeneous stages and temperatures. The results indicated an important role of reliable kinetic model, as significant difference in k(L)a product was obtained with extended and simple approach.

Reduced Chemical Kinetic Mechanisms for Hydrocarbon Fuels

DTIC Science & Technology

2006-01-01

Technologies Reaction Engineering International 77 West 200 South, Suite # 210 Salt Lake City, UT 84101 3Professor Department of Mechanical ... Engineering University of California, Berkeley Berkeley, CA 94720 4Program Leader for Computational Chemistry Lawrence Livermore National Laboratory...species by the error introduced by assuming they are in quasi-steady state. The reduced mechanisms have been compared to detailed chemistry calculations

A Detailed, Finite-Rate, Chemical Kinetics Mechanism for Monomethylhydrazine-Red Fuming Nitric Acid Systems

DTIC Science & Technology

2010-02-01

nitromethane . When the effort to develop the MMH-RFNA mechanism was discontinued in 2005, the mechanism was composed of rate expressions and...results comparable to those predicted by the theory of thermal explosions . Thermochemical parameters for molecules unique to these two mechanisms were...Bendtsen, A. B.; Miller, J. A. Nitromethane Dissociation: Implications for the CH3 + NO2 Reaction. Int. J. Chemical Kinetics 1999, 31, 591–602. Kee, R

LES of Sooting Flames

DTIC Science & Technology

2006-12-01

27], [28] on soot nucleation, and [29] on the soot formation in diesel engines . [27] discussed the unresolved problems in SOx, NOx , and soot...used LEM approach to study aerosol dynamics in engine exhaust plumes. Recently, [41] used detailed NOx mechanism combined with MOM to predict the...combustion engines . For instance, the laminar flamelet approach used by [43, 44, 45], allows the usage of a detailed chemical mechanism but is not

KINETICS AND MECHANISMS OF SOIL BIOGEOCHEMICAL PROCESSES

EPA Science Inventory

The application of kinetic studies to soil chemistry is useful to determine reaction mechanisms and fate of nutrients and environmental contaminants. How deeply one wishes to query the mechanism depends on the detail sought. Reactions that involve chemical species in more than on...

Consistent Chemical Mechanism from Collaborative Data Processing

DOE PAGES

Slavinskaya, Nadezda; Starcke, Jan-Hendrik; Abbasi, Mehdi; ...

2016-04-01

Numerical tool of Process Informatics Model (PrIMe) is mathematically rigorous and numerically efficient approach for analysis and optimization of chemical systems. It handles heterogeneous data and is scalable to a large number of parameters. The Boundto-Bound Data Collaboration module of the automated data-centric infrastructure of PrIMe was used for the systematic uncertainty and data consistency analyses of the H 2/CO reaction model (73/17) and 94 experimental targets (ignition delay times). The empirical rule for evaluation of the shock tube experimental data is proposed. The initial results demonstrate clear benefits of the PrIMe methods for an evaluation of the kinetic datamore » quality and data consistency and for developing predictive kinetic models.« less

Kinetics and mechanism of soot formation in hydrocarbon combustion

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1990-01-01

The focus of this work was on kinetic modeling. The specific objectives were: detailed modeling of soot formation in premixed flames, elucidation of the effects of fuel structure on the pathway to soot, and the development of a numerical technique for accurate modeling of soot particle coagulation and surface growth. Those tasks were successfully completed and are briefly summarized.

Large Eddy Simulation of Turbulent Combustion

DTIC Science & Technology

2005-10-01

a new method to automatically generate skeletal kinetic mechanisms for surrogate fuels, using the directed relation graph method with error...propagation, was developed. These mechanisms are guaranteed to match results obtained using detailed chemistry within a user- defined accuracy for any...specified target. They can be combined together to produce adequate chemical models for surrogate fuels. A library containing skeletal mechanisms of various

The JH2 domain and SH2-JH2 linker regulate JAK2 activity: A detailed kinetic analysis of wild type and V617F mutant kinase domains.

PubMed

Sanz Sanz, Arturo; Niranjan, Yashavanthi; Hammarén, Henrik; Ungureanu, Daniela; Ruijtenbeek, Rob; Touw, Ivo P; Silvennoinen, Olli; Hilhorst, Riet

2014-10-01

JAK2 tyrosine kinase regulates many cellular functions. Its activity is controlled by the pseudokinase (JH2) domain by still poorly understood mechanisms. The V617F mutation in the pseudokinase domain activates JAK2 and causes myeloproliferative neoplasms. We conducted a detailed kinetic analysis of recombinant JAK2 tyrosine kinase domain (JH1) and wild-type and V617F tandem kinase (JH1JH2) domains using peptide microarrays to define the functions of the kinase domains. The results show that i) JAK2 follows a random Bi-Bi reaction mechanism ii) JH2 domain restrains the activity of the JH1 domain by reducing the affinity for ATP and ATP competitive inhibitors iii) V617F decreases affinity for ATP but increases catalytic activity compared to wild-type and iv) the SH2-JH2 linker region participates in controlling activity by reducing the affinity for ATP. Copyright © 2014 Elsevier B.V. All rights reserved.

Computations of steady-state and transient premixed turbulent flames using pdf methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hulek, T.; Lindstedt, R.P.

1996-03-01

Premixed propagating turbulent flames are modeled using a one-point, single time, joint velocity-composition probability density function (pdf) closure. The pdf evolution equation is solved using a Monte Carlo method. The unclosed terms in the pdf equation are modeled using a modified version of the binomial Langevin model for scalar mixing of Valino and Dopazo, and the Haworth and Pope (HP) and Lagrangian Speziale-Sarkar-Gatski (LSSG) models for the viscous dissipation of velocity and the fluctuating pressure gradient. The source terms for the presumed one-step chemical reaction are extracted from the rate of fuel consumption in laminar premixed hydrocarbon flames, computed usingmore » a detailed chemical kinetic mechanism. Steady-state and transient solutions are obtained for planar turbulent methane-air and propane-air flames. The transient solution method features a coupling with a Finite Volume (FV) code to obtain the mean pressure field. The results are compared with the burning velocity measurements of Abdel-Gayed et al. and with velocity measurements obtained in freely propagating propane-air flames by Videto and Santavicca. The effects of different upstream turbulence fields, chemical source terms (different fuels and strained/unstrained laminar flames) and the influence of the velocity statistics models (HP and LSSG) are assessed.« less

Improved removal performance and mechanism investigation of papermaking wastewater treatment using manganese enhanced Fenton reaction.

PubMed

Wang, Yingcai; Wang, Can; Shi, Shuai; Fang, Shuai

2018-06-01

The effects of Mn(II) on Fenton system to treat papermaking wastewater and the mechanism of Mn(II) enhanced Fenton reaction were investigated in this study. The chemical oxygen demand (COD) removal efficiency was enhanced in the presence of Mn(II), which increased by 19% compared with that of the Fenton system alone. The pseudo-first order reaction kinetic rate constant of Mn(II)/Fenton system was 2.11 times higher than that of Fenton system. 67%-81% COD were removed with the increasing Mn(II) concentration from 0 to 0.8 g/L. COD removal efficiency was also enhanced in a wider pH range (3-7), which indicated the operation parameters of Fenton technology could be broadened to a milder condition. The study of the mechanism showed that Mn(II) participated in the oxidation and coagulation stages in Fenton system. In the oxidation stage, Mn(II) promotes the production of HO 2 •/ O 2 • - , then HO 2 •/ O 2 • - reacts with Fe(III) to accelerate the formation of Fe(II), and finally accelerates the production of HO•. Meantime MnMnO 3 and Fe(OH) 3 forms in the coagulation stage, facilitating the removal of suspended substances and a large amount of COD, which enhances the overall COD removal of papermaking wastewater. This study provided a detailed mechanism to improve practical applications of Fenton technology.

Simple model of inhibition of chain-branching combustion processes

NASA Astrophysics Data System (ADS)

Babushok, Valeri I.; Gubernov, Vladimir V.; Minaev, Sergei S.; Miroshnichenko, Taisia P.

2017-11-01

A simple kinetic model has been suggested to describe the inhibition and extinction of flame propagation in reaction systems with chain-branching reactions typical for hydrocarbon systems. The model is based on the generalised model of the combustion process with chain-branching reaction combined with the one-stage reaction describing the thermal mode of flame propagation with the addition of inhibition reaction steps. Inhibitor addition suppresses the radical overshoot in flame and leads to the change of reaction mode from the chain-branching reaction to a thermal mode of flame propagation. With the increase of inhibitor the transition of chain-branching mode of reaction to the reaction with straight-chains (non-branching chain reaction) is observed. The inhibition part of the model includes a block of three reactions to describe the influence of the inhibitor. The heat losses are incorporated into the model via Newton cooling. The flame extinction is the result of the decreased heat release of inhibited reaction processes and the suppression of radical overshoot with the further decrease of the reaction rate due to the temperature decrease and mixture dilution. A comparison of the results of modelling laminar premixed methane/air flames inhibited by potassium bicarbonate (gas phase model, detailed kinetic model) with the results obtained using the suggested simple model is presented. The calculations with the detailed kinetic model demonstrate the following modes of combustion process: (1) flame propagation with chain-branching reaction (with radical overshoot, inhibitor addition decreases the radical overshoot down to the equilibrium level); (2) saturation of chemical influence of inhibitor, and (3) transition to thermal mode of flame propagation (non-branching chain mode of reaction). The suggested simple kinetic model qualitatively reproduces the modes of flame propagation with the addition of the inhibitor observed using detailed kinetic models.

Exact solutions of kinetic equations in an autocatalytic growth model.

PubMed

Jędrak, Jakub

2013-02-01

Kinetic equations are introduced for the transition-metal nanocluster nucleation and growth mechanism, as proposed by Watzky and Finke [J. Am. Chem. Soc. 119, 10382 (1997)]. Equations of this type take the form of Smoluchowski coagulation equations supplemented with the terms responsible for the chemical reactions. In the absence of coagulation, we find complete analytical solutions of the model equations for the autocatalytic rate constant both proportional to the cluster mass, and the mass-independent one. In the former case, ξ(k)=s(k)(ξ(1))[proportionality]ξ(1)(k)/k was obtained, while in the latter, the functional form of s(k)(ξ(1)) is more complicated. In both cases, ξ(1)(t)=h(μ)(M(μ)(t)) is a function of the moments of the mass distribution. Both functions, s(k)(ξ(1)) and h(μ)(M(μ)), depend on the assumed mechanism of autocatalytic growth and monomer production, and not on other chemical reactions present in a system.

Kinetic Analysis of Competitive Electrocatalytic Pathways: New Insights into Hydrogen Production with Nickel Electrocatalysts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiedner, Eric S.; Brown, Houston J.; Helm, Monte L.

2016-01-20

The hydrogen production electrocatalyst Ni(PPh2NPh2)22+ (1) is capable of traversing multiple electrocatalytic pathways. When using dimethylformamidium, DMF(H)+, the mechanism of formation of H2 catalyzed by 1 changes from an ECEC to an EECC mechanism as the potential approaches the Ni(I/0) couple. Two recent electrochemical methods, current-potential analysis and foot-of-the-wave analysis (FOWA), were performed on 1 to measure the detailed chemical kinetics of the competing ECEC and EECC pathways. A sensitivity analysis was performed on the electrochemical methods using digital simulations to gain a better understanding of their strengths and limitations. Notably, chemical rate constants were significantly underestimated when not accountingmore » for electron transfer kinetics, even when electron transfer was fast enough to afford a reversible non-catalytic wave. The EECC pathway of 1 was found to be faster than the ECEC pathway under all conditions studied. Using buffered DMF: DMF(H)+ mixtures led to an increase in the catalytic rate constant (kobs) of the EECC pathway, but kobs for the ECEC pathway did not change when using buffered acid. Further kinetic analysis of the ECEC path revealed that added base increases the rate of isomerization of the exo-protonated Ni(0) isomers to the catalytically active endo-isomers, but decreases the net rate of protonation of Ni(I). FOWA on 1 did not provide accurate rate constants due to incomplete reduction of the exo-protonated Ni(I) intermediate at the foot of the wave, but FOWA could be used to estimate the reduction potential of this previously undetected intermediate. This research was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Numerical study of shock-induced combustion in methane-air mixtures

NASA Technical Reports Server (NTRS)

Yungster, Shaye; Rabinowitz, Martin J.

1993-01-01

The shock-induced combustion of methane-air mixtures in hypersonic flows is investigated using a new reaction mechanism consisting of 19 reacting species and 52 elementary reactions. This reduced model is derived from a full kinetic mechanism via the Detailed Reduction technique. Zero-dimensional computations of several shock-tube experiments are presented first. The reaction mechanism is then combined with a fully implicit Navier-Stokes computational fluid dynamics (CFD) code to conduct numerical simulations of two-dimensional and axisymmetric shock-induced combustion experiments of stoichiometric methane-air mixtures at a Mach number of M = 6.61. Applications to the ram accelerator concept are also presented.

Modeling of the HiPco process for carbon nanotube production. I. Chemical kinetics

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.; Gokcen, Tahir; Meyyappan, M.

2002-01-01

A chemical kinetic model is developed to help understand and optimize the production of single-walled carbon nanotubes via the high-pressure carbon monoxide (HiPco) process, which employs iron pentacarbonyl as the catalyst precursor and carbon monoxide as the carbon feedstock. The model separates the HiPco process into three steps, precursor decomposition, catalyst growth and evaporation, and carbon nanotube production resulting from the catalyst-enhanced disproportionation of carbon monoxide, known as the Boudouard reaction: 2 CO(g)-->C(s) + CO2(g). The resulting detailed model contains 971 species and 1948 chemical reactions. A second model with a reduced reaction set containing 14 species and 22 chemical reactions is developed on the basis of the detailed model and reproduces the chemistry of the major species. Results showing the parametric dependence of temperature, total pressure, and initial precursor partial pressures are presented, with comparison between the two models. The reduced model is more amenable to coupled reacting flow-field simulations, presented in the following article.

Multivariate curve resolution of incomplete fused multiset data from chromatographic and spectrophotometric analyses for drug photostability studies.

PubMed

De Luca, Michele; Ragno, Gaetano; Ioele, Giuseppina; Tauler, Romà

2014-07-21

An advanced and powerful chemometric approach is proposed for the analysis of incomplete multiset data obtained by fusion of hyphenated liquid chromatographic DAD/MS data with UV spectrophotometric data from acid-base titration and kinetic degradation experiments. Column- and row-wise augmented data blocks were combined and simultaneously processed by means of a new version of the multivariate curve resolution-alternating least squares (MCR-ALS) technique, including the simultaneous analysis of incomplete multiset data from different instrumental techniques. The proposed procedure was applied to the detailed study of the kinetic photodegradation process of the amiloride (AML) drug. All chemical species involved in the degradation and equilibrium reactions were resolved and the pH dependent kinetic pathway described. Copyright © 2014 Elsevier B.V. All rights reserved.

Automated Transition State Theory Calculations for High-Throughput Kinetics.

PubMed

Bhoorasingh, Pierre L; Slakman, Belinda L; Seyedzadeh Khanshan, Fariba; Cain, Jason Y; West, Richard H

2017-09-21

A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

“Towards building better linkages between aqueous phase ...

EPA Pesticide Factsheets

Currently, CMAQ’s aqueous phase chemistry routine (AQCHEM-base) assumes Henry’s Law equilibrium and employs a forward Euler method to solve a small set of oxidation equations, considering the additional processes of aitken scavenging and wet deposition in series and employing a bisection method to calculate H+ concentrations. With potentially hundreds of reactions that may be important in cloud water and only seven reactions in the current model, expansion of the existing mechanism is an important area of investigation. However, with the current mechanism hardwired into the solver code, the module is difficult to expand with additional chemistry. It also ignores the impacts of mass transfer limitations on cloud chemistry which may be significant. Here, the Kinetic PreProcessor has been applied to generate a Rosenbrock solver for the CMAQ v5.0.1 aqueous phase chemistry mechanism. The module has been updated to simultaneously solve kinetic mass transfer between the phases, dissociation/association, chemical kinetics, Aitken scavenging, and wet deposition. This will allow for easier expansion of the chemical mechanism in the future and a better link between aqueous phase chemistry and droplet microphysics. The National Exposure Research Laboratory (NERL) Atmospheric Modeling and Analysis Division (AMAD) conducts research in support of EPA mission to protect human health and the environment. AMAD research program is engaged in developing and evaluating pre

Mechanistic and Structural Analysis of Drosophila melanogaster Arylalkylamine N-Acetyltransferases

PubMed Central

2015-01-01

Arylalkylamine N-acetyltransferase (AANAT) catalyzes the penultimate step in the biosynthesis of melatonin and other N-acetylarylalkylamides from the corresponding arylalkylamine and acetyl-CoA. The N-acetylation of arylalkylamines is a critical step in Drosophila melanogaster for the inactivation of the bioactive amines and the sclerotization of the cuticle. Two AANAT variants (AANATA and AANATB) have been identified in D. melanogaster, in which AANATA differs from AANATB by the truncation of 35 amino acids from the N-terminus. We have expressed and purified both D. melanogaster AANAT variants (AANATA and AANATB) in Escherichia coli and used the purified enzymes to demonstrate that this N-terminal truncation does not affect the activity of the enzyme. Subsequent characterization of the kinetic and chemical mechanism of AANATA identified an ordered sequential mechanism, with acetyl-CoA binding first, followed by tyramine. We used a combination of pH–activity profiling and site-directed mutagenesis to study prospective residues believed to function in AANATA catalysis. These data led to an assignment of Glu-47 as the general base in catalysis with an apparent pKa of 7.0. Using the data generated for the kinetic mechanism, structure–function relationships, pH–rate profiles, and site-directed mutagenesis, we propose a chemical mechanism for AANATA. PMID:25406072

Principal component analysis acceleration of rovibrational coarse-grain models for internal energy excitation and dissociation

NASA Astrophysics Data System (ADS)

Bellemans, Aurélie; Parente, Alessandro; Magin, Thierry

2018-04-01

The present work introduces a novel approach for obtaining reduced chemistry representations of large kinetic mechanisms in strong non-equilibrium conditions. The need for accurate reduced-order models arises from compression of large ab initio quantum chemistry databases for their use in fluid codes. The method presented in this paper builds on existing physics-based strategies and proposes a new approach based on the combination of a simple coarse grain model with Principal Component Analysis (PCA). The internal energy levels of the chemical species are regrouped in distinct energy groups with a uniform lumping technique. Following the philosophy of machine learning, PCA is applied on the training data provided by the coarse grain model to find an optimally reduced representation of the full kinetic mechanism. Compared to recently published complex lumping strategies, no expert judgment is required before the application of PCA. In this work, we will demonstrate the benefits of the combined approach, stressing its simplicity, reliability, and accuracy. The technique is demonstrated by reducing the complex quantum N2(g+1Σ) -N(S4u ) database for studying molecular dissociation and excitation in strong non-equilibrium. Starting from detailed kinetics, an accurate reduced model is developed and used to study non-equilibrium properties of the N2(g+1Σ) -N(S4u ) system in shock relaxation simulations.

Quasiglobal reaction model for ethylene combustion

NASA Technical Reports Server (NTRS)

Singh, D. J.; Jachimowski, Casimir J.

1994-01-01

The objective of this study is to develop a reduced mechanism for ethylene oxidation. The authors are interested in a model with a minimum number of species and reactions that still models the chemistry with reasonable accuracy for the expected combustor conditions. The model will be validated by comparing the results to those calculated with a detailed kinetic model that has been validated against the experimental data.

Deuterium Isotope Effects During HMX Combustion: Chemical Kinetic Burn Rate Control Mechanism Verified

DTIC Science & Technology

1989-01-01

experience de gen dieses Experiments. Der 10 KDIE-Wert legt nahe. dab die combustion statique. La valeur de l’effet isotopique primaire laisse...anomaler combustion globale. Des 6tudes publifes par ailleurs confirment cette KDIE-Wert bei 10,4 MPa wirL angegeben. Diese KDIE-Experimente hypoth~se

CHEMICAL TRANSFORMATION MODULES FOR EULERIAN ACID DEPOSITION MODELS. VOLUME 1. THE GAS-PHASE CHEMISTRY

EPA Science Inventory

This study focuses on the review and evaluation of mechanistic and kinetic data for the gas-phase reactions that lead to the production of acidic substances in the environment. A master mechanism is designed that treats oxides, sulfur dioxide, ozone, hydrogen peroxide, ammonia, t...

Accelerating Calculations of Reaction Dissipative Particle Dynamics in LAMMPS

DTIC Science & Technology

2017-05-17

order reaction mechanism, the best acceleration was 6.1 times. For a larger, more chemically detailed mechanism, the best acceleration exceeded 60 times...simulations at previously inaccessible scales. A principle feature of DPD-RX is its ability to model chemical reactions within each CG particle. The...change in composition due to chemical reactions is described by a system of ordinary differential equations (ODEs) that are evaluated at each DPD time

Formulation reproducing the ignition delays simulated by a detailed mechanism: Application to n-heptane combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imbert, Bruno; Lafosse, Fabien; Catoire, Laurent

2008-11-15

This article is part of the project to model the kinetics of high-temperature combustions, occurring behind shock waves and in detonation waves. The ''conventional'' semi-empirical correlations of ignition delays have been reformulated, by keeping the Arrhenius equation form. It is shown how a polynomial with 3{sup N} coefficients (where N element of is the number of adjustable kinetic parameters, likely to be simultaneously chosen among the temperature T, the pressure P, the inert fraction X{sub Ar}, and the equivalence ratio {phi}) can reproduce the delays predicted by the Curran et al. [H.J. Curran, P. Gaffuri, W.J. Pitz, C.K. Westbrook, Combust.more » Flame 129 (2002) 253-280] detailed mechanism (565 species and 2538 reactions), over a wide range of conditions (comparable with the validity domain). The deviations between the simulated times and their fits (typically 1%) are definitely lower than the uncertainties related to the mechanism (at least 25%). In addition, using this new formalism to evaluate these durations is about 10{sup 6} times faster than simulating them with SENKIN (CHEMKIN III package) and only 10 times slower than using the classical correlations. The adaptation of the traditional method for predicting delays is interesting for modeling, because those performances are difficult to obtain simultaneously with other reduction methods (either purely mathematical, chemical, or even mixed). After a physical and mathematical justification of the proposed formalism, some of its potentialities for n-heptane combustion are presented. In particular, the trends of simulated delays and activation energies are shown for {sub T} {sub element} {sub of} {sub [1500} {sub K,1900} {sub K},} {sub P} {sub element} {sub of} {sub [10kPa,1MPa]}, X{sub Ar} element of [0,0.7], and {phi} element of {sub [0.25,4.0]}. (author)« less

Evidence and implications of direct charge excitation as the dominant mechanism in plasmon-mediated photocatalysis

DOE PAGES

Boerigter, Calvin; Campana, Robert; Morabito, Matthew; ...

2016-01-28

Plasmonic metal nanoparticles enhance chemical reactions on their surface when illuminated with light of particular frequencies. It has been shown that these processes are driven by excitation of localized surface plasmon resonance (LSPR). The interaction of LSPR with adsorbate orbitals can lead to the injection of energized charge carriers into the adsorbate, which can result in chemical transformations. The mechanism of the charge injection process (and role of LSPR) is not well understood. Here we shed light on the specifics of this mechanism by coupling optical characterization methods, mainly wavelength-dependent Stokes and anti-Stokes SERS, with kinetic analysis of photocatalytic reactionsmore » in an Ag nanocube–methylene blue plasmonic system. We propose that localized LSPR-induced electric fields result in a direct charge transfer within the molecule–adsorbate system. Lastly, these observations provide a foundation for the development of plasmonic catalysts that can selectively activate targeted chemical bonds, since the mechanism allows for tuning plasmonic nanomaterials in such a way that illumination can selectively enhance desired chemical pathways.« less

Ab initio calculations and kinetic modeling of thermal conversion of methyl chloride: implications for gasification of biomass.

PubMed

Singla, Mallika; Rasmussen, Morten Lund; Hashemi, Hamid; Wu, Hao; Glarborg, Peter; Pelucchi, Matteo; Faravelli, Tiziano; Marshall, Paul

2018-04-25

Limitations in current hot gas cleaning methods for chlorine species from biomass gasification may be a challenge for end use such as gas turbines, engines, and fuel cells, all requiring very low levels of chlorine. During devolatilization of biomass, chlorine is released partly as methyl chloride. In the present work, the thermal conversion of CH3Cl under gasification conditions was investigated. A detailed chemical kinetic model for pyrolysis and oxidation of methyl chloride was developed and validated against selected experimental data from the literature. Key reactions of CH2Cl with O2 and C2H4 for which data are scarce were studied by ab initio methods. The model was used to analyze the fate of methyl chloride in gasification processes. The results indicate that CH3Cl emissions will be negligible for most gasification technologies, but could be a concern for fluidized bed gasifiers, in particular in low-temperature gasification. The present work illustrates how ab initio theory and chemical kinetic modeling can help to resolve emission issues for thermal processes in industrial scale.

Hydrogen and Ethene Plasma Assisted Ignition by NS discharge at Elevated Temperatures

NASA Astrophysics Data System (ADS)

Starikovskiy, Andrey

2015-09-01

The kinetics of ignition in lean H2:O2:Ar and C2H4:O2:Ar mixtures has been studied experimentally and numerically after a high-voltage nanosecond discharge. The ignition delay time behind a reflected shock wave was measured with and without the discharge. It was shown that the initiation of the discharge with a specific deposited energy of 10 - 30 mJ/cm3 leads to an order of magnitude decrease in the ignition delay time. Discharge processes and following chain chemical reactions with energy release were simulated. The generation of atoms, radicals and excited and charged particles was numerically simulated using the measured time - resolved discharge current and electric field in the discharge phase. The calculated densities of the active particles were used as input data to simulate plasma-assisted ignition. Good agreement was obtained between the calculated ignition delay times and the experimental data. It follows from the analysis of the calculated results that the main mechanism of the effect of gas discharge on the ignition of hydrocarbons is the electron impact dissociation of O2 molecules in the discharge phase. Detailed kinetic mechanism for plasma assisted ignition of hydrogen and ethene is elaborated and verified.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 tomore » 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.« less

Modelling and kinetics studies of a corn-rape blend combustion in an oxy-fuel atmosphere.

PubMed

López, R; Fernández, C; Martínez, O; Sánchez, M E

2015-05-01

A kinetic oxy-combustion study of a previously optimized lignocellulose blend is proposed. Kinetic and diffusion control mechanism are considered. The proposed correlations fit properly with the experimental results and diffusion effects are identified as be important enough to be taken into account. Afterwards, with the results obtained in the kinetic study, a detailed consecutive and parallel kinetic scheme is proposed for modelling the oxy-combustion of the blend. A discussion of the temperature and concentration profiles are included. Variation of products final distribution is considered. Smaller particles than 0.001 m are proposed for reducing temperature and concentration profiles and obtaining a good final product distribution. CO2-char reaction is identified as one of the most important step to be optimized for obtaining the lowest final residue. In this study, char is mainly oxidised at 950 K and this situation is attributed to an optimized blending of the bioresidues. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Power of Integrating Kinetic Isotope Effects into the Formalism of the Michaelis-Menten Equation

PubMed Central

Klinman, Judith P.

2014-01-01

The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued to this day. This review discusses a family of eukaryotic copper proteins that includes dopamine β-monooxygenase, tyramine β-monooxygenase, and peptidylglycine α-amidating enzyme, responsible for the synthesis of the neuro-active compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. Highlighted are results that show how combining kinetic isotope effects with initial rate parameters permits an evaluation of: (i) the order of substrate binding to multi-substrate enzymes; (ii) the magnitude of individual rate constants in complex, multi-step reactions; (iii) the identification of chemical intermediates; and (iv) the role of non-classical (tunneling) behavior in C–H activation. PMID:23937475

One-dimensional turbulence modeling of a turbulent counterflow flame with comparison to DNS

DOE PAGES

Jozefik, Zoltan; Kerstein, Alan R.; Schmidt, Heiko; ...

2015-06-01

The one-dimensional turbulence (ODT) model is applied to a reactant-to-product counterflow configuration and results are compared with DNS data. The model employed herein solves conservation equations for momentum, energy, and species on a one dimensional (1D) domain corresponding to the line spanning the domain between nozzle orifice centers. The effects of turbulent mixing are modeled via a stochastic process, while the Kolmogorov and reactive length and time scales are explicitly resolved and a detailed chemical kinetic mechanism is used. Comparisons between model and DNS results for spatial mean and root-mean-square (RMS) velocity, temperature, and major and minor species profiles aremore » shown. The ODT approach shows qualitatively and quantitatively reasonable agreement with the DNS data. Scatter plots and statistics conditioned on temperature are also compared for heat release rate and all species. ODT is able to capture the range of results depicted by DNS. As a result, conditional statistics show signs of underignition.« less

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

NASA Astrophysics Data System (ADS)

Zhang, Rui; Jiang, Shuai; Liu, Yi-Rong; Wen, Hui; Feng, Ya-Juan; Huang, Teng; Huang, Wei

2018-05-01

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid's weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 tomore » 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.« less

A Pre-Steady State Kinetic Analysis of the αY60W mutant of trans-3-Chloroacrylic Acid Dehalogenase: Implications for the Mechanism of the Wild-type Enzyme†

PubMed Central

Huddleston, Jamison P.; Schroeder, Gottfried K.; Johnson, Kenneth A.; Whitman, Christian P.

2012-01-01

The bacterial degradation of the nematicide 1,3-dichloropropene, an isomeric mixture, requires the action of trans- and cis-3-chloracrylic acid dehalogenase (CaaD and cis-CaaD, respectively). Both enzymes are tautomerase superfamily members and share a core catalytic mechanism for the hydrolytic dehalogenation of the respective isomer of 3-haloacrylate. The observation that cis-CaaD requires two additional residues raises the question of how CaaD carries out a comparable reaction with fewer catalytic residues. As part of an effort to determine the basis for the apparently simpler CaaD-catalyzed reaction, the kinetic mechanism was determined by stopped-flow and chemical quench techniques using a fluorescent mutant form of the enzyme, αY60W-CaaD, and trans-3-bromoacrylate as the substrate. The data from these experiments as well as bromide inhibition studies are best accommodated by a six-step model that provides individual rate constants for substrate binding, chemistry, and a proposed conformational change occurring after chemistry followed by release of malonate semialdehyde and bromide. The conformational change and product release rates are comparable and together they limit the rate of turnover. The kinetic analysis and modeling studies validate the αY60W-CaaD mutant as an accurate reporter of active site events during the course of the enzyme-catalyzed reaction. The kinetic mechanism for the αY60W-CaaD-catalyzed reaction is comparable to that obtained for the cis-CaaD-catalyzed reaction. The kinetic model and the validated αY60W-CaaD mutant set the stage for an analysis of active site mutants to explore the contributions of individual catalytic residues and the basis for the simplicity of the reaction. PMID:23110338

Autoignition response of n-butanol and its blend with primary reference fuel constituents of gasoline.

DOE PAGES

Kumar, Kamal; Zhang, Yu; Sung, Chi -Jen; ...

2015-04-13

We study the influence of blending n-butanol on the ignition delay times of n-heptane and iso-octane, the primary reference fuels for gasoline. The ignition delay times are measured using a rapid compression machine, with an emphasis on the low-to-intermediate temperature conditions. The experiments are conducted at equivalence ratios of 0.4 and 1.0, for a compressed pressure of 20 bar, with the temperatures at the end of compression ranging from 613 K to 979 K. The effect of n-butanol addition on the development of the two-stage ignition characteristics for the two primary reference fuels is also examined. The experimental results aremore » compared to predictions obtained using a detailed chemical kinetic mechanism, which has been obtained by a systematic merger of previously reported base models for the combustion of the individual fuel constituents. In conclusion, a sensitivity analysis on the base, and the merged models, is also performed to understand the dependence of autoignition delay times on the model parameters.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Kamal; Zhang, Yu; Sung, Chi -Jen

We study the influence of blending n-butanol on the ignition delay times of n-heptane and iso-octane, the primary reference fuels for gasoline. The ignition delay times are measured using a rapid compression machine, with an emphasis on the low-to-intermediate temperature conditions. The experiments are conducted at equivalence ratios of 0.4 and 1.0, for a compressed pressure of 20 bar, with the temperatures at the end of compression ranging from 613 K to 979 K. The effect of n-butanol addition on the development of the two-stage ignition characteristics for the two primary reference fuels is also examined. The experimental results aremore » compared to predictions obtained using a detailed chemical kinetic mechanism, which has been obtained by a systematic merger of previously reported base models for the combustion of the individual fuel constituents. In conclusion, a sensitivity analysis on the base, and the merged models, is also performed to understand the dependence of autoignition delay times on the model parameters.« less

Evidence of a kinetic isotope effect in nanoaluminum and water combustion.

PubMed

Tappan, Bryce C; Dirmyer, Matthew R; Risha, Grant A

2014-08-25

The normally innocuous combination of aluminum and water becomes violently reactive on the nanoscale. Research in the field of the combustion of nanoparticulate aluminum has important implications in the design of molecular aluminum clusters, hydrogen storage systems, as well as energetic formulations which could use extraterrestrial water for space propulsion. However, the mechanism that controls the reaction speed is poorly understood. While current models for micron-sized aluminum water combustion reactions place heavy emphasis on diffusional limitations, as reaction scales become commensurate with diffusion lengths (approaching the nanoscale) reaction rates have long been suspected to depend on chemical kinetics, but have never been definitely measured. The combustion analysis of nanoparticulate aluminum with H2O or D2O is presented. Different reaction rates resulting from the kinetic isotope effect are observed. The current study presents the first-ever observed kinetic isotope effect in a metal combustion reaction and verifies that chemical reaction kinetics play a major role in determining the global burning rate. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comprehensive experimental and detailed chemical kinetic modelling study of 2,5-dimethylfuran pyrolysis and oxidation

PubMed Central

Somers, Kieran P.; Simmie, John M.; Gillespie, Fiona; Conroy, Christine; Black, Gráinne; Metcalfe, Wayne K.; Battin-Leclerc, Frédérique; Dirrenberger, Patricia; Herbinet, Olivier; Glaude, Pierre-Alexandre; Dagaut, Philippe; Togbé, Casimir; Yasunaga, Kenji; Fernandes, Ravi X.; Lee, Changyoul; Tripathi, Rupali; Curran, Henry J.

2013-01-01

The pyrolytic and oxidative behaviour of the biofuel 2,5-dimethylfuran (25DMF) has been studied in a range of experimental facilities in order to investigate the relatively unexplored combustion chemistry of the title species and to provide combustor relevant experimental data. The pyrolysis of 25DMF has been re-investigated in a shock tube using the single-pulse method for mixtures of 3% 25DMF in argon, at temperatures from 1200–1350 K, pressures from 2–2.5 atm and residence times of approximately 2 ms. Ignition delay times for mixtures of 0.75% 25DMF in argon have been measured at atmospheric pressure, temperatures of 1350–1800 K at equivalence ratios (ϕ) of 0.5, 1.0 and 2.0 along with auto-ignition measurements for stoichiometric fuel in air mixtures of 25DMF at 20 and 80 bar, from 820–1210 K. This is supplemented with an oxidative speciation study of 25DMF in a jet-stirred reactor (JSR) from 770–1220 K, at 10.0 atm, residence times of 0.7 s and at ϕ = 0.5, 1.0 and 2.0. Laminar burning velocities for 25DMF-air mixtures have been measured using the heat-flux method at unburnt gas temperatures of 298 and 358 K, at atmospheric pressure from ϕ = 0.6–1.6. These laminar burning velocity measurements highlight inconsistencies in the current literature data and provide a validation target for kinetic mechanisms. A detailed chemical kinetic mechanism containing 2768 reactions and 545 species has been simultaneously developed to describe the combustion of 25DMF under the experimental conditions described above. Numerical modelling results based on the mechanism can accurately reproduce the majority of experimental data. At high temperatures, a hydrogen atom transfer reaction is found to be the dominant unimolecular decomposition pathway of 25DMF. The reactions of hydrogen atom with the fuel are also found to be important in predicting pyrolysis and ignition delay time experiments. Numerous proposals are made on the mechanism and kinetics of the previously unexplored intermediate temperature combustion pathways of 25DMF. Hydroxyl radical addition to the furan ring is highlighted as an important fuel consuming reaction, leading to the formation of methyl vinyl ketone and acetyl radical. The chemically activated recombination of HȮ2 or CH3Ȯ2 with the 5-methyl-2-furanylmethyl radical, forming a 5-methyl-2-furylmethanoxy radical and ȮH or CH3Ȯ radical is also found to exhibit significant control over ignition delay times, as well as being important reactions in the prediction of species profiles in a JSR. Kinetics for the abstraction of a hydrogen atom from the alkyl side-chain of the fuel by molecular oxygen and HȮ2 radical are found to be sensitive in the estimation of ignition delay times for fuel-air mixtures from temperatures of 820–1200 K. At intermediate temperatures, the resonantly stabilised 5-methyl-2-furanylmethyl radical is found to predominantly undergo bimolecular reactions, and as a result sub-mechanisms for 5-methyl-2-formylfuran and 5-methyl-2-ethylfuran, and their derivatives, have also been developed with consumption pathways proposed. This study is the first to attempt to simulate the combustion of these species in any detail, although future refinements are likely necessary. The current study illustrates both quantitatively and qualitatively the complex chemical behavior of what is a high potential biofuel. Whilst the current work is the most comprehensive study on the oxidation of 25DMF in the literature to date, the mechanism cannot accurately reproduce laminar burning velocity measurements over a suitable range of unburnt gas temperatures, pressures and equivalence ratios, although discrepancies in the experimental literature data are highlighted. Resolving this issue should remain a focus of future work. PMID:24273333

Oxygen Atom Exchange between H2O and Non-Heme Oxoiron(IV) Complexes: Ligand Dependence and Mechanism.

PubMed

Puri, Mayank; Company, Anna; Sabenya, Gerard; Costas, Miquel; Que, Lawrence

2016-06-20

Detailed studies of oxygen atom exchange (OAE) between H2(18)O and synthetic non-heme oxoiron(IV) complexes supported by tetradentate and pentadentate ligands provide evidence that they proceed by a common mechanism but within two different kinetic regimes, with OAE rates that span 2 orders of magnitude. The first kinetic regime involves initial reversible water association to the Fe(IV) complex, which is evidenced by OAE rates that are linearly dependent on [H2(18)O] and H2O/D2O KIEs of 1.6, while the second kinetic regime involves a subsequent rate determining proton-transfer step between the bound aqua and oxo ligands that is associated with saturation behavior with [H2(18)O] and much larger H2O/D2O KIEs of 5-6. [Fe(IV)(O)(TMC)(MeCN)](2+) (1) and [Fe(IV)(O)(MePy2TACN)](2+) (9) are examples of complexes that exhibit kinetic behavior in the first regime, while [Fe(IV)(O)(N4Py)](2+) (3), [Fe(IV)(O)(BnTPEN)](2+) (4), [Fe(IV)(O)(1Py-BnTPEN)](2+) (5), [Fe(IV)(O)(3Py-BnTPEN)](2+) (6), and [Fe(IV)(O)(Me2Py2TACN)](2+) (8) represent complexes that fall in the second kinetic regime. Interestingly, [Fe(IV)(O)(PyTACN)(MeCN)](2+) (7) exhibits a linear [H2(18)O] dependence below 0.6 M and saturation above 0.6 M. Analysis of the temperature dependence of the OAE rates shows that most of these complexes exhibit large and negative activation entropies, consistent with the proposed mechanism. One exception is complex 9, which has a near-zero activation entropy and is proposed to undergo ligand-arm dissociation during the RDS to accommodate H2(18)O binding. These results show that the observed OAE kinetic behavior is highly dependent on the nature of the supporting ligand and are of relevance to studies of non-heme oxoiron(IV) complexes in water or acetonitrile/water mixtures for applications in photocatalysis and water oxidation chemistry.

Chemical mechanism of D-amino acid oxidase from Rhodotorula gracilis: pH dependence of kinetic parameters.

PubMed Central

Ramón, F; Castillón, M; De La Mata, I; Acebal, C

1998-01-01

The variation of kinetic parameters of d-amino acid oxidase from Rhodotorula gracilis with pH was used to gain information about the chemical mechanism of the oxidation of D-amino acids catalysed by this flavoenzyme. d-Alanine was the substrate used. The pH dependence of Vmax and Vmax/Km for alanine as substrate showed that a group with a pK value of 6.26-7.95 (pK1) must be unprotonated and a group with a pK of 10.8-9.90 (pK2) must be protonated for activity. The lower pK value corresponded to a group on the enzyme involved in catalysis and whose protonation state was not important for binding. The higher pK value was assumed to be the amino group of the substrate. Profiles of pKi for D-aspartate as competitive inhibitor showed that binding is prevented when a group on the enzyme with a pK value of 8.4 becomes unprotonated; this basic group was not detected in Vmax/Km profiles suggesting its involvement in binding of the beta-carboxylic group of the inhibitor. PMID:9461524

Precise non-steady-state characterization of solid active materials with no preliminary mechanistic assumptions

DOE PAGES

Constales, Denis; Yablonsky, Gregory S.; Wang, Lucun; ...

2017-04-25

This paper presents a straightforward and user-friendly procedure for extracting a reactivity characterization of catalytic reactions on solid materials under non-steady-state conditions, particularly in temporal analysis of products (TAP) experiments. The kinetic parameters derived by this procedure can help with the development of detailed mechanistic understanding. The procedure consists of the following two major steps: 1) Three “Laplace reactivities” are first determined based on the moments of the exit flow pulse response data; 2) Depending on a select kinetic model, kinetic constants of elementary reaction steps can then be expressed as a function of reactivities and determined accordingly. In particular,more » we distinguish two calculation methods based on the availability and reliability of reactant and product data. The theoretical results are illustrated using a reverse example with given parameters as well as an experimental example of CO oxidation over a supported Au/SiO 2 catalyst. The procedure presented here provides an efficient tool for kinetic characterization of many complex chemical reactions.« less

A detailed kinetic modeling study of aromatics formation in laminar premixed acetylene and ethylene flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, H.; Frenklach, M.

1997-07-01

A computational study was performed for the formation and growth of polycyclic aromatic hydrocarbons (PAHs) in laminar premixed acetylene and ethylene flames. A new detailed reaction mechanism describing fuel pyrolysis and oxidation, benzene formation, and PAH mass growth and oxidation is presented and critically tested. It is shown that the reaction model predicts reasonably well the concentration profiles of major and intermediate species and aromatic molecules in a number of acetylene and ethylene flames reported in the literature. It is demonstrated that reactions of n-C{sub 4}H{sub x} + C{sub 2}H{sub 2} leading to the formation of one-ring aromatics are asmore » important as the propargyl recombination, and hence must be included in kinetic modeling of PAH formation in hydrocarbon flames. It is further demonstrated that the mass growth of PAHs can be accounted for by the previously proposed H-abstraction-C{sub 2}H{sub 2}-addiction mechanism.« less

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate †

PubMed Central

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

2009-01-01

O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes. PMID:18973344

Insights into the Lactonase Mechanism of Serum Paraoxonase 1 (PON1): Experimental and Quantum Mechanics/Molecular Mechanics (QM/MM) Studies.

PubMed

Le, Quang Anh Tuan; Kim, Seonghoon; Chang, Rakwoo; Kim, Yong Hwan

2015-07-30

Serum paraoxonase 1 (PON1) is a versatile enzyme for the hydrolysis of various substrates (e.g., lactones, phosphotriesters) and for the formation of a promising chemical platform γ-valerolactone. Elucidation of the PON1-catalyzed lactonase reaction mechanism is very important for understanding the enzyme function and for engineering this enzyme for specific applications. Kinetic study and hybrid quantum mechanics/molecular mechanics (QM/MM) method were used to investigate the PON1-catalyzed lactonase reaction of γ-butyrolactone (GBL) and (R)-γ-valerolactone (GVL). The activation energies obtained from the QM/MM calculations were in good agreement with the experiments. Interestingly, the QM/MM energy barriers at MP2/3-21G(d,p) level for the lactonase of GVL and GBL were respectively 14.3-16.2 and 11.5-13.1 kcal/mol, consistent with the experimental values (15.57 and 14.73 kcal/mol derived from respective kcat values of 36.62 and 147.21 s(-1)). The QM/MM energy barriers at MP2/6-31G(d) and MP2/6-31G(d,p) levels were also in relatively good agreements with the experiments. Importantly, the difference in the QM/MM energy barriers at MP2 level with all investigated basis sets for the lactonase of GVL and GBL were in excellent agreement with the experiments (0.9-3.1 and 0.8 kcal/mol, respectively). A detailed mechanism for the PON1-catalyzed lactonase reaction was also proposed in this study.

Automated Simplification of Full Chemical Mechanisms

NASA Technical Reports Server (NTRS)

Norris, A. T.

1997-01-01

A code has been developed to automatically simplify full chemical mechanisms. The method employed is based on the Intrinsic Low Dimensional Manifold (ILDM) method of Maas and Pope. The ILDM method is a dynamical systems approach to the simplification of large chemical kinetic mechanisms. By identifying low-dimensional attracting manifolds, the method allows complex full mechanisms to be parameterized by just a few variables; in effect, generating reduced chemical mechanisms by an automatic procedure. These resulting mechanisms however, still retain all the species used in the full mechanism. Full and skeletal mechanisms for various fuels are simplified to a two dimensional manifold, and the resulting mechanisms are found to compare well with the full mechanisms, and show significant improvement over global one step mechanisms, such as those by Westbrook and Dryer. In addition, by using an ILDM reaction mechanism in a CID code, a considerable improvement in turn-around time can be achieved.

Kinetics of liquid-solid reactions in naphthenic acid conversion and Kraft pulping

NASA Astrophysics Data System (ADS)

Yang, Ling

Two liquid-solid reactions, in which the morphology of the solid changes as the reactions proceeds, were examined. One is the NA conversion in oil by decarboxylation on metal oxides and carbonates, and the other is the Kraft pulping in which lignin removal by delignification reaction. In the study of the NA conversion, CaO was chosen as the catalyst for the kinetic study from the tested catalysts based on NA conversion. Two reaction mixtures, carrier oil plus commercial naphthenic acids and heavy vacuum gas oil (HVGO) from Athabasca bitumen, were applied in the kinetic study. The influence of TAN, temperature, and catalyst loading on the NA conversion and decarboxylation were studied systematically. The results showed that the removal rate of TAN and the decarboxylation of NA were both independent of the concentration of NA over the range studied, and significantly dependent on reaction temperature. The data from analyzing the spent catalyst demonstrated that calcium naphthenate was an intermediate of the decarboxylation reaction of NA, and the decomposition of calcium naphthenate was a rate-determining step. In the study on the delignification of the Kraft pulping, a new mechanism was proposed for the heterogeneous delignification reaction during the Kraft pulping process. In particular, the chemical reaction mechanism took into account the heterogeneous nature of Kraft pulping. Lignin reacted in parallel with sodium hydroxide and sodium sulfide. The mechanism consists of three key kinetic steps: (1) adsorption of hydroxide and hydrosulfide ions on lignin; (2) surface reaction on the solid surface to produce degraded lignin products; and (3) desorption of degradation products from the solid surface. The most important step for the delignification process is the surface reaction, rather than the reactions occurring in the liquid phase. A kinetic model has, thus, been developed based on the proposed mechanism. The derived kinetic model showed that the mechanism could be employed to predict the pulping behavior under a variety of conditions with good accuracy.

Homing orientation in salamanders: A mechanism involving chemical cues

NASA Technical Reports Server (NTRS)

Madison, D. M.

1972-01-01

A detailed description is given of experiments made to determine the senses and chemical cues used by salamanders for homing orientation. Sensory impairment and cue manipulative techniques were used in the investigation. All experiments were carried out at night. Results show that sense impaired animals did not home as readily as those who were blind but retained their sensory mechanism. This fact suggests that the olfactory mechanism is necessary for homing in the salamander. It was determined that after the impaired salamander regenerated its sensory mechanism it too returned home. It was concluded that homing ability in salamanders is direction independent, distant dependent, and vision independent.

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave.

PubMed

Gershman, Daniel J; F-Viñas, Adolfo; Dorelli, John C; Boardsen, Scott A; Avanov, Levon A; Bellan, Paul M; Schwartz, Steven J; Lavraud, Benoit; Coffey, Victoria N; Chandler, Michael O; Saito, Yoshifumi; Paterson, William R; Fuselier, Stephen A; Ergun, Robert E; Strangeway, Robert J; Russell, Christopher T; Giles, Barbara L; Pollock, Craig J; Torbert, Roy B; Burch, James L

2017-03-31

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA's Magnetospheric Multiscale (MMS) mission, we utilize Earth's magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electrons confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. The investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.

Kinetic and mechanistic reactivity. Isoprene impact on ozone levels in an urban area near Tijuca Forest, Rio de Janeiro.

PubMed

da Silva, Cleyton Martins; da Silva, Luane Lima; Corrêa, Sergio Machado; Arbilla, Graciela

2016-12-01

Volatile organic compounds (VOCs) play a central role in atmospheric chemistry. In this work, the kinetic and mechanistic reactivities of VOCs are analyzed, and the contribution of the organic compounds emitted by anthropogenic and natural sources is estimated. VOCs react with hydroxyl radicals and other photochemical oxidants, such as ozone and nitrate radicals, which cause the conversion of NO to NO 2 in various potential reaction paths, including photolysis, to form oxygen atoms, which generate ozone. The kinetic reactivity was evaluated based on the reaction coefficients for hydroxyl radicals with VOCs. The mechanistic reactivity was estimated using a detailed mechanism and the incremental reactivity scale that Carter proposed. Different scenarios were proposed and discussed, and a minimum set of compounds, which may describe the tropospheric reactivity in the studied area, was determined. The role of isoprene was analyzed in terms of its contribution to ozone formation.

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

PubMed Central

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.; Boardsen, Scott A.; Avanov, Levon A.; Bellan, Paul M.; Schwartz, Steven J.; Lavraud, Benoit; Coffey, Victoria N.; Chandler, Michael O.; Saito, Yoshifumi; Paterson, William R.; Fuselier, Stephen A.; Ergun, Robert E.; Strangeway, Robert J.; Russell, Christopher T.; Giles, Barbara L.; Pollock, Craig J.; Torbert, Roy B.; Burch, James L.

2017-01-01

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA's Magnetospheric Multiscale (MMS) mission, we utilize Earth's magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electrons confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. The investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations. PMID:28361881

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.

PubMed

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D

2008-11-25

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of enzymes.

Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities.

PubMed

Kitir, Betül; Maolanon, Alex R; Ohm, Ragnhild G; Colaço, Ana R; Fristrup, Peter; Madsen, Andreas S; Olsen, Christian A

2017-09-26

Histone deacetylases (HDACs) are validated targets for treatment of certain cancer types and play numerous regulatory roles in biology, ranging from epigenetics to metabolism. Small molecules are highly important as tool compounds for probing these mechanisms as well as for the development of new medicines. Therefore, detailed mechanistic information and precise characterization of the chemical probes used to investigate the effects of HDAC enzymes are vital. We interrogated Nature's arsenal of macrocyclic nonribosomal peptide HDAC inhibitors by chemical synthesis and evaluation of more than 30 natural products and analogues. This furnished surprising trends in binding affinities for the various macrocycles, which were then exploited for the design of highly potent class I and IIb HDAC inhibitors. Furthermore, thorough kinetic investigation revealed unexpected inhibitory mechanisms of important tool compounds as well as the approved drug Istodax (romidepsin). This work provides novel inhibitors with varying potencies, selectivity profiles, and mechanisms of inhibition and, importantly, affords insight into known tool compounds that will improve the interpretation of their effects in biology and medicine.

Wave-Particle Energy Exchange Directly Observed in a Kinetic Alfven-Branch Wave

NASA Technical Reports Server (NTRS)

Gershman, Daniel J.; F-Vinas, Adolfo; Dorelli, John C.; Boardsen, Scott A. (Inventor); Avanov, Levon A.; Bellan, Paul M.; Schwartz, Steven J.; Lavraud, Benoit; Coffey, Victoria N.; Chandler, Michael O.;

A New Insight into the Mechanism of NADH Model Oxidation by Metal Ions in Non-Alkaline Media.

PubMed

Yang, Jin-Dong; Chen, Bao-Long; Zhu, Xiao-Qing

2018-06-11

For a long time, it has been controversial that the three-step (e-H+-e) or two-step (e-H•) mechanism was used for the oxidations of NADH and its models by metal ions in non-alkaline media. The latter mechanism has been accepted by the majority of researchers. In this work, 1-benzyl-1,4-dihydronicotinamide (BNAH) and 1-phenyl-l,4-dihydronicotinamide (PNAH) are used as NADH models, and ferrocenium (Fc+) metal ion as an electron acceptor. The kinetics for oxidations of the NADH models by Fc+ in pure acetonitrile were monitored by using UV-Vis absorption and quadratic relationship between of kobs and the concentrations of NADH models were found for the first time. The rate expression of the reactions developed according to the three-step mechanism is quite consistent with the quadratic curves. The rate constants, thermodynamic driving forces and KIEs of each elementary step for the reactions were estimated. All the results supported the three-step mechanism. The intrinsic kinetic barriers of the proton transfer from BNAH+• to BNAH and the hydrogen atom transfer from BNAH+• to BNAH+• were estimated, the results showed that the former is 11.8 kcal/mol, and the latter is larger than 24.3 kcal/mol. It is the large intrinsic kinetic barrier of the hydrogen atom transfer that makes the reactions choose the three-step rather than two-step mechanism. Further investigation of the factors affecting the intrinsic kinetic barrier of chemical reactions indicated that the large intrinsic kinetic barrier of the hydrogen atom transfer originated from the repulsion of positive charges between BNAH+• and BNAH+•. The greatest contribution of this work is the discovery of the quadratic dependence of kobs on the concentrations of the NADH models, which is inconsistent with the conventional viewpoint of the "two-step mechanism" on the oxidations of NADH and its models by metal ions in the non-alkaline media.

Kinetic or Dynamic Control on a Bifurcating Potential Energy Surface? An Experimental and DFT Study of Gold-Catalyzed Ring Expansion and Spirocyclization of 2-Propargyl-β-tetrahydrocarbolines.

PubMed

Zhang, Lei; Wang, Yi; Yao, Zhu-Jun; Wang, Shaozhong; Yu, Zhi-Xiang

2015-10-21

In classical transition state theory, a transition state is connected to its reactant(s) and product(s). Recently, chemists found that reaction pathways may bifurcate after a transition state, leading to two or more sets of products. The product distribution for such a reaction containing a bifurcating potential energy surface (bPES) is usually determined by the shape of the bPES and dynamic factors. However, if the bPES leads to two intermediates (other than two products), which then undergo further transformations to give different final products, what factors control the selectivity is still not fully examined. This missing link in transition state theory is founded in the present study. Aiming to develop new methods for the synthesis of azocinoindole derivatives, we found that 2-propargyl-β-tetrahydrocarbolines can undergo ring expansion and spirocyclization under gold catalysis. DFT study revealed that the reaction starts with the intramolecular cyclization of the gold-activated 2-propargyl-β-tetrahydrocarboline with a bPES. The cyclization intermediates can not only interconvert into each other via a [1,5]-alkenyl shift, but also undergo ring expansion (through fragmentation/protodeauration mechanism) or spirocyclization (through deprotonation/protodeauration mechanism). Detailed analysis of the complex PESs for substrates with different substituents indicated that the reaction selectivity is under dynamic control if the interconversion of the intermediates is slower than the ring expansion and spirocyclization processes. Otherwise, the chemical outcome is under typical kinetic control and determined by the relative preference of ring expansion versus spirocyclization pathways. The present study may enrich chemist's understanding of the determinants for selectivities on bPESs.

Two modelling approaches to water-quality simulation in a flooded iron-ore mine (Saizerais, Lorraine, France): a semi-distributed chemical reactor model and a physically based distributed reactive transport pipe network model.

PubMed

Hamm, V; Collon-Drouaillet, P; Fabriol, R

2008-02-19

The flooding of abandoned mines in the Lorraine Iron Basin (LIB) over the past 25 years has degraded the quality of the groundwater tapped for drinking water. High concentrations of dissolved sulphate have made the water unsuitable for human consumption. This problematic issue has led to the development of numerical tools to support water-resource management in mining contexts. Here we examine two modelling approaches using different numerical tools that we tested on the Saizerais flooded iron-ore mine (Lorraine, France). A first approach considers the Saizerais Mine as a network of two chemical reactors (NCR). The second approach is based on a physically distributed pipe network model (PNM) built with EPANET 2 software. This approach considers the mine as a network of pipes defined by their geometric and chemical parameters. Each reactor in the NCR model includes a detailed chemical model built to simulate quality evolution in the flooded mine water. However, in order to obtain a robust PNM, we simplified the detailed chemical model into a specific sulphate dissolution-precipitation model that is included as sulphate source/sink in both a NCR model and a pipe network model. Both the NCR model and the PNM, based on different numerical techniques, give good post-calibration agreement between the simulated and measured sulphate concentrations in the drinking-water well and overflow drift. The NCR model incorporating the detailed chemical model is useful when a detailed chemical behaviour at the overflow is needed. The PNM incorporating the simplified sulphate dissolution-precipitation model provides better information of the physics controlling the effect of flow and low flow zones, and the time of solid sulphate removal whereas the NCR model will underestimate clean-up time due to the complete mixing assumption. In conclusion, the detailed NCR model will give a first assessment of chemical processes at overflow, and in a second time, the PNM model will provide more detailed information on flow and chemical behaviour (dissolved sulphate concentrations, remaining mass of solid sulphate) in the network. Nevertheless, both modelling methods require hydrological and chemical parameters (recharge flow rate, outflows, volume of mine voids, mass of solids, kinetic constants of the dissolution-precipitation reactions), which are commonly not available for a mine and therefore call for calibration data.

Shock tube and chemical kinetic modeling study of the oxidation of 2,5-dimethylfuran.

PubMed

Sirjean, Baptiste; Fournet, René; Glaude, Pierre-Alexandre; Battin-Leclerc, Frédérique; Wang, Weijing; Oehlschlaeger, Matthew A

2013-02-21

A detailed kinetic model describing the oxidation of 2,5-dimethylfuran (DMF), a potential second-generation biofuel, is proposed. The kinetic model is based upon quantum chemical calculations for the initial DMF consumption reactions and important reactions of intermediates. The model is validated by comparison to new DMF shock tube ignition delay time measurements (over the temperature range 1300-1831 K and at nominal pressures of 1 and 4 bar) and the DMF pyrolysis speciation measurements of Lifshitz et al. [ J. Phys. Chem. A 1998 , 102 ( 52 ), 10655 - 10670 ]. Globally, modeling predictions are in good agreement with the considered experimental targets. In particular, ignition delay times are predicted well by the new model, with model-experiment deviations of at most a factor of 2, and DMF pyrolysis conversion is predicted well, to within experimental scatter of the Lifshitz et al. data. Additionally, comparisons of measured and model predicted pyrolysis speciation provides validation of theoretically calculated channels for the oxidation of DMF. Sensitivity and reaction flux analyses highlight important reactions as well as the primary reaction pathways responsible for the decomposition of DMF and formation and destruction of key intermediate and product species.

Mathematical model of alternative mechanism of telomere length maintenance

NASA Astrophysics Data System (ADS)

Kollár, Richard; Bod'ová, Katarína; Nosek, Jozef; Tomáška, L'ubomír

2014-03-01

Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres—nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.

Modeling Macro- and Micro-Scale Turbulent Mixing and Chemistry in Engine Exhaust Plumes

NASA Technical Reports Server (NTRS)

Menon, Suresh

1998-01-01

Simulation of turbulent mixing and chemical processes in the near-field plume and plume-vortex regimes has been successfully carried out recently using a reduced gas phase kinetics mechanism which substantially decreased the computational cost. A detailed mechanism including gas phase HOx, NOx, and SOx chemistry between the aircraft exhaust and the ambient air in near-field aircraft plumes is compiled. A reduced mechanism capturing the major chemical pathways is developed. Predictions by the reduced mechanism are found to be in good agreement with those by the detailed mechanism. With the reduced chemistry, the computer CPU time is saved by a factor of more than 3.5 for the near-field plume modeling. Distributions of major chemical species are obtained and analyzed. The computed sensitivities of major species with respect to reaction step are deduced for identification of the dominant gas phase kinetic reaction pathways in the jet plume. Both the near field plume and the plume-vortex regimes were investigated using advanced mixing models. In the near field, a stand-alone mixing model was used to investigate the impact of turbulent mixing on the micro- and macro-scale mixing processes using a reduced reaction kinetics model. The plume-vortex regime was simulated using a large-eddy simulation model. Vortex plume behind Boeing 737 and 747 aircraft was simulated along with relevant kinetics. Many features of the computed flow field show reasonable agreement with data. The entrainment of the engine plumes into the wing tip vortices and also the partial detrainment of the plume were numerically captured. The impact of fluid mechanics on the chemical processes was also studied. Results show that there are significant differences between spatial and temporal simulations especially in the predicted SO3 concentrations. This has important implications for the prediction of sulfuric acid aerosols in the wake and may partly explain the discrepancy between past numerical studies (that employed parabolic or temporal approximations) and the measured data. Finally to address the major uncertainty in the near-field plume modeling related to the plume processing of sulfur compounds and advanced model was developed to evaluate its impact on the chemical processes in the near wake. A comprehensive aerosol model is developed and it is coupled with chemical kinetics and the axisymmetric turbulent jet flow models. The integrated model is used to simulate microphysical processes in the near-field jet plume, including sulfuric acid and water binary homogeneous nucleation, coagulation, non-equilibrium heteromolecular condensation, and sulfur-induced soot activation. The formation and evolution of aerosols are computed and analyzed. The computed results show that a large number of ultra-fine (0.3--0.6 nm in radius) volatile HSO4 - HO embryos are generated in the near-field plume. These embryos further grow in size by self coagulation and condensation. Soot particles can be activated by both heterogeneous nucleation and scavenging of H2SO4-H2O aerosols. These activated soot particles can serve as water condensation nuclei for contrail formation. Conditions under which ice contrails can form behind aircrafts are studied. The sensitivities of the threshold temperature for contrail formation with respect to aircraft propulsion efficiency, relative humidity, and ambient pressure are evaluated. The computed aerosol properties for different extent of fuel sulfur conversion to S(VI) (SO3 and H2SO4) in engine are examined and the results are found to be sensitive to this conversion fraction.

The single-zone numerical model of homogeneous charge compression ignition engine performance

NASA Astrophysics Data System (ADS)

Fedyanov, E. A.; Itkis, E. M.; Kuzmin, V. N.; Shumskiy, S. N.

2017-02-01

The single-zone model of methane-air mixture combustion in the Homogeneous Charge Compression Ignition engine was developed. First modeling efforts resulted in the selection of the detailed kinetic reaction mechanism, most appropriate for the conditions of the HCCI process. Then, the model was completed so as to simulate the performance of the four-stroke engine and was coupled by physically reasonable adjusting functions. Validation of calculations against experimental data showed acceptable agreement.

A chemical kinetic theory on muscle contraction and spontaneous oscillation

NASA Astrophysics Data System (ADS)

Guo, Wei-Sheng; Luo, Liao-Fu; Li, Qian-Zhong

2002-09-01

From a set of chemical kinetic equations describing the actin-activated myosin ATPase cycle, we show that, in active muscle, the fraction of myosin heads in any given biochemical state is independent of both [ADP] and [P i]. Combining muscle mechanics data of Pate and Cooke, we deduce the muscle state equation in which muscle force is a state variable of the muscle system. The theoretical results are consistent with Baker's experimental data but somewhat different from conventional muscle theory. Based on the muscle state equation with the knowledge of special structure of muscle, we present a physical mechanism which can lead to both contraction and oscillation of sarcomeres. It explains the muscle spontaneous oscillatory contraction in a natural way and agrees well with experimental data. The model will be helpful in studying the oscillatory behavior of cilia and flagella.

Thermodynamic and kinetic analyses of the CO2 chemisorption mechanism on Na2TiO3: Experimental and theoretical evidences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duan, Yuhua

2014-01-01

ABSTRACT: Sodium metatitanate (Na2TiO3) was successfully synthesized via a solid-state reaction. The Na2TiO3 structure and microstructure were characterized using X-ray diffraction, scanning and transmission electron microscopy, and N2 adsorption. Then, the CO2 chemisorption mechanism on Na2TiO3 was systematically analyzed to determine the influence of temperature. The CO2 chemisorption capacity of Na2TiO3 was evaluated both dynamically and isothermally, and the products were reanalyzed to elucidate the Na2TiO3-CO2 reaction mechanism. Different chemical species (Na2CO3, Na2O, and Na4Ti5O12 or Na16Ti10O28) were identified during the CO2 capture process in Na2TiO3. In addition, some CO2 chemisorption kinetic parameters were determined. The ΔH‡ was found tomore » be 140.9 kJ/mol, to the Na2TiO3-CO2 system, between 600 and 780 °C. Results evidenced that CO2 chemisorption on Na2TiO3 highly depends on the reaction temperature. Furthermore, the experiments were theoretically supported by different thermodynamic calculations. The calculated thermodynamic properties of CO2 capture reactions by (Na2TiO3, Na4Ti5O12, and Na16Ti10O28) sodium titanates were fully investigated.« less

First- and second-order metal-insulator phase transitions and topological aspects of a Hubbard-Rashba system

NASA Astrophysics Data System (ADS)

Marcelino, Edgar

2017-05-01

This paper considers a model consisting of a kinetic term, Rashba spin-orbit coupling and short-range Coulomb interaction at zero temperature. The Coulomb interaction is decoupled by a mean-field approximation in the spin channel using field theory methods. The results feature a first-order phase transition for any finite value of the chemical potential and quantum criticality for vanishing chemical potential. The Hall conductivity is also computed using the Kubo formula in a mean-field effective Hamiltonian. In the limit of infinite mass the kinetic term vanishes and all the phase transitions are of second order; in this case the spontaneous symmetry-breaking mechanism adds a ferromagnetic metallic phase to the system and features a zero-temperature quantization of the Hall conductivity in the insulating one.

Effects of CO addition on the characteristics of laminar premixed CH{sub 4}/air opposed-jet flames

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, C.-Y.; Chao, Y.-C.; Chen, C.-P.

2009-02-15

The effects of CO addition on the characteristics of premixed CH{sub 4}/air opposed-jet flames are investigated experimentally and numerically. Experimental measurements and numerical simulations of the flame front position, temperature, and velocity are performed in stoichiometric CH{sub 4}/CO/air opposed-jet flames with various CO contents in the fuel. Thermocouple is used for the determination of flame temperature, velocity measurement is made using particle image velocimetry (PIV), and the flame front position is measured by direct photograph as well as with laser-induced predissociative fluorescence (LIPF) of OH imaging techniques. The laminar burning velocity is calculated using the PREMIX code of Chemkin collectionmore » 3.5. The flame structures of the premixed stoichiometric CH{sub 4}/CO/air opposed-jet flames are simulated using the OPPDIF package with GRI-Mech 3.0 chemical kinetic mechanisms and detailed transport properties. The measured flame front position, temperature, and velocity of the stoichiometric CH{sub 4}/CO/air flames are closely predicted by the numerical calculations. Detailed analysis of the calculated chemical kinetic structures reveals that as the CO content in the fuel is increased from 0% to 80%, CO oxidation (R99) increases significantly and contributes to a significant level of heat-release rate. It is also shown that the laminar burning velocity reaches a maximum value (57.5 cm/s) at the condition of 80% of CO in the fuel. Based on the results of sensitivity analysis, the chemistry of CO consumption shifts to the dry oxidation kinetics when CO content is further increased over 80%. Comparison between the results of computed laminar burning velocity, flame temperature, CO consumption rate, and sensitivity analysis reveals that the effect of CO addition on the laminar burning velocity of the stoichiometric CH{sub 4}/CO/air flames is due mostly to the transition of the dominant chemical kinetic steps. (author)« less

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

PubMed Central

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-01-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data. PMID:19662155

Chemical conversion pathways and kinetic modeling for the OH-initiated reaction of triclosan in gas-phase.

PubMed

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-04-10

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k add/k total and k abs/k total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin.

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

PubMed Central

Zhang, Xue; Zhang, Chenxi; Sun, Xiaomin; Kang, Lingyan; Zhao, Yan

2015-01-01

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of kadd/ktotal and kabs/ktotal at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. PMID:25867482

Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency.

PubMed

Taylor, Mark R; Conrad, John A; Wahl, Daniel; O'Brien, Patrick J

2011-07-01

DNA ligase I (LIG1) catalyzes the ligation of single-strand breaks to complete DNA replication and repair. The energy of ATP is used to form a new phosphodiester bond in DNA via a reaction mechanism that involves three distinct chemical steps: enzyme adenylylation, adenylyl transfer to DNA, and nick sealing. We used steady state and pre-steady state kinetics to characterize the minimal mechanism for DNA ligation catalyzed by human LIG1. The ATP dependence of the reaction indicates that LIG1 requires multiple Mg(2+) ions for catalysis and that an essential Mg(2+) ion binds more tightly to ATP than to the enzyme. Further dissection of the magnesium ion dependence of individual reaction steps revealed that the affinity for Mg(2+) changes along the reaction coordinate. At saturating concentrations of ATP and Mg(2+) ions, the three chemical steps occur at similar rates, and the efficiency of ligation is high. However, under conditions of limiting Mg(2+), the nick-sealing step becomes rate-limiting, and the adenylylated DNA intermediate is prematurely released into solution. Subsequent adenylylation of enzyme prevents rebinding to the adenylylated DNA intermediate comprising an Achilles' heel of LIG1. These ligase-generated 5'-adenylylated nicks constitute persistent breaks that are a threat to genomic stability if they are not repaired. The kinetic and thermodynamic framework that we have determined for LIG1 provides a starting point for understanding the mechanism and specificity of mammalian DNA ligases.

Learning Chemistry from Good and (Why Not?) Problematic Results: Kinetics of the pH-Independent Hydrolysis of 4-Nitrophenyl Chloroformate

ERIC Educational Resources Information Center

El Seoud, Omar A.; Galgano, Paula D.; Are^as, Elizabeth P. G.; Moraes, Jamille M.

2015-01-01

The determination of kinetic data is central to reaction mechanism; science courses usually include experiments on chemical kinetics. Thanks to PC-controlled data acquisition and availability of software, the students calculate rate constants, whether the experiment has been done properly or not. This contrasts with their experience in, e.g.,…

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

PubMed

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-08-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Kinetic calorimetry in the study of the mechanism of low-temperature chemical reactions

NASA Astrophysics Data System (ADS)

Barkalov, I. M.; Kiryukhin, D. P.

Chemical reactions are always followed by a change in the reacting system enthalpy, hence, calorimetry as a method of enthalpy and heat capacity measuring is a universal and, sometimes, even the only possible way of studying chemical reaction kinetics. Throughout its long history, the calorimeter, having preserved the positions of the main method of thermodynamic studies, has conquered a new field of application: that of kinetic study of chemical reactions. The advantages and disadvantages of the kinetic calorimeter are now obvious. First, the advantages are: (1) the possibility of measuring the rate of a chemical reaction without any special requirements being imposed on the reaction medium (solid, viscous, multicomponent systems); (2) the high efficiency: a large volume of kinetic information in one experiment and a non-destructive character of changes; (3) the possibility of measuring directly in the field of ionizing radiation (γ-radiation, accelerated electrons) and light; and (4) recording of the chemical conversion directly at the time of its occurrence. The disadvantages of this method are: (1) the high inertia of standard calorimeter systems (τC⋍102-103S), which restricts the possibilities of studying fast processes; and (2) the complexity of the correct organization of the calorimeter experiment when the parameters of the process are changed (overheating in the sample, conversion of the process to explosive and auto wave regimens). One of the oldest and most universal methods of studying the mechanism of chemical reactions, calorimetry, is now passing through a period of turbulent development due to the advances in electronics and computerization. The wide variety of types of calorimeter set-ups and the large assortment of measurement schemes in the currently described methods complicate the experimental selection of the necessary instrument rather than facilitate it. The basic principles of the method, the types of calorimeters, and the measuring schemes are described [1-5]. However, despite the high working characteristics of modern calorimeters (Perkin-Elmer, Du Pont, LKB, etc.), all of them have one principal disadvantage: a cell with a sample is placed in them at room temperature. In cryochemical investigation, when the sample has metastable formations, the loading is made `from nitrogen to nitrogen', i.e. the sample prepared at 77 K should be loaded into a calorimeter at 77 K. Besides, the existing installations do not allow measurements at the temperatures <110K. For this reason, the Laboratory of Cryochemistry and Radiation Chemistry at the Institute of Chemical Physics in Chernogolovka has created original calorimetric techniques which allow: (1) the carrying out phase analysis and the determination of the main thermodynamic characteristic of individual substances and complicated systems in the temperature range 5 300 K. Sample loading can be conducted at 77 K that allows us to study the systems containing: tetrafiuoroethylene, hexafluoropropylene, ethylene, carbon monoxide, nitrogen, methane, hydrogen, oxygen, ozone, formaldehyde and many other gaseous substances; (2) the study of the dynamics of chemical reactions and to measure the main kinetic parameters of the processes-the elementary rate constants and the activation energies. The experiment can be conducted both under direct action of radiation and UV light and in the post-effect mode [5,6].

Identifying the Oscillatory Mechanism of the Glucose Oxidase-Catalase Coupled Enzyme System.

PubMed

Muzika, František; Jurašek, Radovan; Schreiberová, Lenka; Radojković, Vuk; Schreiber, Igor

2017-10-12

We provide experimental evidence of periodic and aperiodic oscillations in an enzymatic system of glucose oxidase-catalase in a continuous-flow stirred reactor coupled by a membrane with a continuous-flow reservoir supplied with hydrogen peroxide. To describe such dynamics, we formulate a detailed mechanism based on partial results in the literature. Finally, we introduce a novel method for estimation of unknown kinetic parameters. The method is based on matching experimental data at an oscillatory instability with stoichiometric constraints of the mechanism formulated by applying the stability theory of reaction networks. This approach has been used to estimate rate coefficients in the catalase part of the mechanism. Remarkably, model simulations show good agreement with the observed oscillatory dynamics, including apparently chaotic intermittent behavior. Our method can be applied to any reaction system with an experimentally observable dynamical instability.

Thermodynamics and simulation of hard-sphere fluid and solid: Kinetic Monte Carlo method versus standard Metropolis scheme

NASA Astrophysics Data System (ADS)

Ustinov, E. A.

2017-01-01

The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends. The existence of rarefied zones allows one to determine the chemical potential of the crystalline phase and substantially increases its accuracy for the disordered dense phase in the central zone of the simulation box. This method is applicable to both the Metropolis MC and the kMC, but in the latter case, the chemical potential is determined with higher accuracy at the same conditions and the number of MC steps. Thermodynamic functions of the disordered fluid and crystalline face-centered cubic (FCC) phase for the hard-sphere system have been evaluated with the kinetic MC and the standard MC coupled with the Widom procedure over a wide range of density. The melting transition parameters have been determined by the point of intersection of the pressure-chemical potential curves for the disordered HS fluid and FCC crystal using the Gibbs-Duhem equation as a constraint. A detailed thermodynamic analysis of the hard-sphere fluid has provided a rigorous verification of the approach, which can be extended to more complex systems.

A Direct Mechanism of Ultrafast Intramolecular Singlet Fission in Pentacene Dimers

DTIC Science & Technology

2016-08-24

property for materials used in third- generation solar cells and photodetectors, among other optoelectronic devices.1−3 Unfortunately, techno- logical...detailed mechanism of iSF and to establish its relationship to chemical structure. Current literature on the mechanism of xSF is in general agreement...not been identified. We use this ring-breathing mode to generate a two- dimensional potential energy surface (PES) for the excited states along the

Determination of the mechanism of demethylenation of (methylenedioxy)phenyl compounds by cytochrome P450 using deuterium isotope effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fukuto, J.M.; Kumagai, Y.; Cho, A.K.

1991-09-01

The mechanism of demethylenation of (methylenedioxy)benzene (MDB), (methylenedioxy)amphetamine (MDA), and (methylenedioxy)methamphetamine (MDMA) by purified rabbit liver cytochrome P450IIB4 has been investigated by using deuterium isotope effects. A comparison of the magnitude and direction of the observed kinetic isotope effects indicates that the three compounds are demethylenated by different mechanisms. The different mechanisms of demethylenation have been proposed on the basis of comparisons of the observed biochemical isotope effects with the isotope effects from purely chemical systems.

Mimicking Nonequilibrium Steady States with Time-Periodic Driving

NASA Astrophysics Data System (ADS)

Raz, O.; Subaşı, Y.; Jarzynski, C.

2016-04-01

Under static conditions, a system satisfying detailed balance generically relaxes to an equilibrium state in which there are no currents. To generate persistent currents, either detailed balance must be broken or the system must be driven in a time-dependent manner. A stationary system that violates detailed balance evolves to a nonequilibrium steady state (NESS) characterized by fixed currents. Conversely, a system that satisfies instantaneous detailed balance but is driven by the time-periodic variation of external parameters—also known as a stochastic pump (SP)—reaches a periodic state with nonvanishing currents. In both cases, these currents are maintained at the cost of entropy production. Are these two paradigmatic scenarios effectively equivalent? For discrete-state systems, we establish a mapping between nonequilibrium stationary states and stochastic pumps. Given a NESS characterized by a particular set of stationary probabilities, currents, and entropy production rates, we show how to construct a SP with exactly the same (time-averaged) values. The mapping works in the opposite direction as well. These results establish a proof of principle: They show that stochastic pumps are able to mimic the behavior of nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics. Nonequilibrium steady states and stochastic pumps are often used to model, respectively, biomolecular motors driven by chemical reactions and artificial molecular machines steered by the variation of external, macroscopic parameters. Our results loosely suggest that anything a biomolecular machine can do, an artificial molecular machine can do equally well. We illustrate this principle by showing that kinetic proofreading, a NESS mechanism that explains the low error rates in biochemical reactions, can be effectively mimicked by a constrained periodic driving.

Probing Aluminum Reactions in Combustion and Explosion Via the Kinetic Isotope Effect

NASA Astrophysics Data System (ADS)

Tappan, Bryce

2015-06-01

The mechanism that controls the reaction speed of aluminum in explosion and combustion is poorly understood, and experimentally difficult to measure. Recently, work in our laboratory has demonstrated that during the combustion of nanoparticulate aluminum with H2O or D2O, different reaction rates due to the kinetic isotope effect are observed. This result is the first-ever observed kinetic isotope effect in a metal combustion reaction and verifies that chemical reaction kinetics play a major role in determining the global burning rate. During or shortly after a detonation, however, the reaction rates are dramatically faster and the physical mechanism controlling Al reaction is likely different than during combustion events. To utilize the kinetic isotope effect to probe Al reactions in detonation, formulations were produced that contain powdered Al in deuterated high explosives and high-fidelity detonation velocity were determined along with PDV measurements to observe early wall velocity expansion measurements. The JWL equation of state was solved to determine temperature, pressure and energies at specific time periods, in addition of Gurney energies, which enables the elucidation of Al reaction extent. By comparison of the Al oxidation with LiF, data indicate that Al oxidation occurs on an extremely fast time scale and isotope effects in both the HE detonation and post-detonation Al reactions are discussed.

Methods for Kinetic and Thermodynamic Analysis of Aminoacyl-tRNA Synthetases

PubMed Central

Francklyn, Christopher S.; First, Eric A.; Perona, John J.; Hou, Ya-Ming

2008-01-01

The accuracy of protein synthesis relies on the ability of aminoacyl-tRNA synthetases (aaRSs) to discriminate among true and near cognate substrates. To date, analysis of aaRSs function, including identification of residues of aaRS participating in amino acid and tRNA discrimination, has largely relied on the steady state kinetic pyrophosphate exchange and aminoacylation assays. Pre-steady state kinetic studies investigating a more limited set of aaRS systems have also been undertaken to assess the energetic contributions of individual enzyme-substrate interactions, particularly in the adenylation half reaction. More recently, a renewed interest in the use of rapid kinetics approaches for aaRSs has led to their application to several new aaRS systems, resulting in the identification of mechanistic differences that distinguish the two structurally distinct aaRS classes. Here, we review the techniques for thermodynamic and kinetic analysis of aaRS function. Following a brief survey of methods for the preparation of materials and for steady state kinetic analysis, this review will describe pre-steady state kinetic methods employing rapid quench and stopped-flow fluorescence for analysis of the activation and aminoacyl transfer reactions. Application of these methods to any aaRS system allows the investigator to derive detailed kinetic mechanisms for the activation and aminoacyl transfer reactions, permitting issues of substrate specificity, stereochemical mechanism, and inhibitor interaction to be addressed in a rigorous and quantitative fashion. PMID:18241792

Kinetic and mechanism formation reaction of complex compound Cu with di-n-buthildithiocarbamate (dbdtc) ligand

NASA Astrophysics Data System (ADS)

Haryani, S.; Kurniawan, C.; Kasmui

2018-04-01

Synthesis of complex compound is one field of research which intensively studied. Metal-dithiocarbamate complexes find wide-ranging applications in nanomaterial and metal separation science, and have potential use as chemotherapeutic, pesticides, and as additives to lubricants. However, the information about is reaction kinetic and mechanism are very much lacking. The research and analyzes results show that reaction synthesis ligand DBDTC and complex compounds Cu-DBDTC. Optimum reaction condition of formation of complex compounds Cu with DBDTC at pH=3, [DBDTC] = 4.10-3 M, and the time of reaction 5 minutes. Based the analysis varian reaction of complex compounds at pH 3 and 4, diffrence significance at the other pH: 5; 5,5; 6; 6,5 ; 7; and 8. The various of mole with reactants comosition difference sigbificance, those the time reaction for 5 and 6 minutes diffrence by significance with the other time, it is 3,4,8, and 10 minutes. The great product to at condition pH 6, the time optimum at 5 minutes and molar ratio of logam: ligand = 1:2. The reaction kinetic equation of complex compound Cu with chelathing ligand DBDTC is V=0.917106 [Cu2+]0.87921 [DBDTC]2.03021. Based on the kinetic data, and formed complex compounds estimation, the mechanism explaining by 2 stages. In the first stage formation of [Cu(DBDTC)], and then [Cu(DBDTC)2] with the last structure geomethry planar rectangle. The result of this research will be more useful if an effort is being done in reaction mechanism by chemical computation method for obtain intermediate, and for constant “k” in same stage, k1.k2. and compound complex constanta (β).

Chemical kinetics of octane sensitivity in a spark-ignition engine (Chemical Kinetics of Octane Sensitivity in a Spark Ignition Engine)

DOE PAGES

Westbrook, Charles K.; Mehl, Marco; Pitz, William J.; ...

2016-07-11

This article uses a chemical kinetic modeling approach to study the influences of fuel molecular structure on Octane Sensitivity (OS) in Spark Ignition (SI) engines. Octane Sensitivity has the potential to identify fuels that can be used in next-generation high compression, turbocharged SI engines to avoid unwanted knocking conditions and extend the range of operating conditions that can be used in such engines. While the concept of octane numbers of different fuels has been familiar for many years, the variations of their values and their role in determining Octane Sensitivity have not been addressed previously in terms of the basicmore » structures of the fuel molecules. In particular, the importance of electron delocalization on low temperature hydrocarbon reactivity and its role in determining OS in engine fuel is described here for the first time. Finally, the role of electron delocalization on fuel reactivity and Octane Sensitivity is illustrated for a very wide range of engine fuel types, including n-alkane, 1-olefin, n-alcohol, and n-alkyl benzenes, and the unifying features of these fuels and their common trends, using existing detailed chemical kinetic reaction mechanisms that have been collected and unified to produce an overall model with unprecedented capabilities.« less

Kinetics in the real world: linking molecules, processes, and systems.

PubMed

Kohse-Höinghaus, Katharina; Troe, Jürgen; Grabow, Jens-Uwe; Olzmann, Matthias; Friedrichs, Gernot; Hungenberg, Klaus-Dieter

2018-04-25

Unravelling elementary steps, reaction pathways, and kinetic mechanisms is key to understanding the behaviour of many real-world chemical systems that span from the troposphere or even interstellar media to engines and process reactors. Recent work in chemical kinetics provides detailed information on the reactive changes occurring in chemical systems, often on the atomic or molecular scale. The optimisation of practical processes, for instance in combustion, catalysis, battery technology, polymerisation, and nanoparticle production, can profit from a sound knowledge of the underlying fundamental chemical kinetics. Reaction mechanisms can combine information gained from theory and experiments to enable the predictive simulation and optimisation of the crucial process variables and influences on the system's behaviour that may be exploited for both monitoring and control. Chemical kinetics, as one of the pillars of Physical Chemistry, thus contributes importantly to understanding and describing natural environments and technical processes and is becoming increasingly relevant for interactions in and with the real world.

Stabilization of the Simplest Criegee Intermediate from the Reaction between Ozone and Ethylene: A High-Level Quantum Chemical and Kinetic Analysis of Ozonolysis.

PubMed

Nguyen, Thanh Lam; Lee, Hyunwoo; Matthews, Devin A; McCarthy, Michael C; Stanton, John F

2015-06-04

The fraction of the collisionally stabilized Criegee species CH2OO produced from the ozonolysis of ethylene is calculated using a two-dimensional (E, J)-grained master equation technique and semiclassical transition-state theory based on the potential energy surface obtained from high-accuracy quantum chemical calculations. Our calculated yield of 42 ± 6% for the stabilized CH2OO agrees well, within experimental error, with available (indirect) experimental results. Inclusion of angular momentum in the master equation is found to play an essential role in bringing the theoretical results into agreement with the experiment. Additionally, yields of HO and HO2 radical products are predicted to be 13 ± 6% and 17 ± 6%, respectively. In the kinetic simulation, the HO radical product is produced mostly from the stepwise decomposition mechanism of primary ozonide rather than from dissociation of hot CH2OO.

Chemical kinetics of octane sensitivity in a spark-ignition engine (Chemical Kinetics of Octane Sensitivity in a Spark Ignition Engine)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Westbrook, Charles K.; Mehl, Marco; Pitz, William J.

This article uses a chemical kinetic modeling approach to study the influences of fuel molecular structure on Octane Sensitivity (OS) in Spark Ignition (SI) engines. Octane Sensitivity has the potential to identify fuels that can be used in next-generation high compression, turbocharged SI engines to avoid unwanted knocking conditions and extend the range of operating conditions that can be used in such engines. While the concept of octane numbers of different fuels has been familiar for many years, the variations of their values and their role in determining Octane Sensitivity have not been addressed previously in terms of the basicmore » structures of the fuel molecules. In particular, the importance of electron delocalization on low temperature hydrocarbon reactivity and its role in determining OS in engine fuel is described here for the first time. Finally, the role of electron delocalization on fuel reactivity and Octane Sensitivity is illustrated for a very wide range of engine fuel types, including n-alkane, 1-olefin, n-alcohol, and n-alkyl benzenes, and the unifying features of these fuels and their common trends, using existing detailed chemical kinetic reaction mechanisms that have been collected and unified to produce an overall model with unprecedented capabilities.« less

An experimental and kinetic investigation of premixed furan/oxygen/argon flames.

PubMed

Tian, Zhenyu; Yuan, Tao; Fournet, Rene; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Zhang, Kuiwen; Qi, Fei

2011-04-01

The detailed chemical structures of three low-pressure (35 Torr) premixed laminar furan/oxygen/argon flames with equivalence ratios of 1.4, 1.8 and 2.2 have been investigated by using tunable synchrotron vacuum ultraviolet (VUV) photoionization and molecular-beam mass spectrometry. About 40 combustion species including hydrocarbons and oxygenated intermediates have been identified by measurements of photoionization efficiency spectra. Mole fraction profiles of the flame species including reactants, intermediates and products have been determined by scanning burner position with some selected photon energies near ionization thresholds. Flame temperatures have been measured by a Pt-6%Rh/Pt-30%Rh thermocouple. A new mechanism involving 206 species and 1368 reactions has been proposed whose predictions are in reasonable agreement with measured species profiles for the three investigated flames. Rate-of-production and sensitivity analyses have been performed to track the key reaction paths governing furan consumption for different equivalence ratios. Both experimental and modeling results indicate that few aromatics could be formed in these flames. Furthermore, the current model has been validated against previous pyrolysis results of the literature obtained behind shock waves and the agreement is reasonable as well.

Numerical Study of Contaminant Effects on Combustion of Hydrogen, Ethane, and Methane in Air

NASA Technical Reports Server (NTRS)

Lai, H. T.; Thomas, S. R.

1995-01-01

A numerical study was performed to assess the effects of vitiated air on the chemical kinetics of hydrogen, ethane, and methane combustion with air. A series of calculations in static reacting systems was performed, where the initial temperature was specified and reactions occurred at constant pressure. Three different types of test flow contaminants were considered: NP, H2O, and a combustion of H2O and CO2. These contaminants are present in the test flows of facilities used for hypersonic propulsion testing. The results were computed using a detailed reaction mechanism and are presented in terms of ignition and reaction times. Calculations were made for a wide range of contaminant concentrations, temperatures and pressures. The results indicate a pronounced kinetic effect over a range of temperatures, especially with NO contamination and, to a lesser degree, with H2O contamination. In all cases studied, CO2 remained kinetically inert, but had a thermodynamic effect on results by acting as a third body. The largest effect is observed with combustion using hydrogen fuel, less effect is seen with combustion of ethane, and little effect of contaminants is shown with methane combustion.

Numerical study of contaminant effects on combustion of hydrogen, ethane, and methane in air

NASA Technical Reports Server (NTRS)

Lai, H. T.; Thomas, S. R.

1995-01-01

A numerical study was performed to assess the effects of vitiated air on the chemical kinetics of hydrogen, ethane, and methane combustion with air. A series of calculations in static reacting systems was performed, where the initial temperature was specified and reactions occurred at constant pressure. Three different types of test flow contaminants were considered: NO, H2O, and a combination of H2O and CO2. These contaminants are present in the test flows of facilities used for hypersonic propulsion testing. The results were computed using a detailed reaction mechanism and are presented in terms of ignition and reaction times. Calculations were made for a wide range of contaminant concentrations, temperatures and pressures. The results indicate a pronounced kinetic effect over a range of temperatures, especially with NO contamination and, to a lesser degree, with H2O contamination. In all cases studied, CO2 remained kinetically inert, but had a thermodynamically effect on results by acting as a third body. The largest effect is observed with combustion using hydrogen fuel, less effect is seen with combustion of ethane, and little effect of contaminants is shown with methane combustion.

Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

PubMed

Pan, Xiaoliang; Schwartz, Steven D

2015-04-30

It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA’s Magnetospheric Multiscale (MMS) mission, we utilize Earth’s magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electronsmore » confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. As a result, the investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.« less

Wave-particle energy exchange directly observed in a kinetic Alfvén-branch wave

DOE PAGES

Gershman, Daniel J.; F-Viñas, Adolfo; Dorelli, John C.; ...

2017-03-31

Alfvén waves are fundamental plasma wave modes that permeate the universe. At small kinetic scales, they provide a critical mechanism for the transfer of energy between electromagnetic fields and charged particles. These waves are important not only in planetary magnetospheres, heliospheres and astrophysical systems but also in laboratory plasma experiments and fusion reactors. Through measurement of charged particles and electromagnetic fields with NASA’s Magnetospheric Multiscale (MMS) mission, we utilize Earth’s magnetosphere as a plasma physics laboratory. Here we confirm the conservative energy exchange between the electromagnetic field fluctuations and the charged particles that comprise an undamped kinetic Alfvén wave. Electronsmore » confined between adjacent wave peaks may have contributed to saturation of damping effects via nonlinear particle trapping. As a result, the investigation of these detailed wave dynamics has been unexplored territory in experimental plasma physics and is only recently enabled by high-resolution MMS observations.« less

Nucleation and growth of WSe2: enabling large grain transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Yue, Ruoyu; Nie, Yifan; Walsh, Lee A.; Addou, Rafik; Liang, Chaoping; Lu, Ning; Barton, Adam T.; Zhu, Hui; Che, Zifan; Barrera, Diego; Cheng, Lanxia; Cha, Pil-Ryung; Chabal, Yves J.; Hsu, Julia W. P.; Kim, Jiyoung; Kim, Moon J.; Colombo, Luigi; Wallace, Robert M.; Cho, Kyeongjae; Hinkle, Christopher L.

2017-12-01

The limited grain size (<200 nm) for transition metal dichalcogenides (TMDs) grown by molecular beam epitaxy (MBE) reported in the literature thus far is unsuitable for high-performance device applications. In this work, the fundamental nucleation and growth behavior of WSe2 is investigated through a detailed experimental design combined with on-lattice, diffusion-based first principles kinetic modeling to enable large area TMD growth. A three-stage adsorption-diffusion-attachment mechanism is identified and the adatom stage is revealed to play a significant role in the nucleation behavior. To limit the nucleation density and promote 2D layered growth, it is necessary to have a low metal flux in conjunction with an elevated substrate temperature. At the same time, providing a Se-rich environment further limits the formation of W-rich nuclei which suppresses vertical growth and promotes 2D growth. The fundamental understanding gained through this investigation has enabled an increase of over one order of magnitude in grain size for WSe2 thus far, and provides valuable insight into improving the growth of other TMD compounds by MBE and other growth techniques such as chemical vapor deposition (CVD).

Experimental and Computational Studies of Oxidizer and Fuel Side Addition of Ethanol to Opposed Flow Air/Ethylene Flames

DTIC Science & Technology

2005-02-01

literature to be used in modeling of the results (10). 2. Background The separation of the regions of highest particulate and aromatic concentrations... modeling calculations incorporating the well-characterized C2 combustion mechanism of Frenklach et al. (10). This mechanism was developed for...experimentally and modeled , and shown to occur via different pathways within the context of a detailed chemical mechanism. In particular, ethanol

Large eddy simulation of a reacting spray flame with multiple realizations under compression ignition engine conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pei, Yuanjiang; Som, Sibendu; Pomraning, Eric

2015-12-01

An n-dodecane spray flame (Spray A from Engine Combustion Network) was simulated using a detailed combustion model along with a dynamic structure LES model to evaluate its performance at engine-relevant conditions and understand the transient behavior of this turbulent flame. The liquid spray was treated with a traditional Lagrangian method and the gas-phase reaction was modeled using a detailed combustion model. A 103-species skeletal mechanism was used for the n-dodecane chemical kinetic model. Significantly different flame structures and ignition processes are observed for the LES compared to those of RANS predictions. The LES data suggests that the first ignition initiatesmore » in lean mixture and propagates to rich mixture, and the main ignition happens in rich mixture, preferable less than 0.14 in mixture fraction space. LES was observed to have multiple ignition spots in the mixing layer simultaneously while the main ignition initiates in a clearly asymmetric fashion. The temporal flame development also indicates the flame stabilization mechanism is auto-ignition controlled and modulated by flame propagation. Soot predictions by LES present much better agreement with experiments compared to RANS both qualitatively and quantitatively. Multiple realizations for LES were performed to understand the realization to realization variation and to establish best practices for ensemble-averaging diesel spray flames. The relevance index analysis suggests that an average of 2 and 5 realizations can reach 99\\% of similarity to the target average of 16 realizations on the temperature and mixture fraction fields, respectively. However, more realizations are necessary for OH and soot mass fraction due to their high fluctuations.« less

Numerical Analysis of the Trailblazer Inlet Flowfield for Hypersonic Mach Numbers

NASA Technical Reports Server (NTRS)

Steffen, C. J., Jr.; DeBonis, J. R.

1999-01-01

A study of the Trailblazer vehicle inlet was conducted using the Global Air Sampling Program (GASP) code for flight Mach numbers ranging from 4-12. Both perfect gas and finite rate chemical analysis were performed with the intention of making detailed comparisons between the two results. Inlet performance was assessed using total pressure recovery and kinetic energy efficiency. These assessments were based upon a one-dimensional stream-thrust-average of the axisymmetric flowfield. Flow visualization utilized to examine the detailed shock structures internal to this mixed-compression inlet. Kinetic energy efficiency appeared to be the least sensitive to differences between the perfect gas and finite rate chemistry results. Total pressure recovery appeared to be the most sensitive discriminator between the perfect gas and finite rate chemistry results for flight Mach numbers above Mach 6. Adiabatic wall temperature was consistently overpredicted by the perfect gas model for flight Mach numbers above Mach 4. The predicted shock structures were noticeably different for Mach numbers from 6-12. At Mach 4, the perfect gas and finite rate chemistry models collapse to the same result.

Kinetics of SiHCl3 chemical vapor deposition and fluid dynamic simulations.

PubMed

Cavallotti, Carlo; Masi, Maurizio

2011-09-01

Though most of the current silicon photovoltaic technology relies on trichlorosilane (SiHCl3) as a precursor gas to deposit Si, only a few studies have been devoted to the investigation of its gas phase and surface kinetics. In the present work we propose a new kinetic mechanism apt to describe the gas phase and surface chemistry active during the deposition of Si from SiHCl3. Kinetic constants of key reactions were either taken from the literature or determined through ab initio calculations. The capability of the mechanism to reproduce experimental data was tested through the implementation of the kinetic scheme in a fluid dynamic model and in the simulation of both deposition and etching of Si in horizontal reactors. The results of the simulations show that the reactivity of HCl is of key importance in order to control the Si deposition rate. When HCl reaches a critical concentration in the gas phase it starts etching the Si surface, so that the net deposition rate is the net sum of the adsorption rate of the gas phase precursors and the etching rate due to HCl. In these conditions the possibility to further deposit Si is directly related to the rate of consumption of HCl through its reaction with SiHCl3 to give SiCl4. The proposed reaction mechanism was implemented in a 3D fluid dynamic model of a simple Siemens reactor. The simulation results indicate that the proposed interpretation of the growth process applies also to this class of reactors, which operate in what can be defined as a mixed kinetic-transport controlled regime.

Heterogeneous Oxidation of Atmospheric Organic Aerosol: Kinetics of Changes to the Amount and Oxidation State of Particle-Phase Organic Carbon.

PubMed

Kroll, Jesse H; Lim, Christopher Y; Kessler, Sean H; Wilson, Kevin R

2015-11-05

Atmospheric oxidation reactions are known to affect the chemical composition of organic aerosol (OA) particles over timescales of several days, but the details of such oxidative aging reactions are poorly understood. In this study we examine the rates and products of a key class of aging reaction, the heterogeneous oxidation of particle-phase organic species by the gas-phase hydroxyl radical (OH). We compile and reanalyze a number of previous studies from our laboratories involving the oxidation of single-component organic particles. All kinetic and product data are described on a common basis, enabling a straightforward comparison among different chemical systems and experimental conditions. Oxidation chemistry is described in terms of changes to key ensemble properties of the OA, rather than to its detailed molecular composition, focusing on two quantities in particular, the amount and the oxidation state of the particle-phase carbon. Heterogeneous oxidation increases the oxidation state of particulate carbon, with the rate of increase determined by the detailed chemical mechanism. At the same time, the amount of particle-phase carbon decreases with oxidation, due to fragmentation (C-C scission) reactions that form small, volatile products that escape to the gas phase. In contrast to the oxidation state increase, the rate of carbon loss is nearly uniform among most systems studied. Extrapolation of these results to atmospheric conditions indicates that heterogeneous oxidation can have a substantial effect on the amount and composition of atmospheric OA over timescales of several days, a prediction that is broadly in line with available measurements of OA evolution over such long timescales. In particular, 3-13% of particle-phase carbon is lost to the gas phase after one week of heterogeneous oxidation. Our results indicate that oxidative aging represents an important sink for particulate organic carbon, and more generally that fragmentation reactions play a major role in the lifecycle of atmospheric OA.

Study on COD removal mechanism and reaction kinetics of oilfield wastewater.

PubMed

Yin, Xian-Qing; Jing, Bo; Chen, Wen-Juan; Zhang, Jian; Liu, Qian; Chen, Wu

2017-11-01

The chemical oxygen demand (COD) removal mechanism and reaction kinetics were mainly studied in the treatment of oilfield oily sewage containing polymer by three-dimensional electrode reactor. The results proved that the residual active oxides O 3 , H 2 O 2 , •OH and active chlorine in the system of electrochemical reaction could be effectively detected, and the COD removal mechanism was co-oxidation of active oxides; Under these experimental conditions: the electrolysis current of 6 A, surface/volume ratio of 6/25(cm 2 ·L -1 ), the reaction time of 50 min, the COD cr of treated sewage was no more than 50 mg·L -1 ; the removal reaction of COD conformed to apparent second-order reaction kinetic model, the correlation coefficient R 2 was 0.9728, and the apparent reaction rate constant was k = 3.58 × 10 -4 (L·min -1 ·mg -1 ·m -2 ). To reach the goal, the COD cr was no more than 50 mg·L -1 in treated sewage, and the theory minimum processing time was 45.73 min. The verification of experimental results was consistent with kinetic equations.

Non-thermal plasma destruction of allyl alcohol in waste gas: kinetics and modelling

NASA Astrophysics Data System (ADS)

DeVisscher, A.; Dewulf, J.; Van Durme, J.; Leys, C.; Morent, R.; Van Langenhove, H.

2008-02-01

Non-thermal plasma treatment is a promising technique for the destruction of volatile organic compounds in waste gas. A relatively unexplored technique is the atmospheric negative dc multi-pin-to-plate glow discharge. This paper reports experimental results of allyl alcohol degradation and ozone production in this type of plasma. A new model was developed to describe these processes quantitatively. The model contains a detailed chemical degradation scheme, and describes the physics of the plasma by assuming that the fraction of electrons that takes part in chemical reactions is an exponential function of the reduced field. The model captured the experimental kinetic data to less than 2 ppm standard deviation.

A Model of Reduced Kinetics for Alkane Oxidation Using Constituents and Species for N-Heptane

NASA Technical Reports Server (NTRS)

Harstad, Kenneth G.; Bellan, Josette

2011-01-01

The reduction of elementary or skeletal oxidation kinetics to a subgroup of tractable reactions for inclusion in turbulent combustion codes has been the subject of numerous studies. The skeletal mechanism is obtained from the elementary mechanism by removing from it reactions that are considered negligible for the intent of the specific study considered. As of now, there are many chemical reduction methodologies. A methodology for deriving a reduced kinetic mechanism for alkane oxidation is described and applied to n-heptane. The model is based on partitioning the species of the skeletal kinetic mechanism into lights, defined as those having a carbon number smaller than 3, and heavies, which are the complement of the species ensemble. For modeling purposes, the heavy species are mathematically decomposed into constituents, which are similar but not identical to groups in the group additivity theory. From analysis of the LLNL (Lawrence Livermore National Laboratory) skeletal mechanism in conjunction with CHEMKIN II, it is shown that a similarity variable can be formed such that the appropriately non-dimensionalized global constituent molar density exhibits a self-similar behavior over a very wide range of equivalence ratios, initial pressures and initial temperatures that is of interest for predicting n-heptane oxidation. Furthermore, the oxygen and water molar densities are shown to display a quasi-linear behavior with respect to the similarity variable. The light species ensemble is partitioned into quasi-steady and unsteady species. The reduced model is based on concepts consistent with those of Large Eddy Simulation (LES) in which functional forms are used to replace the small scales eliminated through filtering of the governing equations; in LES, these small scales are unimportant as far as the overwhelming part of dynamic energy is concerned. Here, the scales thought unimportant for recovering the thermodynamic energy are removed. The concept is tested by using tabular information from the LLNL skeletal mechanism in conjunction with CHEMKIN II utilized as surrogate ideal functions replacing the necessary functional forms. The test reveals that the similarity concept is indeed justified and that the combustion temperature is well predicted, but that the ignition time is over-predicted, a fact traced to neglecting a detailed description of the processes leading to the heavies chemical decomposition. To palliate this deficiency, functional modeling is incorporated into this conceptual reduction in addition to the modeling the evolution of the global constituent molar density, the enthalpy evolution of the heavies, the contribution to the reaction rate of the unsteady lights from other light species and from the heavies, the molar density evolution of oxygen and water, and the mole fractions of the quasisteady light species. The model is compact in that there are only nine species-related progress variables. Results are presented showing the performance of the model for predicting the temperature and species evolution. The model reproduces the ignition time over a wide range of equivalence ratios, initial pressure, and initial temperature.

Probing the antagonistic effect of toluene as a component in surrogate fuel models at low temperatures and high pressures. A case study of toluene/dimethyl ether mixtures

DOE PAGES

Zhang, Yingjia; Somers, Kieran P.; Mehl, Marco; ...

2016-07-12

There is a dearth of experimental data which examine the fundamental low-temperature ignition (T < 900 K) behavior of toluene resulting in a lack of data for the construction, validation, and interpretation of chemical kinetic models for commercial fuels. In order to gain a better understanding of its combustion chemistry, dimethyl ether (DME) has been used as a radical initiator to induce ignition in this highly knock resistant aromatic, and its influence on the combustion of toluene ignition was studied in both shock tube and rapid compression machines as a function of temperature (624–1459 K), pressure (20–40 atm), equivalence ratiomore » (0.5–2.0), and blending ratio (100% toluene, 76% toluene (76T/24D), 58% toluene (58T/42D), 26% toluene (26T/74D) and 100% DME). We use several literature chemical kinetic models to interpret our experimental results. For mixtures containing high concentrations of toluene at low-temperatures none of these are capable of reproducing experiment. This then implies an incomplete understanding of the low-temperature oxidation pathways which control its ignition in our experimental reactors, and by extension, in spark- (SI) and compression-ignition (CI) engines, and an updated detailed chemical kinetic model is presented for engineering applications. Model analyses indicate that although the initial fate of the fuel is dominated by single-step H-atom abstraction reactions from both the benzylic and phenylic sites, the subsequent fate of the allylic and vinylic radicals formed is much more complex. Further experimental and theoretical endeavors are required to gain a holistic qualitative and quantitative chemical kinetics based understanding of the combustion of pure toluene, toluene blends, and commercial fuels containing other aromatic components, at temperatures of relevance to SI and CI engines.« less

Probing the antagonistic effect of toluene as a component in surrogate fuel models at low temperatures and high pressures. A case study of toluene/dimethyl ether mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yingjia; Somers, Kieran P.; Mehl, Marco

There is a dearth of experimental data which examine the fundamental low-temperature ignition (T < 900 K) behavior of toluene resulting in a lack of data for the construction, validation, and interpretation of chemical kinetic models for commercial fuels. In order to gain a better understanding of its combustion chemistry, dimethyl ether (DME) has been used as a radical initiator to induce ignition in this highly knock resistant aromatic, and its influence on the combustion of toluene ignition was studied in both shock tube and rapid compression machines as a function of temperature (624–1459 K), pressure (20–40 atm), equivalence ratiomore » (0.5–2.0), and blending ratio (100% toluene, 76% toluene (76T/24D), 58% toluene (58T/42D), 26% toluene (26T/74D) and 100% DME). We use several literature chemical kinetic models to interpret our experimental results. For mixtures containing high concentrations of toluene at low-temperatures none of these are capable of reproducing experiment. This then implies an incomplete understanding of the low-temperature oxidation pathways which control its ignition in our experimental reactors, and by extension, in spark- (SI) and compression-ignition (CI) engines, and an updated detailed chemical kinetic model is presented for engineering applications. Model analyses indicate that although the initial fate of the fuel is dominated by single-step H-atom abstraction reactions from both the benzylic and phenylic sites, the subsequent fate of the allylic and vinylic radicals formed is much more complex. Further experimental and theoretical endeavors are required to gain a holistic qualitative and quantitative chemical kinetics based understanding of the combustion of pure toluene, toluene blends, and commercial fuels containing other aromatic components, at temperatures of relevance to SI and CI engines.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doktorov, Alexander B., E-mail: doktorov@kinetics.nsc.ru

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

Implementation of an online chemical mechanism within a global-regional atmospheric model: design and initial steps

NASA Astrophysics Data System (ADS)

Jorba, O.; Pérez, C.; Baldasano, J. M.

2009-04-01

Chemical processes in air quality modelling systems are usually treated independently from the meteorological models. This approach is computationally attractive since off-line chemical transport simulations only require a single meteorological dataset to produce many chemical simulations. However, this separation of chemistry and meteorology produces a loss of important information about atmospheric processes and does not allow for feedbacks between chemistry and meteorology. To take into account such processes current models are evolving to an online coupling of chemistry and meteorology to produce consistent chemical weather predictions. The Earth Sciences Department of the Barcelona Supercomputing Center (BSC) develops the NMMB/BSC-DUST (Pérez et al., 2008), an online dust model within the global-regional NCEP/NMMB numerical weather prediction model (Janjic and Black, 2007) under development at National Centers for Environmental Prediction (NCEP). Current implementation is based on the well established regional dust model and forecast system DREAM (Nickovic et al., 2001). The most relevant characteristics of NMMB/BSC-DUST are its on-line coupling of the dust scheme with the meteorological driver, the wide range of applications from meso to global scales, and the inclusion of dust radiative effects allowing feedbacks between aerosols and meteorology. In order to complement such development, BSC works also in the implementation of a fully coupled online chemical mechanism within NMMB/BSC-DUST. The final objective is to develop a fully chemical weather prediction system able to resolve gas-aerosol-meteorology interactions from global to local scales. In this contribution we will present the design of the chemistry coupling and the current progress of its implementation. Following the NCEP/NMMB approach, the chemistry part will be coupled through the Earth System Modeling Framework (ESMF) as a pluggable component. The chemical mechanism and chemistry solver is based on the Kinetic PreProcessor KPP (Sandu and Sander, 2006) package with the main purpose to maintain a wide flexibility when configuring the model. Such approach will allow using a simple general chemical mechanism for global applications or a more complex mechanism for regional to local applications at higher resolution. REFERENCES Janjic, Z.I., and Black, T.L., 2007. An ESMF unified model for a broad range of spatial and temporal scales, Geophysical Research Abstracts, 9, 05025. Nickovic, S., Papadopoulos, A., Kakaliagou, O., and Kallos, G., 2001. Model for prediciton of desert dust cycle in the atmosphere. J. Geophys. Res., 106, 18113-18129. Pérez, C., Haustein, K., Janjic, Z.I., Jorba, O., Baldasano, J.M., Black, T.L., and Nickovic, S., 2008. An online dust model within the meso to global NMMB: current progress and plans. AGU Fall Meeting, San Francisco, A41K-03, 2008. Sandu, A., and Sander, R., 2006. Technical note:Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1. Atmos. Chem. and Phys., 6, 187-195.

Hydrogen production by aqueous phase reforming of light oxygenated hydrocarbons

NASA Astrophysics Data System (ADS)

Shabaker, John William

Aqueous phase reforming (APR) of renewable oxygenated hydrocarbons (e.g., methanol, ethylene glycol, glycerol, sorbitol, glucose) is a promising new technology for the catalytic production of high-purity hydrogen for fuel cells and chemical processing. Supported Pt catalysts are effective catalysts for stable and rapid H2 production at temperatures near 500 K (H 2 turnover frequencies near 10 min-1). Inexpensive Raney Ni-based catalysts have been developed using a combination of fundamental and high-throughput studies that have similar catalytic properties as Pt-based materials. Promotion of Raney Ni with Sn by controlled surface reaction of organometallic tin compounds is necessary to control formation of thermodynamically-favorable alkane byproducts. Detailed characterization by Mossbauer spectroscopy, electron microscopy, adsorption studies, and x-ray photoelectron spectroscopy (XPS/ESCA) has shown that NiSn alloys are formed during heat treatment, and may be responsible for enhanced stability and selectivity for hydrogen production. Detailed kinetic studies led to the development of a kinetic mechanism for the APR reaction on Pt and NiSn catalysts, in which the oxygenate decomposes through C--H and O--H cleavage, followed by C--C cleavage and water gas shift of the CO intermediate. The rate limiting step on Pt surfaces is the initial dehydrogenation, while C--C cleavage appears rate limiting over NiSn catalysts. Tin promotion of Raney Ni catalysts suppresses C--O bond scission reactions that lead to alkane formation without inhibiting fast C--C and C--H cleavage steps that are necessary for high rates of reforming. A window of operating temperature, pressure, and reactor residence time has been identified for use of the inexpensive NiSn catalysts as a Pt substitute. Concentrated feed stocks and aggressive pretreatments have been found to counteract catalyst deactivation by sintering in the hydrothermal APR environment and allow stable, long-term production of H2 over Raney-NiSn materials.

Mechanism of Rifampicin Inactivation in Nocardia farcinica

PubMed Central

Abdelwahab, Heba; Martin Del Campo, Julia S.; Dai, Yumin; Adly, Camelia; El-Sohaimy, Sohby; Sobrado, Pablo

2016-01-01

A novel mechanism of rifampicin (Rif) resistance has recently been reported in Nocardia farcinica. This new mechanism involves the activity of rifampicin monooxygenase (RifMO), a flavin-dependent monooxygenase that catalyzes the hydroxylation of Rif, which is the first step in the degradation pathway. Recombinant RifMO was overexpressed and purified for biochemical analysis. Kinetic characterization revealed that Rif binding is necessary for effective FAD reduction. RifMO exhibits only a 3-fold coenzyme preference for NADPH over NADH. RifMO catalyzes the incorporation of a single oxygen atom forming an unstable intermediate that eventually is converted to 2′-N-hydroxy-4-oxo-Rif. Stable C4a-hydroperoxyflavin was not detected by rapid kinetics methods, which is consistent with only 30% of the activated oxygen leading to product formation. These findings represent the first reported detailed biochemical characterization of a flavin-monooxygenase involved in antibiotic resistance. PMID:27706151

Self-Assembly of Human Serum Albumin: A Simplex Phenomenon

PubMed Central

Thakur, Garima; Prashanthi, Kovur; Jiang, Keren; Thundat, Thomas

2017-01-01

Spontaneous self-assemblies of biomolecules can generate geometrical patterns. Our findings provide an insight into the mechanism of self-assembled ring pattern generation by human serum albumin (HSA). The self-assembly is a process guided by kinetic and thermodynamic parameters. The generated protein ring patterns display a behavior which is geometrically related to a n-simplex model and is explained through thermodynamics and chemical kinetics. PMID:28930179

Electron-beam generated porous dextran gels: experimental and quantum chemical studies.

PubMed

Naumov, Sergej; Knolle, Wolfgang; Becher, Jana; Schnabelrauch, Matthias; Reichelt, Senta

2014-06-01

The aim of this work was to investigate the reaction mechanism of electron-beam generated macroporous dextran cryogels by quantum chemical calculation and electron paramagnetic resonance measurements. Electron-beam radiation was used to initiate the cross-linking reaction of methacrylated dextran in semifrozen aqueous solutions. The pore morphology of the resulting cryogels was visualized by scanning electron microscopy. Quantum chemical calculations and electron paramagnetic resonance studies provided information on the most probable reaction pathway and the chain growth radicals. The most probable reaction pathway was a ring opening reaction and the addition of a C-atom to the double-bond of the methacrylated dextran molecule. First detailed quantum chemical calculation on the reaction mechanism of electron-beam initiated cross-linking reaction of methacrylated dextran are presented.

Kinetic multi-layer model of aerosol surface and bulk chemistry (KM-SUB): the influence of interfacial transport and bulk diffusion on the oxidation of oleic acid by ozone

NASA Astrophysics Data System (ADS)

Shiraiwa, Manabu; Pfrang, Christian; Pöschl, Ulrich

2010-05-01

Aerosols are ubiquitous in the atmosphere and have strong effects on climate and public health. Gas-particle interactions can significantly change the physical and chemical properties of aerosols such as toxicity, reactivity, hygroscopicity and radiative properties. Chemical reactions and mass transport lead to continuous transformation and changes in the composition of atmospheric aerosols ("chemical aging"). Resistor model formulations are widely used to describe and investigate heterogeneous reactions and multiphase processes in laboratory, field and model studies of atmospheric chemistry. The traditional resistor models, however, are usually based on simplifying assumptions such as steady state conditions, homogeneous mixing, and limited numbers of non-interacting species and processes. In order to overcome these limitations, Pöschl, Rudich and Ammann have developed a kinetic model framework (PRA framework) with a double-layer surface concept and universally applicable rate equations and parameters for mass transport and chemical reactions at the gas-particle interface of aerosols and clouds [1]. Based on the PRA framework, we present a novel kinetic multi-layer model that explicitly resolves mass transport and chemical reaction at the surface and in the bulk of aerosol particles (KM-SUB) [2]. The model includes reversible adsorption, surface reactions and surface-bulk exchange as well as bulk diffusion and reaction. Unlike earlier models, KM-SUB does not require simplifying assumptions about steady-state conditions and radial mixing. The temporal evolution and concentration profiles of volatile and non-volatile species at the gas-particle interface and in the particle bulk can be modeled along with surface concentrations and gas uptake coefficients. In this study we explore and exemplify the effects of bulk diffusion on the rate of reactive gas uptake for a simple reference system, the ozonolysis of oleic acid particles, in comparison to experimental data and earlier model studies. We demonstrate how KM-SUB can be used to interpret and analyze experimental data from laboratory studies, and how the results can be extrapolated to atmospheric conditions. In particular, we show how interfacial transport and bulk transport, i.e., surface accommodation, bulk accommodation and bulk diffusion, influence the kinetics of the chemical reaction. Sensitivity studies suggest that in fine air particulate matter oleic acid and compounds with similar reactivity against ozone (C=C double bonds) can reach chemical life-times of multiple hours only if they are embedded in a (semi-)solid matrix with very low diffusion coefficients (~10-10 cm2 s-1). Depending on the complexity of the investigated system, unlimited numbers of volatile and non-volatile species and chemical reactions can be flexibly added and treated with KM-SUB. We propose and intend to pursue the application of KM-SUB as a basis for the development of a detailed master mechanism of aerosol chemistry as well as for the derivation of simplified but realistic parameterizations for large-scale atmospheric and climate models. References [1] Pöschl et al., Atmos. Chem. and Phys., 7, 5989-6023 (2007). [2] Shiraiwa et al., Atmos. Chem. Phys. Discuss., 10, 281-326 (2010).

Detailed reaction mechanism of macrophomate synthase. Extraordinary enzyme catalyzing five-step transformation from 2-pyrones to benzoates.

PubMed

Watanabe, K; Mie, T; Ichihara, A; Oikawa, H; Honma, M

2000-12-08

Macrophomate synthase from the fungus Macrophoma commelinae IFO 9570 is a Mg(II)-dependent dimeric enzyme that catalyzes an extraordinary, complex five-step chemical transformation from 2-pyrone and oxalacetate to benzoate involving decarboxylation, C-C bond formation, and dehydration. The catalytic mechanism of the whole pathway was investigated in three separate chemical steps. In the first decarboxylation step, the enzyme loses oxalacetate decarboxylation activity upon incubation with EDTA. Activity is fully restored by addition of Mg(II) and is not restored with other divalent metal cations. The dissociation constant of 0.93 x 10(-)(7) for Mg(II) and atomic absorption analysis established a 1:1 stoichiometric complex. Inhibition of pyruvate formation with 2-pyrone revealed that the actual product in the first step is a pyruvate enolate, which undergoes C-C bond formation in the presence of 2-pyrone. Incubation of substrate analogs provided aberrant adducts that were produced via C-C bond formation and rearrangement. This strongly indicates that the second step is two C-C bond formations, affording a bicyclic intermediate. Based on the stereospecificity, involvement of a Diels-Alder reaction at the second step is proposed. Incubation of the stereospecifically deuterium-labeled malate with 2-pyrones in the presence of malate dehydrogenase provided information for the stereochemical course of the reaction catalyzed by macrophomate synthase, indicating that the first decarboxylation provides pyruvate (Z)-[3-(2)H]enolate and that dehydration at the final step occurs with anti-elimination accompanied by concomitant decarboxylation. Examination of kinetic parameters in the individual steps suggests that the third step is the rate-determining step of the overall transformation.

Kinetic energy budgets near the turbulent/nonturbulent interface in jets

NASA Astrophysics Data System (ADS)

Taveira, Rodrigo R.; da Silva, Carlos B.

2013-01-01

The dynamics of the kinetic energy near the turbulent/nonturbulent (T/NT) interface separating the turbulent from the irrotational flow regions is analysed using three direct numerical simulations of turbulent planar jets, with Reynolds numbers based on the Taylor micro-scale across the jet shear layer in the range Reλ ≈ 120-160. Important levels of kinetic energy are already present in the irrotational region near the T/NT interface. The mean pressure and kinetic energy are well described by the Bernoulli equation in this region and agree with recent results obtained from rapid distortion theory in the turbulent region [M. A. C. Teixeira and C. B. da Silva, "Turbulence dynamics near a turbulent/non-turbulent interface," J. Fluid Mech. 695, 257-287 (2012)], 10.1017/jfm.2012.17 while the normal Reynolds stresses agree with the theoretical predictions from Phillips ["The irrotational motion outside a free turbulent boundary," Proc. Cambridge Philos. Soc. 51, 220 (1955)], 10.1017/S0305004100030073. The use of conditional statistics in relation to the distance from the T/NT interface allow a detailed study of the build up of kinetic energy across the T/NT interface, pointing to a very different picture than using classical statistics. Conditional kinetic energy budgets show that apart from the viscous dissipation of kinetic energy, the maximum of all the mechanisms governing the kinetic energy are concentrated in a very narrow region distancing about one to two Taylor micro-scales from the T/NT interface. The (total and fluctuating) kinetic energy starts increasing in the irrotational region by pressure-velocity interactions - a mechanism that can act at distance, and continue to grow by advection (for the total kinetic energy) and turbulent diffusion (for the turbulent kinetic energy) inside the turbulent region. These mechanisms tend to occur preferentially around the core of the large-scale vortices existing near T/NT interface. The production of turbulent kinetic energy then becomes the dominating mechanism and the so called "peak production" is located at about one Taylor micro-scale from the T/NT interface. Simple analytical estimates are given for the peaks of pressure strain, turbulent diffusion, and production near the T/NT interface. The growth of kinetic energy across the T/NT interface is an inertial process, since the viscous terms (diffusion and dissipation) are negligible during this process. The present results highlight the importance of the region near the T/NT interface in the entire jet development.

Thermodynamic and kinetic analysis of heterogeneous photocatalysis for semiconductor systems.

PubMed

Liu, Baoshun; Zhao, Xiujian; Terashima, Chiaki; Fujishima, Akira; Nakata, Kazuya

2014-05-21

Since the report of the Honda-Fujishima effect, heterogeneous photocatalysis has attracted much attention around the world because of its potential energy and environmental applications. Although great progresses have been made in recent years, most were focused on preparing highly-active photocatalysts and investigating visible light utilization. In fact, we are still unclear on the thermodynamic and kinetic nature of photocatalysis to date, which sometimes leads to misunderstandings for experimental results. It is timely to give a review and discussion on the thermodynamics and kinetics of photocatalysis, so as to direct future researches. However, there is an absence of a detailed review on this topic until now. In this article, we tried to review and discuss the thermodynamics and kinetics of photocatalysis. We explained the thermodynamic driving force of photocatalysis, and distinguished the functions of light and heat in photocatalysis. The Langmuir-Hinshelwood kinetic model, the ˙OH oxidation mechanism, and the direct-indirect (D-I) kinetic model were reviewed and compared. Some applications of the D-I model to study photocatalytic kinetics were also discussed. The electron transport mode and its importance in photocatalysis were investigated. Finally, the intrinsic relation between the kinetics and the thermodynamics of photocatalytic reactions was discussed.

How fast monoamine oxidases decompose adrenaline? Kinetics of isoenzymes A and B evaluated by empirical valence bond simulation.

PubMed

Oanca, Gabriel; Stare, Jernej; Mavri, Janez

2017-12-01

This work scrutinizes kinetics of decomposition of adrenaline catalyzed by monoamine oxidase (MAO) A and B enzymes, a process controlling the levels of adrenaline in the central nervous system and other tissues. Experimental kinetic data for MAO A and B catalyzed decomposition of adrenaline are reported only in the form of the maximum reaction rate. Therefore, we estimated the experimental free energy barriers form the kinetic data of closely related systems using regression method, as was done in our previous study. By using multiscale simulation on the Empirical Valence Bond (EVB) level, we studied the chemical reactivity of the MAO A catalyzed decomposition of adrenaline and we obtained a value of activation free energy of 17.3 ± 0.4 kcal/mol. The corresponding value for MAO B is 15.7 ± 0.7 kcal/mol. Both values are in good agreement with the estimated experimental barriers of 16.6 and 16.0 kcal/mol for MAO A and MAO B, respectively. The fact that we reproduced the kinetic data and preferential catalytic effect of MAO B over MAO A gives additional support to the validity of the proposed hydride transfer mechanism. Furthermore, we demonstrate that adrenaline is preferably involved in the reaction in a neutral rather than in a protonated form due to considerably higher barriers computed for the protonated adrenaline substrate. The results are discussed in the context of chemical mechanism of MAO enzymes and possible applications of multiscale simulation to rationalize the effects of MAO activity on adrenaline level. © 2017 Wiley Periodicals, Inc.

On the mechanism of flow evolution in shock-tube experiments

NASA Astrophysics Data System (ADS)

Kiverin, Alexey; Yakovenko, Ivan

2018-02-01

The paper studies numerically the flow development behind the shock wave propagating inside the tube. The detailed analysis of the flow patterns behind the shock wave allows determination of the gas-dynamical origins of the temperature non-uniformities responsible for the subsequent localized start of chemical reactions in the test mixture. In particular, it is shown that the temperature field structure is determined mainly by the mechanisms of boundary layer instability development. The kinetic energy dissipation related to the flow deceleration inside boundary layer results in local heating of the test gas. At the same time, the heat losses to the tube wall lead to the cooling of the gas. Therefore the temperature stratification takes place on the scales of the boundary layer. As soon as the shock wave reflected from the end-wall of the tube interacts with the developed boundary layer the localized hot regions arise at a certain distance from the end wall. The position of these hot regions is associated with the zones of shock wave interaction with roller vortices at the margin between the boundary layer and the bulk flow. Formulated mechanism of the temperature field evolution can be used to explain the peculiarities of non-steady shock-induced ignition of combustible mixtures with moderate ignition delay times, where the ignition starts inside localized kernels at distance from the end wall.

Study on kinetics of adsorption of humic acid modified by ferric chloride on U(VI)

NASA Astrophysics Data System (ADS)

Zhang, Y. Y.; Lv, J. W.; Song, Y.; Dong, X. J.; Fang, Q.

2017-11-01

In order to reveal the adsorption mechanism of the ferric chloride modified humic acid on uranium, the influence of pH value and contact time of adsorption on uranium was studied through a series of batch experiments. Meanwhile, the adsorption kinetics was analyzed with pseudo-first order kinetic model and pseudo-second order kinetic model. The results show that adsorption is affected by the pH value of the solution and by contract time, and the best condition for adsorption on uranium is at pH=5 and the adsorption equilibrium time is about 80 min. Kinetics of HA-Fe adsorption on uranium accords with pseudo-second order kinetic model. The adsorption is mainly chemical adsorption, and complexes were produced by the reaction between uranium ions and the functional groups on the surface of HA-Fe, which can provide reference for further study of humic acid effecting on the migration of U(VI) in soil.

Radioactive Cobalt(II) Removal from Aqueous Solutions Using a Reusable Nanocomposite: Kinetic, Isotherms, and Mechanistic Study

PubMed Central

Wang, Ximing; Chen, Zhangjing

2017-01-01

A lignocellulose/montmorillonite (LMT) nanocomposite was prepared as a reusable adsorbent for cobalt(II) ions, and characterized by nitrogen (N2) adsorption/desorption isotherm, X-ray Diffraction (XRD), Scanning Electron Microscope (SEM), Transmission Electron Microscopy (TEM), and Fourier Transform Infrared Spectroscopy (FTIR). LMT exhibited efficient adsorption of cobalt ions (Co(II)), and the adsorbed Co(II) was readily desorbed by nitric acid (HNO3). All parameters affecting the adsorption and/or desorption of Co(II), including initial Co(II) concentration, pH value, temperature, HNO3 concentration, and time, were optimized. The kinetic data analysis showed that the adsorption followed the pseudo-second-order kinetic model and fit well into the Langmuir isotherm equation. Notably, the nanocomposite can be used four times without significantly losing adsorbent capability. The Energy-Dispersive X-ray (EDX) and FTIR spectra analysis also revealed that the adsorption mechanism may be mainly a chemical adsorption dominated process. PMID:29186794

A New Method for Evaluating the Carbon Isotope Characteristics of Carbonate Formed Under Cryogenic Conditions Analogous to Mars

NASA Technical Reports Server (NTRS)

Niles, P. B.; Socki, R. A.; Hredzak, P. L.

2007-01-01

The two upcoming robotic missions to Mars, Phoenix and MSL, will both have the capability of measuring the carbon isotopic composition of CO2 in the martian atmosphere, as well as possible CO2 trapped in carbonate minerals in the Martian soil. Results from orbital and landed missions now clearly indicate that no large scale deposits of carbonate materials exist at the surface. However, some results from orbital remote sensing have been interpreted to indicate that carbonate minerals are present as fine particles interspersed at low concentrations (approx. 2%) in the martian dust. One likely mechanism for the production of these carbonates is during the freezing of transient water near the surface. Large deposits of near surface ice and photographic evidence for flowing water on the surface suggest that transient melting and refreezing of H2O is an active process on Mars. Any exposure of these fluids to the CO2 rich atmosphere should al-low the production of HCO3- solutions. Carbonates are likely precipitates from these solutions during freezing as extensive CO2 degassing, driven by the fluid s decreasing volume, drives CO2 out. This rapid CO2 degassing increases the pH of the solution and drives carbonate precipitation. It has been shown in previous studies that this rapid CO2 degassing also results in a kinetic isotopic fractionation where the CO2 gas has a much lighter isotopic composition causing a large isotope enrichment of C-13 in the precipitated carbonate. This kinetic isotope enrichment may be very common in the current martian environment, and may be a very important factor in understanding the very high deltaC-13 values of carbonates found in the martian meteorites. However, while previous studies have succeeded in generally quantifying the magnitude of this effect, detailed studies of the consistency of this effect, and the freezing rates needed to produce it are needed to understand any carbon isotope analyses from carbonate minerals in the martian soil or dust. This study demonstrates an innovative new method for measuring the isotopic composition of gas evolved from the freezing of carbonate solutions in real time, which allows for a much clearer view of the chemical processes involved. This method now sets the stage for detailed analysis of the chemical and isotopic mechanisms that produce cryogenic carbonates.

Thermodynamically Feasible Kinetic Models of Reaction Networks

PubMed Central

Ederer, Michael; Gilles, Ernst Dieter

2007-01-01

The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts the concepts of potentials and forces from irreversible thermodynamics to kinetic modeling. In the proposed formalism, the thermokinetic potential of a compound is proportional to its concentration. The proportionality factor is a compound-specific parameter called capacity. The thermokinetic force of a reaction is a function of the potentials. Every reaction has a resistance that is the ratio of thermokinetic force and reaction rate. For mass-action type kinetics, the resistances are constant. Since it relies on the thermodynamic concept of potentials and forces, the TKM formalism structurally observes detailed balance for all values of capacities and resistances. Thus, it provides an easy way to formulate physically feasible, kinetic models of biological reaction networks. The TKM formalism is useful for modeling large biological networks that are subject to many detailed balance relations. PMID:17208985

Detailed kinetics and regulation of mammalian 2-oxoglutarate dehydrogenase

PubMed Central

2011-01-01

Background Mitochondrial 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The catalytic mechanism and allosteric regulation of this large enzyme complex are not fully understood. Here computer simulation is used to test possible catalytic mechanisms and mechanisms of allosteric regulation of the enzyme by nucleotides (ATP, ADP), pH, and metal ion cofactors (Ca2+ and Mg2+). Results A model was developed based on an ordered ter-ter enzyme kinetic mechanism combined with con-formational changes that involve rotation of one lipoic acid between three catalytic sites inside the enzyme complex. The model was parameterized using a large number of kinetic data sets on the activity of OGDHC, and validated by comparison of model predictions to independent data. Conclusions The developed model suggests a hybrid rapid-equilibrium ping-pong random mechanism for the kinetics of OGDHC, consistent with previously reported mechanisms, and accurately describes the experimentally observed regulatory effects of cofactors on the OGDHC activity. This analysis provides a single consistent theoretical explanation for a number of apparently contradictory results on the roles of phosphorylation potential, NAD (H) oxidation-reduction state ratio, as well as the regulatory effects of metal ions on ODGHC function. PMID:21943256

Density-dependent liquid nitromethane decomposition: molecular dynamics simulations based on ReaxFF.

PubMed

Rom, Naomi; Zybin, Sergey V; van Duin, Adri C T; Goddard, William A; Zeiri, Yehuda; Katz, Gil; Kosloff, Ronnie

2011-09-15

The decomposition mechanism of hot liquid nitromethane at various compressions was studied using reactive force field (ReaxFF) molecular dynamics simulations. A competition between two different initial thermal decomposition schemes is observed, depending on compression. At low densities, unimolecular C-N bond cleavage is the dominant route, producing CH(3) and NO(2) fragments. As density and pressure rise approaching the Chapman-Jouget detonation conditions (∼30% compression, >2500 K) the dominant mechanism switches to the formation of the CH(3)NO fragment via H-transfer and/or N-O bond rupture. The change in the decomposition mechanism of hot liquid NM leads to a different kinetic and energetic behavior, as well as products distribution. The calculated density dependence of the enthalpy change correlates with the change in initial decomposition reaction mechanism. It can be used as a convenient and useful global parameter for the detection of reaction dynamics. Atomic averaged local diffusion coefficients are shown to be sensitive to the reactions dynamics, and can be used to distinguish between time periods where chemical reactions occur and diffusion-dominated, nonreactive time periods. © 2011 American Chemical Society

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

Temporal cross-correlation asymmetry and departure from equilibrium in a bistable chemical system.

PubMed

Bianca, C; Lemarchand, A

2014-06-14

This paper aims at determining sustained reaction fluxes in a nonlinear chemical system driven in a nonequilibrium steady state. The method relies on the computation of cross-correlation functions for the internal fluctuations of chemical species concentrations. By employing Langevin-type equations, we derive approximate analytical formulas for the cross-correlation functions associated with nonlinear dynamics. Kinetic Monte Carlo simulations of the chemical master equation are performed in order to check the validity of the Langevin equations for a bistable chemical system. The two approaches are found in excellent agreement, except for critical parameter values where the bifurcation between monostability and bistability occurs. From the theoretical point of view, the results imply that the behavior of cross-correlation functions cannot be exploited to measure sustained reaction fluxes in a specific nonlinear system without the prior knowledge of the associated chemical mechanism and the rate constants.

Gas Fluxing of Molten Aluminum: An Overview

NASA Astrophysics Data System (ADS)

Sigworth, Geoffrey K.; Williams, Edward M.; Chesonis, D. Corleen

The aluminum industry is under continual pressure to improve metal quality, while at the same time reduce costs. Although a reasonably mature technology, there has been a continual evolution in degassing equipment over the years. A detailed review and theoretical analysis is given of the chemical and kinetic factors which control the metal quality after gas fluxing, and the evolution of degassing technology in Alcoa is summarized. Particular emphasis is placed on hydrogen removal, minimization of chlorine use, reduced operating costs and minimization of environmental emissions. Considerations related to inclusion removal are also discussed briefly.

Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.

Computed rate coefficients and product yields for c-C5H5 + CH3 --> products.

PubMed

Sharma, Sandeep; Green, William H

2009-08-06

Using quantum chemical methods, we have explored the region of the C6H8 potential energy surface that is relevant in predicting the rate coefficients of various wells and major product channels following the reaction between cyclopentadienyl radical and methyl radical, c-C5H5 + CH3. Variational transition state theory is used to calculate the high-pressure-limit rate coefficient for all of the barrierless reactions. RRKM theory and the master equation are used to calculate the pressure dependent rate coefficients for 12 reactions. The calculated results are compared with the limited experimental data available in the literature and the agreement between the two is quite good. All of the rate coefficients calculated in this work are tabulated and can be used in building detailed chemical kinetic models.

Environmental Biotechnology: Moving from the Flask to the Field

DTIC Science & Technology

1991-09-30

biosorption , Biosorption of metal ions is a phenome- non exhibited by both alive and dead microbial cells. The detailed investigation of the mechanism of... biosorption has revealed that biosorption is a physical-chemical process whereby selected areas of the microbial cell exhibit high selectivity and...dead cells than by the same cells alive. The use of proper chemical solutions (eluants) is capable of reversing the equilibrium of biosorption

Pre-Steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase: Analysis and Implications†

PubMed Central

Robertson, Brooklyn A.; Schroeder, Gottfried K.; Jin, Zhinan; Johnson, Kenneth A.; Whitman, Christian P.

2009-01-01

Isomer-specific 3-chloroacrylic acid dehalogenases catalyze the hydrolytic dehalogenation of the cis- and trans-isomers of 3-chloroacrylate to yield malonate semialdehyde. These reactions represent key steps in the degradation of the nematocide, 1,3-dichloropropene. The kinetic mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) has now been examined using stopped-flow and chemical-quench techniques. Stopped-flow analysis of the reaction, following the fluorescence of an active site tryptophan, is consistent with a minimal three-step model involving substrate binding, chemistry, and product release. Chemical quench experiments show burst kinetics, indicating that product release is at least partially rate limiting. Global fitting of all of the kinetic results by simulation is best accommodated by a four-step mechanism. In the final kinetic model, the enzyme binds substrate and isomerizes to an alternate fluorescent form, chemistry occurs, and is followed by the ordered release of two products, with the release of the first product as the rate-limiting step. Bromide ion is a competitive inhibitor of the reaction indicating that it binds to the free enzyme rather than to the enzyme with one product still bound. This observation suggests that malonate semialdehyde is the first product released by the enzyme (rate limiting), followed by halide. A comparison of the unliganded cis-CaaD crystal structure with that of an inactivated cis-CaaD where the prolyl nitrogen of Pro-1 is covalently attached to (R)-2-hydroxypropanoate provides a possible explanation for the isomerization step. The structure of the covalently modified enzyme shows that a 7-residue loop comprised of residues 32-38 is closed down on the active site cavity where the backbone amides of two residues (Phe-37 and Leu-38) interact with the carboxylate group of the adduct. In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop to close down on the active site and sequester the reaction from the external environment. PMID:19856961

Miming the cancer-immune system competition by kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bianca, Carlo; Lemarchand, Annie

2016-10-01

In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance.

pyJac: Analytical Jacobian generator for chemical kinetics

NASA Astrophysics Data System (ADS)

Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

2017-06-01

Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using pyJac via matrix evaluation timing comparisons; the routines produced by pyJac outperformed first-order finite differences by 3-7.5 times and the existing analytical Jacobian software TChem by 1.1-2.2 times on a single-threaded basis. It is noted that TChem is not thread-safe, while pyJac is easily parallelized, and hence can greatly outperform TChem on multicore CPUs. The Jacobian matrix generator we describe here will be useful for reducing the cost of integrating chemical source terms with implicit algorithms in particular and algorithms that require an accurate Jacobian matrix in general. Furthermore, the open-source release of the program and Python-based implementation will enable wide adoption.

A framework for expanding aqueous chemistry in the ...

EPA Pesticide Factsheets

This paper describes the development and implementation of an extendable aqueous-phase chemistry option (AQCHEM − KMT(I)) for the Community Multiscale Air Quality (CMAQ) modeling system, version 5.1. Here, the Kinetic PreProcessor (KPP), version 2.2.3, is used to generate a Rosenbrock solver (Rodas3) to integrate the stiff system of ordinary differential equations (ODEs) that describe the mass transfer, chemical kinetics, and scavenging processes of CMAQ clouds. CMAQ's standard cloud chemistry module (AQCHEM) is structurally limited to the treatment of a simple chemical mechanism. This work advances our ability to test and implement more sophisticated aqueous chemical mechanisms in CMAQ and further investigate the impacts of microphysical parameters on cloud chemistry. Box model cloud chemistry simulations were performed to choose efficient solver and tolerance settings, evaluate the implementation of the KPP solver, and assess the direct impacts of alternative solver and kinetic mass transfer on predicted concentrations for a range of scenarios. Month-long CMAQ simulations for winter and summer periods over the US reveal the changes in model predictions due to these cloud module updates within the full chemical transport model. While monthly average CMAQ predictions are not drastically altered between AQCHEM and AQCHEM − KMT, hourly concentration differences can be significant. With added in-cloud secondary organic aerosol (SOA) formation from bio

Microwave Assisted Enzymatic Kinetic Resolution of (±)-1-Phenyl-2-propyn-1-ol in Nonaqueous Media

PubMed Central

Devendran, Saravanan; Yadav, Ganapati D.

2014-01-01

Kinetic resolution of 1-phenyl-2-propyn-1-ol, an important chiral synthon, was studied through trans-esterification with acyl acetate to investigate synergism between microwave irradiation and enzyme catalysis. Lipases from different microbial origins were employed for the kinetic resolution of (R/S)-1-phenyl-2-propyn-1-ol, among which Candida antarctica lipase B, immobilized on acrylic resin (Novozym 435), was found to be the best catalyst in n-hexane as solvent. Vinyl acetate was the most effective among different acyl esters studied. The effect of various parameters was studied in a systematic manner. Definite synergism between microwave and enzyme was observed. The initial rate was improved around 1.28 times under microwave irradiation than conventional heating. Under optimum conditions, maximum conversion (48.78%) and high enantiomeric excess (93.25%) were obtained in 2 h. From modeling studies, it is concluded that the reaction follows the Ping-Pong bi-bi mechanism with dead end alcohol inhibition. Kinetic parameters were obtained by using nonlinear regression. This process is green, clean, and easily scalable as compared to the chemical process. PMID:24707487

Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms

NASA Astrophysics Data System (ADS)

Druschel, Gregory K.; Emerson, David; Sutka, R.; Suchecki, P.; Luther, George W., III

2008-07-01

Neutrophilic iron oxidizing bacteria (FeOB) must actively compete with rapid abiotic processes governing Fe(II) oxidation and as a result have adapted to primarily inhabit low-O 2 environments where they can more successfully compete with abiotic Fe(II) oxidation. The spatial distribution of these microorganisms can be observed through the chemical gradients they affect, as measured using in situ voltammetric analysis for dissolved Fe(II), Fe(III), O 2, and FeS (aq). Field and laboratory determination of the chemical environments inhabited by the FeOB were coupled with detailed kinetic competition studies for abiotic and biotic oxidation processes using a pure culture of FeOB to quantify the geochemical niche these organisms inhabit. In gradient culture tubes, the maximum oxygen levels, which were associated with growth bands of Sideroxydans lithotrophicus (ES-1, a novel FeOB), were 15-50 μM. Kinetic measurements made on S. lithotrophicus compared biotic/abiotic (killed control) Fe oxidation rates. The biotic rate can be a significant and measurable fraction of the total Fe oxidation rate below O 2 concentrations of approximately 50 μM, but biotic Fe(II) oxidation (via the biotic/abiotic rate comparison) becomes difficult to detect at higher O 2 levels. These results are further supported by observations of conditions supporting FeOB communities in field settings. Variablity in cell densities and cellular activity as well as variations in hydrous ferrous oxide mineral quantities significantly affect the laboratory kinetic rates. The microbial habitat (or geochemical niche) where FeOB are active is thus largely controlled by the competition between abiotic and biotic kinetics, which are dependent on Fe(II) concentration, P O2, temperature and pH in addition to the surface area of hydrous ferric oxide minerals and the cell density/activity of FeOB. Additional field and lab culture observations suggest a potentially important role for the iron-sulfide aqueous molecular cluster, FeS (aq), in the overall cycling of iron associated with the environments these microorganisms inhabit.

Chemical Kinetic Influences of Alkyl Chain Structure on the High Pressure and Temperature Oxidation of a Representative Unsaturated Biodiesel: Methyl Nonenoate.

PubMed

Fridlyand, Aleksandr; Goldsborough, S Scott; Brezinsky, Kenneth

2015-07-16

The high pressure and temperature oxidation of methyl trans-2-nonenoate, methyl trans-3-nonenoate, 1-octene, and trans-2-octene are investigated experimentally to probe the influence of the double bond position on the chemical kinetics of long esters and alkenes. Single pulse shock tube experiments are performed in the ranges p = 3.8-6.2 MPa and T = 850-1500 K, with an average reaction time of 2 ms. Gas chromatographic measurements indicate increased reactivity for trans-2-octene compared to 1-octene, whereas both methyl nonenoate isomers have reactivities similar to that of 1-octene. A difference in the yield of stable intermediates is observed for the octenes when compared to the methyl nonenoates. Chemical kinetic models are developed with the aid of the Reaction Mechanism Generator to interpret the experimental results. The models are created using two different base chemistry submodels to investigate the influence of the foundational chemistry (i.e., C0-C4), whereas Monte Carlo simulations are performed to examine the quality of agreement with the experimental results. Significant uncertainties are found in the chemistry of unsaturated esters with the double bonds located close to the ester groups. This work highlights the importance of the foundational chemistry in predictive chemical kinetics of biodiesel combustion at engine relevant conditions.

PROGRESS IN DETAILED KINETIC MODELING OF THE COMBUSTION OF OXYGENATED COMPONENTS OF BIOFUELS

PubMed Central

Sy Tran, Luc; Sirjean, Baptiste; Glaude, Pierre-Alexandre; Fournet, René; Battin-Leclerc, Frédérique

2013-01-01

Due to growing environmental concerns and diminishing petroleum reserves, a wide range of oxygenated species has been proposed as possible substitutes to fossil fuels: alcohols, methyl esters, acyclic and cyclic ethers. After a short review the major detailed kinetic models already proposed in the literature for the combustion of these molecules, the specific classes of reactions considered for modeling the oxidation of acyclic and cyclic oxygenated molecules respectively, are detailed. PMID:23700355

Combining experimental techniques with non-linear numerical models to assess the sorption of pesticides on soils

NASA Astrophysics Data System (ADS)

Magga, Zoi; Tzovolou, Dimitra N.; Theodoropoulou, Maria A.; Tsakiroglou, Christos D.

2012-03-01

The risk assessment of groundwater pollution by pesticides may be based on pesticide sorption and biodegradation kinetic parameters estimated with inverse modeling of datasets from either batch or continuous flow soil column experiments. In the present work, a chemical non-equilibrium and non-linear 2-site sorption model is incorporated into solute transport models to invert the datasets of batch and soil column experiments, and estimate the kinetic sorption parameters for two pesticides: N-phosphonomethyl glycine (glyphosate) and 2,4-dichlorophenoxy-acetic acid (2,4-D). When coupling the 2-site sorption model with the 2-region transport model, except of the kinetic sorption parameters, the soil column datasets enable us to estimate the mass-transfer coefficients associated with solute diffusion between mobile and immobile regions. In order to improve the reliability of models and kinetic parameter values, a stepwise strategy that combines batch and continuous flow tests with adequate true-to-the mechanism analytical of numerical models, and decouples the kinetics of purely reactive steps of sorption from physical mass-transfer processes is required.

[Mechanisms of congenital erythrocyte enzyme deficiencies associated with hemolytic anemia].

PubMed

Boivin, P; Kahn, A

1976-01-01

The search for a mechanism for red cell enzyme deficiency associated with congenital hemolytic anemia, requires one to determine the kinetic and thermodynamic properties of the enzyme reaction and study the physico-chemical and immunological characteristics of the protein which supports enzyme activity. The technique of iso-electric focalisation and the use of specific anti-enzyme antibodies, is the reason for recent progress in the understanding of the mechanism of these deficiencies. Examples of application of these techniques are given in relation to glucose-6-dehydrogenase, pyruvate kinase, glucose phosphate isomerase, phosphofructokinase and phosphoglycerate kinase of deficiencies showing the multiplicity of the molecular mechanisms.

Inhibition of turbulence in inertial-confinement-fusion hot spots by viscous dissipation.

PubMed

Weber, C R; Clark, D S; Cook, A W; Busby, L E; Robey, H F

2014-05-01

Achieving ignition in inertial confinement fusion (ICF) requires the formation of a high-temperature (>10 keV) central hot spot. Turbulence has been suggested as a mechanism for degrading the hot-spot conditions by altering transport properties, introducing colder, mixed material, or reducing the conversion of radially directed kinetic energy to hot-spot heating. We show, however, that the hot spot is very viscous, and the assumption of turbulent conditions in the hot spot is incorrect. This work presents the first high-resolution, three-dimensional simulations of National Ignition Facility (NIF) implosion experiments using detailed knowledge of implosion dynamics and instability seeds and including an accurate model of physical viscosity. We find that when viscous effects are neglected, the hot spot can exhibit a turbulent kinetic energy cascade. Viscous effects, however, are significant and strongly damp small-scale velocity structures, with a hot-spot Reynolds number in the range of only 10-100.

Inhibition of turbulence in inertial-confinement-fusion hot spots by viscous dissipation

NASA Astrophysics Data System (ADS)

Weber, C. R.; Clark, D. S.; Cook, A. W.; Busby, L. E.; Robey, H. F.

2014-05-01

Achieving ignition in inertial confinement fusion (ICF) requires the formation of a high-temperature (>10 keV) central hot spot. Turbulence has been suggested as a mechanism for degrading the hot-spot conditions by altering transport properties, introducing colder, mixed material, or reducing the conversion of radially directed kinetic energy to hot-spot heating. We show, however, that the hot spot is very viscous, and the assumption of turbulent conditions in the hot spot is incorrect. This work presents the first high-resolution, three-dimensional simulations of National Ignition Facility (NIF) implosion experiments using detailed knowledge of implosion dynamics and instability seeds and including an accurate model of physical viscosity. We find that when viscous effects are neglected, the hot spot can exhibit a turbulent kinetic energy cascade. Viscous effects, however, are significant and strongly damp small-scale velocity structures, with a hot-spot Reynolds number in the range of only 10--100.

Impact of biochar produced from post-harvest residue on the adsorption behavior of diesel oil on loess soil.

PubMed

Jiang, Yu Feng; Sun, Hang; Yves, Uwamungu J; Li, Hong; Hu, Xue Fei

2016-02-01

The primary objective of this study was to investigate the effect of biochar, produced from wheat residue at different temperatures, on the adsorption of diesel oil by loess soil. Kinetic and equilibrium data were processed to understand the adsorption mechanism of diesel by biochar-affected loess soil; dynamic and thermodynamic adsorption experiments were conducted to characterize this adsorption. The surface features and chemical structure of biochar, modified at varying pyrolytic temperatures, were investigated using surface scanning electron microscopy and Fourier transform infrared analysis. The kinetic data showed that the adsorption of diesel oil onto loess soil could be described by a pseudo-second-order kinetic model, with the rate-controlling step being intraparticle diffusion. However, in the presence of biochar, boundary layer control and intraparticle diffusion were both involved in the adsorption. Besides, the adsorption equilibrium data were well described by the Freundlich isothermal model. The saturated adsorption capacity weakened as temperature increased, suggesting a spontaneous exothermic process. Thermodynamic parameter analysis showed that adsorption was mainly a physical process and was enhanced by chemical adsorption. The adsorption capacity of loess soil for diesel oil was weakened with increasing pH. The biochar produced by pyrolytic wheat residue increased the adsorption behavior of petroleum pollutants in loess soil.

Recent structural and mechanistic insights into post-translational enzymatic glycosylation.

PubMed

Hurtado-Guerrero, Ramon; Davies, Gideon J

2012-12-01

Enzymatic glycosylation of proteins, a post-transitional modification of great significance, is carried out by diverse glycosyltransferases (GTs) that harness activated sugar donors, typically nucleotide or lipid-phosphate linked species. Recent work has seen a major increase in the study of the 3D structure and reaction mechanism of these enzymes. Key advances include the dissection of the classical O-glycosylating and N-glycosylating apparatus, revealing unusual folds and hitherto unconsidered chemical mechanisms for acceptor activation. There has been considerable success in the application of kinetic isotope effects and quantum simulations to address the controversial issue of the reaction mechanism of retaining GTs. New roles for old modifications, exemplified by potential epigenetic roles for glycosylation, have been discovered and there has also been a plethora of studies into important mammalian glycosylations that play key roles in cellular biology, opening up new targets for chemical intervention approaches. Copyright © 2012 Elsevier Ltd. All rights reserved.

Elucidating the reaction pathways in the synthesis of organolead trihalide perovskite for high-performance solar cells.

PubMed

Wang, Baohua; Young Wong, King; Xiao, Xudong; Chen, Tao

2015-05-28

The past two years have witnessed unprecedentedly rapid development of organic-inorganic halide perovskite-based solar cells. The solution-processability and high efficiency make this technology extraordinarily attractive. The intensive investigations have accumulated rich experiences in the perovskite fabrication; while the mechanism of the chemical synthesis still remains unresolved. Here, we set up the chemical equation of the synthesis and elucidate the reactions from both thermodynamic and kinetic perspectives. Our study shows that gaseous products thermodynamically favour the reaction, while the activation energy and "collision" probability synergistically determine the reaction rate. These understandings enable us to finely tune the crystal size for high-quality perovskite film, leading to a record fill factor among similar device structures in the literature. This investigation provides a general strategy to explore the mechanism of perovskite synthesis and benefits the fabrication of high-efficiency perovskite photoactive layer.

Discrete kinetic models from funneled energy landscape simulations.

PubMed

Schafer, Nicholas P; Hoffman, Ryan M B; Burger, Anat; Craig, Patricio O; Komives, Elizabeth A; Wolynes, Peter G

2012-01-01

A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

Impact of carbon, oxygen and sulfur content of microscale zerovalent iron particles on its reactivity towards chlorinated aliphatic hydrocarbons.

PubMed

Velimirovic, Milica; Larsson, Per-Olof; Simons, Queenie; Bastiaens, Leen

2013-11-01

Zerovalent iron (ZVI) abiotically degrades several chlorinated aliphatic hydrocarbons (CAHs) via reductive dechlorination, which offers perspectives for in situ groundwater remediation applications. The difference in reactivity between ZVI particles is often linked with their specific surface area. However, other parameters may influence the reactivity as well. Earlier, we reported for a set of microscale zerovalent iron (mZVI) particles the disappearance kinetic of different CAHs which were collected under consistent experimental conditions. In the present study, these kinetic data were correlated with the carbon, oxygen and sulfur content of mZVI particles. It was confirmed that not only the specific surface area affects the disappearance kinetic of CAHs, but also the chemical composition of the mZVI particles. The chemical composition, in addition, influences CAHs removal mechanism inducing sorption onto mZVI particles instead of dechlorination. Generally, high disappearance kinetic of CAHs was observed for particles containing less oxygen. A high carbon content, on the other hand, induced nonreactive sorption of the contaminants on the mZVI particles. To obtain efficient remediation of CAHs by mZVI particles, this study suggested that the carbon and oxygen content should not exceed 0.5% and 1% respectively. Finally, the efficiency of the mZVI particles may be improved to some extent by enriching them with sulfur. However, the impact of sulfur content on the reactivity of mZVI particles is less pronounced than that of the carbon and oxygen content. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isotope effect studies of the chemical mechanism of nicotinamide adenine dinucleotide malic enzyme from Crassula

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grissom, C.B.; Willeford, O.; Wedding, R.T.

1987-05-05

The /sup 13/C primary kinetic isotope effect on the decarboxylation of malate by nicotinamide adenine dinucleotide malic enzyme from Crassula argentea is 1.0199 +/- 0.0006 with proteo L-malate-2-H and 1.0162 +/- 0.0003 with malate-2-d. The primary deuterium isotope effect is 1.45 +/- 0.10 on V/K and 1.93 +/- 0.13 on V/sub max/. This indicates a stepwise conversion of malate to pyruvate and CO/sub 2/ with hydride transfer preceding decarboxylation, thereby suggesting a discrete oxaloacetate intermediate. This is in agreement with the stepwise nature of the chemical mechanism of other malic enzymes despite the Crassula enzyme's inability to reduce or decarboxylatemore » oxaloacetate. Differences in morphology and allosteric regulation between enzymes suggest specialization of the Crassula malic enzyme for the physiology of crassulacean and acid metabolism while maintaining the catalytic events founds in malic enzymes from animal sources.« less

An experimental and kinetic investigation of premixed furan/oxygen/argon flames

PubMed Central

Tian, Zhenyu; Yuan, Tao; Fournet, Rene; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Battin-Leclerc, Frédérique; Zhang, Kuiwen; Qi, Fei

2013-01-01

The detailed chemical structures of three low-pressure (35 Torr) premixed laminar furan/oxygen/argon flames with equivalence ratios of 1.4, 1.8 and 2.2 have been investigated by using tunable synchrotron vacuum ultraviolet (VUV) photoionization and molecular-beam mass spectrometry. About 40 combustion species including hydrocarbons and oxygenated intermediates have been identified by measurements of photoionization efficiency spectra. Mole fraction profiles of the flame species including reactants, intermediates and products have been determined by scanning burner position with some selected photon energies near ionization thresholds. Flame temperatures have been measured by a Pt-6%Rh/Pt-30%Rh thermocouple. A new mechanism involving 206 species and 1368 reactions has been proposed whose predictions are in reasonable agreement with measured species profiles for the three investigated flames. Rate-of-production and sensitivity analyses have been performed to track the key reaction paths governing furan consumption for different equivalence ratios. Both experimental and modeling results indicate that few aromatics could be formed in these flames. Furthermore, the current model has been validated against previous pyrolysis results of the literature obtained behind shock waves and the agreement is reasonable as well. PMID:23814311

Reduced Equations for Calculating the Combustion Rates of Jet-A and Methane Fuel

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2003-01-01

Simplified kinetic schemes for Jet-A and methane fuels were developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) that is being developed at Glenn. These kinetic schemes presented here result in a correlation that gives the chemical kinetic time as a function of initial overall cell fuel/air ratio, pressure, and temperature. The correlations would then be used with the turbulent mixing times to determine the limiting properties and progress of the reaction. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentration of carbon monoxide as a function of fuel air ratio, pressure, and temperature. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates and the values obtained from the equilibrium correlations were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide, and NOx were obtained for both Jet-A fuel and methane.

Solar-pumped gas laser development

NASA Technical Reports Server (NTRS)

Wilson, J. W.

1980-01-01

A survey of gas properties through detailed kinetic models led to the identification of critical gas parameters for use in choosing appropriate gas combinations for solar pumped lasers. Broadband photoabsorption in the visible or near UV range is required to excite large volumes of gas and to insure good solar absorption efficiency. The photoexcitation density is independent of the absorption bandwidth. The state excited must be a metastable state which is not quenched by the parent gas. The emission bandwidth must be less than 10 A to insure lasing threshold over reasonable gain lengths. The system should show a high degree of chemical reversibility and an insensitivity to increasing temperature. Other properties such as good quantum efficiency and kinetic efficiency are also implied. Although photoexcitation of electronic vibrational transitions is considered as a possible system if the emission bands sufficiently narrow, it appears that photodissociation into atomic metastables is more likely to result in a successful solar pumped laser system.

A method for generating reduced-order combustion mechanisms that satisfy the differential entropy inequality

NASA Astrophysics Data System (ADS)

Ream, Allen E.; Slattery, John C.; Cizmas, Paul G. A.

2018-04-01

This paper presents a new method for determining the Arrhenius parameters of a reduced chemical mechanism such that it satisfies the second law of thermodynamics. The strategy is to approximate the progress of each reaction in the reduced mechanism from the species production rates of a detailed mechanism by using a linear least squares method. A series of non-linear least squares curve fittings are then carried out to find the optimal Arrhenius parameters for each reaction. At this step, the molar rates of production are written such that they comply with a theorem that provides the sufficient conditions for satisfying the second law of thermodynamics. This methodology was used to modify the Arrhenius parameters for the Westbrook and Dryer two-step mechanism and the Peters and Williams three-step mechanism for methane combustion. Both optimized mechanisms showed good agreement with the detailed mechanism for species mole fractions and production rates of most major species. Both optimized mechanisms showed significant improvement over previous mechanisms in minor species production rate prediction. Both optimized mechanisms produced no violations of the second law of thermodynamics.

Simulating flame lift-off characteristics of diesel and biodiesel fuels using detailed chemical-kinetic mechanisms and LES turbulence model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Som, S; Longman, D. E.; Luo, Z

2012-01-01

Combustion in direct-injection diesel engines occurs in a lifted, turbulent diffusion flame mode. Numerous studies indicate that the combustion and emissions in such engines are strongly influenced by the lifted flame characteristics, which are in turn determined by fuel and air mixing in the upstream region of the lifted flame, and consequently by the liquid breakup and spray development processes. From a numerical standpoint, these spray combustion processes depend heavily on the choice of underlying spray, combustion, and turbulence models. The present numerical study investigates the influence of different chemical kinetic mechanisms for diesel and biodiesel fuels, as well asmore » Reynolds-averaged Navier-Stokes (RANS) and large eddy simulation (LES) turbulence models on predicting flame lift-off lengths (LOLs) and ignition delays. Specifically, two chemical kinetic mechanisms for n-heptane (NHPT) and three for biodiesel surrogates are investigated. In addition, the RNG k-{epsilon} (RANS) model is compared to the Smagorinsky based LES turbulence model. Using adaptive grid resolution, minimum grid sizes of 250 {micro}m and 125 {micro}m were obtained for the RANS and LES cases respectively. Validations of these models were performed against experimental data from Sandia National Laboratories in a constant volume combustion chamber. Ignition delay and flame lift-off validations were performed at different ambient temperature conditions. The LES model predicts lower ignition delays and qualitatively better flame structures compared to the RNG k-{epsilon} model. The use of realistic chemistry and a ternary surrogate mixture, which consists of methyl decanoate, methyl 9-decenoate, and NHPT, results in better predicted LOLs and ignition delays. For diesel fuel though, only marginal improvements are observed by using larger size mechanisms. However, these improved predictions come at a significant increase in computational cost.« less

Chemical Peels in Melasma: A Review with Consensus Recommendations by Indian Pigmentary Expert Group.

PubMed

Sarkar, Rashmi; Arsiwala, Shehnaz; Dubey, Neha; Sonthalia, Sidharth; Das, Anupam; Arya, Latika; Gokhale, Narendra; Torsekar, R G; Somani, V K; Majid, Imran; Godse, Kiran; Ravichandran, G; Singh, Mohan; Aurangabadkar, Sanjeev; Salim, T; Shah, Swapnil; Sinha, Surabhi

2017-01-01

Melasma is a notorious dermatosis, often resistant to treatment. Chemical peeling constitutes an acceptable option of management of melasma (of any type and duration). In this article, as a group of experts from Pigmentary Disorders Society (PDS) in collaboration with South Asian Pigmentary Forum (SPF), we have tried to elaborate the various chemical peeling agents for the treatment of melasma. Besides, we have reviewed the indications, mechanism of action, rationality and the detailed procedure of peeling. The evidence in favor of various peeling agents have been summarized as well.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

The Low Temperature Oxidation of 2,7-Dimethyloctane in a Pressurized Flow Reactor

NASA Astrophysics Data System (ADS)

Farid, Farinaz

The complexity of real fuels has fostered the use of simple mixtures of hydrocarbons whose combustion behavior approximates that of real fuels in both experimental and computational studies to develop models of the combustion of the real fuel. These simple mixtures have been called surrogates. Lightly branched paraffins are an important class of constituents in gasoline, diesel and aviation turbine fuels and therefore are primary candidates for use as a component in a surrogate. Unfortunately, fundamental studies on combustion characteristics of high molecular weight mono- and di-methylated iso-paraffins are scarce. Therefore, this study was designed to investigate the low-temperature oxidation of 2,7-dimethyloctane (2,7-DMO) (C10H22), a lightly branched isomer of decane. Replicate 2,7-DMO oxidation experiments were conducted in a pressurized flow reactor (PFR) over the temperature range of 550 -- 850 K, at a pressure of 8 atm and an equivalence ratio of 0.3 in 4.21% oxygen / nitrogen. The reactivity was mapped by continuous monitoring of CO, CO 2, and O2 using a non-dispersive infrared (NDIR) carbon monoxide / carbon dioxide analyzer and an electrochemical oxygen sensor. For examining the underlying reaction chemistry, detailed speciation of samples was performed at selected temperatures using a gas chromatograph with a flame ionization detector coupled to a mass spectrometer. Comparable oxidation experiments for n-decane were carried out to examine the unique effects of branching on fuel reactivity and distribution of major stable intermediates. For both isomers, the onset of negative temperature coefficient (NTC) region was observed near 700 K, with the reactivity decreasing with increasing the temperature. The flow reactor study of n-decane oxidation confirmed that the isomerization reduces the amount of CO produced at peak reactivity. In addition to reaction inhibition, branching affected the distribution of C2-C 4 olefin intermediates. While the oxidation of n-decane resulted primarily in the formation of ethene near the NTC start, propene and isobutene were the major olefins produced from 2,7-DMO. A comparative analysis of experimental data with respect to a detailed chemical kinetic model for 2,7-DMO was performed and discrepancies were noted. Based on these results, a collaborative effort with Dr. Charles Westbrook (Lawrence Livermore National Laboratory) was initiated to refine the model predictions in the low temperature and NTC regimes. The effort resulted in an updated version of the 2,7-DMO mechanism, improving some of the key features such as calculated CO2 profile and final yields of iso-butene over the studied range of temperature. Fuel pyrolysis in the intermediate temperature regime, 850 -- 1000 K, also was investigated for the first time in the PFR facility. However, preliminary n-decane experiments measured only a small amount of fuel decomposition, indicating that higher temperature operation would be beneficial. The major species produced from n-decane decomposition, in descending order of molar fraction, were ethene, propene, and 1-butene. These results were compared with the predictions of two existing chemical kinetic models and the sources of variations between the experiments and the models as well as among the mechanisms were investigated. At 1000 K, the mechanisms predicted higher levels of fuel depletion and ethene production. Also, while the mechanisms were similar in their predicted pathways for fuel depletion and formation of ethene, inconsistencies were observed in relative contribution of these pathways to the final yields as well as the rate parameter determination for several sensitive reactions with respect to n-decane and ethene. Overall, the research aided in achieving a data set quantifying the oxidation characteristics of 2,7-DMO (and n-decane for comparison) as well as an elucidation of critical reaction pathways based on experimental results. Preliminary pyrolysis experiments were carried out using n-decane and the limitations on companion 2,7-DMO pyrolysis experiments were established. The data was compared with the predictions of several chemical kinetic mechanisms and, using tools such as rate of production analysis and sensitivity analysis, the sources of deviations from experimental data as well as possible areas of improvement were identified. The findings from 2,7-DMO study was directly used to refine an existing chemical kinetic model for 2,7-DMO, in line with the ultimate goal of feeding the much needed experimental database for validation and refinement of kinetic models of jet fuel surrogates.

Influence of Antimony-Halogen Additives on Flame Propagation*

PubMed Central

Babushok, Valeri I.; Deglmann, Peter; Krämer, Roland; Linteris, Gregory T.

2016-01-01

A kinetic model for flame inhibition by antimony-halogen compounds in hydrocarbon flames is developed. Thermodynamic data for the relevant species are assembled from the literature, and calculations are performed for a large set of additional species of Sb-Br-C-H-O system. The main Sb- and Br-containing species in the combustion products and reaction zone are determined using flame equilibrium calculations with a set of possible Sb-Br-C-H-O species, and these are used to develop the species and reactions in a detailed kinetic model for antimony flame inhibition. The complete thermodynamic data set and kinetic mechanism are presented. Laminar burning velocity simulations are used to validate the mechanism against available data in the literature, as well as to explore the relative performance of the antimony-halogen compounds. Further analysis of the premixed flame simulations has unraveled the catalytic radical recombination cycle of antimony. It includes (primarily) the species Sb, SbO, SbO2, and HOSbO, and the reactions: Sb+O+M=SbO+M; Sb+O2+M=SbO2+M; SbO+H=Sb+OH; SbO+O=Sb+O2; SbO+OH+M=HOSbO+M; SbO2+H2O=HOSbO+OH; HOSbO+H=SbO+H2O; SbO+O+M=SbO2+M. The inhibition cycles of antimony are shown to be more effective than those of bromine, and intermediate between the highly effective agents CF3Br and trimethylphosphate. Preliminary examination of a Sb/Br gas-phase system did not show synergism in the gas-phase catalytic cycles (i.e., they acted essentially independently). PMID:28133390

Plasma Assisted Ignition and Combustion at Low Initial Gas Temperatures: Development of Kinetic Mechanism

DTIC Science & Technology

2016-10-05

the complexity of the air flow, plasma and combustion interaction can be obtained from papers where the ignition of supersonic and fast subsonic gas ...AFRL-AFOSR-JP-TR-2016-0083 Plasma Assisted Ignition and Combustion at Low Initial Gas Temperatures: Development of Kinetic Mechanism Svetlana...Combustion at Low Initial Gas Temperatures: Development of Kinetic Mechanism 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-13-1-4064 5c.  PROGRAM ELEMENT

Systematic development of reduced reaction mechanisms for dynamic modeling

NASA Technical Reports Server (NTRS)

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

1986-01-01

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

Modelling total OH reactivity: atmospheric implications of the missing OH sink

NASA Astrophysics Data System (ADS)

Ferracci, V.; Archibald, A. T.; Heimann, I.; Pyle, J. A.

2016-12-01

The removal of the majority of reactive trace gases emitted into the atmosphere is initiated by reaction with the hydroxyl radical (OH). Over the last decade, a number of field campaigns have measured the chemical loss rate of OH, also known as total OH reactivity, in a variety of regions across the planet, from urban areas to remote forests. In most cases, comparison of the measured total OH reactivity with that calculated from the sum of the individual OH sinks (obtained via the simultaneous detection of species such as VOCs and NOx) highlighted the presence of "missing" reactivity (up to 80 % of the total measured reactivity), indicating that a significant sink of the hydroxyl radical is currently not accounted for in tropospheric oxidation schemes. Potential candidates for the missing OH reactivity are previously undetected biogenic VOCs, reactive intermediates of the oxidation of known biogenic VOCs (mainly isoprene), or a combination of the two. In this work the Met Office's Unified Model with the United Kingdom Chemistry and Aerosols scheme (UM-UKCA) was used to investigate the potential impacts of a simulated missing OH sink. UM-UKCA is a chemistry-climate model which includes detailed tropospheric chemistry derived from a combination of the JPL-NASA and IUPAC kinetic evaluations as well as the Master Chemical Mechanism database. The missing OH sink was simulated in a number of scenarios: initially, by including in the model chemical reactions that were only recently characterised (e.g., peroxy radicals + OH), then by adding a new chemical tracer, along with its reaction with OH, that would account for most of the missing reactivity observed in the various campaigns across the globe. Sensitivity of the model to the abundance and regional distribution of the new chemical tracer, and to the kinetics and hypothetical products of its reaction with OH are discussed, as well as the impacts of the missing OH sink on the tropospheric ozone budget and methane lifetime, with associated implications for air quality and global warming respectively.

Simulation of the effects of sub-breakdown electric fields on the chemical kinetics in nonpremixed counterflow methane/air flames

NASA Astrophysics Data System (ADS)

Belhi, Memdouh; Im, Hong; Computational Reacting Flows Laboratory, Clean Combustion Research Center Team

2017-11-01

The effects of an electric field on the combustion kinetics in nonpremixed counterflow methane/air flames were investigated via one-dimensional numerical simulations. A classical fluid model coupling Poison's equation with transport equations for combustion species and electric field-induced particles was used. A methane-air reaction mechanism accounting for the natural ionization in flames was combined with a set of reactions that describe the formation of active particles induced by the electric field. Kinetic parameters for electron-impact reactions and transport coefficients of electrons were modeled as functions of reduced electric field via solutions to the Boltzmann kinetic equation using the BOLSIG code. Mobility of ions was computed based on the (n,6,4) and coulomb interaction potentials, while the diffusion coefficient was approximated from the mobility using Einstein relation. Contributions of electron dissociation, excitation and ionization processes were characterized quantitatively. An analysis to identify the plasma regime where the electric field can alter the combustion kinetic was proposed.

Mössbauer spectroscopy.

PubMed

Huynh, Boi Hanh

2011-01-01

Mössbauer spectroscopy has contributed significantly to the studies of Fe-containing proteins. Early applications yielded detailed electronic characterizations of hemeproteins, and thus enhanced our understanding of the chemical properties of this important class of proteins. The next stage of the applications was marked by major discoveries of several novel Fe clusters of complex structures, including the 8Fe7S P cluster and the mixed metal 1Mo7Fe M center in nitrogenase. Since early 1990 s, rapid kinetic techniques have been used to arrest enzymatic reactions for Mössbauer studies. A number of reaction intermediates were discovered and characterized, both spectroscopically and kinetically, providing unprecedented detailed molecular-level mechanistic information. This chapter gives a brief summary of the historical accounts and a concise description of some experimental and theoretical elements in Mössbauer spectroscopy that are essential for understanding Mössbauer spectra. Major biological applications are summarized at the end.

A Gas-Kinetic Scheme for Multimaterial Flows and Its Application in Chemical Reaction

NASA Technical Reports Server (NTRS)

Lian, Yongsheng; Xu, Kun

1999-01-01

This paper concerns the extension of the multicomponent gas-kinetic BGK-type scheme to multidimensional chemical reactive flow calculations. In the kinetic model, each component satisfies its individual gas-kinetic BGK equation and the equilibrium states of both components are coupled in space and time due to the momentum and energy exchange in the course of particle collisions. At the same time, according to the chemical reaction rule one component can be changed into another component with the release of energy, where the reactant and product could have different gamma. Many numerical test cases are included in this paper, which show the robustness and accuracy of kinetic approach in the description of multicomponent reactive flows.

A counterflow diffusion flame study of branched octane isomers

DOE PAGES

Sarathy, S. Mani; Niemann, Ulrich; Yeung, Coleman; ...

2012-09-25

Conventional petroleum, Fischer–Tropsch (FT), and other alternative hydrocarbon fuels typically contain a high concentration of lightly methylated iso-alkanes. However, until recently little work has been done on this important class of hydrocarbon components. In order to better understand the combustion characteristics of real fuels, this study presents new experimental data for 3-methylheptane and 2,5-dimethylhexane in counterflow diffusion flames. This new dataset includes flame ignition, extinction, and speciation profiles. The high temperature oxidation of these fuels has been modeled using an extended transport database and a high temperature skeletal chemical kinetic model. The skeletal model is generated from a detailed modelmore » reduced using the directed relation graph with expert knowledge (DRG-X) methodology. The proposed skeletal model contains sufficient chemical fidelity to accurately predict the experimental speciation data in flames. The predictions are compared to elucidate the effects of number and location of the methyl substitutions. The location is found to have little effect on ignition and extinction in these counterflow diffusion flames. However, increasing the number of methyl substitutions was found to inhibit ignition and promote extinction. Chemical kinetic modelling simulations were used to correlate a fuel’s extinction propensity with its ability to populate the H radical concentration. In conclusion, species composition measurements indicate that the location and number of methyl substitutions was found to particularly affect the amount and type of alkenes observed.« less

Reassessing the atmospheric oxidation mechanism of toluene

NASA Astrophysics Data System (ADS)

Ji, Yuemeng; Zhao, Jun; Terazono, Hajime; Misawa, Kentaro; Levitt, Nicholas P.; Li, Yixin; Lin, Yun; Peng, Jianfei; Wang, Yuan; Duan, Lian; Pan, Bowen; Zhang, Fang; Feng, Xidan; An, Taicheng; Marrero-Ortiz, Wilmarie; Secrest, Jeremiah; Zhang, Annie L.; Shibuya, Kazuhiko; Molina, Mario J.; Zhang, Renyi

2017-08-01

Photochemical oxidation of aromatic hydrocarbons leads to tropospheric ozone and secondary organic aerosol (SOA) formation, with profound implications for air quality, human health, and climate. Toluene is the most abundant aromatic compound under urban environments, but its detailed chemical oxidation mechanism remains uncertain. From combined laboratory experiments and quantum chemical calculations, we show a toluene oxidation mechanism that is different from the one adopted in current atmospheric models. Our experimental work indicates a larger-than-expected branching ratio for cresols, but a negligible formation of ring-opening products (e.g., methylglyoxal). Quantum chemical calculations also demonstrate that cresols are much more stable than their corresponding peroxy radicals, and, for the most favorable OH (ortho) addition, the pathway of H extraction by O2 to form the cresol proceeds with a smaller barrier than O2 addition to form the peroxy radical. Our results reveal that phenolic (rather than peroxy radical) formation represents the dominant pathway for toluene oxidation, highlighting the necessity to reassess its role in ozone and SOA formation in the atmosphere.

In vivo multiphoton kinetic imaging of the toxic effect of carbon tetrachloride on hepatobiliary metabolism.

PubMed

Lin, Chih-Ju; Lee, Sheng-Lin; Lee, Hsuan-Shu; Dong, Chen-Yuan

2018-06-01

We used intravital multiphoton microscopy to study the recovery of hepatobiliary metabolism following carbon tetrachloride (CCl4) induced hepatotoxicity in mice. The acquired images were processed by a first order kinetic model to generate rate constant resolved images of the mouse liver. We found that with progression of hepatotoxicity, the spatial gradient of hepatic function disappeared. A CCl4-induced damage mechanism involves the compromise of membrane functions, resulting in accumulation of processed 6-carboxyfluorescein molecules. At day 14 following induction, a restoration of the mouse hepatobiliary function was found. Our approach allows the study of the response of hepatic functions to chemical agents in real time and is useful for studying pharmacokinetics of drug molecules through optical microscopic imaging. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Biological proton pumping in an oscillating electric field

PubMed Central

Kim, Young C.; Furchtgott, Leon A.; Hummer, Gerhard

2010-01-01

Time-dependent external perturbations provide powerful probes of the function of molecular machines. Here we study biological proton pumping in an oscillating electric field. The protein cytochrome c oxidase is the main energy transducer in aerobic life, converting chemical energy into an electric potential by pumping protons across a membrane. With the help of master-equation descriptions that recover the key thermodynamic and kinetic properties of this biological “fuel cell,” we show that the proton pumping efficiency and the electronic currents in steady state both depend significantly and distinctly on the frequency and amplitude of the applied field, allowing us to distinguish between different microscopic mechanisms of the machine. A spectral analysis reveals dominant kinetic modes that show reaction steps consistent with an electron-gated pumping mechanism. PMID:20366348

Lattice based Kinetic Monte Carlo Simulations of a complex chemical reaction network

NASA Astrophysics Data System (ADS)

Danielson, Thomas; Savara, Aditya; Hin, Celine

Lattice Kinetic Monte Carlo (KMC) simulations offer a powerful alternative to using ordinary differential equations for the simulation of complex chemical reaction networks. Lattice KMC provides the ability to account for local spatial configurations of species in the reaction network, resulting in a more detailed description of the reaction pathway. In KMC simulations with a large number of reactions, the range of transition probabilities can span many orders of magnitude, creating subsets of processes that occur more frequently or more rarely. Consequently, processes that have a high probability of occurring may be selected repeatedly without actually progressing the system (i.e. the forward and reverse process for the same reaction). In order to avoid the repeated occurrence of fast frivolous processes, it is necessary to throttle the transition probabilities in such a way that avoids altering the overall selectivity. Likewise, as the reaction progresses, new frequently occurring species and reactions may be introduced, making a dynamic throttling algorithm a necessity. We present a dynamic steady-state detection scheme with the goal of accurately throttling rate constants in order to optimize the KMC run time without compromising the selectivity of the reaction network. The algorithm has been applied to a large catalytic chemical reaction network, specifically that of methanol oxidative dehydrogenation, as well as additional pathways on CeO2(111) resulting in formaldehyde, CO, methanol, CO2, H2 and H2O as gas products.

Wintertime ozone and nitrogen oxide photochemistry and nighttime chemistry in a Western oil and gas basin

NASA Astrophysics Data System (ADS)

Brown, S. S.; Edwards, P. M.; Patel, S.; Dube, W. P.; Williams, E. J.; Roberts, J. M.; McLaren, R.; Kercher, J. P.; Gilman, J. B.; Lerner, B. M.; Warneke, C.; Geiger, F.; De Gouw, J. A.; Tsai, C.; Stutz, J.; Young, C. J.; Washenfelder, R. A.; Parrish, D. D.

2012-12-01

Oil and gas development in mountain basins of the Western United States has led to frequent exceedences of National Ambient Air Quality Standards for ozone during the winter season. The Uintah Basin Winter Ozone Study took place during February and March 2012 in northeast Utah with the goal of providing detailed chemical and meteorological data to understand this phenomenon. Although snow and cold pool stagnation conditions that lead to winter ozone buildup were not encountered during the study period, the detailed measurements did provide a unique data set to understand the chemistry of key air pollutants in a desert environment during winter. This presentation will examine both the photochemistry and the nighttime chemistry of nitrogen oxides, ozone and VOCs, with the goal of understanding the observed photochemistry and its relationship to nighttime chemistry through a set of box models. The photochemical box model is based on the master chemical mechanism (MCM), a detailed model for VOC degradation and ozone production. The presentation will examine the sensitivity of ozone photochemistry to different parameters, including pollutant concentrations likely to be characteristic of cold pool conditions, and the strength of radical sources derived from heterogeneous chemical reactions. The goal of the analysis will be to identify the factors most likely to be responsible for the higher ozone events that have been observed during colder years with less detailed chemical measurements.

Probing plasma fluorinated graphene via spectromicroscopy.

PubMed

Struzzi, C; Scardamaglia, M; Reckinger, N; Sezen, H; Amati, M; Gregoratti, L; Colomer, J-F; Ewels, C; Snyders, R; Bittencourt, C

2017-11-29

Plasma fluorination of graphene is studied using a combination of spectroscopy and microscopy techniques, giving insight into the yield and fluorination mechanism for functionalization of supported graphene with both CF 4 and SF 6 gas precursors. Ion acceleration during fluorination is used to probe the effect on grafting functionalities. Adatom clustering, which occurs with CF 4 plasma treatment, is suppressed when higher kinetic energy is supplied to the ions. During SF 6 plasma functionalization, the sulfur atoms tend to bond to bare copper areas instead of affecting the graphene chemistry, except when the kinetic energy of the ions is restricted. Using scanning photoelectron microscopy, with a 100 nm spatial resolution, the chemical bonding environment is evaluated in the fluorinated carbon network at selected regions and the functionalization homogeneity is controlled in individual graphene flakes.

The ozone acetylene reaction: concerted or non-concerted reaction mechanism? A quantum chemical investigation

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Kraka, Elfi; Crehuet, Ramon; Anglada, Josep; Gräfenstein, Jürgen

2001-10-01

The ozone-acetylene reaction is found to proceed via an intermediate van der Waals complex (rather than a biradical), which is the precursor for a concerted symmetry-allowed [4+2] cycloaddition reaction leading to 1,2,3-trioxolene. CCSD(T)/6-311G+(2d, 2p) and CCSD(T)/CBS (complete basis set) calculations predict the ozone-acetylene van der Waals complex to be stable by 2.2 kcal mol -1, the calculated activation enthalpy for the cycloaddition reaction is 9.6 kcal mol -1 and the reaction enthalpy -55.5 kcal mol -1. Calculated kinetic data for the overall reaction ( k=0.8 l mol -1 s-1, A=1.71×10 6 l mol -1 s-1, E a=8.6 kcal mol -1) suggest that there is a need for refined kinetic measurements.

Aircraft Emissions: Potential Effects on Ozone and Climate - A Review and Progress Report

DTIC Science & Technology

1977-03-01

which itself absorbs and reemits energy over a wide spectral range. In addition to such direct effects, various possible feedback effects can be...4.3.3 COMESA Climatic Effect Studies 4-17 4.4 Computed Mean Temperature Effects--Fleet Effects 4-24 4.4.1 Introduction 4-24 4.4.2 Mean Temperature Impact ...M B-13 B-2 The Chemical Kinetic Mechanism Used In . Model A B-19 B-3 Rate Coefficients for Model B (with Activation Energy in cal/mole) B-20 B-4

The Magnetorotational Instability in a Collisionless Plasma

NASA Astrophysics Data System (ADS)

Quataert, Eliot; Dorland, William; Hammett, Gregory W.

2002-09-01

We consider the linear axisymmetric stability of a differentially rotating collisionless plasma in the presence of a weak magnetic field; we restrict our analysis to wavelengths much larger than the proton Larmor radius. This is the kinetic version of the magnetorotational instability explored extensively as a mechanism for magnetic field amplification and angular momentum transport in accretion disks. The kinetic calculation is appropriate for hot accretion flows onto compact objects and for the growth of very weak magnetic fields, where the collisional mean free path is larger than the wavelength of the unstable modes. We show that the kinetic instability criterion is the same as in MHD, namely that the angular velocity decrease outward. However, nearly every mode has a linear kinetic growth rate that differs from its MHD counterpart. The kinetic growth rates also depend explicitly on β, i.e., on the ratio of the gas pressure to the pressure of the seed magnetic field. For β~1 the kinetic growth rates are similar to the MHD growth rates, while for β>>1 they differ significantly. For β>>1, the fastest growing mode has a growth rate ~sqrt(3)Ω for a Keplerian disk, larger than its MHD counterpart; there are also many modes whose growth rates are negligible, <~β-1/2Ω<<Ω. We provide a detailed physical interpretation of these results and show that gas pressure forces, rather than just magnetic forces, are central to the behavior of the magnetorotational instability in a collisionless plasma. We also discuss the astrophysical implications of our analysis.

Transition from Gaseous Compounds to Aerosols in Titan's Atmosphere

NASA Technical Reports Server (NTRS)

Lebonnois, Sebastien; Bakes, E. L. O.; McKay, Christopher P.; DeVincenzi, Donald (Technical Monitor)

2002-01-01

We investigate the chemical transition of simple molecules like C2H2 and HCN into aerosol particles in the context of Titan's atmosphere. Experiments that synthesize analogs (tholins) for these aerosols can help understand and constrain these polymerization mechanisms. Using information available from these experiments, we suggest chemical pathways that can link simple molecules to macromolecules, that will be the precursors to aerosol particles: polymers of acetylene and cyanoacetylene, polycyclic aromatics (PAHs), polymers of HCN and other nitriles, and polynes. Although our goal here is not to build a detailed kinetic model for this transition, we propose parameterizations to estimate the production rates of these macromolecules, their C/N and C/H ratios, and the loss of parent molecules (C2H2, HCN, HC3N and other nitriles, C6H6) from the gas phase to the haze. We use a 1-dimensional photochemical model of Titan's atmosphere to estimate the formation rate of precursors macromolecules. We find a production zone slightly lower than 200 km altitude with a total production rate of 4 x 10(exp -14) g/ sq cm s and a C/N approx. = 4. These results are compared with experimental data, and to microphysical models requirements. The Cassini/Huygens mission will bring a detailed picture of the haze distribution and properties, that will be a great challenge for our understanding of those chemical processes.

Hyperon polarization in heavy-ion collisions and holographic gravitational anomaly

NASA Astrophysics Data System (ADS)

Baznat, Mircea; Gudima, Konstantin; Sorin, Alexander; Teryaev, Oleg

2018-04-01

We study the energy dependence of global polarization of Λ hyperons in peripheral Au-Au collisions. We combine the calculation of vorticity and strange chemical potential in the framework of the kinetic quark-gluon-string model with the anomalous mechanism related to the axial vortical effect. We pay special attention to the temperature-dependent contribution related to the holographic gravitational anomaly and find that the preliminary data from the BNL Relativistic Heavy Ion Collider are compatible with its suppression discovered earlier in lattice calculations.

Recent advances in modeling Hugoniots with Cheetah

NASA Astrophysics Data System (ADS)

Glaesemann, Kurt

2005-07-01

The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and thermodynamic chemical equilibrium. Unfortunately, little is known concerning the detailed chemical kinetics of reacting energetic materials. Cheetah uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. Cheetah supports a wide range of elements and condensed detonation products and can also be applied to gas phase reactions. Improvements have been made to Cheetah's equilibrium solver, that allow it to find a wider range of thermodynamic states. Many of the difficulties experienced by users in earlier versions of Cheetah have been fixed. New capabilities have also been added. The ultimate result is a code that can be applied to a wide range of shock problems involving both energetic and non-energetic materials. New experimental validations of Cheetah's equation of state methodology have been performed, including both reacted and unreacted Hugoniots. This work was performed under the auspices of the U.S. Department of Energy by the University of California Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Analytical study of mechanisms for nitric oxide formation during combustion of methane in a jet-stirred combustor

NASA Technical Reports Server (NTRS)

Jachimowski, C. J.

1975-01-01

The role of chemical kinetics in the formation of nitric oxide during the combustion of methane was examined analytically by means of a detailed chemical mechanism for the oxidation of methane, for the reaction between hydrocarbon fragments, and for the formation of nitric oxide. By comparing predicted nitric oxide levels with values reported in the literature from jet-stirred combuster experiments, it was determined that the nitric oxide levels observed in fuel-rich flames cannot be described by a mechanism in which the rate of nitric oxide formation is controlled solely by the kinetics of oxygen atom formation. A proposed mechanism for the formation of nitric oxide in methane-rich flames reproduces the observed levels. The oxidation of hydrogen cyanide appears to be an important factor in nitric oxide formation.

Kinetic energy of Ps formed by Ore mechanism in Ar gas

NASA Astrophysics Data System (ADS)

Sano, Yosuke; Kino, Yasushi; Oka, Toshitaka; Sekine, Tsutomu

2015-06-01

In order to investigate kinetic energy of positronium(Ps) formed by Ore mechanism, we performed positron annihilation age-momentum correlation (AMOC) measurements in Argas for 5.0 MPa and 7.5 MPa at room temperature. From the time dependence of Doppler broadening of para-Ps (p-Ps) self-annihilation gramma-ray component, we observed Ps slowing down process. Using a simple slowing down model, we obtained the initial kinetic energy of Ps formed by Ore mechanism and Ps-Armomentum transfer cross section. The initial kinetic energy was 3.9 eV which was higher than the kinetic energy of Ps formed at the upper limit of Ore gap. The momentum transfer cross section was 0.019 ± 0.010 nm2 in between 1 eV and 3.9 eV, and was close to the theoretical calculation.

A Reaction Between High Mn-High Al Steel and CaO-SiO2-Type Molten Mold Flux: Part II. Reaction Mechanism, Interface Morphology, and Al2O3 Accumulation in Molten Mold Flux

NASA Astrophysics Data System (ADS)

Kang, Youn-Bae; Kim, Min-Su; Lee, Su-Wan; Cho, Jung-Wook; Park, Min-Seok; Lee, Hae-Geon

2013-04-01

Following a series of laboratory-scale experiments, the mechanism of a chemical reaction 4[{Al}] + 3({SiO}_2) = 3[{Si}] + 2({Al}_2{O}_3) between high-alloyed TWIP (TWin-Induced Plasticity) steel containing Mn and Al and molten mold flux composed mainly of CaO-SiO2 during the continuous casting process is discussed in the present article in the context of kinetic analysis, morphological evolution at the reaction interface. By the kinetic analysis using a two-film theory, a rate-controlling step of the chemical reaction at the interface between the molten steel and the molten flux is found to be mass transport of Al in a boundary layer of the molten steel, as long as the molten steel and the molten flux phases are concerned. Mass transfer coefficient of the Al in the boundary layer (k_{{Al}}) is estimated to be 0.9 to 1.2 × 10-4 m/s at 1773 K (1500 ^{circ}C). By utilizing experimental data at various temperatures, the following equation is obtained for the k_{{Al}}; ln k_{{Al}} = -14,290/T - 1.1107. Activation energy for the mass transfer of Al in the boundary layer is 119 kJ/mol, which is close to a value of activation energy for mass transfer in metal phase. The composition evolution of Al in the molten steel was well explained by the mechanism of Al mass transfer. On the other hand, when the concentration of Al in the steel was high, a significant deviation of the composition evolution of Al in the molten steel was observed. By observing reaction interface between the molten steel and the molten flux, it is thought that the chemical reaction controlled by the mass transfer of Al seemed to be disturbed by formation of a solid product layer of MgAl2O4. A model based on a dynamic mass balance and the reaction mechanism of mass transfer of Al in the boundary layer for the low Al steel was developed to predict (pct Al2O3) accumulation rate in the molten mold flux.

What Air Quality Models Tell Us About Sources and Sinks of Atmospheric Aldehydes

NASA Astrophysics Data System (ADS)

Luecken, D.; Hutzell, W. T.; Phillips, S.

2010-12-01

Atmospheric aldehydes play important roles in several aspects of air quality: they are critical radical sources that drive ozone formation, they are hazardous air pollutants that are national drivers for cancer risk, they participate in aqueous chemistry and potentially aerosol formation, and are key species for evaluating the accuracy of isoprene emissions. For these reasons, it is important to accurately understand their sources and sinks, and the sensitivity of their concentrations to emission controls. While both compounds have been included in air quality modeling for many years, current, state-of-the-science chemical mechanisms have difficulty reproducing measured values of aldehydes, which calls into question the robustness of ozone, HAPs and aerosol predictions. In the past, we have attributed discrepancies to measurement errors, inventory errors, or the focus on high-NOx urban regimes. Despite improvements in all of these areas, the measurements still diverge from model predictions, with formaldehyde often underpredicted by 50% and acetaldehyde showing a large degree of scatter - from 20% overprediction to 50% underprediction. To better examine the sources of aldehydes, we implemented the new SAPRC07T mechanism in the Community Multi-Scale Air Quality (CMAQ) model. This mechanism incorporates current recommendations for kinetic data and has the most detailed representation of product formation under a wide variety of conditions of any mechanism used in regional air quality models. We use model simulations to pinpoint where and when aldehyde concentrations tend to deviate from measurements. We demonstrate the role of secondary production versus primary emissions in aldehdye concentrations and find that secondary sources produce the largest deviations from measurements. We identify which VOCs are most responsible for aldehyde secondary production in the areas of the U.S. where the largest health effects are seen, and discuss how this affects consideration of control strategies.

Development of an integrated chemical weather prediction system for environmental applications at meso to global scales: NMMB/BSC-CHEM

NASA Astrophysics Data System (ADS)

Jorba, O.; Pérez, C.; Karsten, K.; Janjic, Z.; Dabdub, D.; Baldasano, J. M.

2009-09-01

This contribution presents the ongoing developments of a new fully on-line chemical weather prediction system for meso to global scale applications. The modeling system consists of a mineral dust module and a gas-phase chemistry module coupled on-line to a unified global-regional atmospheric driver. This approach allows solving small scale processes and their interactions at local to global scales. Its unified environment maintains the consistency of all the physico-chemical processes involved. The atmospheric driver is the NCEP/NMMB numerical weather prediction model (Janjic and Black, 2007) developed at National Centers for Environmental Prediction (NCEP). It represents an evolution of the operational WRF-NMME model extending from meso to global scales. Its unified non-hydrostatic dynamical core supports regional and global simulations. The Barcelona Supercomputing Center is currently designing and implementing a chemistry transport model coupled online with the new global/regional NMMB. The new modeling system is intended to be a powerful tool for research and to provide efficient global and regional chemical weather forecasts at sub-synoptic and mesoscale resolutions. The online coupling of the chemistry follows the approach similar to that of the mineral dust module already coupled to the atmospheric driver, NMMB/BSC-DUST (Pérez et al., 2008). Chemical species are advected and mixed at the corresponding time steps of the meteorological tracers using the same numerical scheme. Advection is eulerian, positive definite and monotone. The chemical mechanism and chemistry solver is based on the Kinetic PreProcessor KPP (Damian et al., 2002) package with the main purpose of maintaining a wide flexibility when configuring the model. Such approach will allow using a simplified chemical mechanism for global applications or a more complete mechanism for high-resolution local or regional studies. Moreover, it will permit the implementation of a specific configuration for forecasting applications in regional or global domains. An emission process allows the coupling of different emission inventories sources such as RETRO, EDGAR and GEIA for the global domain, EMEP for Europe and HERMES for Spain. The photolysis scheme is based on the Fast-J scheme, coupled with physics of each model layer (e.g., aerosols, clouds, absorbers as ozone) and it considers grid-scale clouds from the atmospheric driver. The dry deposition scheme follows the deposition velocity analogy for gases, enabling the calculation of deposition fluxes from airborne concentrations. No cloud-chemistry processes are included in the system yet (no wet deposition, scavenging and aqueous chemistry). The modeling system developments will be presented and first results of the gas-phase chemistry at global scale will be discussed. REFERENCES Janjic, Z.I., and Black, T.L., 2007. An ESMF unified model for a broad range of spatial and temporal scales, Geophysical Research Abstracts, 9, 05025. Pérez, C., Haustein, K., Janjic, Z.I., Jorba, O., Baldasano, J.M., Black, T.L., and Nickovic, S., 2008. An online dust model within the meso to global NMMB: current progress and plans. AGU Fall Meeting, San Francisco, A41K-03, 2008. Damian, V., Sandu, A., Damian, M., Potra, F., and Carmichael, G.R., 2002. The kinetic preprocessor KPP - A software environment for solving chemical kinetics. Comp. Chem. Eng., 26, 1567-1579. Sandu, A., and Sander, R., 2006. Technical note:Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1. Atmos. Chem. and Phys., 6, 187-195.

A Gas-Kinetic Scheme for Reactive Flows

NASA Technical Reports Server (NTRS)

Lian,Youg-Sheng; Xu, Kun

1998-01-01

In this paper, the gas-kinetic BGK scheme for the compressible flow equations is extended to chemical reactive flow. The mass fraction of the unburnt gas is implemented into the gas kinetic equation by assigning a new internal degree of freedom to the particle distribution function. The new variable can be also used to describe fluid trajectory for the nonreactive flows. Due to the gas-kinetic BGK model, the current scheme basically solves the Navier-Stokes chemical reactive flow equations. Numerical tests validate the accuracy and robustness of the current kinetic method.

Conversion and origin of normal and abnormal temperature dependences of kinetic isotope effect in hydride transfer reactions.

PubMed

Zhu, Xiao-Qing; Li, Xiu-Tao; Han, Su-Hui; Mei, Lian-Rui

2012-05-18

The effects of substituents on the temperature dependences of kinetic isotope effect (KIE) for the reactions of the hydride transfer from the substituted 5-methyl-6-phenyl-5,6-dihydrophenanthridine (G-PDH) to thioxanthylium (TX(+)) in acetonitrile were examined, and the results show that the temperature dependences of KIE for the hydride transfer reactions can be converted by adjusting the nature of the substituents in the molecule of the hydride donor. In general, electron-withdrawing groups can make the KIE to have normal temperature dependence, but electron-donating groups can make the KIE to have abnormal temperature dependence. Thermodynamic analysis on the possible pathways of the hydride transfer from G-PDH to TX(+) in acetonitrile suggests that the transfers of the hydride anion in the reactions are all carried out by the concerted one-step mechanism whether the substituent is an electron-withdrawing group or an electron-donating group. But the examination of Hammett-type free energy analysis on the hydride transfer reactions supports that the concerted one-step hydride transfer is not due to an elementary chemical reaction. The experimental values of KIE at different temperatures for the hydride transfer reactions were modeled by using a kinetic equation formed according to a multistage mechanism of the hydride transfer including a returnable charge-transfer complex as the reaction intermediate; the real mechanism of the hydride transfer and the root that why the temperature dependences of KIE can be converted as the nature of the substituents are changed were discovered.

Modelling the influence of carbon content on material behavior during forging

NASA Astrophysics Data System (ADS)

Korpała, G.; Ullmann, M.; Graf, M.; Wester, H.; Bouguecha, A.; Awiszus, B.; Behrens, B.-A.; Kawalla, R.

2017-10-01

Nowadays the design of single process steps and even of whole process chains is realized by the use of numerical simulation, in particular finite element (FE) based methods. A detailed numerical simulation of hot forging processes requires realistic models, which consider the relevant material-specific parameters to characterize the material behavior, the surface phenomena, the dies as well as models for the machine kinematic. This data exists partial for several materials, but general information on steel groups depending on alloying elements are not available. In order to generate the scientific input data regarding to material modelling, it is necessary to take into account the mathematical functions for deformation behavior as well as recrystallization kinetic, which depends alloying elements, initial microstructure and reheating mode. Besides the material flow characterization, a detailed description of surface changes caused by oxide scale is gaining in importance, as these phenomena affect the material flow and the component quality. Experiments to investigate the influence of only one chemical element on the oxide scale kinetic and the inner structure at high temperatures are still not available. Most data concerning these characteristics is provided for the steel grade C45, so this steel will be used as basis for the tests. In order to identify the effect of the carbon content on the material and oxidation behavior, the steel grades C15 and C60 will be investigated. This paper gives first approaches with regard to the influence of the carbon content on the oxide scale kinetic and the flow stresses combined with the initial microstructure.

Another Unprecedented Wieland Mechanism Confirmed: Hydrogen Formation from Hydrogen Peroxide, Formaldehyde, and Sodium Hydroxide.

PubMed

Czochara, Robert; Litwinienko, Grzegorz; Korth, Hans-Gert; Ingold, Keith U

2018-03-26

In 1923, Wieland and Wingler reported that in the molecular hydrogen producing reaction of hydrogen peroxide with formaldehyde in basic solution, free hydrogen atoms (H . ) are not involved. They postulated that bis(hydroxymethyl)peroxide, HOCH 2 OOCH 2 OH, is the intermediate, which decomposes to yield H 2 and formate, proposing a mechanism that would nowadays be considered as a "concerted process". Since then, several other (conflicting) "mechanisms" have been suggested. Our NMR and Raman spectroscopic and kinetic studies, particularly the determination of the deuterium kinetic isotope effect (DKIE), now confirm that in this base-dependent reaction, both H atoms of H 2 derive from the CH 2 hydrogen atoms of formaldehyde, and not from the OH groups of HOCH 2 OOCH 2 OH or from water. Quantum-chemical CBS-QB3 and W1BD computations show that H 2 release proceeds through a concerted process, which is strongly accelerated by double deprotonation of HOCH 2 OOCH 2 OH, thereby ruling out a free radical pathway. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid fixation of methylene chloride by a macrocyclic amine.

PubMed

Lee, Jung-Jae; Stanger, Keith J; Noll, Bruce C; Gonzalez, Carlos; Marquez, Manuel; Smith, Bradley D

2005-03-30

A simple macrocyclic amine is alkylated by methylene chloride to give a quaternary ammonium chloride salt. When methylene chloride is the solvent, the reaction exhibits pseudo-first-order kinetics, and the reaction half-life at 25.0 degrees C is 2.0 min. The reaction half-life for a structurally related, acyclic amine is approximately 50 000 times longer. Detailed calculations favor a mechanism where the methylene chloride associates with the macrocycle to form an activated prereaction complex. The macrocyclic nitrogen subsequently attacks the methylene chloride with a classic SN2 trajectory, and although the carbon-chlorine bond breaks, the chloride leaving group does not separate from the newly formed cationic macrocycle, such that the product is a tightly associated ion-pair. X-ray crystal structures of the starting amine and the product salt, as well as kinetic data, support this mechanism.

A possible mechanism of metabolic regulation in Gibberella fujikuroi using a mixed carbon source of glucose and corn oil inferred from analysis of the kinetics data obtained in a stirrer tank bioreactor.

PubMed

Rios-Iribe, Erika Y; Hernández-Calderón, Oscar M; Reyes-Moreno, C; Contreras-Andrade, I; Flores-Cotera, Luis B; Escamilla-Silva, Eleazar M

2013-01-01

A nonstructured model was used to study the dynamics of gibberellic acid production in a stirred tank bioreactor. Experimental data were obtained from submerged batch cultures of Gibberella fujikuroi (CDBB H-984) grown in varying ratios of glucose-corn oil as the carbon source. The nitrogen depletion effect was included in mathematical model by considering the specific kinetic constants as a linear function of the normalized nitrogen consumption rate. The kinetics of biomass growth and consumption of phosphate and nitrogen were based on the logistic model. The traditional first-order kinetic model was used to describe the specific consumption of glucose and corn oil. The nitrogen effect was solely included in the phosphate and corn oil consumption and biomass growth. The model fit was satisfactory, revealing the dependence of the kinetics with respect to the nitrogen assimilation rate. Through simulations, it was possible to make diagrams of specific growth rate and specific rate of substrate consumptions, which was a powerful tool for understanding the metabolic interactions that occurred during the various stages of fermentation process. This kinetic analysis provided the proposal of a possible mechanism of regulation on growth, substrate consumptions, and production of gibberellic acid (GA3 ) in G. fujikuroi. © 2013 American Institute of Chemical Engineers.

Mechanism and Substrate Recognition of Human Holo ACP Synthase

PubMed Central

Bunkoczi, Gabor; Pasta, Saloni; Joshi, Anil; Wu, Xiaoqiu; Kavanagh, Kathryn L.; Smith, Stuart; Oppermann, Udo

2007-01-01

Summary Mammals utilize a single phosphopantetheinyl transferase for the posttranslational modification of at least three different apoproteins: the carrier protein components of cytosolic and mitochondrial fatty acid synthases and the aminoadipate semialdehyde reductase involved in lysine degradation. We determined the crystal structure of the human phosphopantetheinyl transferase, a eukaryotic phosphopantetheinyl transferase characterized, complexed with CoA and Mg2+, and in ternary complex with CoA and ACP. The involvement of key residues in ligand binding and catalysis was confirmed by mutagenesis and kinetic analysis. Human phosphopantetheinyl transferase exhibits an α/β fold and 2-fold pseudosymmetry similar to the Sfp phosphopantetheinyl transferase from Bacillus subtilis. Although the bound ACP exhibits a typical four-helix structure, its binding is unusual in that it is facilitated predominantly by hydrophobic interactions. A detailed mechanism is proposed describing the substrate binding and catalytic process. PMID:18022563

Presenting a new kinetic model for methanol to light olefins reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson mechanism

NASA Astrophysics Data System (ADS)

Javad Azarhoosh, Mohammad; Halladj, Rouein; Askari, Sima

2017-10-01

In this study, a new kinetic model for methanol to light olefins (MTO) reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson (LHHW) mechanism was presented and the kinetic parameters was obtained using a genetic algorithm (GA) and genetic programming (GP). Several kinetic models for the MTO reactions have been presented. However, due to the complexity of the reactions, most reactions are considered lumped and elementary, which cannot be deemed a completely accurate kinetic model of the process. Therefore, in this study, the LHHW mechanism is presented as kinetic models of MTO reactions. Because of the non-linearity of the kinetic models and existence of many local optimal points, evolutionary algorithms (GA and GP) are used in this study to estimate the kinetic parameters in the rate equations. Via the simultaneous connection of the code related to modelling the reactor and the GA and GP codes in the MATLAB R2013a software, optimization of the kinetic models parameters was performed such that the least difference between the results from the kinetic models and experiential results was obtained and the best kinetic parameters of MTO process reactions were achieved. A comparison of the results from the model with experiential results showed that the present model possesses good accuracy.

Simplified Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2005-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two time step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting rates of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx are obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

Selective and slow-binding inhibition of shikonin derivatives isolated from Lithospermum erythrorhizon on glycosyl hydrolase 33 and 34 sialidases.

PubMed

Kim, Ji Young; Jeong, Hyung Jae; Park, Ji-Young; Kim, Young Min; Park, Su-Jin; Cho, Jung Keun; Park, Ki Hun; Ryu, Young Bae; Lee, Woo Song

2012-03-01

Sialidases are enzymes that catalyze the hydrolysis of sialic acid residues from various glycoconjugates, which are widely found in a number of viral and microbial pathogens. In this study, we investigated the biological evaluation of isolated six shikonins (1-6) and three shikonofurans (7-9) from Lithospermum erythrorhizon. The nine isolated compounds 1-9 showed strong and selective inhibition of glycosyl hydrolase (GH) 33 and -34 sialidases activities. In GH33 bacterial-sialidase inhibition assay, the inhibitory activities against GH33 siadliase of all shikonofuran derivatives (7-9) were greater than shikonin derivatives (1-6). Shikonofuran E (8) exhibited the most potent inhibitory activity toward GH33 sialidases (IC(50)=0.24μM). Moreover, our detailed kinetic analysis of these species unveiled that they are all competitive and simple reversible slow-binding inhibitors. Otherwise, they showed different inhibitory capacities and kinetic modes to GH34 viral-sialidase activity. All the naphthoquinone derivatives (1-6) were of almost equal efficiency with IC(50) value of 40μM and shikonofurans (7-9) did not show the significant inhibitory effect to GH34 sialidase. Kinetic analyses indicated that naphthoquinones acted via a noncompetitive mechanism. Copyright © 2012 Elsevier Ltd. All rights reserved.

Novel approach to investigation of semiconductor MOCVD by microreactor technology

NASA Astrophysics Data System (ADS)

Konakov, S. A.; Krzhizhanovskaya, V. V.

2017-11-01

Metal-Organic Chemical Vapour Deposition is a very complex technology that requires further investigation and optimization. We propose to apply microreactors to (1) replace multiple expensive time-consuming macroscale experiments by just one microreactor deposition with many points on one substrate; (2) to derive chemical reaction rates from individual deposition profiles using theoretical analytical solution. In this paper we also present the analytical solution of a simplified equation describing the deposition rate dependency on temperature. It allows to solve an inverse problem and to obtain detailed information about chemical reaction mechanism of MOCVD process.

Chemical Peels in Melasma: A Review with Consensus Recommendations by Indian Pigmentary Expert Group

PubMed Central

Sarkar, Rashmi; Arsiwala, Shehnaz; Dubey, Neha; Sonthalia, Sidharth; Das, Anupam; Arya, Latika; Gokhale, Narendra; Torsekar, RG; Somani, VK; Majid, Imran; Godse, Kiran; Ravichandran, G.; Singh, Mohan; Aurangabadkar, Sanjeev; Salim, T; Shah, Swapnil; Sinha, Surabhi

2017-01-01

Melasma is a notorious dermatosis, often resistant to treatment. Chemical peeling constitutes an acceptable option of management of melasma (of any type and duration). In this article, as a group of experts from Pigmentary Disorders Society (PDS) in collaboration with South Asian Pigmentary Forum (SPF), we have tried to elaborate the various chemical peeling agents for the treatment of melasma. Besides, we have reviewed the indications, mechanism of action, rationality and the detailed procedure of peeling. The evidence in favor of various peeling agents have been summarized as well. PMID:29263530

Gas-phase Precursors to Anthropogenic SOA: Using the MCM to Probe Detailed Observations of Aromatic Photo-oxidation

NASA Astrophysics Data System (ADS)

Rickard, A. R.; Wyche, K. P.; Metzger, A.; Monks, P. S.; Ellis, A. M.; Baltensperger, U.; Pilling, M. J.; Jenkin, M. E.

2008-12-01

The formation of photochemical ozone and particulate matter are major priorities in the determination of European air quality policies. Predictions of the future state of the atmosphere and the development of appropriate mitigation strategies rely on models, which necessarily incorporate chemistry. The Master Chemical Mechanism (MCM, http://mcm.leeds.ac.uk/MCM) is a near-explicit chemical mechanism originally conceived to model ozone formation in Europe but now also employed as a benchmark mechanism in a wide variety of applications where chemical detail is required. The MCM currently describes the detailed gas- phase tropospheric degradation of a 135 primary emitted volatile organic compounds (VOCs) leading to a mechanism containing ca. 5900 species and 13500 reactions. In order that the MCM continues to be a state-of-the-art resource for the atmospheric science community it resides under a constant regime of evaluation, development and improvement. Individual VOC photochemical mechanisms are evaluated using data obtained, under a variety of atmospheric conditions, from highly instrumented smog chambers. Smog chamber experiments are crucial, not only for mechanism evaluation, but also for mechanism development. Findings obtained from combined model and chamber studies can additionally provide key insight for guiding the directions of future laboratory experiments. Recently, the MCM was updated to MCMv3.1 in order to take into account recent advancements in the understanding of aromatic photo-oxidation, an important class of anthropogenic VOCs. As well as constituting precursors to secondary organic aerosol (SOA), aromatics generally have high photochemical ozone creation potentials (POCPs) and hence contribute significantly towards tropospheric ozone formation. In the work presented, a detailed gas-phase photochemical chamber box model, incorporating the MCMv3.1 degradation mechanism for 1,3,5-trimethylbenzene (TMB), has been used to simulate data measured during a series of chamber experiments carried out at the Paul Scherrer Institute Aerosol Chamber in order to evaluate the mechanism under a variety of VOC/NOx conditions. More specifically, the model was used in the interpretation of data recorded by the University of Leicester's Chemical Ionisation Reaction Time-of- Flight Mass Spectrometer (CIR-TOF-MS), a novel instrument used to provide comprehensive, high (mass and time) resolution measurements of the organic gaseous oxidation products formed from the TMB precursor. Additional supporting gas and aerosol measurements also enable us to explore the "missing link" between the gas and aerosol phases. Model-measurement comparisons have been used to gain an insight into the complex array of oxygenated products formed, including the peroxide bicyclic ring opening products (gamma-dicarbonyls and furanones) and the O2-bridged peroxide bicyclic ring retaining products (diol, ketone and nitrate). To our knowledge this is the first time these O2-bridged species have been identified in the gas-phase. The model was also used to give insights into which gas-phase species were participating in SOA formation, with the primary and secondary peroxide products, formed primarily under NOx-limiting conditions ([NO] approaches zero), identified as likely candidates.

Numerical simulation of detonation reignition in H 2-O 2 mixtures in area expansions

NASA Astrophysics Data System (ADS)

Jones, D. A.; Kemister, G.; Tonello, N. A.; Oran, E. S.; Sichel, M.

Time-dependent, two-dimensional, numerical simulations of a transmitted detonation show reignition occuring by one of two mechanisms. The first mechanism involves the collision of triple points as they expand along a decaying shock front. In the second mechanism ignition results from the coalescence of a number of small, relatively high pressure regions left over from the decay of weakened transverse waves. The simulations were performed using an improved chemical kinetic model for stoichiometric H 2-O 2 mixtures. The initial conditions were a propagating, two-dimensional detonation resolved enough to show transverse wave structure. The calculations provide clarification of the reignition mechanism seen in previous H 2-O 2-Ar simulations, and again demonstrate that the transverse wave structure of the detonation front is critical to the reignition process.

Effect of Vertical Concentration Gradient on Globally Planar Detonation with Detailed Reaction Mechanism

NASA Astrophysics Data System (ADS)

Song, Qingguana; Wang, Cheng; Han, Yong; Gao, Dayuan; Duan, Yingliang

2017-06-01

Since detonation often initiates and propagates in the non-homogeneous mixtures, investigating its behavior in non-uniform mixtures is significant not only for the industrial explosion in the leakage combustible gas, but also for the experimental investigations with a vertical concentration gradient caused by the difference in the molecular weight of gas mixture. Objective of this work is to show the detonation behavior in the mixture with different concentration gradients with detailed chemical reaction mechanism. A globally planar detonation in H2-O2 system is simulated by a high-resolution code based on the fifth-order weighted essentially non-oscillatory (WENO) scheme in spatial discretization and the third-order Additive Runge-Kutta schemes in time discretization. The different shocked combustion modes appear in the rich-fuel and poor-fuel layers due to the concentration gradient effect. Globally, for the cases with the lower gradient detonation can be sustained in a way of the alternation of the multi-heads mode and single-head mode, whereas for the cases with the higher gradient detonation propagates with a single-head mode. Institute of Chemical Materials, CAEP.

Ab initio investigation of the thermal decomposition of n-butylcyclohexane.

PubMed

Ali, Mohamad Akbar; Dillstrom, V Tyler; Lai, Jason Y W; Violi, Angela

2014-02-13

Environmental and energy security concerns have motivated an increased focus on developing clean, efficient combustors, which increasingly relies on insight into the combustion chemistry of fuels. In particular, naphthenes (cycloalkanes and alkylcycloalkanes) are important chemical components of distillate fuels, such as diesel and jet fuels. As such, there is a growing interest in describing napthene reactivity with kinetic mechanisms. Use of these mechanisms in predictive combustion models aids in the development of combustors. This study focuses on the pyrolysis of n-butylcyclohexane (n-BCH), an important representative of naphthenes in jet fuels. Seven different unimolecular decomposition pathways of C-C bond fission were explored utilizing ab initio/DFT methods. Accurate reaction energies were computed using the high-level quantum composite G3B3 method. Variational transition state theory, Rice-Ramsperger-Kassel-Marcus/master equation simulations provided temperature- and pressure-dependent rate constants. Implementation of these pathways into an existing chemical kinetic mechanism improved the prediction of experimental OH radical and H2O speciation in shock tube oxidation. Simulations of this combustion showed a change in the expected decomposition chemistry of n-BCH, predicting increased production of cyclic alkyl radicals instead of straight-chain alkenes. The most prominent reaction pathway for the decomposition of n-BCH is n-BCH = C3H7 + C7H13. The results of this study provide insight into the combustion of n-BCH and will aid in the future development of naphthene kinetic mechanisms.

New Reduced Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

NASA Technical Reports Server (NTRS)

Molnar, Melissa; Marek, C. John

2004-01-01

A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes that are being developed at Glenn. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx were obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering the turbine (T4) was also correlated as a function of the initial combustor temperature (T3), equivalence ratio, water to fuel mass ratio, and pressure.

A predictive computational model of the kinetic mechanism of stimulus-induced transducer methylation and feedback regulation through CheY in archaeal phototaxis and chemotaxis.

PubMed

Streif, Stefan; Oesterhelt, Dieter; Marwan, Wolfgang

2010-03-18

Photo- and chemotaxis of the archaeon Halobacterium salinarum is based on the control of flagellar motor switching through stimulus-specific methyl-accepting transducer proteins that relay the sensory input signal to a two-component system. Certain members of the transducer family function as receptor proteins by directly sensing specific chemical or physical stimuli. Others interact with specific receptor proteins like the phototaxis photoreceptors sensory rhodopsin I and II, or require specific binding proteins as for example some chemotaxis transducers. Receptor activation by light or a change in receptor occupancy by chemical stimuli results in reversible methylation of glutamate residues of the transducer proteins. Both, methylation and demethylation reactions are involved in sensory adaptation and are modulated by the response regulator CheY. By mathematical modeling we infer the kinetic mechanisms of stimulus-induced transducer methylation and adaptation. The model (deterministic and in the form of ordinary differential equations) correctly predicts experimentally observed transducer demethylation (as detected by released methanol) in response to attractant and repellent stimuli of wildtype cells, a cheY deletion mutant, and a mutant in which the stimulated transducer species is methylation-deficient. We provide a kinetic model for signal processing in photo- and chemotaxis in the archaeon H. salinarum suggesting an essential role of receptor cooperativity, antagonistic reversible methylation, and a CheY-dependent feedback on transducer demethylation.

Fuzzy Performance between Surface Fitting and Energy Distribution in Turbulence Runner

PubMed Central

Liang, Zhongwei; Liu, Xiaochu; Ye, Bangyan; Brauwer, Richard Kars

2012-01-01

Because the application of surface fitting algorithms exerts a considerable fuzzy influence on the mathematical features of kinetic energy distribution, their relation mechanism in different external conditional parameters must be quantitatively analyzed. Through determining the kinetic energy value of each selected representative position coordinate point by calculating kinetic energy parameters, several typical algorithms of complicated surface fitting are applied for constructing microkinetic energy distribution surface models in the objective turbulence runner with those obtained kinetic energy values. On the base of calculating the newly proposed mathematical features, we construct fuzzy evaluation data sequence and present a new three-dimensional fuzzy quantitative evaluation method; then the value change tendencies of kinetic energy distribution surface features can be clearly quantified, and the fuzzy performance mechanism discipline between the performance results of surface fitting algorithms, the spatial features of turbulence kinetic energy distribution surface, and their respective environmental parameter conditions can be quantitatively analyzed in detail, which results in the acquirement of final conclusions concerning the inherent turbulence kinetic energy distribution performance mechanism and its mathematical relation. A further turbulence energy quantitative study can be ensured. PMID:23213287

Quantum chemical and kinetic study of formation of 2-chlorophenoxy radical from 2-chlorophenol: unimolecular decomposition and bimolecular reactions with H, OH, Cl, and O2.

PubMed

Altarawneh, Mohammednoor; Dlugogorski, Bogdan Z; Kennedy, Eric M; Mackie, John C

2008-04-24

This study investigates the kinetic parameters of the formation of the chlorophenoxy radical from the 2-chlorophenol molecule, a key precursor to polychlorinated dibenzo-p-dioxins and dibenzofurans (PCCD/F), in unimolecular and bimolecular reactions in the gas phase. The study develops the reaction potential energy surface for the unimolecular decomposition of 2-chlorophenol. The migration of the phenolic hydrogen to the ortho-C bearing the hydrogen atom produces 2-chlorocyclohexa-2,4-dienone through an activation barrier of 73.6 kcal/mol (0 K). This route holds more importance than the direct fission of Cl or the phenolic H. Reaction rate constants for the bimolecular reactions, 2-chlorophenol + X --> X-H + 2-chlorophenoxy (X = H, OH, Cl, O2) are calculated and compared with the available experimental kinetics for the analogous reactions of X with phenol. OH reaction with 2-chlorophenol produces 2-chlorophenoxy by direct abstraction rather than through addition and subsequent water elimination. The results of the present study will find applications in the construction of detailed kinetic models describing the formation of PCDD/F in the gas phase.

A statistical approach to develop a detailed soot growth model using PAH characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raj, Abhijeet; Celnik, Matthew; Shirley, Raphael

A detailed PAH growth model is developed, which is solved using a kinetic Monte Carlo algorithm. The model describes the structure and growth of planar PAH molecules, and is referred to as the kinetic Monte Carlo-aromatic site (KMC-ARS) model. A detailed PAH growth mechanism based on reactions at radical sites available in the literature, and additional reactions obtained from quantum chemistry calculations are used to model the PAH growth processes. New rates for the reactions involved in the cyclodehydrogenation process for the formation of 6-member rings on PAHs are calculated in this work based on density functional theory simulations. Themore » KMC-ARS model is validated by comparing experimentally observed ensembles on PAHs with the computed ensembles for a C{sub 2}H{sub 2} and a C{sub 6}H{sub 6} flame at different heights above the burner. The motivation for this model is the development of a detailed soot particle population balance model which describes the evolution of an ensemble of soot particles based on their PAH structure. However, at present incorporating such a detailed model into a population balance is computationally unfeasible. Therefore, a simpler model referred to as the site-counting model has been developed, which replaces the structural information of the PAH molecules by their functional groups augmented with statistical closure expressions. This closure is obtained from the KMC-ARS model, which is used to develop correlations and statistics in different flame environments which describe such PAH structural information. These correlations and statistics are implemented in the site-counting model, and results from the site-counting model and the KMC-ARS model are in good agreement. Additionally the effect of steric hindrance in large PAH structures is investigated and correlations for sites unavailable for reaction are presented. (author)« less

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Exergy parametric study of carbon monoxide oxidation in moist air

NASA Astrophysics Data System (ADS)

Souidi, Ferhat; Benmalek, Toufik; Yesaad, Billel; Baik, Mouloud

2015-12-01

This study aims to analyze the oxidation of carbon monoxide in moist air from the second thermodynamic law aspect. A mathematical model of laminar premixed flame in a stagnation point flow has been achieved by numerical solution of the boundary layer equation using a self-made code. The chemical kinetic mechanism for flameless combustion of fuel, which is a mixture of carbon monoxide, oxygen, and water vapor, is modeled by 34 elementary reactions that incorporate (09) nine chemical species: CO, O, CO2, O2, H2O, H, H2, HO2, and OH. The salient point is that for all the parameters we considered, the exergy of the process is completely destroyed by irreversibilities. From the chemical viewpoint, the OH radical plays an essential role in CO oxidation. This latter point has already been mentioned by previous investigators.

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE PAGES

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

2016-12-09

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Structural and Kinetic Isotope Effect Studies of Nicotinamidase (Pnc1) from Saccharomyces cerevisiae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Brian C.; Anderson, Mark A.; Hoadley, Kelly A.

2012-05-08

Nicotinamidases catalyze the hydrolysis of nicotinamide to nicotinic acid and ammonia. Nicotinamidases are absent in mammals but function in NAD{sup +} salvage in many bacteria, yeast, plants, protozoa, and metazoans. We have performed structural and kinetic investigations of the nicotinamidase from Saccharomyces cerevisiae (Pnc1). Steady-state product inhibitor analysis revealed an irreversible reaction in which ammonia is the first product released, followed by nicotinic acid. A series of nicotinamide analogues acting as inhibitors or substrates were examined, revealing that the nicotinamide carbonyl oxygen and ring nitrogen are critical for binding and reactivity. X-ray structural analysis revealed a covalent adduct between nicotinaldehydemore » and Cys167 of Pnc1 and coordination of the nicotinamide ring nitrogen to the active-site zinc ion. Using this structure as a guide, the function of several residues was probed via mutagenesis and primary {sup 15}N and {sup 13}C kinetic isotope effects (KIEs) on V/K for amide bond hydrolysis. The KIE values of almost all variants were increased, indicating that C-N bond cleavage is at least partially rate limiting; however, a decreased KIE for D51N was indicative of a stronger commitment to catalysis. In addition, KIE values using slower alternate substrates indicated that C-N bond cleavage is at least partially rate limiting with nicotinamide to highly rate limiting with thionicotinamide. A detailed mechanism involving nucleophilic attack of Cys167, followed by elimination of ammonia and then hydrolysis to liberate nicotinic acid, is discussed. These results will aid in the design of mechanism-based inhibitors to target pathogens that rely on nicotinamidase activity.« less

Astronomical chemistry.

PubMed

Klemperer, William

2011-01-01

The discovery of polar polyatomic molecules in higher-density regions of the interstellar medium by means of their rotational emission detected by radioastronomy has changed our conception of the universe from essentially atomic to highly molecular. We discuss models for molecule formation, emphasizing the general lack of thermodynamic equilibrium. Detailed chemical kinetics is needed to understand molecule formation as well as destruction. Ion molecule reactions appear to be an important class for the generally low temperatures of the interstellar medium. The need for the intrinsically high-quality factor of rotational transitions to definitively pin down molecular emitters has been well established by radioastronomy. The observation of abundant molecular ions both positive and, as recently observed, negative provides benchmarks for chemical kinetic schemes. Of considerable importance in guiding our understanding of astronomical chemistry is the fact that the larger molecules (with more than five atoms) are all organic.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-06-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Kinetic and Mechanism Study of Vanadium Acid Leaching from Black Shale Using Microwave Heating Method

NASA Astrophysics Data System (ADS)

Wang, Jing-peng; Zhang, Yi-min; Huang, Jing; Liu, Tao

2018-04-01

The leaching kinetics of the vanadium leaching process were investigated by the comparison of microwave heating and conventional heating methods. Microwave heating with CaF2 had a synergistic effect and improved the vanadium leaching efficiency. In contrast to conventional heating leaching, microwave heating accelerated the vanadium leaching rate by approximately 1-3% and by approximately 15% when CaF2 was also used. The kinetics analysis showed that the calculated activation energy decreased in the microwave heating method in the presence and absence of CaF2. The control procedure of leaching also changed from a chemical reaction control step to a mixed chemical diffusion control step upon the addition of CaF2. Microwave heating was shown to be suitable for leaching systems with diffusion or mixed chemical diffusion control steps when the target mineral does not have a microwave absorbing ability.

Density-functional study on the dopant-segregation mechanism: Chemical potential dependence of dopant-defect complex at Si/SiO2 interface

NASA Astrophysics Data System (ADS)

Kawai, Hiroki; Nakasaki, Yasushi; Kanemura, Takahisa; Ishihara, Takamitsu

2018-04-01

Dopant segregation at Si/SiO2 interface has been a serious problem in silicon device technology. This paper reports a comprehensive density-functional study on the segregation mechanisms of boron, phosphorous, and arsenic at the Si/SiO2 interface. We found that three kinds of interfacial defects, namely, interstitial oxygen, oxygen vacancy, and silicon vacancy with two oxygen atoms, are stable in the possible chemical potential range. Thus, we consider these defects as trap sites for the dopants. For these defects, the dopant segregation energies, the electrical activities of the trapped dopants, and the kinetic energy barriers of the trapping/detrapping processes are calculated. As a result, trapping at the interstitial oxygen site is indicated to be the most plausible mechanism of the dopant segregation. The interstitial oxygen works as a major trap site since it has a high areal density at the Si/SiO2 interface due to the low formation energy.

Oxygen Reduction Reaction on Ag(111) in Alkaline Solution: A Combined Density Functional Theory and Kinetic Monte Carlo Study

DOE PAGES

Liu, Shizhong; White, Michael G.; Liu, Ping

2018-01-25

We reported a detailed mechanistic study of the oxygen reduction reaction (ORR) on the model Ag(111) surface in alkaline solution by using density functional theory (DFT) and Kinetic Monte Carlo (KMC) simulations, in which multiple pathways involving either 2 e - or 4 e - mechanisms were included. The theoretical modelling presented here is able to reproduce the experimentally measured polarization curves in both low and high potential regions. An electrochemical 4 e - network including both a chemisorbed water (*H 2O)-mediated 4 e - associative pathway and the conventional associative pathway was identified to dominate the ORR mechanism. Onmore » the basis of the mechanistic understanding derived from these calculations, the ways to promote the ORR on Ag(111) were provided, including facilitating *OH removal, **O 2 reduction by *H 2O, and suppressing **O 2 desorption. Finally, the origin of the different ORR behaviors of Ag(111) and Pt(111) was also discussed in detail.« less

Unraveling reaction pathways and specifying reaction kinetics for complex systems.

PubMed

Vinu, R; Broadbelt, Linda J

2012-01-01

Many natural and industrial processes involve a complex set of competing reactions that include several different species. Detailed kinetic modeling of such systems can shed light on the important pathways involved in various transformations and therefore can be used to optimize the process conditions for the desired product composition and properties. This review focuses on elucidating the various components involved in modeling the kinetics of pyrolysis and oxidation of polymers. The elementary free radical steps that constitute the chain reaction mechanism of gas-phase/nonpolar liquid-phase processes are outlined. Specification of the rate coefficients of the various reaction families, which is central to the theme of kinetics, is described. Construction of the reaction network on the basis of the types of end groups and reactive moieties in a polymer chain is discussed. Modeling frameworks based on the method of moments and kinetic Monte Carlo are evaluated using illustrations. Finally, the prospects and challenges in modeling biomass conversion are addressed.

Detailed mechanism of the NO + CO reaction on Rh(1 0 0) and Rh(1 1 1): A first-principles study

NASA Astrophysics Data System (ADS)

Tan, Lu; Huang, Liangliang; Liu, Yingchun; Wang, Qi

2018-06-01

Through DFT calculations, the detailed mechanism of the catalytic NO + CO reaction, a prototypical system with great practical applications especially in the automobile-exhaust aftertreatment, was determined on Rh(1 0 0) and Rh(1 1 1). The elementary steps and their energy evolution were revealed. These steps include NO dissociation, N2 formation through N recombination, CO2 formation, and N2O formation, transformation, and dissociation. The reaction steps of NO2 formation and direct reaction between NO and CO were also studied, and were verified to be relatively insignificant in this reaction system. Results shed light on the atomic-level origin why Rh(1 0 0) is more active for this reaction system and more selective for the production of N2 versus N2O compared with Rh(1 1 1). Meanwhile, the preference between the two routes for N2 production, i.e., N atoms recombination and N2O as intermediate, was found to be dependent on the distribution of surface species and the interaction among them intricately. This work provides a basis for further kinetic modeling to investigate the catalytic properties on a realistic scale.

Influence of Antimony-Halogen Additives on Flame Propagation.

PubMed

Babushok, Valeri I; Deglmann, Peter; Krämer, Roland; Linteris, Gregory T

2017-01-01

A kinetic model for flame inhibition by antimony-halogen compounds in hydrocarbon flames is developed. Thermodynamic data for the relevant species are assembled from the literature, and calculations are performed for a large set of additional species of Sb-Br-C-H-O system. The main Sb- and Br-containing species in the combustion products and reaction zone are determined using flame equilibrium calculations with a set of possible Sb-Br-C-H-O species, and these are used to develop the species and reactions in a detailed kinetic model for antimony flame inhibition. The complete thermodynamic data set and kinetic mechanism are presented. Laminar burning velocity simulations are used to validate the mechanism against available data in the literature, as well as to explore the relative performance of the antimony-halogen compounds. Further analysis of the premixed flame simulations has unraveled the catalytic radical recombination cycle of antimony. It includes (primarily) the species Sb, SbO, SbO 2 , and HOSbO, and the reactions: Sb+O+M=SbO+M; Sb+O 2 +M=SbO 2 +M; SbO+H=Sb+OH; SbO+O=Sb+O 2 ; SbO+OH+M=HOSbO+M; SbO 2 +H 2 O=HOSbO+OH; HOSbO+H=SbO+H 2 O; SbO+O+M=SbO 2 +M. The inhibition cycles of antimony are shown to be more effective than those of bromine, and intermediate between the highly effective agents CF 3 Br and trimethylphosphate. Preliminary examination of a Sb/Br gas-phase system did not show synergism in the gas-phase catalytic cycles (i.e., they acted essentially independently).

Quantifying atom addition reactions on amorphous solid water: a review of recent laboratory advances

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-06-01

Complex organic molecules found in space are mostly formed on and in the ice mantle covering interstellar dust grains. In clouds where ionizing irradiation is insignificant, chemical reactions on the ice mantle are dominated by thermal processes. Modeling of grain surface chemistry requires detailed information from the laboratory, including sticking coefficients, binding energies, diffusion energy barriers, mechanism of reaction, and chemical desorption rates. In this talk, recent laboratory advances in obtaining these information would be reviewed. Specifically, this talk will focus on the efforts in our group in: 1) Determining the mechanism of atomic hydrogen addition reactions on amorphous solid water (ASW); 2) Measuring the chemical desorption coefficient of H+O3-->O2+OH using the time-resolved scattering technique; and 3) Measuring the diffusion energy barrier of volatile molecules on ASW. Further laboratory studies will be suggested.This research was supported by NSF Astronomy & Astrophysics Research Grant #1615897.

Adsorption mechanisms and impact factors of oxytetracycline on activated sludge

NASA Astrophysics Data System (ADS)

Xiancai, Song; Dongfang, Liu; Lejun, Zhao

2017-03-01

The adsorption mechanisms and the effect of Oxytetracycline (OTC) onto activated sludge were studied. The results show that the adsorption of Oxytetracycline (OTC) onto activated sludge was coincident with the Pseudo-second-order kinetic model which suggested that chemical adsorption mechanism was dominant. The influences including pH and metal ions on the OTC were examined. It was demonstrated that the adsorption process was highly pH-dependant, which indicate that cationic exchange mechanisms may play an important role in the adsorption process. Na+, K+, Ca2+, Mg2+ and Cd2+ ions more or less inhibited the adsorption of OTC on activated sludge while Cu2+ enhanced the adsorption ability. The phenomenon may reflect the result that a surface complexation mechanism could involved in the adsorption.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kodavasal, Janardhan; Kolodziej, Christopher P.; Ciatti, Stephen A.

Gasoline compression ignition (GCI) is a low temperature combustion (LTC) concept that has been gaining increasing interest over the recent years owing to its potential to achieve diesel-like thermal efficiencies with significantly reduced engine-out nitrogen oxides (NOx) and soot emissions compared to diesel engines. In this work, closed-cycle computational fluid dynamics (CFD) simulations are performed of this combustion mode using a sector mesh in an effort to understand effects of model settings on simulation results. One goal of this work is to provide recommendations for grid resolution, combustion model, chemical kinetic mechanism, and turbulence model to accurately capture experimental combustionmore » characteristics. Grid resolutions ranging from 0.7 mm to 0.1 mm minimum cell sizes were evaluated in conjunction with both Reynolds averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES) based turbulence models. Solution of chemical kinetics using the multi-zone approach is evaluated against the detailed approach of solving chemistry in every cell. The relatively small primary reference fuel (PRF) mechanism (48 species) used in this study is also evaluated against a larger 312-species gasoline mechanism. Based on these studies the following model settings are chosen keeping in mind both accuracy and computation costs – 0.175 mm minimum cell size grid, RANS turbulence model, 48-species PRF mechanism, and multi-zone chemistry solution with bin limits of 5 K in temperature and 0.05 in equivalence ratio. With these settings, the performance of the CFD model is evaluated against experimental results corresponding to a low load start of injection (SOI) timing sweep. The model is then exercised to investigate the effect of SOI on combustion phasing with constant intake valve closing (IVC) conditions and fueling over a range of SOI timings to isolate the impact of SOI on charge preparation and ignition. Simulation results indicate that there is an optimum SOI timing, in this case -30?aTDC (after top dead center), which results in the most stable combustion. Advancing injection with respect to this point leads to significant fuel mass burning in the colder squish region, leading to retarded phasing and ultimately misfire for SOI timings earlier than -42?aTDC. On the other hand, retarding injection beyond this optimum timing results in reduced residence time available for gasoline ignition kinetics, and also leads to retarded phasing, with misfire at SOI timings later than -15?aTDC.« less

Oxygen Reduction Reaction on Ag(111) in Alkaline Solution: A Combined Density Functional Theory and Kinetic Monte Carlo Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Shizhong; White, Michael G.; Liu, Ping

We reported a detailed mechanistic study of the oxygen reduction reaction (ORR) on the model Ag(111) surface in alkaline solution by using density functional theory (DFT) and Kinetic Monte Carlo (KMC) simulations, in which multiple pathways involving either 2 e - or 4 e - mechanisms were included. The theoretical modelling presented here is able to reproduce the experimentally measured polarization curves in both low and high potential regions. An electrochemical 4 e - network including both a chemisorbed water (*H 2O)-mediated 4 e - associative pathway and the conventional associative pathway was identified to dominate the ORR mechanism. Onmore » the basis of the mechanistic understanding derived from these calculations, the ways to promote the ORR on Ag(111) were provided, including facilitating *OH removal, **O 2 reduction by *H 2O, and suppressing **O 2 desorption. Finally, the origin of the different ORR behaviors of Ag(111) and Pt(111) was also discussed in detail.« less

Predicting kinetic nanocrystal shapes through multi-scale theory and simulation: Polyvinylpyrrolidone-mediated growth of Ag nanocrystals

NASA Astrophysics Data System (ADS)

Balankura, Tonnam; Qi, Xin; Zhou, Ya; Fichthorn, Kristen A.

2016-10-01

In the shape-controlled synthesis of colloidal Ag nanocrystals, structure-directing agents, particularly polyvinylpyrrolidone (PVP), are known to be a key additive in making nanostructures with well-defined shapes. Although many Ag nanocrystals have been successfully synthesized using PVP, the mechanism by which PVP actuates shape control remains elusive. Here, we present a multi-scale theoretical framework for kinetic Wulff shape predictions that accounts for the chemical environment, which we used to probe the kinetic influence of the adsorbed PVP film. Within this framework, we use umbrella-sampling molecular dynamics simulations to calculate the potential of mean force and diffusion coefficient profiles of Ag atom deposition onto Ag(100) and Ag(111) in ethylene glycol solution with surface-adsorbed PVP. We use these profiles to calculate the mean-first passage times and implement extensive Brownian dynamics simulations, which allows the kinetic effects to be quantitatively evaluated. Our results show that PVP films can regulate the flux of Ag atoms to be greater towards Ag(111) than Ag(100). PVP's preferential binding towards Ag(100) over Ag(111) gives PVP its flux-regulating capabilities through the lower free-energy barrier of Ag atoms to cross the lower-density PVP film on Ag(111) and enhanced Ag trapping by the extended PVP film on Ag(111). Under kinetic control, {100}-faceted nanocrystals will be formed when the Ag flux is greater towards Ag(111). The predicted kinetic Wulff shapes are in agreement with the analogous experimental system.

Numerical simulation of capacitively coupled RF plasma flowing through a tube for the synthesis of silicon nanocrystals

NASA Astrophysics Data System (ADS)

Le Picard, Romain; Song, Sang-Heon; Porter, David; Kushner, Mark; Girshick, Steven

2014-10-01

Silicon nanocrystals (SiNCs) are of interest for applications in the photonics, electronics, and biomedical areas. Nonthermal plasmas offer several potential advantages for synthesizing SiNCs. In this work, we have developed a numerical model of a capacitively coupled RF plasma used for the synthesis of SiNCs. The plasma, consisting of silane diluted in argon at a total pressure of about 2 Torr, flows through a narrow quartz tube with two ring electrodes. The numerical model is 2D, assuming axisymmetry. An aerosol sectional model is added to the Hybrid Plasma Equipment Model developed by Kushner and coworkers. The aerosol module solves for aerosol size distributions and size-dependent charge distributions. A detailed chemical kinetic mechanism considering silicon hydride species containing up to 5 Si atoms is used to model particle nucleation and surface growth. The sectional model calculates coagulation, particle transport by electric force, neutral drag and ion drag, and particle charging using orbital motion limited theory. Simulation results are presented for selected operating conditions, and are compared to experimental results. This work was partially supported by the US Dept. of Energy Office of Fusion Energy Science (DE-SC0001939), the US National Science Foundation (CHE-124752), and the Minnesota Supercomputing Institute.

Evolution of atomic structure during nanoparticle formation

DOE PAGES

Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

2014-04-14

Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structuremore » is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries.« less

A classical but new kinetic equation for hydride transfer reactions.

PubMed

Zhu, Xiao-Qing; Deng, Fei-Huang; Yang, Jin-Dong; Li, Xiu-Tao; Chen, Qiang; Lei, Nan-Ping; Meng, Fan-Kun; Zhao, Xiao-Peng; Han, Su-Hui; Hao, Er-Jun; Mu, Yuan-Yuan

2013-09-28

A classical but new kinetic equation to estimate activation energies of various hydride transfer reactions was developed according to transition state theory using the Morse-type free energy curves of hydride donors to release a hydride anion and hydride acceptors to capture a hydride anion and by which the activation energies of 187 typical hydride self-exchange reactions and more than thirty thousand hydride cross transfer reactions in acetonitrile were safely estimated in this work. Since the development of the kinetic equation is only on the basis of the related chemical bond changes of the hydride transfer reactants, the kinetic equation should be also suitable for proton transfer reactions, hydrogen atom transfer reactions and all the other chemical reactions involved with breaking and formation of chemical bonds. One of the most important contributions of this work is to have achieved the perfect unity of the kinetic equation and thermodynamic equation for hydride transfer reactions.

Modelling the contribution of biogenic volatile organic compounds to new particle formation in the Jülich plant atmosphere chamber

NASA Astrophysics Data System (ADS)

Roldin, P.; Liao, L.; Mogensen, D.; Dal Maso, M.; Rusanen, A.; Kerminen, V.-M.; Mentel, T. F.; Wildt, J.; Kleist, E.; Kiendler-Scharr, A.; Tillmann, R.; Ehn, M.; Kulmala, M.; Boy, M.

2015-09-01

We used the Aerosol Dynamics gas- and particle-phase chemistry model for laboratory CHAMber studies (ADCHAM) to simulate the contribution of BVOC plant emissions to the observed new particle formation during photooxidation experiments performed in the Jülich Plant-Atmosphere Chamber and to evaluate how well smog chamber experiments can mimic the atmospheric conditions during new particle formation events. ADCHAM couples the detailed gas-phase chemistry from Master Chemical Mechanism with a novel aerosol dynamics and particle phase chemistry module. Our model simulations reveal that the observed particle growth may have either been controlled by the formation rate of semi- and low-volatility organic compounds in the gas phase or by acid catalysed heterogeneous reactions between semi-volatility organic compounds in the particle surface layer (e.g. peroxyhemiacetal dimer formation). The contribution of extremely low-volatility organic gas-phase compounds to the particle formation and growth was suppressed because of their rapid and irreversible wall losses, which decreased their contribution to the nano-CN formation and growth compared to the atmospheric situation. The best agreement between the modelled and measured total particle number concentration (R2 > 0.95) was achieved if the nano-CN was formed by kinetic nucleation involving both sulphuric acid and organic compounds formed from OH oxidation of BVOCs.

Isoprene derived secondary organic aerosol in a global aerosol chemistry climate model

NASA Astrophysics Data System (ADS)

Stadtler, Scarlet; Kühn, Thomas; Taraborrelli, Domenico; Kokkola, Harri; Schultz, Martin

2017-04-01

Secondary organic aerosol (SOA) impacts earth's climate and human health. Since its precursor chemistry and its formation are not fully understood, climate models cannot catch its direct and indirect effects. Global isoprene emissions are higher than any other non-methane hydrocarbons. Therefore, SOA from isoprene-derived, low volatile species (iSOA) is simulated using a global aerosol chemistry climate model ECHAM6-HAM-SALSA-MOZ. Isoprene oxidation in the chemistry model MOZ is following a novel semi-explicit scheme, embedded in a detailed atmospheric chemical mechanism. For iSOA formation four low volatile isoprene oxidation products were identified. The group method by Nanoonlal et al. 2008 was used to estimate their evaporation enthalpies ΔHvap. To calculate the saturation concentration C∗(T) the sectional aerosol model SALSA uses the gas phase concentrations simulated by MOZ and their corresponding ΔHvap to obtain the saturation vapor pressure p∗(T) from the Clausius Clapeyron equation. Subsequently, the saturation concentration is used to calculate the explicit kinetic partitioning of these compounds forming iSOA. Furthermore, the irreversible heterogeneous reactions of IEPOX and glyoxal from isoprene were included. The possibility of reversible heterogeneous uptake was ignored at this stage, leading to an upper estimate of the contribution of glyoxal to iSOA mass.

Marangoni Effect-Driven Motion of Miniature Robots and Generation of Electricity on Water.

PubMed

Zhang, Lidong; Yuan, Yihui; Qiu, Xiaxin; Zhang, Ting; Chen, Qing; Huang, Xinhua

2017-11-07

The well-known Marangoni effect perfectly supports the dynamic mechanism of organic solvent-swollen gels on water. On this basis, we report a series of energy conversion processes of concentrated droplets of polyvinylidene fluoride/dimethyl formamide (PVDF/DMF) that can transfer chemical-free energy to kinetic energy to rapidly rotate itself on water. This droplet (22.2 mg) is capable to offer kinetic energy of 0.099 μJ to propel an artificial paper rocket of 31.8 mg to move over 560 cm on water at an initial velocity of 7.9 cm s -1 . As the droplet increases to 35.0 mg, a paper goldfish of 10.6 mg can be driven to swim longer at a higher initial velocity of 20 cm s -1 . The kinetic energy of the droplet can be further converted to electrical energy through an electromagnetic generator, in which as a 0.5 MΩ resistor is loaded, the peak output reaches 6.5 mV that corresponds to the power density of 0.293 μW kg -1 . We believe that this report would open up a promising avenue to exploit energies for applications in miniature robotics.

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

3D DNS of Turbulent Premixed Flame with over 50 Species and 300 Elementary Reactions

NASA Astrophysics Data System (ADS)

Shimura, Masayasu; Yenerdag, Basmil; Naka, Yoshitsugu; Nada, Yuzuru; Tanahashi, Mamoru

2014-11-01

Three-dimensional direct numerical simulation of methane-air premixed planar flame propagating in homogenous isotropic turbulence is conducted to investigate local flame structure in thin reaction zones. Detailed kinetic mechanism, GRI-Mech 3.0 which includes 53 species and 325 elementary reactions, is used to represent methane-air reaction, and temperature dependences of transport and thermal properties are considered. For a better understanding of the local flame structure in thin reaction zones regime, distributions of mass fractions of major species, heat release rate, temperature and turbulent structures are investigated. Characteristic flame structures, such as radical fingering and multi-layered-like flame structures, are observed. The most expected maximum heat release rate in flame elements is lower than that of laminar flame with same mixture. To clarify mechanism of the decrease in local heat release rate, effects of strain rates tangential to flame front on local heat release rate are investigated.

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

PubMed Central

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-01-01

Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

Kinetic analysis of a Michaelis-Menten mechanism in which the enzyme is unstable.

PubMed Central

Garrido-del Solo, C; García-Cánovas, F; Havsteen, B H; Varón-Castellanos, R

1993-01-01

A kinetic analysis of the Michaelis-Menten mechanism is made for the cases in which the free enzyme, or the enzyme-substrate complex, or both, are unstable, either spontaneously or as a result of the addition of a reagent. The explicit time-course equations of all of the species involved has been derived under conditions of limiting enzyme concentration. The validity of these equations has been checked by using numerical simulations. An experimental design and a kinetic data analysis allowing the evaluation of the parameters and kinetic constants are recommended. PMID:8373361

Single-molecule enzymology of steroid transforming enzymes: Transient kinetic studies and what they tell us.

PubMed

Penning, Trevor M

2016-07-01

Structure-function studies on steroid transforming enzymes often use site-directed mutagenesis to inform mechanisms of catalysis and effects on steroid binding, and data are reported in terms of changes in steady state kinetic parameters kcat, Km and kcat/Km. However, this dissection of function is limited since kcat is governed by the rate-determining step and Km is a complex macroscopic kinetic constant. Often site-directed mutagenesis can lead to a change in the rate-determining step which cannot be revealed by just reporting a decrease in kcat alone. These issues are made more complex when it is considered that many steroid transforming enzymes have more than one substrate and product. We present the case for using transient-kinetics performed with stopped-flow spectrometry to assign rate constants to discrete steps in these multi-substrate reactions and their use to interpret enzyme mechanism and the effects of disease and engineered mutations. We demonstrate that fluorescence kinetic transients can be used to measure ligand binding that may be accompanied by isomerization steps, revealing the existence of new enzyme intermediates. We also demonstrate that single-turnover reactions can provide a klim for the chemical step and Ks for steroid-substrate binding and that when coupled with kinetic isotope effect measurements can provide information on transition state intermediates. We also demonstrate how multiple turnover experiments can provide evidence for either "burst-phase" kinetics, which can reveal a slow product release step, or linear-phase kinetics, in which the chemical step can be rate-determining. With these assignments it becomes more straightforward to analyze the effects of mutations. We use examples from the hydroxysteroid dehydrogenases (AKR1Cs) and human steroid 5β-reductase (AKR1D1) to illustrate the utility of the approach, which are members of the aldo-keto reductase (AKR) superfamily. Copyright © 2015 Elsevier Ltd. All rights reserved.

Deep-inelastic multinucleon transfer processes in the 16O+27Al reaction

NASA Astrophysics Data System (ADS)

Roy, B. J.; Sawant, Y.; Patwari, P.; Santra, S.; Pal, A.; Kundu, A.; Chattopadhyay, D.; Jha, V.; Pandit, S. K.; Parkar, V. V.; Ramachandran, K.; Mahata, K.; Nayak, B. K.; Saxena, A.; Kailas, S.; Nag, T. N.; Sahoo, R. N.; Singh, P. P.; Sekizawa, K.

2018-03-01

The reaction mechanism of deep-inelastic multinucleon transfer processes in the 16O+27Al reaction at an incident 16O energy (Elab=134 MeV) substantially above the Coulomb barrier has been studied both experimentally and theoretically. Elastic-scattering angular distribution, total kinetic energy loss spectra, and angular distributions for various transfer channels have been measured. The Q -value- and angle-integrated isotope production cross sections have been deduced. To obtain deeper insight into the underlying reaction mechanism, we have carried out a detailed analysis based on the time-dependent Hartree-Fock (TDHF) theory. A recently developed method, TDHF+GEMINI, has been applied to evaluate production cross sections for secondary products. From a comparison between the experimental and theoretical cross sections, we find that the theory qualitatively reproduces the experimental data. Significant effects of secondary light-particle emissions are demonstrated. Possible interplay among fusion-fission, deep-inelastic, multinucleon transfer, and particle evaporation processes is discussed.

Comparative kinetic analysis on thermal degradation of some cephalosporins using TG and DSC data

PubMed Central

2013-01-01

Background The thermal decomposition of cephalexine, cefadroxil and cefoperazone under non-isothermal conditions using the TG, respectively DSC methods, was studied. In case of TG, a hyphenated technique, including EGA, was used. Results The kinetic analysis was performed using the TG and DSC data in air for the first step of cephalosporin’s decomposition at four heating rates. The both TG and DSC data were processed according to an appropriate strategy to the following kinetic methods: Kissinger-Akahira-Sunose, Friedman, and NPK, in order to obtain realistic kinetic parameters, even if the decomposition process is a complex one. The EGA data offer some valuable indications about a possible decomposition mechanism. The obtained data indicate a rather good agreement between the activation energy’s values obtained by different methods, whereas the EGA data and the chemical structures give a possible explanation of the observed differences on the thermal stability. A complete kinetic analysis needs a data processing strategy using two or more methods, but the kinetic methods must also be applied to the different types of experimental data (TG and DSC). Conclusion The simultaneous use of DSC and TG data for the kinetic analysis coupled with evolved gas analysis (EGA) provided us a more complete picture of the degradation of the three cephalosporins. It was possible to estimate kinetic parameters by using three different kinetic methods and this allowed us to compare the Ea values obtained from different experimental data, TG and DSC. The thermodegradation being a complex process, the both differential and integral methods based on the single step hypothesis are inadequate for obtaining believable kinetic parameters. Only the modified NPK method allowed an objective separation of the temperature, respective conversion influence on the reaction rate and in the same time to ascertain the existence of two simultaneous steps. PMID:23594763

Chemical kinetic modeling of benzene and toluene oxidation behind shock waves

NASA Technical Reports Server (NTRS)

Mclain, A. G.; Jachimowski, C. J.; Wilson, C. H.

1979-01-01

The oxidation of stoichiometric mixtures of benzene and toluene behind incident shock waves was studied for a temperature range from 1700 to 2800 K and a pressure range from 1.1 to 1.7 atm. The concentration of CO and CO2 produced were measured as well as the product of the oxygen atom and carbon monoxide concentrations. Comparisons between the benzene experimental data and results calculated by use of a reaction mechanism published in the open literature were carried out. With some additional reactions and changes in rate constants to reflect the pressure-temperature range of the experimental data, a good agreement was achieved between computed and experimental results. A reaction mechanism was developed for toluene oxidation based on analogous rate steps from the benzene mechanism. Measurements of NOx levels in an actual flame device, a jet-stirred combustor, were reproduced successfully by use of the reaction mechanism developed from the shock-tube experiments on toluene. These experimental measurements of NOx levels were reproduced from a computer simulation of a jet-stirred combustor.

Experimental and analytical study of nitric oxide formation during combustion of propane in a jet-stirred combustor

NASA Technical Reports Server (NTRS)

Wakelyn, N. T.; Jachimowski, C. J.; Wilson, C. H.

1978-01-01

A jet-stirred combustor, constructed of castable zirconia and with an Inconel injector, was used to study nitric oxide formation in propane-air combustion with residence times in the range from 3.2 to 3.3 msec and equivalence ratios varying from 0.7 to 1.4. Measurements were made of combustor operating temperature and of nitric oxide concentration. Maximum nitric oxide concentrations of the order of 55 ppm were found in the range of equivalence ratio from 1.0 to 1.1. A finite-rate chemical kinetic mechanism for propane combustion and nitric oxide formation was assembled by coupling an existing propane oxidation mechanism with the Zeldovich reactions and reactions of molecular nitrogen with hydrocarbon fragments. Analytical studies using this mechanism in a computer simulation of the experimental conditions revealed that the hydrocarbon-fragment-nitrogen reactions play a significant role in nitric oxide formation during fuel-rich combustion.

CO2 valorization by means of Dielectric Barrier Discharge

NASA Astrophysics Data System (ADS)

Machrafi, H.; Cavadias, S.; Amouroux, J.

2011-01-01

As atmospheric pollution is causing several environmental problems it is incumbent to reduce the impact of pollution on the environment. One particular problem is the production of CO2 by many transport and industrial applications. Instead of stocking CO2 and instead of being a product, it can be used as a source. The case considered is the CO2 reformation of methane producing hydrogen and CO. It is an endothermic reaction, for which the activation barrier needs to be surpassed. This can be done efficiently by the method of Dielectric Barrier Discharge. The process relies on the collision of electrons, which are accelerated under an electrical field that is created in the discharge area. This leads to the formation of reactive species, which facilitate the abovementioned reaction. This study is performed using a Matlab program with the Reaction Engineering module in COMSOL (with an incorporated kinetic mechanism) in order to model the discharge phase. Then COMSOL (continuity and Navier-Stokes equations) is used to model the flow in the post-discharge phase. The results showed that both a 2D and 3D model can be used to model the chemical-plasma process. These methods need strongly reduced kinetic mechanism, which in some cases can cause loss of precision.

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

NASA Astrophysics Data System (ADS)

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; Park, Beomseok; Shim, Yoonjung; Kim, Youngchang; Liu, Lili; van Houten, Bennett; He, Chuan; Ansari, Anjum; Min, Jung-Hyun

2015-01-01

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.

Mono- and dinuclear oxidovanadium(v) complexes of an amine-bis(phenolate) ligand with bromo-peroxidase activities: synthesis, characterization, catalytic, kinetic and computational studies.

PubMed

Debnath, Mainak; Dolai, Malay; Pal, Kaberi; Bhunya, Sourav; Paul, Ankan; Lee, Hon Man; Ali, Mahammad

2018-02-20

The mono- and dinuclear oxidovanadium(v) complexes [V V O(L 1 )(Cl)] (1) and [L 1 V V O(μ 2 -O)VO(L 1 )] (2) of ONNO donor amine-bis(phenolate) ligand (H 2 L 1 ) were readily synthesized by the reaction between H 2 L 1 and VCl 3 .(THF) 3 or VO(acac) 2 in MeOH or MeCN, respectively, and then characterized through mass spectroscopy, 1 H-NMR and FTIR techniques. Both the complexes possess distorted octahedral geometry around each V centre. Upon the addition of 1 equivalent or more acid to a MeCN solution of complex 1, it immediately turned into the protonated form, which might be in equilibrium as: [L 1 ClV V [double bond, length as m-dash]OH] + ↔ [L 1 ClV V -OH] + (in the case of [L 1 ClV V [double bond, length as m-dash]OH] + oxo-O is just protonated, whereas in [L 1 ClV V -OH] + it is a hydroxo species), with the shift in λ max from 610 nm to 765 nm. Similar was the case for complex 2. The complexes 1 and 2 could efficiently catalyze the oxidative bromination of salicylaldehyde in the presence of H 2 O 2 to produce 5-bromo salicylaldehyde as the major product with TONs of 405 and 450, respectively, in the mixed solvent system (H 2 O : MeOH : THF = 4 : 3 : 2, v/v). The kinetic analysis of the bromide oxidation reaction indicated a first-order mechanism in the protonated peroxidovanadium complex and a bromide ion and limiting first-order mechanism on [H + ]. The evaluated k Br and k H values were 5.78 ± 0.20 and 11.01 ± 0.50 M -1 s -1 for complex 1 and 6.21 ± 0.13 and 20.14 ± 0.72 M -1 s -1 for complex 2, respectively. The kinetic and thermodynamic acidities of the protonated oxido species of complexes 1 and 2 were pK a = 2.55 (2.35) and 2.16 (2.19), respectively, which were far more acidic than those reported by Pecoraro et al. for peroxido-protonation instead of oxido protonation. On the basis of the chemistry observed for these model compounds, a mechanism of halide oxidation and a detailed catalytic cycle are proposed for the vanadium haloperoxidase enzyme and these were substantiated by detailed DFT calculations.

Simulation of semi-explicit mechanisms of SOA formation from glyoxal in a 3-D model

NASA Astrophysics Data System (ADS)

Knote, C.; Hodzic, A.; Jimenez, J. L.; Volkamer, R.; Orlando, J. J.; Baidar, S.; Brioude, J.; Fast, J.; Gentner, D. R.; Goldstein, A. H.; Hayes, P. L.; Knighton, W. B.; Oetjen, H.; Setyan, A.; Stark, H.; Thalman, R.; Tyndall, G.; Washenfelder, R.; Waxman, E.; Zhang, Q.

2013-10-01

New pathways to form secondary organic aerosols (SOA) have been postulated recently. Glyoxal, the smallest dicarbonyl, is one of the proposed precursors. It has both anthropogenic and biogenic sources, and readily partitions into the aqueous-phase of cloud droplets and deliquesced aerosols where it undergoes both reversible and irreversible chemistry. In this work we extend the regional scale chemistry transport model WRF-Chem to include a detailed gas-phase chemistry of glyoxal formation as well as a state-of-the-science module describing its partitioning and reactions in the aqueous-phase of aerosols. A comparison of several proposed mechanisms is performed to quantify the relative importance of different formation pathways and their regional variability. The CARES/CalNex campaigns over California in summer 2010 are used as case studies to evaluate the model against observations. In all simulations the LA basin was found to be the hotspot for SOA formation from glyoxal, which contributes between 1% and 15% of the model SOA depending on the mechanism used. Our results indicate that a mechanism based only on a simple uptake coefficient, as frequently employed in global modeling studies, leads to higher SOA contributions from glyoxal compared to a more detailed description that considers aerosol phase state and chemical composition. In the more detailed simulations, surface uptake is found to be the main contributor to SOA mass compared to a volume process and reversible formation. We find that contribution of the latter is limited by the availability of glyoxal in aerosol water, which is in turn controlled by an increase in the Henry's law constant depending on salt concentrations ("salting-in"). A kinetic limitation in this increase prevents substantial partitioning of glyoxal into aerosol water at high salt concentrations. If this limitation is removed, volume pathways contribute >20% of glyoxal SOA mass, and the total mass formed (5.8% of total SOA in the LA basin) is about a third of the simple uptake coefficient formulation without consideration of aerosol phase state and composition. All these model formulations are based on very limited and recent field or laboratory data and we conclude that the current uncertainty on glyoxal SOA formation spans a factor of 10 in this domain and time period.

Kinetic gating mechanism of DNA damage recognition by Rad4/XPC

DOE PAGES

Chen, Xuejing; Velmurugu, Yogambigai; Zheng, Guanqun; ...

2015-01-06

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivitymore » arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Lastly, kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.« less

Polycyclic aromatic hydrocarbon formation in carbon-rich stellar envelopes

NASA Technical Reports Server (NTRS)

Cherchneff, Isabelle; Barker, John R.; Tielens, Alexander G. G. M.

1992-01-01

A detailed chemical kinetic scheme is applied to stellar envelope profiles of gas density and temperature profiles in order to study the formation of PAH molecules in carbon-rich stellar outflows. Chemical concentration profiles are calculated for several envelope models by integrating the coupled continuity equations that include spherically expanding flows from an inner boundary at the shock formation radius. The influence of the 'inverse greenhouse' effect experienced by small PAHs is investigated and shown to increase the PAH yield by many orders of magnitude. It is shown that the route through propargyl radicals could be an important channel to produce benzene. PAH formation yields are found to be extremely sensitive to gas density and temperature and are much smaller than values inferred from the observed dust content of late-type carbon-rich stellar envelopes. It is therefore unlikely that aromatic molecules are generated in the stellar outflow itself.

Equilibrium, kinetic and thermodynamic studies on aluminum biosorption by a mycelial biomass (Streptomyces rimosus).

PubMed

Tassist, Amina; Lounici, Hakim; Abdi, Nadia; Mameri, Nabil

2010-11-15

This work focused on kinetic, equilibrium and thermodynamic studies on aluminum biosorption by Streptomyces rimosus biomass. Infrared spectroscopy analysis shows that S. rimosus present some groups: hydroxyl, methyl, carboxyl, amine, thiol and phosphate. The maximum biosorption capacity of S. rimosus biomass was found to be 11.76 mg g(-1) for the following optimum conditions: particle size, [250-560] μm, pH 4-4.25, biomass content of 25 g L(-1), agitation of 250 rpm and temperature of 25 °C. Langmuir, Freundlich and Dubinin-Radushkevich (D-R) models were applied to describe the biosorption isotherms at free pH (pH(i) 4) and fixed pH (pH(f) 4). Langmuir model is the most adequate. With fixed pH, the maximum biosorption capacity is enhanced from 6.62 mg g(-1) to 11.76 mg g(-1). The thermodynamic parameters (ΔG°, ΔH° and ΔS°) showed the feasibility, endothermic and spontaneous nature of the biosorption at 10-80 °C. The activation energy (Ea) was determined as 52.18 kJ mol(-1) using the Arrhenius equation and the rate constant of pseudo-second-order model (the most adequate kinetic model). The mean free energy was calculated as 12.91 kJ mol(-1) using the D-R isotherm model. The mechanism of Al(III) biosorption on S. rimosus could be a chemical ion exchange and carboxyl groups are mainly involved in this mechanism. Copyright © 2010 Elsevier B.V. All rights reserved.

Detailed surface reaction mechanism in a three-way catalyst.

PubMed

Chatterjee, D; Deutschmann, O; Warnatz, J

2001-01-01

Monolithic three-way catalysts are applied to reduce the emission of combustion engines. The design of such a catalytic converter is a complex process involving the optimization of different physical and chemical parameters (in the simplest case, e.g., length, cell densities or metal coverage of the catalyst). Numerical simulation can be used as an effective tool for the investigation of the catalytic properties of a catalytic converter and for the prediction of the performance of the catalyst. To attain this goal, a two-dimensional flow-field description is coupled with a detailed surface reaction model (gas-phase reactions can be neglected in three-way catalysts). This surface reaction mechanism (with C3H6 taken as representative of unburnt hydrocarbons) was developed using sub-mechanisms recently developed for hydrogen, carbon monoxide and methane oxidation, literature values for C3H6 oxidation, and estimates for the remaining unknown reactions. Results of the simulation of a monolithic single channel are used to validate the surface reaction mechanism. The performance of the catalyst was simulated under lean, nearly stoichiometric and rich conditions. For these characteristic conditions, the oxidation of propene and carbon monoxide and the reduction of NO on a typical Pt/Rh coated three-way catalyst were simulated as a function of temperature. The numerically predicted conversion data are compared with experimentally measured data. The simulation further reveals the coupling between chemical reactions and transport processes within the monolithic channel.

Spectral optimization and uncertainty quantification in combustion modeling

NASA Astrophysics Data System (ADS)

Sheen, David Allan

Reliable simulations of reacting flow systems require a well-characterized, detailed chemical model as a foundation. Accuracy of such a model can be assured, in principle, by a multi-parameter optimization against a set of experimental data. However, the inherent uncertainties in the rate evaluations and experimental data leave a model still characterized by some finite kinetic rate parameter space. Without a careful analysis of how this uncertainty space propagates into the model's predictions, those predictions can at best be trusted only qualitatively. In this work, the Method of Uncertainty Minimization using Polynomial Chaos Expansions is proposed to quantify these uncertainties. In this method, the uncertainty in the rate parameters of the as-compiled model is quantified. Then, the model is subjected to a rigorous multi-parameter optimization, as well as a consistency-screening process. Lastly, the uncertainty of the optimized model is calculated using an inverse spectral optimization technique, and then propagated into a range of simulation conditions. An as-compiled, detailed H2/CO/C1-C4 kinetic model is combined with a set of ethylene combustion data to serve as an example. The idea that the hydrocarbon oxidation model should be understood and developed in a hierarchical fashion has been a major driving force in kinetics research for decades. How this hierarchical strategy works at a quantitative level, however, has never been addressed. In this work, we use ethylene and propane combustion as examples and explore the question of hierarchical model development quantitatively. The Method of Uncertainty Minimization using Polynomial Chaos Expansions is utilized to quantify the amount of information that a particular combustion experiment, and thereby each data set, contributes to the model. This knowledge is applied to explore the relationships among the combustion chemistry of hydrogen/carbon monoxide, ethylene, and larger alkanes. Frequently, new data will become available, and it will be desirable to know the effect that inclusion of these data has on the optimized model. Two cases are considered here. In the first, a study of H2/CO mass burning rates has recently been published, wherein the experimentally-obtained results could not be reconciled with any extant H2/CO oxidation model. It is shown in that an optimized H2/CO model can be developed that will reproduce the results of the new experimental measurements. In addition, the high precision of the new experiments provide a strong constraint on the reaction rate parameters of the chemistry model, manifested in a significant improvement in the precision of simulations. In the second case, species time histories were measured during n-heptane oxidation behind reflected shock waves. The highly precise nature of these measurements is expected to impose critical constraints on chemical kinetic models of hydrocarbon combustion. The results show that while an as-compiled, prior reaction model of n-alkane combustion can be accurate in its prediction of the detailed species profiles, the kinetic parameter uncertainty in the model remains to be too large to obtain a precise prediction of the data. Constraining the prior model against the species time histories within the measurement uncertainties led to notable improvements in the precision of model predictions against the species data as well as the global combustion properties considered. Lastly, we show that while the capability of the multispecies measurement presents a step-change in our precise knowledge of the chemical processes in hydrocarbon combustion, accurate data of global combustion properties are still necessary to predict fuel combustion.

Mechanism of silver-mediated di-tert-butylsilylene transfer from a silacyclopropane to an alkene.

PubMed

Driver, Tom G; Woerpel, K A

2004-08-18

Kinetic studies of the reactions of cyclohexene silacyclopropane 1 and monosubstituted alkenes in the presence of 5 mol % of (Ph3P)2AgOTf suggested a possible mechanism for silver-mediated di-tert-butylsilylene transfer. The kinetic order in cyclohexene silacyclopropane 1 was determined to be one. Inverse kinetic saturation behavior (rate inhibition) was observed in monosubstituted alkene and cyclohexene concentrations. Saturation kinetic behavior in catalyst concentration was observed. A reactive intermediate, a silylsilver complex, was observed using low temperature 29Si NMR spectroscopy. Competition experiments between substituted styrenes and a deficient amount of 1 correlated well with the Hammett equation and provided a rho value of -0.62 +/- 0.02 using sigmap constants. These data support a mechanism involving reversible silver-promoted di-tert-butylsilylene extrusion from 1 followed by irreversible concerted electrophilic attack of the silylsilver intermediate on the alkene.

Opposed Jet Burner Approach for Characterizing Flameholding Potentials of Hydrocarbon Scramjet Fuels

NASA Technical Reports Server (NTRS)

Pellett, Gerald L.; Convery, Janet L.; Wilson, Lloyd G.

2006-01-01

Opposed Jet Burner (OJB) tools have been used extensively by the authors to measure Flame Strength (FS) extinction limits of laminar H2/N2 air and (recently) hydrocarbon (HC) air Counterflow Diffusion Flames (CFDFs) at one atm. This paper details normalization of FSs of N2- diluted H2 and HC systems to account for effects of fuel composition, temperature, pressure, jet diameter, inflow Reynolds number, and inflow velocity profile (plug, contoured nozzle; and parabolic, straight tube). Normalized results exemplify a sensitive accurate means of validating, globally, reduced chemical kinetic models at approx. 1 atm and the relatively low temperatures approximating the loss of non-premixed idealized flameholding, e.g., in scramjet combustors. Laminar FS is defined locally as maximum air input velocity, U(sub air), that sustains combustion of a counter-jet of g-fuel at extinction. It uniquely characterizes a fuel. And global axial strain rate at extinction (U(sub air) normalized by nozzle or tube diameter, D(sub n or (sub t)) can be compared directly with computed extinction limits, determined using either a 1-D Navier Stokes stream-function solution, using detailed transport and finite rate chemistry, or (better yet) a detailed 2-D Navier Stokes numerical simulation. The experimental results define an idealized flameholding reactivity scale that shows wide ranging (50 x) normalized FS s for various vaporized-liquid and gaseous HCs, including, in ascending order: JP-10, methane, JP-7, n-heptane, n-butane, propane, ethane, and ethylene. Results from H2 air produce a unique and exceptionally strong flame that agree within approx. 1% of a recent 2-D numerically simulated FS for a 3 mm tube-OJB. Thus we suggest that experimental FS s and/or FS ratios, for various neat and blended HCs w/ and w/o additives, offer accurate global tests of chemical kinetic models at the Ts and Ps of extinction. In conclusion, we argue the FS approach is more direct and fundamental, for assessing, e.g., idealized scramjet flameholding potentials, than measurements of laminar burning velocity or blowout in a Perfectly Stirred Reactor, because the latter characterize premixed combustion in the absence of aerodynamic strain. And FS directly measures a chemical kinetic characteristic of non-premixed combustion at typical flameholding temperatures. It mimics conditions where gfuels are typically injected into a subsonic flameholding recirculation zone that captures air, where the effects of aerodynamic strain and associated multi-component diffusion become important.

Chemical probes and engineered constructs reveal a detailed unfolding mechanism for a solvent-free multi-domain protein

PubMed Central

Eschweiler, Joseph D.; Martini, Rachel M.; Ruotolo, Brandon T.

2017-01-01

Despite the growing application of gas-phase measurements in structural biology and drug discovery, the factors that govern protein stabilities and structures in a solvent-free environment are still poorly understood. Here, we examine the solvent-free unfolding pathway for a group of homologous serum albumins. Utilizing a combination of chemical probes and non-covalent reconstructions, we draw new specific conclusions regarding the unfolding of albumins in the gas-phase, as well as more-general inferences regarding the sensitivity of collision induced unfolding to changes in protein primary and tertiary structure. Our findings suggest that the general unfolding pathway of low charge state albumin ions is largely unaffected by changes in primary structure; however, the stabilities of intermediates along these pathways vary widely as sequences diverge. Additionally, we find that human albumin follows a domain associated unfolding pathway, and are able to assign each unfolded form observed in our gas-phase dataset to the disruption of specific domains within the protein. The totality of our data informs the first detailed mechanism for multi-domain protein unfolding in the gas phase, and highlights key similarities and differences from the known the solution-phase pathway. PMID:27959526

Mechanistic Kinetic Modeling of Thiol-Michael Addition Photopolymerizations via Photocaged "Superbase" Generators: An Analytical Approach.

PubMed

Claudino, Mauro; Zhang, Xinpeng; Alim, Marvin D; Podgórski, Maciej; Bowman, Christopher N

2016-11-08

A kinetic mechanism and the accompanying mathematical framework are presented for base-mediated thiol-Michael photopolymerization kinetics involving a photobase generator. Here, model kinetic predictions demonstrate excellent agreement with a representative experimental system composed of 2-(2-nitrophenyl)propyloxycarbonyl-1,1,3,3-tetramethylguanidine (NPPOC-TMG) as a photobase generator that is used to initiate thiol-vinyl sulfone Michael addition reactions and polymerizations. Modeling equations derived from a basic mechanistic scheme indicate overall polymerization rates that follow a pseudo-first-order kinetic process in the base and coreactant concentrations, controlled by the ratio of the propagation to chain-transfer kinetic parameters ( k p / k CT ) which is dictated by the rate-limiting step and controls the time necessary to reach gelation. Gelation occurs earlier as the k p / k CT ratio reaches a critical value, wherefrom gel times become nearly independent of k p / k CT . The theoretical approach allowed determining the effect of induction time on the reaction kinetics due to initial acid-base neutralization for the photogenerated base caused by the presence of protic contaminants. Such inhibition kinetics may be challenging for reaction systems that require high curing rates but are relevant for chemical systems that need to remain kinetically dormant until activated although at the ultimate cost of lower polymerization rates. The pure step-growth character of this living polymerization and the exhibited kinetics provide unique potential for extended dark-cure reactions and uniform material properties. The general kinetic model is applicable to photobase initiators where photolysis follows a unimolecular cleavage process releasing a strong base catalyst without cogeneration of intermediate radical species.

Kinetics, mechanism, and spectroscopy of the reversible binding of nitric oxide to aquated iron(II). An undergraduate text book reaction revisited.

PubMed

Wanat, Alicja; Schneppensieper, Thorsten; Stochel, Grazyna; van Eldik, Rudi; Bill, Eckhard; Wieghardt, Karl

2002-01-14

A detailed kinetic and mechanistic analysis of the classical "brown-ring" reaction of [Fe(H(2)O)(6)](2+) with NO was performed using stopped-flow and laser flash photolysis techniques at ambient and high pressure. The kinetic parameters for the "on" and "off" reactions at 25 degrees C were found to be k(on) = 1.42 x 10(6) M(-1) s(-1), DeltaH(++)(on) = 37.1 +/- 0.5 kJ mol(-1), DeltaS(++)(on) = -3 +/- 2 J K(-1) mol(-1), DeltaV(++)(on) = +6.1 +/- 0.4 cm(3) mol(-1), and k(off) = 3240 +/- 750 s(-1), DeltaH(++)(off) = 48.4 +/- 1.4 kJ mol(-1), DeltaS(++)(off) = -15 +/- 5 J K(-1) mol(-1), DeltaV(++)(off) = +1.3 +/- 0.2 cm(3) mol(-1). These parameters suggest that both reactions follow an interchange dissociative (I(d)) ligand substitution mechanism, which correlates well with the suggested mechanism for the water exchange reaction on [Fe(H(2)O)(6)](2+). In addition, Mössbauer spectroscopy and EPR measurements were performed on the reaction product [Fe(H(2)O)(5)(NO)](2+). The Mössbauer and EPR parameters closely resemble those of the [FeNO](7) units in any of the other well-characterized nitrosyl complexes. It is concluded that its electronic structure is best described by the presence of high-spin Fe(III) antiferromagnetically coupled to NO(-) (S = 1) yielding the observed spin quartet ground state (S = (3)/(2)), i.e., [Fe(III)(H(2)O)(5)(NO(-))](2+), and not [Fe(I)(H(2)O)(5)(NO(+))](2+) as usually quoted in undergraduate text books.

Quantum chemical approaches to [NiFe] hydrogenase.

PubMed

Vaissier, Valerie; Van Voorhis, Troy

2017-05-09

The mechanism by which [NiFe] hydrogenase catalyses the oxidation of molecular hydrogen is a significant yet challenging topic in bioinorganic chemistry. With far-reaching applications in renewable energy and carbon mitigation, significant effort has been invested in the study of these complexes. In particular, computational approaches offer a unique perspective on how this enzyme functions at an electronic and atomistic level. In this article, we discuss state-of-the art quantum chemical methods and how they have helped deepen our comprehension of [NiFe] hydrogenase. We outline the key strategies that can be used to compute the (i) geometry, (ii) electronic structure, (iii) thermodynamics and (iv) kinetic properties associated with the enzymatic activity of [NiFe] hydrogenase and other bioinorganic complexes. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Kinetics of (3-aminopropyl)triethoxylsilane (APTES) silanization of superparamagnetic iron oxide nanoparticles.

PubMed

Liu, Yue; Li, Yueming; Li, Xue-Mei; He, Tao

2013-12-10

Silanization of magnetic ironoxide nanoparticles with (3-aminopropyl)triethoxylsilane (APTES) is reported. The kinetics of silanization toward saturation was investigated using different solvents including water, water/ethanol (1/1), and toluene/methanol (1/1) at different reaction temperature with different APTES loading. The nanoparticles were characterized by Fourier transform infrared spectroscopy, vibrating sample magnetometry, transmission electron microscopy, and thermal gravimetric analysis (TGA). Grafting density data based on TGA were used for the kinetic modeling. It is shown that initial silanization takes place very fast but the progress toward saturation is very slow, and the mechanism may involve adsorption, chemical sorption, and chemical diffusion processes. The highest equilibrium grafting density of 301 mg/g was yielded when using toluene/methanol mixture as the solvent at a reaction temperature of 70 °C.

LSENS - GENERAL CHEMICAL KINETICS AND SENSITIVITY ANALYSIS CODE

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1994-01-01

LSENS has been developed for solving complex, homogeneous, gas-phase, chemical kinetics problems. The motivation for the development of this program is the continuing interest in developing detailed chemical reaction mechanisms for complex reactions such as the combustion of fuels and pollutant formation and destruction. A reaction mechanism is the set of all elementary chemical reactions that are required to describe the process of interest. Mathematical descriptions of chemical kinetics problems constitute sets of coupled, nonlinear, first-order ordinary differential equations (ODEs). The number of ODEs can be very large because of the numerous chemical species involved in the reaction mechanism. Further complicating the situation are the many simultaneous reactions needed to describe the chemical kinetics of practical fuels. For example, the mechanism describing the oxidation of the simplest hydrocarbon fuel, methane, involves over 25 species participating in nearly 100 elementary reaction steps. Validating a chemical reaction mechanism requires repetitive solutions of the governing ODEs for a variety of reaction conditions. Analytical solutions to the systems of ODEs describing chemistry are not possible, except for the simplest cases, which are of little or no practical value. Consequently, there is a need for fast and reliable numerical solution techniques for chemical kinetics problems. In addition to solving the ODEs describing chemical kinetics, it is often necessary to know what effects variations in either initial condition values or chemical reaction mechanism parameters have on the solution. Such a need arises in the development of reaction mechanisms from experimental data. The rate coefficients are often not known with great precision and in general, the experimental data are not sufficiently detailed to accurately estimate the rate coefficient parameters. The development of a reaction mechanism is facilitated by a systematic sensitivity analysis which provides the relationships between the predictions of a kinetics model and the input parameters of the problem. LSENS provides for efficient and accurate chemical kinetics computations and includes sensitivity analysis for a variety of problems, including nonisothermal conditions. LSENS replaces the previous NASA general chemical kinetics codes GCKP and GCKP84. LSENS is designed for flexibility, convenience and computational efficiency. A variety of chemical reaction models can be considered. The models include static system, steady one-dimensional inviscid flow, reaction behind an incident shock wave including boundary layer correction, and the perfectly stirred (highly backmixed) reactor. In addition, computations of equilibrium properties can be performed for the following assigned states, enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. For static problems LSENS computes sensitivity coefficients with respect to the initial values of the dependent variables and/or the three rates coefficient parameters of each chemical reaction. To integrate the ODEs describing chemical kinetics problems, LSENS uses the packaged code LSODE, the Livermore Solver for Ordinary Differential Equations, because it has been shown to be the most efficient and accurate code for solving such problems. The sensitivity analysis computations use the decoupled direct method, as implemented by Dunker and modified by Radhakrishnan. This method has shown greater efficiency and stability with equal or better accuracy than other methods of sensitivity analysis. LSENS is written in FORTRAN 77 with the exception of the NAMELIST extensions used for input. While this makes the code fairly machine independent, execution times on IBM PC compatibles would be unacceptable to most users. LSENS has been successfully implemented on a Sun4 running SunOS and a DEC VAX running VMS. With minor modifications, it should also be easily implemented on other platforms with FORTRAN compilers which support NAMELIST input. LSENS required 4Mb of RAM under SunOS 4.1.1 and 3.4Mb of RAM under VMS 5.5.1. The standard distribution medium for LSENS is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 1600 BPI 9-track magnetic tape or a TK50 tape cartridge in DEC VAX BACKUP format. Alternate distribution media and formats are available upon request. LSENS was developed in 1992.

Comparisons of dense-plasma-focus kinetic simulations with experimental measurements.

PubMed

Schmidt, A; Link, A; Welch, D; Ellsworth, J; Falabella, S; Tang, V

2014-06-01

Dense-plasma-focus (DPF) Z-pinch devices are sources of copious high-energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood and past optimization efforts of these devices have been largely empirical. Previously we reported on fully kinetic simulations of a DPF and compared them with hybrid and fluid simulations of the same device. Here we present detailed comparisons between fully kinetic simulations and experimental data on a 1.2 kJ DPF with two electrode geometries, including neutron yield and ion beam energy distributions. A more intensive third calculation is presented which examines the effects of a fully detailed pulsed power driver model. We also compare simulated electromagnetic fluctuations with direct measurement of radiofrequency electromagnetic fluctuations in a DPF plasma. These comparisons indicate that the fully kinetic model captures the essential physics of these plasmas with high fidelity, and provide further evidence that anomalous resistivity in the plasma arises due to a kinetic instability near the lower hybrid frequency.

Catalytic combustion of hydrogen-air mixtures in stagnation flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeda, H.; Libby, P.A.; Williams, F.A.

1993-04-01

The interaction between heterogeneous and homogeneous reactions arising when a mixture of hydrogen and air impinges on a platinum plate at elevated temperature is studied. A reasonably complete description of the kinetic mechanism for homogeneous reactions is employed along with a simplified model for heterogeneous reactions. Four regimes are identified depending on the temperature of the plate, on the rate of strain imposed on the flow adjacent to the plate and on the composition and temperature of the reactant stream: (1) surface reaction alone; (2) surface reaction inhibiting homogeneous reaction; (3) homogeneous reaction inhibiting surface reaction; and (4) homogeneous reactionmore » alone. These regimes are related to those found earlier for other chemical systems and form the basis of future experimental investigation of the chemical system considered in the present study.« less

Explaining rISC and 100% efficient TADF (Conference Presentation)

NASA Astrophysics Data System (ADS)

Monkman, Andrew P.; Etherington, Marc; Graves, David; Data, Przemyslaw; Dos Santos, Paloma Lays; Nobuyasu, Roberto; Baiao Dias, Fernando M.

2016-09-01

Detailed photophysical measurements of intramolecular charge transfer (ICT) states have been made both in solution and solid state. Temperature dependent time resolved emission, delayed emission and photoinduced absorption are used to map the energy levels involved in molecule decay, and through detailed kinetic modelling of the thermally activated processes observed, true electron exchange energies and other energy barriers of the systems determined with the real states involved in the reversed intersystem crossing mechanism elucidated. For specific donor acceptor molecules, the CT singlet and local triplet states (of donor or acceptor) are found to be the lowest lying excited states of the molecule with very small energy barrier between them ? kT. In these cases the decay kinetics of the molecules become significantly different to normal molecules, and the effect of rapid recycling between CT singlet and local triplet states is observed which gives rise to the true triplet harvesting mechanism in TADF. Using a series of different TADF emitters we will show how the energy level ordering effects or does not effect TADF and how ultimate OLED performance is dictated by energy level ordering, from 5% to 22% external quantum efficiency. From this understanding, we are able to define three criterion for TADF in different molecules and these will be discussed.

Functional Studies on Oligotropha carboxidovorans Molybdenum-Copper CO Dehydrogenase Produced in Escherichia coli.

PubMed

Kaufmann, Paul; Duffus, Benjamin R; Teutloff, Christian; Leimkühler, Silke

2018-04-30

The Mo/Cu-dependent CO dehydrogenase (CODH) from Oligotropha carboxidovorans is an enzyme that is able to catalyze both the oxidation of CO to CO 2 and the oxidation of H 2 to protons and electrons. Despite the close to atomic resolution structure (1.1 Å), significant uncertainties have remained with regard to the reaction mechanism of substrate oxidation at the unique Mo/Cu center, as well as the nature of intermediates formed during the catalytic cycle. So far, the investigation of the role of amino acids at the active site was hampered by the lack of a suitable expression system that allowed for detailed site-directed mutagenesis studies at the active site. Here, we report on the establishment of a functional heterologous expression system of O. carboxidovorans CODH in Escherichia coli. We characterize the purified enzyme in detail by a combination of kinetic and spectroscopic studies and show that it was purified in a form with characteristics comparable to those of the native enzyme purified from O. carboxidovorans. With this expression system in hand, we were for the first time able to generate active-site variants of this enzyme. Our work presents the basis for more detailed studies of the reaction mechanism for CO and H 2 oxidation of Mo/Cu-dependent CODHs in the future.

Modeling the detailed kinetics of mitochondrial cytochrome c oxidase: Catalytic mechanism and nitric oxide inhibition

PubMed Central

Pannala, Venkat R.; Camara, Amadou K. S.

2016-01-01

Cytochrome c oxidase (CcO) catalyzes the exothermic reduction of O2 to H2O by using electrons from cytochrome c, and hence plays a crucial role in ATP production. Although details on the enzyme structure and redox centers involved in O2 reduction have been known, there still remains a considerable ambiguity on its mechanism of action, e.g., the number of sequential electrons donated to O2 in each catalytic step, the sites of protonation and proton pumping, and nitric oxide (NO) inhibition mechanism. In this work, we developed a thermodynamically constrained mechanistic mathematical model for the catalytic action of CcO based on available kinetic data. The model considers a minimal number of redox centers on CcO and couples electron transfer and proton pumping driven by proton motive force (PMF), and accounts for the inhibitory effects of NO on the reaction kinetics. The model is able to fit well all the available kinetic data under diverse experimental conditions with a physiologically realistic unique parameter set. The model predictions show that: 1) the apparent Km of O2 varies considerably and increases from fully reduced to fully oxidized cytochrome c depending on pH and the energy state of mitochondria, and 2) the intermediate enzyme states depend on pH and cytochrome c redox fraction and play a central role in coupling mitochondrial respiration to PMF. The developed CcO model can easily be integrated into existing mitochondrial bioenergetics models to understand the role of the enzyme in controlling oxidative phosphorylation in normal and disease conditions. PMID:27633738

Kinetics and mechanism of styrene epoxidation by chlorite: role of chlorine dioxide.

PubMed

Leigh, Jessica K; Rajput, Jonathan; Richardson, David E

2014-07-07

An investigation of the kinetics and mechanism for epoxidation of styrene and para-substituted styrenes by chlorite at 25 °C in the pH range of 5-6 is described. The proposed mechanism in water and water/acetonitrile includes seven oxidation states of chlorine (-I, 0, I, II, III, IV, and V) to account for the observed kinetics and product distributions. The model provides an unusually detailed quantitative mechanism for the complex reactions that occur in mixtures of chlorine species and organic substrates, particularly when the strong oxidant chlorite is employed. Kinetic control of the reaction is achieved by the addition of chlorine dioxide to the reaction mixture, thereby eliminating a substantial induction period observed when chlorite is used alone. The epoxidation agent is identified as chlorine dioxide, which is continually formed by the reaction of chlorite with hypochlorous acid that results from ClO produced by the epoxidation reaction. The overall stoichiometry is the result of two competing chain reactions in which the reactive intermediate ClO reacts with either chlorine dioxide or chlorite ion to produce hypochlorous acid and chlorate or chloride, respectively. At high chlorite ion concentrations, HOCl is rapidly eliminated by reaction with chlorite, minimizing side reactions between HOCl and Cl2 with the starting material. Epoxide selectivity (>90% under optimal conditions) is accurately predicted by the kinetic model. The model rate constant for direct reaction of styrene with ClO2(aq) to produce epoxide is (1.16 ± 0.07) × 10(-2) M(-1) s(-1) for 60:40 water/acetonitrile with 0.20 M acetate buffer. Rate constants for para substituted styrenes (R = -SO3(-), -OMe, -Me, -Cl, -H, and -NO2) with ClO2 were determined. The results support the radical addition/elimination mechanism originally proposed by Kolar and Lindgren to account for the formation of styrene oxide in the reaction of styrene with chlorine dioxide.

Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles

PubMed Central

Rosenzweig, Rina; Sekhar, Ashok; Nagesh, Jayashree; Kay, Lewis E

2017-01-01

The Hsp70 chaperone system is integrated into a myriad of biochemical processes that are critical for cellular proteostasis. Although detailed pictures of Hsp70 bound with peptides have emerged, correspondingly detailed structural information on complexes with folding-competent substrates remains lacking. Here we report a methyl-TROSY based solution NMR study showing that the Escherichia coli version of Hsp70, DnaK, binds to as many as four distinct sites on a small 53-residue client protein, hTRF1. A fraction of hTRF1 chains are also bound to two DnaK molecules simultaneously, resulting in a mixture of DnaK-substrate sub-ensembles that are structurally heterogeneous. The interactions of Hsp70 with a client protein at different sites results in a fuzzy chaperone-substrate ensemble and suggests a mechanism for Hsp70 function whereby the structural heterogeneity of released substrate molecules enables them to circumvent kinetic traps in their conformational free energy landscape and fold efficiently to the native state. DOI: http://dx.doi.org/10.7554/eLife.28030.001 PMID:28708484

Electron transfer and reaction mechanism of laccases.

PubMed

Jones, Stephen M; Solomon, Edward I

2015-03-01

Laccases are part of the family of multicopper oxidases (MCOs), which couple the oxidation of substrates to the four electron reduction of O2 to H2O. MCOs contain a minimum of four Cu's divided into Type 1 (T1), Type 2 (T2), and binuclear Type 3 (T3) Cu sites that are distinguished based on unique spectroscopic features. Substrate oxidation occurs near the T1, and electrons are transferred approximately 13 Å through the protein via the Cys-His pathway to the T2/T3 trinuclear copper cluster (TNC), where dioxygen reduction occurs. This review outlines the electron transfer (ET) process in laccases, and the mechanism of O2 reduction as elucidated through spectroscopic, kinetic, and computational data. Marcus theory is used to describe the relevant factors which impact ET rates including the driving force, reorganization energy, and electronic coupling matrix element. Then, the mechanism of O2 reaction is detailed with particular focus on the intermediates formed during the two 2e(-) reduction steps. The first 2e(-) step forms the peroxide intermediate, followed by the second 2e(-) step to form the native intermediate, which has been shown to be the catalytically relevant fully oxidized form of the enzyme.

Detailed energy distributions in laser-produced plasmas of solid gold and foam gold planar targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Yunsong; Department of Engineering Physics, Tsinghua University, Beijing 100084; Zhang, Lu

Foam gold was proposed to increase the laser to x-ray conversion efficiency due to its important applications. To understand the mechanism of x-ray enhancement, the detailed energy distributions and plasma profiles for laser-irradiated solid gold and foam gold targets were studied comparatively by hydrodynamic simulations using the code Multi-1D. It is confirmed that the radiation heat wave is subsonic for the normal solid gold target, while supersonic for the foam gold target. The shock wave, which is behind the supersonic radiation heat wave for the foam gold target, generates a plasma temperature gradient with high temperature near the shock wavemore » front to produce an additional net outward radiation for enhancement of the x-ray emission. Much larger inward plasma velocity is also driven by the shock wave as an initial plasma velocity for the laser deposition and electron thermal conduct zone, which decreases the expanding plasma kinetic energy loss and helps to increase the x-ray radiation.« less

Metadynamics Simulations Reveal a Na+ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT

PubMed Central

Bisha, Ina; Rodriguez, Alex; Laio, Alessandro; Magistrato, Alessandra

2014-01-01

Sodium-Galactose Transporter (SGLT) is a secondary active symporter which accumulates sugars into cells by using the electrochemical gradient of Na+ across the membrane. Previous computational studies provided insights into the release process of the two ligands (galactose and sodium ion) into the cytoplasm from the inward-facing conformation of Vibrio parahaemolyticus sodium/galactose transporter (vSGLT). Several aspects of the transport mechanism of this symporter remain to be clarified: (i) a detailed kinetic and thermodynamic characterization of the exit path of the two ligands is still lacking; (ii) contradictory conclusions have been drawn concerning the gating role of Y263; (iii) the role of Na+ in modulating the release path of galactose is not clear. In this work, we use bias-exchange metadynamics simulations to characterize the free energy profile of the galactose and Na+ release processes toward the intracellular side. Surprisingly, we find that the exit of Na+ and galactose is non-concerted as the cooperativity between the two ligands is associated to a transition that is not rate limiting. The dissociation barriers are of the order of 11–12 kcal/mol for both the ion and the substrate, in line with kinetic information concerning this type of transporters. On the basis of these results we propose a branched six-state alternating access mechanism, which may be shared also by other members of the LeuT-fold transporters. PMID:25522004

A critical analysis of the accuracy of several numerical techniques for combustion kinetic rate equations

NASA Technical Reports Server (NTRS)

Radhadrishnan, Krishnan

1993-01-01

A detailed analysis of the accuracy of several techniques recently developed for integrating stiff ordinary differential equations is presented. The techniques include two general-purpose codes EPISODE and LSODE developed for an arbitrary system of ordinary differential equations, and three specialized codes CHEMEQ, CREK1D, and GCKP4 developed specifically to solve chemical kinetic rate equations. The accuracy study is made by application of these codes to two practical combustion kinetics problems. Both problems describe adiabatic, homogeneous, gas-phase chemical reactions at constant pressure, and include all three combustion regimes: induction, heat release, and equilibration. To illustrate the error variation in the different combustion regimes the species are divided into three types (reactants, intermediates, and products), and error versus time plots are presented for each species type and the temperature. These plots show that CHEMEQ is the most accurate code during induction and early heat release. During late heat release and equilibration, however, the other codes are more accurate. A single global quantity, a mean integrated root-mean-square error, that measures the average error incurred in solving the complete problem is used to compare the accuracy of the codes. Among the codes examined, LSODE is the most accurate for solving chemical kinetics problems. It is also the most efficient code, in the sense that it requires the least computational work to attain a specified accuracy level. An important finding is that use of the algebraic enthalpy conservation equation to compute the temperature can be more accurate and efficient than integrating the temperature differential equation.

Activation mechanism of melB tyrosinase from Aspergillus oryzae by acidic treatment.

PubMed

Fujieda, Nobutaka; Murata, Michiaki; Yabuta, Shintaro; Ikeda, Takuya; Shimokawa, Chizu; Nakamura, Yukihiro; Hata, Yoji; Itoh, Shinobu

2013-01-01

The pro form of recombinant tyrosinase from Aspergillus oryzae (melB) shows no catalytic activity, but acid treatment (around pH 3.5) of protyrosinase activates it to induce tyrosinase activity. Circular dichroism spectra, gel filtration analysis, and colorimetric assay have indicated that acid treatment around pH 3.5 induced the disruption of the conformation of the C-terminal domain covering the enzyme active site. These structural changes induced by the acid treatment may open the entrance to the enzyme active site for substrate incorporation. To compare the mechanism of hydroxylation by the acid-treated tyrosinase with that by trypsin-treated tyrosinase, a detailed steady-state kinetic analysis of the phenolase activity was performed by monitoring the O(2)-consumption rate using a Clark-type oxygen electrode. The results clearly show that the phenolase activity (phenol hydroxylation) of the activated tyrosinase involves an electrophilic aromatic substitution mechanism as in the case of mushroom tyrosinase (Yamazaki and Itoh in J. Am. Chem. Soc. 125:13034-13035, 2003) and activated hemocyanin with urea (Morioka et al. in J. Am. Chem. Soc. 128:6788-6789, 2006).

Comparison of detailed and reduced kinetics mechanisms of silane oxidation in the basis of detonation wave structure problem

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Tropin, D. A.; Fomin, P. A.

2018-03-01

The paper deals with the problem of the structure of detonation waves in the silane-air mixture within the framework of mathematical model of a nonequilibrium gas dynamics. Detailed kinetic scheme of silane oxidation as well as the newly developed reduced kinetic model of detonation combustion of silane are used. On its basis the detonation wave (DW) structure in stoichiometric silane - air mixture and dependences of Chapman-Jouguet parameters of mixture on stoichiometric ratio between the fuel (silane) and an oxidizer (air) were obtained.

Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9.

PubMed

Raper, Austin T; Stephenson, Anthony A; Suo, Zucai

2018-02-28

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.

The Dissociative Recombination of OH(+)

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1995-01-01

Theoretical quantum chemical calculations of the cross sections and rates for the dissociative recombination of the upsilon = 0 level of the ground state of OH(+) show that recombination occurs primarily along the 2 (2)Pi diabatic route. The products are 0((1)D) and a hot H atom with 6.1 eV kinetic energy. The coupling to the resonances is very small and the indirect recombination mechanism plays only a minor role. The recommended value for the rate coefficient is (6.3 +/- 0.7) x 10(exp -9)x (T(e)/1300)(exp -0.48) cu.cm/s for 10 less than T(e) less than 1000 K.

A Comparison of Two Chemical Mechanisms Using Data from the Southern Oxidant and Aerosol Study

NASA Astrophysics Data System (ADS)

Green, S. B.; Saylor, R. D.

2016-12-01

The Atmospheric Chemistry and Canopy Exchange Simulation System (ACCESS) is a 1-D column model of the physical and chemical processes occurring from the Earth's surface to the top of the planetary boundary layer (PBL). In this study, we couple ACCESS with environmental data from the Southern Oxidant and Aerosol Study (SOAS) intensive field measurement campaign to simulate the chemical evolution of biogenic hydrocarbons above a forest canopy over two time periods: a four-day period from June 29-July 2, 2013 and a three-day period from June 21-23, 2013. We quantify the efficacy of the model by calculating R2 values between SOAS chemical measurements and simulation results of isoprene, methyl vinyl ketone (MVK), methacrolein (MACR), α-pinene, and limonene. Two kinetic mechanisms, one from Browne et al. (2014) (RACM2+) and another from Schwantes et al. (2015) (CIT), were implemented in ACCESS and used in independent simulations to determine which mechanism better represents the SOAS data through daytime and nighttime periods. The results demonstrate that RACM2+ and CIT perform at comparable levels for simulating the evolution of isoprene, MVK, and MACR, but both differ substantially from measurements of α-pinene and limonene. The mechanisms perform equally well during both daytime and nighttime periods and thus, substantiated by our results, there is no strong justification for implementing one mechanism over the other.

Chemical kinetics of homogeneous atmospheric oxidation of sulfur dioxide

NASA Technical Reports Server (NTRS)

Sander, S. P.; Seinfeld, J. H.

1976-01-01

A systematic evaluation of known homogeneous SO2 reactions which might be important in air pollution chemistry is carried out. A mechanism is developed to represent the chemistry of NOx/hydrocarbon/SO2 systems, and the mechanism is used to analyze available experimental data appropriate for quantitative analysis of SO2 oxidation kinetics. Detailed comparisons of observed and predicted concentration behavior are presented. In all cases, observed SO2 oxidation rates cannot be explained solely on the basis of those SO2 reactions for which rate constants have been measured. The role of ozone-olefin reactions in SO2 oxidation is elucidated.

Mechanism and Kinetics of the Formation and Transport of Aerosol Particles in the Lower Stratosphere

NASA Astrophysics Data System (ADS)

Aloyan, A. E.; Ermakov, A. N.; Arutyunyan, V. O.

2018-03-01

Field and laboratory observation data on aerosol particles in the lower stratosphere are considered. The microphysics of their formation, mechanisms of heterogeneous chemical reactions involving reservoir gases (e.g., HCl, ClONO2, etc.) and their kinetic characteristics are analyzed. A new model of global transport of gaseous and aerosol admixtures in the lower stratosphere is described. The preliminary results from a numerical simulation of the formation of sulfate particles of the Junge layer and particles of polar stratospheric clouds (PSCs, types Ia, Ib, and II) are presented, and their effect on the gas and aerosol composition is analyzed.

Quantifying the influence of boreal biomass burning emissions on tropospheric oxidant chemistry over the North Atlantic using BORTAS measurements

NASA Astrophysics Data System (ADS)

Parrington, Mark; Palmer, Paul I.; Rickard, Andrew; Young, Jennifer; Lewis, Ally; Lee, James; Henze, Daven; Tarasick, David; Hyer, Edward; Yantosca, Robert; Bowman, Kevin; Worden, John; Griffin, Debora; Franklin, Jonathan; Helmig, Detlev

2013-04-01

We use the GEOS-Chem chemistry transport model to quantify the impact of boreal biomass burning on tropospheric oxidant chemistry over the North Atlantic region during summer of 2011. The GEOS-Chem model is used at a spatial resolution of 1/2 degree latitude by 2/3 degree longitude for a domain covering eastern North America, the North Atlantic Ocean and western Europe. We initialise the model with biomass burning emissions from the Fire Locating and Monitoring of Burning Emissions (FLAMBE) inventory and use a modified chemical mechanism providing a detailed description of ozone photochemistry in boreal biomass burning outflow derived from the Master Chemical Mechanism (MCM). We evaluate the 3-D model distribution of ozone and tracers associated with biomass burning against measurements made by the UK FAAM BAe-146 research aircraft, ozonesondes, ground-based and satellite instruments as part of the BORTAS experiment between 12 July and 3 August 2011. We also use the GEOS-Chem model adjoint to fit the model to BORTAS measurements to analyse the sensitivity of the model chemical mechanism and ozone distribution to wildfire emissions in central Canada.

Investigation and modeling of the effects of light spectrum and incident angle on the growth of Chlorella vulgaris in photobioreactors.

PubMed

Souliès, Antoine; Legrand, Jack; Marec, Hélène; Pruvost, Jérémy; Castelain, Cathy; Burghelea, Teodor; Cornet, Jean-François

2016-03-01

An in-depth investigation of how various illumination conditions influence microalgal growth in photobioreactors (PBR) has been presented. Effects of both the light emission spectrum (white and red) and the light incident angle (0° and 60°) on the PBR surface were investigated. The experiments were conducted in two fully controlled lab-scale PBRs, a torus PBR and a thin flat-panel PBR for high cell density culture. The results obtained in the torus PBR were used to build the kinetic growth model of Chlorella vulgaris taken as a model species. The PBR model was then applied to the thin flat-panel PBR, which was run with various illumination conditions. Its detailed representation of local rate of photon absorption under various conditions (spectral calculation of light attenuation, incident angle influence) enabled the model to take into account all the tested conditions with no further adjustment. This allowed a detailed investigation of the coupling between radiation field and photosynthetic growth. Effects of all the radiation conditions together with pigment acclimation, which was found to be relevant, were investigated in depth. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:247-261, 2016. © 2016 American Institute of Chemical Engineers.

Sum over Histories Representation for Kinetic Sensitivity Analysis: How Chemical Pathways Change When Reaction Rate Coefficients Are Varied

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bai, Shirong; Davis, Michael J.; Skodje, Rex T.

2015-11-12

The sensitivity of kinetic observables is analyzed using a newly developed sum over histories representation of chemical kinetics. In the sum over histories representation, the concentrations of the chemical species are decomposed into the sum of probabilities for chemical pathways that follow molecules from reactants to products or intermediates. Unlike static flux methods for reaction path analysis, the sum over histories approach includes the explicit time dependence of the pathway probabilities. Using the sum over histories representation, the sensitivity of an observable with respect to a kinetic parameter such as a rate coefficient is then analyzed in terms of howmore » that parameter affects the chemical pathway probabilities. The method is illustrated for species concentration target functions in H-2 combustion where the rate coefficients are allowed to vary over their associated uncertainty ranges. It is found that large sensitivities are often associated with rate limiting steps along important chemical pathways or by reactions that control the branching of reactive flux« less

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

PubMed

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

2007-06-16

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

Detailed physico-chemical characterization of microplastics from North Atlantic Gyre

NASA Astrophysics Data System (ADS)

ter Halle, A.; Ladirat, L.; Gendre, X.; Goudouneche, D.; Pusineri, C.; Routaboul, C.; Tenailleau, C.; Duployer, B.; Perez, E.

2016-02-01

More than 260 million tonnes of plastic are used each year. Based on population density and economic status of costal countries the mass of land based plastic waste entering the ocean was recently estimated between 4.8 to 12.7 million metric tons per year1. Most striking is the estimation for 2025 that this amount will increase by an order of magnitude if waste management infrastructures are not improved. Plastic debris is abundant and widespread in the marine habitat. Marine plastic pollution has been recently recognized as a global environmental threat2. There is still a need for detailed research in terms of estimating the global scale of plastic inputs, their fate in the environment as well as the biological responses to plastic exposure in a variety of marine organisms. In this context, the present study aimed at giving a detailed physico-chemical characterization of the microplastics collected at the surface of the North Atlantic accumulation zone. A detailed description of the plastics is given in terms of size, width, density and weight together with a microscopic and infrared spectroscopy characterization. In this study, also we introduce a new fragmentation mechanism of the microplastics based on the physico-chemical data collected. This approach will be helpful for oceanographic modelling. The results will be also very useful to better understand the biological response to the plastic in terms of transfer of chemical in case of ingestion or to better understand the formation and development of the plastisphere. 1 Jambeck, J. R.; Geyer, R.; Wilcox, C.; Siegler, T. R.; Perryman, M.; Andrady, A.; Narayan, R.; Lavender Law, K., Plastic waste inputs from land into the ocean 2 Moore, C. J., Synthetic polymers in the marine environment: A rapidly increasing, long-term threat. Environmental Research 2008, 108, (2), 131-139.

Kinetic Studies with Ion Selective Electrodes: Determination of Creatinine in Urine with a Picrate Ion Selective Electrode: A Laboratory Experiment.

ERIC Educational Resources Information Center

Diamandis, E. P.; And Others

1983-01-01

The kinetic of the Jaffe reaction with picrate ion selective electrode (ISE) and a kinetic method for determining creatinine in urine is presented. The experiment could be used to familarize students with the application of ISE in kinetic studies and chemical analysis. (Author/JN)

STATIC AND KINETIC SITE-SPECIFIC PROTEIN-DNA PHOTOCROSSLINKING: ANALYSIS OF BACTERIAL TRANSCRIPTION INITIATION COMPLEXES

PubMed Central

Naryshkin, Nikolai; Druzhinin, Sergei; Revyakin, Andrei; Kim, Younggyu; Mekler, Vladimir; Ebright, Richard H.

2009-01-01

Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking--involving rapid-quench-flow mixing and pulsed-laser irradiation--permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes. PMID:19378179

High speed turbulent reacting flows: DNS and LES

NASA Technical Reports Server (NTRS)

Givi, Peyman

1990-01-01

Work on understanding the mechanisms of mixing and reaction in high speed turbulent reacting flows was continued. Efforts, in particular, were concentrated on taking advantage of modern computational methods to simulate high speed turbulent flows. In doing so, two methodologies were used: large eddy simulations (LES) and direct numerical simulations (DNS). In the work related with LES the objective is to study the behavior of the probability density functions (pdfs) of scalar properties within the subgrid in reacting turbulent flows. The data base obtained by DNS for a detailed study of the pdf characteristics within the subgrid was used. Simulations are performed for flows under various initializations to include the effects of compressibility on mixing and chemical reactions. In the work related with DNS, a two-dimensional temporally developing high speed mixing layer under the influence of a second-order non-equilibrium chemical reaction of the type A + B yields products + heat was considered. Simulations were performed with different magnitudes of the convective Mach numbers and with different chemical kinetic parameters for the purpose of examining the isolated effects of the compressibility and the heat released by the chemical reactions on the structure of the layer. A full compressible code was developed and utilized, so that the coupling between mixing and chemical reactions is captured in a realistic manner.

Mechanism of catalytic gasification of coal char. Quarterly technical report No. 5, October 1 to December 31, 1981

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wood, B. J.; Sancier, K. M.; Sheridan, D. R.

1982-02-26

The purpose of this study is to determine the mechanisms involved in the catalytic reactions of coal char and to identify the specific reaction steps and the parameters that control the catalytic process. The mode of action of the catalyst can be viewed in two ways. In one view, the catalyst participates in a reduction/oxidation cycle. The initial reaction between the carbon and the catalyst reduces the KOH to potassium accompanied by the gaseous reactant (H/sub 2/O or CO/sub 2/), producing further gaseous products (CO and H/sub 2/) and regenerating the initial state of the catalyst. In an alternative view,more » the catalyst initially forms an alkali metal addition compound with the carbon network of the char. The carbon-carbon bonds are altered by the formation of the metal-carbon linkage, possibly by electron transfer from the alkali metal atom to the carbon structure. As a result, the carbon structure is more readily attacked by the gaseous reactant (CO or H/sub 2/O) to produce the products of gasification. The following areas were investigated to provide experimental evidence for these catalytic modes of action: chemical kinetic measurements; thermodynamic measurements; free radicals in reacting carbon; electrical conductivity measurements. A detailed discussion on the catalyst-carbon interaction and on the reaction intermediate is provided.« less

Detailed and Simplified Chemical Kinetics of Aviation Fuels and Surrogates

DTIC Science & Technology

2009-09-01

Cyclopentene and Methyl-Cyclopentadiene Mixtures, Proc. Comb. Inst. 29:2291-2298 (2002). [13] Final Report, Computational Fluid Dynamics for...Determination of Total and Polycyclic Aromatic Hydrocarbons in Aviation Jet Fuel, Journal of Chromatography A (1- 2) 985 (2003), 197-203. [10] C. K...DiNaro, J. B. Howard, W. H. Green, J. W. Tester and J. W. Bozzelli, Elementary Reaction Mechanism for Benzene Oxidation in Supercritical Water, J

Detailed and Simplified Chemical Kinetics of Aviation Fuels and Surrogates

DTIC Science & Technology

2009-11-12

Cyclopentene and Methyl-Cyclopentadiene Mixtures, Proc. Comb. Inst. 29:2291-2298 (2002). [13] Final Report, Computational Fluid Dynamics for...Determination of Total and Polycyclic Aromatic Hydrocarbons in Aviation Jet Fuel, Journal of Chromatography A (1- 2) 985 (2003), 197-203. [10] C. K...DiNaro, J. B. Howard, W. H. Green, J. W. Tester and J. W. Bozzelli, Elementary Reaction Mechanism for Benzene Oxidation in Supercritical Water, J

Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways

PubMed Central

Cheon, Mookyung; Hall, Carol K.; Chang, Iksoo

2015-01-01

Discovering the mechanisms by which proteins aggregate into fibrils is an essential first step in understanding the molecular level processes underlying neurodegenerative diseases such as Alzheimer’s and Parkinson's. The goal of this work is to provide insights into the structural changes that characterize the kinetic pathways by which amyloid-β peptides convert from monomers to oligomers to fibrils. By applying discontinuous molecular dynamics simulations to PRIME20, a force field designed to capture the chemical and physical aspects of protein aggregation, we have been able to trace out the entire aggregation process for a system containing 8 Aβ17–42 peptides. We uncovered two fibrillization mechanisms that govern the structural conversion of Aβ17–42 peptides from disordered oligomers into protofilaments. The first mechanism is monomeric conversion templated by a U-shape oligomeric nucleus into U-shape protofilament. The second mechanism involves a long-lived and on-pathway metastable oligomer with S-shape chains, having a C-terminal turn, en route to the final U-shape protofilament. Oligomers with this C-terminal turn have been regarded in recent experiments as a major contributing element to cell toxicity in Alzheimer’s disease. The internal structures of the U-shape protofilaments from our PRIME20/DMD simulation agree well with those from solid state NMR experiments. The approach presented here offers a simple molecular-level framework to describe protein aggregation in general and to visualize the kinetic evolution of a putative toxic element in Alzheimer’s disease in particular. PMID:25955249

Effect of Na+ impregnated activated carbon on the adsorption of NH4(+)-N from aqueous solution.

PubMed

Shi, Mo; Wang, Zhengfang; Zheng, Zheng

2013-08-01

Two kinds of activated carbons modified by Na+ impregnation after pre-treatments involving oxidation by nitric acid or acidification by hydrochloric acid (denoted as AC/N-Na and AC/HCl-Na, respectively), were used as adsorbents to remove NH4(+)-N. The surface features of samples were investigated by BET, SEM, XRD and FT-IR. The adsorption experiments were conducted in equilibrium and kinetic conditions. Influencing factors such as initial solution pH and initial concentration were investigated. A possible mechanism was proposed. Results showed that optimal NH4(+)-N removal efficiency was achieved at a neutral pH condition for the modified ACs. The Langmuir isotherm adsorption equation provided a better fit than other models for the equilibrium study. The adsorption kinetics followed both the pseudo second-order kinetics model and intra-particle kinetic model. Chemical surface analysis indicated that Na+ ions form ionic bonds with available surface functional groups created by pre-treatment, especially oxidation by nitric acid, thus increasing the removal efficiency of the modified ACs for NH4(+)-N. Na(+)-impregnated ACs had a higher removal capability in removing NH4(+)-N than unmodified AC, possibly resulting from higher numbers of surface functional groups and better intra-particle diffusion. The good fit of Langmuir isotherm adsorption to the data indicated the presence of monolayer NH4(+)-N adsorption on the active homogenous sites within the adsorbents. The applicability of pseudo second-order and intra-particle kinetic models revealed the complex nature of the adsorption mechanism. The intra-particle diffusion model revealed that the adsorption process consisted not only of surface adsorption but also intra-particle diffusion.

FAGE measurements of tropospheric HO with measurements and model of interferences

NASA Technical Reports Server (NTRS)

Hard, T. M.; Mehrabzadeh, A. A.; Chan, C. Y.; O'Brien, R. J.

1992-01-01

Ambient HO measurements by low-pressure laser-excited fluorescence with chemical modulation, and supporting ozone and water-vapor data, are presented for periods in May and August 1987. The observed peak daytime ambient HO concentrations are in the range (2.5 to 8) x 10 exp 6 molecules/cu cm and show small negative offsets due to photochemical interference. Direct measurements of the interference at fixed (O3) give the dependence on ambient (H2O) and on the modulating reagent (isobutane). At ambient (O3) = 30 ppb and 10 torr H2O, with excitation and detection at a total pressure of 4 torr, the net interference is equal to (HO) = -1.3 x 10 exp 6 molecules/cu cm. Production of HO by the reaction of isobutane with O(1D) accounts for the negative interference. Quenching of HO fluorescence by the modulating reagent contributes a smaller positive term to the interference; kinetic measurements of the quenching rate coefficient are reported. The experimental interference results are compared with a detailed kinetic model of HO production, excitation, relaxation, and detection; reasonable agreement is found.

Heterogeneous selenite reduction by zero valent iron steel wool.

PubMed

Li, Ziyan; Huang, Donglin; McDonald, Louis M

2017-02-01

Mine drainage from the low-sulfur surface coal mines in southern West Virginia, USA, is circumneutral (pH > 6) but contains elevated selenium (Se) concentrations. Removal of selenite ions from aqueous solutions under anoxic condition at pH 6-8.5 by zero valent iron steel wool (ZVI-SW) was investigated in bench-scale kinetic experiments using wet chemical, microscopic and spectroscopic techniques (X-ray photoelectron spectroscopy). ZVI-SW could effectively and efficiently remove Se IV from solution with pH 6-8.5. A two-step removal mechanism was identified for Se IV reduction by ZVI-SW. The proposed mechanism was electrochemical reduction of Se IV by Fe 0 in an initial lag stage, followed by a faster heterogeneous reduction, mediated by an Fe II -bearing phase (hydroxide or green rust). Solution pH was a critical factor for the kinetic rate in the lag stage (0.33 h -1 for pH > 8 and 0.10 h -1 for pH 6-8). The length of lag stage was 20-30 min as determined by the time for dissolved Fe II concentration to reach 0.30 ± 0.04 mg L -1 which was critical for induction of the faster stage. About 65% of the initial Se IV was reduced to Se 0 , the primary reductive product in both stages.

Preparation and biophysical characterization of recombinant Pseudomonas aeruginosa phosphorylcholine phosphatase.

PubMed

Beassoni, Paola R; Berti, Federico Pérez de; Otero, Lisandro H; Risso, Valeria A; Ferreyra, Raul G; Lisa, Angela T; Domenech, Carlos E; Ermácora, Mario R

2010-06-01

Pseudomonas aeruginosa infections constitute a widespread health problem with high economical and social impact, and the phosphorylcholine phosphatase (PchP) of this bacterium is a potential target for antimicrobial treatment. However, drug design requires high-resolution structural information and detailed biophysical knowledge not available for PchP. An obstacle in the study of PchP is that current methods for its expression and purification are suboptimal and allowed only a preliminary kinetic characterization of the enzyme. Herein, we describe a new procedure for the efficient preparation of recombinant PchP overexpressed in Escherichia coli. The enzyme is purified from urea solubilized inclusion bodies and refolded by dialysis. The product of PchP refolding is a mixture of native PchP and a kinetically-trapped, alternatively-folded aggregate that is very slowly converted into the native state. The properly folded and fully active enzyme is isolated from the refolding mixture by size-exclusion chromatography. PchP prepared by the new procedure was subjected to chemical and biophysical characterization, and its basic optical, hydrodynamic, metal-binding, and catalytic properties are reported. The unfolding of the enzyme was also investigated, and its thermal stability was determined. The obtained information should help to compare PchP with other phosphatases and to obtain a better understanding of its catalytic mechanism. In addition, preliminary trials showed that PchP prepared by the new protocol is suitable for crystallization, opening the way for high-resolution studies of the enzyme structure.

Chemical oscillator as a generalized Rayleigh oscillator.

PubMed

Ghosh, Shyamolina; Ray, Deb Shankar

2013-10-28

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.

Methodology for extracting local constants from petroleum cracking flows

DOEpatents

Chang, Shen-Lin; Lottes, Steven A.; Zhou, Chenn Q.

2000-01-01

A methodology provides for the extraction of local chemical kinetic model constants for use in a reacting flow computational fluid dynamics (CFD) computer code with chemical kinetic computations to optimize the operating conditions or design of the system, including retrofit design improvements to existing systems. The coupled CFD and kinetic computer code are used in combination with data obtained from a matrix of experimental tests to extract the kinetic constants. Local fluid dynamic effects are implicitly included in the extracted local kinetic constants for each particular application system to which the methodology is applied. The extracted local kinetic model constants work well over a fairly broad range of operating conditions for specific and complex reaction sets in specific and complex reactor systems. While disclosed in terms of use in a Fluid Catalytic Cracking (FCC) riser, the inventive methodology has application in virtually any reaction set to extract constants for any particular application and reaction set formulation. The methodology includes the step of: (1) selecting the test data sets for various conditions; (2) establishing the general trend of the parametric effect on the measured product yields; (3) calculating product yields for the selected test conditions using coupled computational fluid dynamics and chemical kinetics; (4) adjusting the local kinetic constants to match calculated product yields with experimental data; and (5) validating the determined set of local kinetic constants by comparing the calculated results with experimental data from additional test runs at different operating conditions.

Comparison of cadmium absorption, translocation, subcellular distribution and chemical forms between two radish cultivars (Raphanus sativus L.).

PubMed

Xin, Juan; Zhao, Xiaohu; Tan, Qiling; Sun, Xuecheng; Hu, Chengxiao

2017-11-01

Cadmium (Cd) absorption and accumulation vary greatly not only among plant species but also among cultivars within the same species. In order to better understand the mechanisms of Cd absorption, transportation and distribution, we examined the differences of Cd absorption, translocation, subcellular distribution and chemical forms between L19, a Cd-tolerant genotype, and H4, a Cd-sensitive genotype, using kinetic analysis and soil culture experiment. Kinetic assays showed that the different Cd concentrations between the two cultivars might be ascribed to root absorption and translocation from root to shoot. The investigations of subcellular distribution and chemical forms verified that Cd concentrations of all subcellular fractions in H4 were all higher than in L19. Meanwhile, most of the Cd was associated with cell walls in the root of H4, but the Cd in the root of L19 and leaf of the two cultivars was mainly stored in soluble fraction, which could be one possible mechanism of tolerance to Cd toxicity. In addition, Cd fractions extracted by 1M NaCl and 2% HAC were predominant in root and leaf of both cultivars and the concentrations and proportions extracted by water and 80% ethanol in root and 1M NaCl in leaf were all higher in H4 than in L19. These results indicate that the Cd in H4 is more active than L19, which could be responsible for the sensitivity of H4 to Cd damage. Copyright © 2017 Elsevier Inc. All rights reserved.

Some aspects of modeling hydrocarbon oxidation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gal, D.; Botar, L.; Danoczy, E.

1981-01-01

A modeling procedure for the study of hydrocarbon oxidation is suggested, and its effectiveness for the oxidation of ethylbenzene is demonstrated. As a first step in modeling, systematization involves compilation of possible mechanisms. Then, by introduction of the concept of kinetic communication, the chaotic set of possible mechanisms is systematized into a network. Experimentation serves both as feedback to the systematic arrangement of information and source of new information. Kinetic treatment of the possible mechanism has been accomplished by two different approaches: by classical inductive calculations starting with a small mechanism and using kinetic approximations, and by computer simulation. Themore » authors have compiled a so-called Main Contributory Mechanism, involving processes - within the possible mechanism - which contribute basically to the formation and consumption of the intermediates, to the consumption of the starting compounds and to the formation of the end products. 24 refs.« less

A Novel Selective Inverse Agonist of the CB2 Receptor as a Radiolabeled Tool Compound for Kinetic Binding Studies.

PubMed

Martella, Andrea; Sijben, Huub; Rufer, Arne C; Grether, Uwe; Fingerle, Juergen; Ullmer, Christoph; Hartung, Thomas; IJzerman, Adriaan P; van der Stelt, Mario; Heitman, Laura H

2017-10-01

The endocannabinoid system, and in particular the cannabinoid type 2 receptor (CB2R), raised the interest of many medicinal chemistry programs for its therapeutic relevance in several (patho)physiologic processes. However, the physico-chemical properties of tool compounds for CB2R (e.g., the radioligand [ 3 H]CP55,940) are not optimal, despite the research efforts in developing effective drugs to target this system. At the same time, the importance of drug-target binding kinetics is growing since the kinetic binding profile of a ligand may provide important insights for the resulting in vivo efficacy. In this context we synthesized and characterized [ 3 H]RO6957022, a highly selective CB2R inverse agonist, as a radiolabeled tool compound. In equilibrium and kinetic binding experiments [ 3 H]RO6957022 showed high affinity for human CB2R with fast association ( k on ) and moderate dissociation ( k off ) kinetics. To demonstrate the robustness of [ 3 H]RO6957022 binding, affinity studies were carried out for a wide range of CB2R reference ligands, spanning the range of full, partial, and inverse agonists. Finally, we used [ 3 H]RO6957022 to study the kinetic binding profiles (i.e., k on and k off values) of selected synthetic and endogenous (i.e., 2-arachidonoylglycerol, anandamide, and noladin ether) CB2R ligands by competition association experiments. All tested ligands, and in particular the endocannabinoids, displayed distinct kinetic profiles, shedding more light on their mechanism of action and the importance of association rates in the determination of CB2R affinity. Altogether, this study shows that the use of a novel tool compound, i.e., [ 3 H]RO6957022, can support the development of novel ligands with a repertoire of kinetic binding profiles for CB2R. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by Its dodecameric structure

DOE PAGES

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy; ...

2015-01-23

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence ofmore » a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.« less

Fundamental insights into interfacial catalysis.

PubMed

Gong, Jinlong; Bao, Xinhe

2017-04-03

Surface and interfacial catalysis plays a vital role in chemical industries, electrochemistry and photochemical reactions. The challenges of modern chemistry are to optimize the chemical reaction processes and understand the detailed mechanism of chemical reactions. Since the early 1960s, the foundation of surface science systems has allowed the study of surface and interfacial phenomena on atomic/molecular level, and thus brought a number of significant developments to fundamental and technological processes, such as catalysis, material science and biochemistry, just to name a few. This themed issue describes the recent advances and developments in the fundamental understanding of surface and interfacial catalysis, encompassing areas of knowledge from metal to metal oxide, carbide, graphene, hexagonal boron nitride, and transition metal dichalcogenides under ultrahigh vacuum conditions, as well as under realistic reaction conditions.

[Construction of automatic elucidation platform for mechanism of traditional Chinese medicine].

PubMed

Zhang, Bai-xia; Luo, Si-jun; Yan, Jing; Gu, Hao; Luo, Ji; Zhang, Yan-ling; Tao, Ou; Wang, Yun

2015-10-01

Aim at the two problems in the field of traditional Chinese medicine (TCM) mechanism elucidation, one is the lack of detailed biological processes information, next is the low efficient in constructing network models, we constructed an auxiliary elucidation system for the TCM mechanism and realize the automatic establishment of biological network model. This study used the Entity Grammar Systems (EGS) as the theoretical framework, integrated the data of formulae, herbs, chemical components, targets of component, biological reactions, signaling pathways and disease related proteins, established the formal models, wrote the reasoning engine, constructed the auxiliary elucidation system for the TCM mechanism elucidation. The platform provides an automatic modeling method for biological network model of TCM mechanism. It would be benefit to perform the in-depth research on TCM theory of natures and combination and provides the scientific references for R&D of TCM.

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure

PubMed Central

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Ballicora, Miguel A.

2015-01-01

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key towards understanding the regulation of polyamine levels in bacteria during pathogenesis. PMID:25623305

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by Its dodecameric structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Filippova, Ekaterina V.; Kuhn, Misty L.; Osipiuk, Jerzy

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence ofmore » a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis.« less

Adsorption Kinetics of Manganese (II) in wastewater of Chemical laboratory with Column Method using Sugarcane Bagasse as Adsorbent

NASA Astrophysics Data System (ADS)

Zaini, H.; Abubakar, S.; Saifuddin

2018-01-01

The purpose of this research is to separate manganese (II) metal in the wastewater using sugarcane bagasse as an adsorbent. Experimental design, the independent variables are contact time (0; 30; 60; 90; 120; 150; 180; 210; 240 minutes, respectively) and activation treatment (without activation, physical activation, activation by H2SO4 0.5 N and activation by NaOH 0.5 N. Fixed variables consist of adsorbent mass (50 g), adsorbent particle size (30 mesh), flow rate (7 L/min) and volume of adsorbent (10 L). The dependent variable is the concentration of manganese. The results showed that the separation process of manganese by adsorption method was influenced by contact time and activation type. The kinetic studies show that the adsorption mechanism satisfies the pseudo-second-order kinetics model. Maximum adsorption capacity (qm) for adsorbents without treatment is 0.971 mg/g, physical treatment is 0.889 mg/g, chemical treatment by H2SO4 is 0.858 mg/g and chemical treatment by NaOH is 1.016 mg/g.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

Mechanism Reduction for the Formation of Secondary Organic Aerosol for Integration into a 3-Dimensional Regional Air Quality Model

NASA Astrophysics Data System (ADS)

Xia, A.; Michelangeli, D.; Makar, P.

2006-12-01

Secondary Organic Aerosol (SOA) plays an important role in atmospheric chemistry, regional and global climate, and human health. It is important to develop a reduced yet accurate chemical mechanism for the formation of both ozone and SOA in a regional air quality model to alleviate CPU time and memory burden. A subset of a near-explicit Master Chemical Mechanism (MCM v3.1) describing alpha-pinene oxidation (976 reactions and 331 compounds), coupled with a gas/particle absorptive partitioning model, is used as a benchmark for the study of SOA formation within a box model. Results from the detailed mechanism show that total SOA mass decreases as the NOx/HC ratio increases. Aerosol fractions for the PAN-like compounds and the nitrates increase with increasing NOx/HC ratio, and the aerosol fractions for the organic peroxides and organic acids decrease with increasing NOx/HC ratio. In addition, 28 out of 149 condensable products are identified as important compounds for the SOA formation and mechanism reduction purposes. The detailed alpha-pinene oxidation mechanism was reduced systematically through five mechanism reduction techniques, in sequence, to create reduced mechanism preserving the properties of the original mechanism, while using less species. Specifically, a directed relation graph method with error propagation (DRGEP) based on resolving species interaction has been shown, in the first stage, to remove efficiently a large number of redundant species and reactions under a wide range of conditions. Next, the application of principal component analysis (PCA) of the rate sensitivity matrix and the use of quasi-steady-state approximation (QSSA) have been used to eliminate some reactions and remove some QSS species, respectively. The fourth stage is to use an iterative screening method to remove redundant species and reactions simultaneously. Last, a new lumping approach, depended on the NOx/HC ratio, is developed and implemented to reduce the number of species in the final stage. This methodology results in a reduction ratio of 3 for the number of species and reactions compared with the full mechanism. The simplified mechanism is demonstrated to reproduce well the important gas and aerosol phase species, four functional groups (PANs, Nitrates, organic peroxides, and organic acids), and the total SOA mass accurately within 16% under a wide range of conditions.

A novel polyamine allosteric site of SpeG from Vibrio cholerae is revealed by its dodecameric structure.

PubMed

Filippova, Ekaterina V; Kuhn, Misty L; Osipiuk, Jerzy; Kiryukhina, Olga; Joachimiak, Andrzej; Ballicora, Miguel A; Anderson, Wayne F

2015-03-27

Spermidine N-acetyltransferase, encoded by the gene speG, catalyzes the initial step in the degradation of polyamines and is a critical enzyme for determining the polyamine concentrations in bacteria. In Escherichia coli, studies have shown that SpeG is the enzyme responsible for acetylating spermidine under stress conditions and for preventing spermidine toxicity. Not all bacteria contain speG, and many bacterial pathogens have developed strategies to either acquire or silence it for pathogenesis. Here, we present thorough kinetic analyses combined with structural characterization of the VCA0947 SpeG enzyme from the important human pathogen Vibrio cholerae. Our studies revealed the unexpected presence of a previously unknown allosteric site and an unusual dodecameric structure for a member of the Gcn5-related N-acetyltransferase superfamily. We show that SpeG forms dodecamers in solution and in crystals and describe its three-dimensional structure in several ligand-free and liganded structures. Importantly, these structural data define the first view of a polyamine bound in an allosteric site of an N-acetyltransferase. Kinetic characterization of SpeG from V. cholerae showed that it acetylates spermidine and spermine. The behavior of this enzyme is complex and exhibits sigmoidal curves and substrate inhibition. We performed a detailed non-linear regression kinetic analysis to simultaneously fit families of substrate saturation curves to uncover a simple kinetic mechanism that explains the apparent complexity of this enzyme. Our results provide a fundamental understanding of the bacterial SpeG enzyme, which will be key toward understanding the regulation of polyamine levels in bacteria during pathogenesis. Copyright © 2015. Published by Elsevier Ltd.

[Medical aspects of common non-lethal weapons].

PubMed

Kunz, Sebastian Niko; Grove, Christina; Monticelli, Fabio

2014-03-01

The development and provision of non-lethal weapons (NLW) allow military and law enforcement personnel to exploit gradual engagement in countering potentially hazardous threats. Chemical, kinetic and electrical weapons systems are used to curb violence in civilian crowds. With inappropriate usage, these technologies can cause potentially fatal injuries that are not only of clinical, but also of legal relevance. In this context, the practicing physician is faced with treatment as well as assessment issues of new forms of injuries. In order to assure medical care and to be able to draw competent expert's conclusions, a detailed knowledge of the medical effects of these NLW is necessary. The review at hand presents today's most popular NLW and gives an overview of their possible injury potential and required treatments.

Development of a database for chemical mechanism assignments for volatile organic emissions.

PubMed

Carter, William P L

2015-10-01

The development of a database for making model species assignments when preparing total organic gas (TOG) emissions input for atmospheric models is described. This database currently has assignments of model species for 12 different gas-phase chemical mechanisms for over 1700 chemical compounds and covers over 3000 chemical categories used in five different anthropogenic TOG profile databases or output by two different biogenic emissions models. This involved developing a unified chemical classification system, assigning compounds to mixtures, assigning model species for the mechanisms to the compounds, and making assignments for unknown, unassigned, and nonvolatile mass. The comprehensiveness of the assignments, the contributions of various types of speciation categories to current profile and total emissions data, inconsistencies with existing undocumented model species assignments, and remaining speciation issues and areas of needed work are also discussed. The use of the system to prepare input for SMOKE, the Speciation Tool, and for biogenic models is described in the supplementary materials. The database, associated programs and files, and a users manual are available online at http://www.cert.ucr.edu/~carter/emitdb . Assigning air quality model species to the hundreds of emitted chemicals is a necessary link between emissions data and modeling effects of emissions on air quality. This is not easy and makes it difficult to implement new and more chemically detailed mechanisms in models. If done incorrectly, it is similar to errors in emissions speciation or the chemical mechanism used. Nevertheless, making such assignments is often an afterthought in chemical mechanism development and emissions processing, and existing assignments are usually undocumented and have errors and inconsistencies. This work is designed to address some of these problems.

Explosives and pyrotechnic propellants for use in long term deep space missions

NASA Technical Reports Server (NTRS)

Gorzynski, C. S., Jr.; Maycock, J. N.

1973-01-01

Explosives and pyrotechnic propellant materials which will withstand heat sterilization cycling at 125 C and ten year deep space aging under 10 to the minus 6th power torr and 66 C have been selected. The selection was accomplished through a detailed literature survey and an analytical evaluation of the physicochemical properties of the materials. The chemical components of the electroexplosive devices used in U.S. missiles and spacecraft were categorized into primary explosives, secondary explosives, and propellant ingredients. Kinetic data on such parameters as thermal decomposition and sublimation were obtained for these materials and used as a basis for the ten year life prediction. From these experimental data and some analytical calculations, a listing of candidate materials for deep space missions was made.

Characterization of the In Vitro Kinetic Interaction of Chlorpyrifos-Oxon with Rat Salivary Cholinesterase: A Potential Biomonitoring Matrix

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kousba, Ahmed A.; Poet, Torka S.; Timchalk, Charles

2003-02-12

Chlorpyrifos (CPF) is a commonly used organophosphate insecticide (OP). The primary mechanism of action for CPF involves the inhibition of acetylcholinesterase (AChE) by the active metabolite, CPF-oxon, with subsequent accumulation of acetylcholine (ACh) resulting in a wide range of neutotoxicity. CPF-oxon, can likewise inhibit other non-target cholinesterases (ChE) such as butyrylcholinesterase (BuChE), which represents a detoxification mechanism and a potential biomarker of exposure/response. Biological monitoring for OPs has focused on measuring parent chemical or metabolite in blood and urine or blood ChE inhibition. Salivary biomonitoring has recently been explored as a practical method for examination of chemical exposure; however, theremore » are a limited number of studies exploring its use for OPs. To evaluate the use of salivary ChE as a biological monitor for OP exposure, the current study characterized salivary ChE activity in Sprague-Dawley rats through its comparison with brain and plasma ChE using BW284C51 and iso-OMPA as selective inhibitors of AChE and BuChE, respectively. The study also estimated the kinetic constants describing BuChE interaction with CPF-oxon. A modified Ellman assay in conjunction with pharmacodynamic (PD) modeling was used to characterize the in vitro titration of diluted rat salivary ChE enzyme with CPF-oxon. The results indicated that, more than 95% of rat salivary ChE activity was associated with BuChE activity, total BuChE active site concentration was 0.0012 0.00013 nmol/ml saliva, reactivation rate constant (Kr) was 0.068 0.008 h-1 and inhibitory (Ki) rate constant of 8.825 and 9.80 nM-1h-1 determined experimentally and using model optimization respectively. These study results would be helpful for further evaluating the potential utility of salivary ChE as a practical tool for biological monitor of OP exposures.« less

Nucleation, growth, and repair of a cobalt-based oxygen evolving catalyst.

PubMed

Surendranath, Yogesh; Lutterman, Daniel A; Liu, Yi; Nocera, Daniel G

2012-04-11

The mechanism of nucleation, steady-state growth, and repair is investigated for an oxygen evolving catalyst prepared by electrodeposition from Co(2+) solutions in weakly basic electrolytes (Co-OEC). Potential step chronoamperometry and atomic force microscopy reveal that nucleation of Co-OEC is progressive and reaches a saturation surface coverage of ca. 70% on highly oriented pyrolytic graphite substrates. Steady-state electrodeposition of Co-OEC exhibits a Tafel slope approximately equal to 2.3 × RT/F. The electrochemical rate law exhibits a first order dependence on Co(2+) and inverse orders on proton (third order) and proton acceptor, methylphosphonate (first order for 1.8 mM ≤ [MeP(i)] ≤ 18 mM and second order dependence for 32 mM ≤ [MeP(i)] ≤ 180 mM). These electrokinetic studies, combined with recent XAS studies of catalyst structure, suggest a mechanism for steady state growth at intermediate MeP(i) concentration (1.8-18 mM) involving a rapid solution equilibrium between aquo Co(II) and Co(III) hydroxo species accompanied with a rapid surface equilibrium involving electrolyte dissociation and deprotonation of surface bound water. These equilibria are followed by a chemical rate-limiting step for incorporation of Co(III) into the growing cobaltate clusters comprising Co-OEC. At higher concentrations of MeP(i) ([MeP(i)] ≥ 32 mM), MePO(3)(2-) equilibrium binding to Co(II) in solution is suggested by the kinetic data. Consistent with the disparate pH profiles for oxygen evolution electrocatalysis and catalyst formation, NMR-based quantification of catalyst dissolution as a function of pH demonstrates functional stability and repair at pH values >6 whereas catalyst corrosion prevails at lower pH values. These kinetic insights provide a basis for developing and operating functional water oxidation (photo)anodes under benign pH conditions. © 2012 American Chemical Society

A graphical user interface for a method to infer kinetics and network architecture (MIKANA).

PubMed

Mourão, Márcio A; Srividhya, Jeyaraman; McSharry, Patrick E; Crampin, Edmund J; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis-Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1).

A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA)

PubMed Central

Mourão, Márcio A.; Srividhya, Jeyaraman; McSharry, Patrick E.; Crampin, Edmund J.; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis–Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1). PMID:22096591

Identified particle distributions in pp and Au+Au collisions at square root of (sNN)=200 GeV.

PubMed

Adams, J; Adler, C; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Badyal, S K; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bezverkhny, B I; Bhardwaj, S; Bhaskar, P; Bhati, A K; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Botje, M; Boucham, A; Brandin, A; Bravar, A; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Carroll, J; Castillo, J; Castro, M; Cebra, D; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, Y; Chernenko, S P; Cherney, M; Chikanian, A; Choi, B; Christie, W; Coffin, J P; Cormier, T M; Cramer, J G; Crawford, H J; Das, D; Das, S; Derevschikov, A A; Didenko, L; Dietel, T; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Majumdar, M R; Eckardt, V; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faine, V; Faivre, J; Fatemi, R; Filimonov, K; Filip, P; Finch, E; Fisyak, Y; Flierl, D; Foley, K J; Fu, J; Gagliardi, C A; Ganti, M S; Gutierrez, T D; Gagunashvili, N; Gans, J; Gaudichet, L; Germain, M; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Grachov, O; Grigoriev, V; Gronstal, S; Grosnick, D; Guedon, M; Guertin, S M; Gupta, A; Gushin, E; Hallman, T J; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Heppelmann, S; Herston, T; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horsley, M; Huang, H Z; Huang, S L; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Janik, M; Johnson, I; Jones, P G; Judd, E G; Kabana, S; Kaneta, M; Kaplan, M; Keane, D; Kiryluk, J; Kisiel, A; Klay, J; Klein, S R; Klyachko, A; Koetke, D D; Kollegger, T; Konstantinov, A S; Kopytine, M; Kotchenda, L; Kovalenko, A D; Kramer, M; Kravtsov, P; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunde, G J; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lansdell, C P; Lasiuk, B; Laue, F; Lauret, J; Lebedev, A; Lednický, R; Leontiev, V M; LeVine, M J; Li, C; Li, Q; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Z; Liu, Q J; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Ludlam, T; Lynn, D; Ma, J; Ma, Y G; Magestro, D; Mahajan, S; Mangotra, L K; Mahapatra, D P; Majka, R; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J; Matis, H S; Matulenko, Yu A; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Messer, M; Miller, M L; Milosevich, Z; Minaev, N G; Mironov, C; Mishra, D; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Mora-Corral, M J; Morozov, V; de Moura, M M; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Nevski, P; Nikitin, V A; Nogach, L V; Norman, B; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pandey, S U; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Perevoztchikov, V; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Ruan, L J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schweda, K; Seger, J; Seliverstov, D; Seyboth, P; Shahaliev, E; Shao, M; Sharma, M; Shestermanov, K E; Shimanskii, S S; Singaraju, R N; Simon, F; Skoro, G; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Spinka, H M; Srivastava, B; Stanislaus, S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Struck, C; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; de Toledo, A Szanto; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Thein, D; Thomas, J H; Tikhomirov, V; Tokarev, M; Tonjes, M B; Trainor, T A; Trentalange, S; Tribble, R E; Trivedi, M D; Trofimov, V; Tsai, O; Ullrich, T; Underwood, D G; Van Buren, G; VanderMolen, A M; Vasiliev, A N; Vasiliev, M; Vigdor, S E; Viyogi, Y P; Voloshin, S A; Waggoner, W; Wang, F; Wang, G; Wang, X L; Wang, Z M; Ward, H; Watson, J W; Wells, R; Westfall, G D; Whitten, C; Wieman, H; Willson, R; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yakutin, A E; Yamamoto, E; Yang, J; Yepes, P; Yurevich, V I; Zanevski, Y V; Zborovský, I; Zhang, H; Zhang, H Y; Zhang, W M; Zhang, Z P; Zołnierczuk, P A; Zoulkarneev, R; Zoulkarneeva, J; Zubarev, A N

2004-03-19

Transverse mass and rapidity distributions for charged pions, charged kaons, protons, and antiprotons are reported for square root of [sNN]=200 GeV pp and Au+Au collisions at Relativistic Heary Ion Collider (RHIC). Chemical and kinetic equilibrium model fits to our data reveal strong radial flow and long duration from chemical to kinetic freeze-out in central Au+Au collisions. The chemical freeze-out temperature appears to be independent of initial conditions at RHIC energies.

Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics

PubMed Central

Smirnov, Ivan; Carletti, Eugénie; Kurkova, Inna; Nachon, Florian; Nicolet, Yvain; Mitkevich, Vladimir A.; Débat, Hélène; Avalle, Bérangère; Belogurov, Alexey A.; Kuznetsov, Nikita; Reshetnyak, Andrey; Masson, Patrick; Tonevitsky, Alexander G.; Ponomarenko, Natalia; Makarov, Alexander A.; Friboulet, Alain; Tramontano, Alfonso; Gabibov, Alexander

2011-01-01

Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic antibody variable fragment library that uses a nucleophilic mechanism. Specific phosphonylation at a single tyrosine within the variable light-chain framework was confirmed in a recombinant IgG construct. High-resolution crystallographic structures of unmodified and phosphonylated Fabs display a 15-Å-deep two-chamber cavity at the interface of variable light (VL) and variable heavy (VH) fragments having a nucleophilic tyrosine at the base of the site. The depth and structure of the pocket are atypical of antibodies in general but can be compared qualitatively with the catalytic site of cholinesterases. A structurally disordered heavy chain complementary determining region 3 loop, constituting a wall of the cleft, is stabilized after covalent modification by hydrogen bonding to the phosphonate tropinol moiety. These features and presteady state kinetics analysis indicate that an induced fit mechanism operates in this reaction. Mutations of residues located in this stabilized loop do not interfere with direct contacts to the organophosphate ligand but can interrogate second shell interactions, because the H3 loop has a conformation adjusted for binding. Kinetic and thermodynamic parameters along with computational docking support the active site model, including plasticity and simple catalytic components. Although relatively uncomplicated, this catalytic machinery displays both stereo- and chemical selectivity. The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes. PMID:21896761

A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases.

PubMed

Tuckerman, Mark E; Chandra, Amalendu; Marx, Dominik

2010-09-28

Extraction of relaxation times, lifetimes, and rates associated with the transport of topological charge defects in hydrogen-bonded networks from molecular dynamics simulations is a challenge because proton transfer reactions continually change the identity of the defect core. In this paper, we present a statistical mechanical theory that allows these quantities to be computed in an unbiased manner. The theory employs a set of suitably defined indicator or population functions for locating a defect structure and their associated correlation functions. These functions are then used to develop a chemical master equation framework from which the rates and lifetimes can be determined. Furthermore, we develop an integral equation formalism for connecting various types of population correlation functions and derive an iterative solution to the equation, which is given a graphical interpretation. The chemical master equation framework is applied to the problems of both hydronium and hydroxide transport in bulk water. For each case it is shown that the theory establishes direct links between the defect's dominant solvation structures, the kinetics of charge transfer, and the mechanism of structural diffusion. A detailed analysis is presented for aqueous hydroxide, examining both reorientational time scales and relaxation of the rotational anisotropy, which is correlated with recent experimental results for these quantities. Finally, for OH(-)(aq) it is demonstrated that the "dynamical hypercoordination mechanism" is consistent with available experimental data while other mechanistic proposals are shown to fail. As a means of going beyond the linear rate theory valid from short up to intermediate time scales, a fractional kinetic model is introduced in the Appendix in order to describe the nonexponential long-time behavior of time-correlation functions. Within the mathematical framework of fractional calculus the power law decay ∼t(-σ), where σ is a parameter of the model and depends on the dimensionality of the system, is obtained from Mittag-Leffler functions due to their long-time asymptotics, whereas (stretched) exponential behavior is found for short times.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations.

PubMed

Becerra, Rosa; Cannady, J Pat; Dormer, Guy; Walsh, Robin

2009-07-14

Time-resolved kinetic studies of the reactions of silylene, SiH(2), and dideutero-silylene, SiD(2), generated by laser flash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH(3)C[triple bond, length as m-dash]CCH(3). The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF(6) bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(1)/RTIn10log(k(D)(Infinity)/cm(3) molecule(-1) s(-1) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTIn10. Additionally, pressure-dependent rate coefficients for the reaction of SiH(2) with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC(4)H(8) reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH(2)C(CH(3))[double bond, length as m-dash]C(CH(3))-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH(3)CH[double bond, length as m-dash]C(CH(3))SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H-D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Utilization of oil palm biodiesel solid residue as renewable sources for preparation of granular activated carbon by microwave induced KOH activation.

PubMed

Foo, K Y; Hameed, B H

2013-02-01

In this work, preparation of granular activated carbon from oil palm biodiesel solid residue, oil palm shell (PSAC) by microwave assisted KOH activation has been attempted. The physical and chemical properties of PSAC were characterized using scanning electron microscopy, volumetric adsorption analyzer and elemental analysis. The adsorption behavior was examined by performing batch adsorption experiments using methylene blue as dye model compound. Equilibrium data were simulated using the Langmuir, Freundlich and Temkin isotherm models. Kinetic modeling was fitted to the pseudo-first-order, pseudo-second-order and Elovich kinetic models, while the adsorption mechanism was determined using the intraparticle diffusion and Boyd equations. The result was satisfactory fitted to the Langmuir isotherm model with a monolayer adsorption capacity of 343.94mg/g at 30°C. The findings support the potential of oil palm shell for preparation of high surface area activated carbon by microwave assisted KOH activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Preparation, non-isothermal decomposition kinetics, heat capacity and adiabatic time-to-explosion of NTOxDNAZ.

PubMed

Ma, Haixia; Yan, Biao; Li, Zhaona; Guan, Yulei; Song, Jirong; Xu, Kangzhen; Hu, Rongzu

2009-09-30

NTOxDNAZ was prepared by mixing 3,3-dinitroazetidine (DNAZ) and 3-nitro-1,2,4-triazol-5-one (NTO) in ethanol solution. The thermal behavior of the title compound was studied under a non-isothermal condition by DSC and TG/DTG methods. The kinetic parameters were obtained from analysis of the DSC and TG/DTG curves by Kissinger method, Ozawa method, the differential method and the integral method. The main exothermic decomposition reaction mechanism of NTOxDNAZ is classified as chemical reaction, and the kinetic parameters of the reaction are E(a)=149.68 kJ mol(-1) and A=10(15.81)s(-1). The specific heat capacity of the title compound was determined with continuous C(p) mode of microcalorimeter. The standard mole specific heat capacity of NTOxDNAZ was 352.56 J mol(-1)K(-1) in 298.15K. Using the relationship between C(p) and T and the thermal decomposition parameters, the time of the thermal decomposition from initialization to thermal explosion (adiabatic time-to-explosion) was obtained.

Surface kinetic roughening caused by dental erosion: An atomic force microscopy study

NASA Astrophysics Data System (ADS)

Quartarone, Eliana; Mustarelli, Piercarlo; Poggio, Claudio; Lombardini, Marco

2008-05-01

Surface kinetic roughening takes place both in case of growth and erosion processes. Teeth surfaces are eroded by contact with acid drinks, such as those used to supplement mineral salts during sporting activities. Calcium-phosphate based (CPP-ACP) pastes are known to reduce the erosion process, and to favour the enamel remineralization. In this study we used atomic force microscopy (AFM) to investigate the surface roughening during dental erosion, and the mechanisms at the basis of the protection role exerted by a commercial CPP-ACP paste. We found a statistically significant difference (p<0.01) in the roughness of surfaces exposed and not exposed to the acid solutions. The treatment with the CPP-ACP paste determined a statistically significant reduction of the roughness values. By interpreting the AFM results in terms of fractal scaling concepts and continuum stochastic equations, we showed that the protection mechanism of the paste depends on the chemical properties of the acid solution.

Reduced chemical kinetics for propane combustion

NASA Technical Reports Server (NTRS)

Ying, Shuh-Jing; Nguyen, Hung Lee

1990-01-01

It is pointed out that a detailed chemical kinetics mechanism for the combustion of propane consists of 40 chemical species and 118 elementary chemical reactions. An attempt is made to reduce the number of chemical species and elementary chemical reactions so that the computer run times and storage requirements may be greatly reduced in three-dimensional gas turbine combustion flow calculations, while maintaining accurate predictions of the propane combustion and exhaust emissions. By way of a sensitivity analysis, the species of interest and chemical reactions are classified in descending order of importance. Nineteen species are chosen, and their pressure, temperature, and concentration profiles are presented for the reduced mechanisms, which are then compared with those from the full 118 reactions. It is found that 45 reactions involving 27 species have to be kept for comparable agreement. A comparison of the results obtained from the 45 reactions to that of the full 118 shows that the pressure and temperature profiles and concentrations of C3H8, O2, N2, H2O, CO, and CO2 are within 10 percent of maximum change.

IMMUNOREACTIONS INVOLVING PLATELETS

PubMed Central

Shulman, N. Raphael

1958-01-01

A steric and kinetic model for the sequence and mechanism of reactions leading to formation of a complex from an antibody, a haptene (quinidine), and a cell membrane (platelets), and to fixation of complement by the complex was deduced from the effects of varying the initial concentration of each component of the complex on the amount of complement fixed, from kinetic aspects of the sequential reactions, and from other chemical and physical properties of the various components involved. Theoretical results calculated using equations based on the model, which were derived by Dr. Terrell L. Hill, were similar in all respects to experimental results. Results of this study were consistent with the possibilities that the protein moiety of a haptenic antigen involved in development of an antibody which attaches to a cell is not necessarily a component of the cell, and that the cell reacts with the antibody by virtue of having a surface favorable for non-specific adsorption of certain haptene-antibody complexes. PMID:13525578

Chemical sensor system

NASA Technical Reports Server (NTRS)

Darrach, Murray R. (Inventor); Chutjian, Ara (Inventor)

2008-01-01

A chemical sensing apparatus and method for the detection of sub parts-per-trillion concentrations of molecules in a sample by optimizing electron utilization in the formation of negative ions is provided. A variety of media may be sampled including air, seawater, dry sediment, or undersea sediment. An electrostatic mirror is used to reduce the kinetic energy of an electron beam to zero or near-zero kinetic energy.

Impact of Diurnal Variations of Precursors on the Prediction of Ozone

NASA Astrophysics Data System (ADS)

Hamer, P. D.; Bowman, K. W.; Henze, D. K.; Singh, K.

2009-12-01

Using a photochemical box model and its adjoint, constructed using the Kinetic Pre-Processor, we investigate the impacts of changing observational capacity, observation frequency and quality upon the ability to both understand and predict the nature of peak ozone events within a variety of polluted environments. The model consists of a chemical mechanism based on the Master Chemical Mechanism utilising 171 chemical species and 524 chemical reactions interacting with emissions, dry deposition and mixing schemes. The model was run under a variety of conditions designed to simulate a range of summertime polluted environments spanning a range of NOx and volatile organic compound regimes (VOCs). Using the forward model we were able to generate simulated atmospheric conditions representative of a particular polluted environment, which could in turn be used to generate a set of pseudo observations of key photochemical constituents. The model was then run under somewhat less polluted conditions to generate a background and then perturbed back towards the polluted trajectory using sequential data assimilation and the pseudo observations. Using a combination of the adjoint sensitivity analysis and the sequential data assimilation described here we assess the optimal time of observation and the diversity of observed chemical species required to provide acceptable forecast estimates of ozone concentrations. As the photochemical regime changes depending on NOx and VOC concentrations different observing strategies become favourable. The impact of using remote sensing based observations of the free tropospheric photochemical state are investigated to demonstrate the advantage of gaining knowledge of atmospheric trace gases away from the immediate photochemical environment.

A quantum chemical study of the mechanism for proton-coupled electron transfer leading to proton pumping in cytochrome c oxidase

NASA Astrophysics Data System (ADS)

Blomberg, Margareta R. A.; Siegbahn, Per E. M.

2010-10-01

The proton pumping mechanism in cytochrome c oxidase, the terminal enzyme in the respiratory chain, has been investigated using hybrid DFT with large chemical models. In previous studies, a gating mechanism was suggested based on electrostatic interpretations of kinetic experiments. The predictions from that analysis are tested here. The main result is that the suggestion of a positively charged transition state for proton transfer is confirmed, while some other suggestions for the gating are not supported. It is shown that a few critical relative energy values from the earlier studies are reproduced with quite high accuracy using the present model calculations. Examples are the forward barrier for proton transfer from the N-side of the membrane to the pump-loading site when the heme a cofactor is reduced, and the corresponding back leakage barrier when heme a is oxidised. An interesting new finding is an unexpected double-well potential for proton transfer from the N-side to the pump-loading site. In the intermediate between the two transition states found, the proton is bound to PropD on heme a. A possible purpose of this type of potential surface is suggested here. The accuracy of the present values are discussed in terms of their sensitivity to the choice of dielectric constant. Only one energy value, which is not critical for the present mechanism, varies significantly with this choice and is therefore less certain.

Flame ignition studies of conventional and alternative jet fuels and surrogate components

NASA Astrophysics Data System (ADS)

Liu, Ning

Practical jet fuels are widely used in air-breathing propulsion, but the chemical mechanisms that control their combustion are not yet understood. Thousands of components are contained in conventional and alternative jet fuels, making thus any effort to model their combustion behavior a daunting task. That has been the motivation behind the development of surrogate fuels that contain typically a small number of neat components, whose physical properties and combustion behavior mimic those of the real jet fuel, and whose kinetics could be modeled with increased degree of confidence. Towards that end, a large number of experimental data are required both for the real fuels and the attendant surrogate components that could be used to develop and validate detailed kinetic models. Those kinetic models could be used then upon reduction to model a combustor and eventually optimize its performance. Among all flame phenomena, ignition is rather sensitive to the oxidative and pyrolytic propensity of the fuel as well as to its diffusivity. The counterflow configuration is ideal in probing both the fuel reactivity and diffusivity aspects of the ignition process and it was used in the present work to determine the ignition temperatures of premixed and non-premixed flames of a variety of fuels relevant to air-breathing propulsion. The experiments were performed at atmospheric pressure, elevated unburned fuel mixture temperatures, and various strain rates that were measured locally. Several recent kinetic models were used in direct numerical simulations of the experiments and the computed results were tested against the experimental data. Furthermore, through sensitivity, reaction path, and structure analyses of the computed flames, insight was provided into the dominant mechanisms that control ignition. It was found that ignition is primarily sensitive to fuel diffusion and secondarily sensitive to chemical kinetics and intermediate species diffusivities under the low fuel concentrations. As for the detailed high temperature oxidation chemistry, ignition of normal, branched, and cyclic alkane flames were found to be sensitive largely to H2/CO and C1-C4 small hydrocarbon chemistry, while for branched alkanes fuel-related reactions do have accountable effect on ignition due to the low rate of initial fuel decomposition that limits the overall reactions preceding ignition. Analyses of the computed flame structures revealed that the concentrations of ignition-promoting radicals such as H, HCO, C2H3, and OH, and ignition-inhibiting radicals such as C3H6, aC3H5, and CH3 are key to the occurrence of ignition. Finally, the ignition characteristics of conventional and alternative jet fuels were studied and were to correlate with the chemical classifications and diffusivities of the neat species that are present in the practical fuel.

Low-temperature wafer direct bonding of silicon and quartz glass by a two-step wet chemical surface cleaning

NASA Astrophysics Data System (ADS)

Wang, Chenxi; Xu, Jikai; Zeng, Xiaorun; Tian, Yanhong; Wang, Chunqing; Suga, Tadatomo

2018-02-01

We demonstrate a facile bonding process for combining silicon and quartz glass wafers by a two-step wet chemical surface cleaning. After a post-annealing at 200 °C, strong bonding interfaces with no defects or microcracks were obtained. On the basis of the detailed surface and bonding interface characterizations, the bonding mechanism was explored and discussed. The amino groups terminated on the cleaned surfaces might contribute to the bonding strength enhancement during the annealing. This cost-effective bonding process has great potentials for silicon- and glass-based heterogeneous integrations without requiring a vacuum system.

Potential and kinetic energetic analysis of phonon modes in varied molecular solids

NASA Astrophysics Data System (ADS)

Kraczek, Brent

2015-03-01

We calculate partitioned kinetic and potential energies of the phonon modes in molecular solids to illuminate the dynamical behavior of the constituent molecules. This enables analysis of the relationship between the characteristics of sets of phonon modes, molecular structure and chemical reactivity by partitioning the kinetic energy into the translational, rotational and vibrational motions of groups of atoms (including molecules), and the potential energy into the energy contained within interatomic interactions. We consider three solids of differing size and rigidity: naphthalene (C1 0 H6), nitromethane (CH3NO2)andα-HMX(C4H8N8O8). Naphthalene and nitromethane mostly act in the semi-rigid manner often expected in molecular solids. HMX exhibits behavior that is significantly less-rigid. While there are definite correlations between the kinetic and potential energetic analyses, there are also differences, particularly in the excitation of chemical bonds by low-frequency lattice modes. This suggests that in many cases computational and experimental methods dependent on atomic displacements may not identify phonon modes active in chemical reactivity.

On the origin of emission and thermal quenching of SRSO:Er3+ films grown by ECR-PECVD

PubMed Central

2013-01-01

Silicon nanocrystals embedded in a silicon-rich silicon oxide matrix doped with Er3+ ions have been fabricated by electron cyclotron resonance plasma-enhanced chemical vapor deposition. Indirect excitation of erbium photoluminescence via silicon nanocrystals has been investigated. Temperature quenching of the photoluminescence originating from the silicon nanocrystals and the erbium ions has been observed. Activation energies of the thermally activated quenching process were estimated for different excitation wavelengths. The temperature quenching mechanism of the emission is discussed. Also, the origin of visible emission and kinetic properties of Er-related emission have been discussed in details. PMID:23433189

A framework for expanding aqueous chemistry in the Community Multiscale Air Quality (CMAQ) model version 5.1

NASA Astrophysics Data System (ADS)

Fahey, Kathleen M.; Carlton, Annmarie G.; Pye, Havala O. T.; Baek, Jaemeen; Hutzell, William T.; Stanier, Charles O.; Baker, Kirk R.; Wyat Appel, K.; Jaoui, Mohammed; Offenberg, John H.

2017-04-01

This paper describes the development and implementation of an extendable aqueous-phase chemistry option (AQCHEM - KMT(I)) for the Community Multiscale Air Quality (CMAQ) modeling system, version 5.1. Here, the Kinetic PreProcessor (KPP), version 2.2.3, is used to generate a Rosenbrock solver (Rodas3) to integrate the stiff system of ordinary differential equations (ODEs) that describe the mass transfer, chemical kinetics, and scavenging processes of CMAQ clouds. CMAQ's standard cloud chemistry module (AQCHEM) is structurally limited to the treatment of a simple chemical mechanism. This work advances our ability to test and implement more sophisticated aqueous chemical mechanisms in CMAQ and further investigate the impacts of microphysical parameters on cloud chemistry. Box model cloud chemistry simulations were performed to choose efficient solver and tolerance settings, evaluate the implementation of the KPP solver, and assess the direct impacts of alternative solver and kinetic mass transfer on predicted concentrations for a range of scenarios. Month-long CMAQ simulations for winter and summer periods over the US reveal the changes in model predictions due to these cloud module updates within the full chemical transport model. While monthly average CMAQ predictions are not drastically altered between AQCHEM and AQCHEM - KMT, hourly concentration differences can be significant. With added in-cloud secondary organic aerosol (SOA) formation from biogenic epoxides (AQCHEM - KMTI), normalized mean error and bias statistics are slightly improved for 2-methyltetrols and 2-methylglyceric acid at the Research Triangle Park measurement site in North Carolina during the Southern Oxidant and Aerosol Study (SOAS) period. The added in-cloud chemistry leads to a monthly average increase of 11-18 % in cloud SOA at the surface in the eastern United States for June 2013.

Competition between Primary Nucleation and Autocatalysis in Amyloid Fibril Self-Assembly

PubMed Central

Eden, Kym; Morris, Ryan; Gillam, Jay; MacPhee, Cait E.; Allen, Rosalind J.

2015-01-01

Kinetic measurements of the self-assembly of proteins into amyloid fibrils are often used to make inferences about molecular mechanisms. In particular, the lag time—the quiescent period before aggregates are detected—is often found to scale with the protein concentration as a power law, whose exponent has been used to infer the presence or absence of autocatalytic growth processes such as fibril fragmentation. Here we show that experimental data for lag time versus protein concentration can show signs of kinks: clear changes in scaling exponent, indicating changes in the dominant molecular mechanism determining the lag time. Classical models for the kinetics of fibril assembly suggest that at least two mechanisms are at play during the lag time: primary nucleation and autocatalytic growth. Using computer simulations and theoretical calculations, we investigate whether the competition between these two processes can account for the kinks which we observe in our and others’ experimental data. We derive theoretical conditions for the crossover between nucleation-dominated and growth-dominated regimes, and analyze their dependence on system volume and autocatalysis mechanism. Comparing these predictions to the data, we find that the experimentally observed kinks cannot be explained by a simple crossover between nucleation-dominated and autocatalytic growth regimes. Our results show that existing kinetic models fail to explain detailed features of lag time versus concentration curves, suggesting that new mechanistic understanding is needed. More broadly, our work demonstrates that care is needed in interpreting lag-time scaling exponents from protein assembly data. PMID:25650930

Morphology-preserving chemical conversion of bioorganic and inorganic templates

NASA Astrophysics Data System (ADS)

Vernon, Jonathan Paul

The generation of nanostructured assemblies with complex (three-dimensional, 3D) self-assembled morphologies and with complex (multicomponent) tailorable inorganic compositions is of considerable technological and scientific interest. This dissertation demonstrates self-assembled 3D organic templates of biogenic origin can be converted into replicas comprised of numerous other functional nanocrystalline inorganic materials. Nature provides a spectacular variety of biologically-assembled 3D organic structures with intricate, hierarchical (macro-to-micro-to-nanoscale) morphologies. Such processing on readily-available structurally complex templates provides a framework for chemical conversion of synthetic organic templates and, potentially, production of organic/inorganic composites. Four specific research thrusts are detailed in this document. First, chemical conversion of a nanostructured bioorganic template into a multicomponent oxide compound (tetragonal BaTiO3) via SSG coating and subsequent morphology-preserving microwave hydrothermal processing is demonstrated. Second, morphology-preserving chemical conversion of bioorganic templates into hierarchical photoluminescent microparticles is demonstrated to reveal both the dramatic change in properties such processing can provide, and the potential utility of chemically transformed templates in anti-counterfeiting / authentication applications. Third, determination of the reaction mechanism(s) for morphology-preserving microwave hydrothermal conversion of TiO2 to BaTiO3, through Au inert markers on single crystal rutile titania, is detailed. Finally, utilization of constructive coating techniques (SSG) and moderate temperature (< 500°C) heat treatments to modify and replicate structural color is coupled with deconstructive focused ion beam microsurgery to prepare samples for microscale structure interrogation. Specifically, the effects of coating thickness and composition on reflection spectra of structurally colored templates are examined. Also, the effects of the replacement of natural material with higher index of refraction inorganic materials on optical properties are discussed. The three processing research thrusts constituting chapters 1, 2 and 4 take advantage of moderate temperature processing to ensure nanocrystalline materials, either for shape preservation or to prevent scattering in optical applications. The research thrust detailed in chapter 3 examines hydrothermal conversion of TiO2 to BaTiO3, not only to identify the reaction mechanism(s) involved in hydrothermal conversion under morphology-preserving conditions, but also to introduce inert marker experiments to the field of microwave hydrothermal processing.

The accumulation mechanism of the hypoxia imaging probe "FMISO" by imaging mass spectrometry: possible involvement of low-molecular metabolites.

PubMed

Masaki, Yukiko; Shimizu, Yoichi; Yoshioka, Takeshi; Tanaka, Yukari; Nishijima, Ken-Ichi; Zhao, Songji; Higashino, Kenichi; Sakamoto, Shingo; Numata, Yoshito; Yamaguchi, Yoshitaka; Tamaki, Nagara; Kuge, Yuji

2015-11-19

(18)F-fluoromisonidazole (FMISO) has been widely used as a hypoxia imaging probe for diagnostic positron emission tomography (PET). FMISO is believed to accumulate in hypoxic cells via covalent binding with macromolecules after reduction of its nitro group. However, its detailed accumulation mechanism remains unknown. Therefore, we investigated the chemical forms of FMISO and their distributions in tumours using imaging mass spectrometry (IMS), which visualises spatial distribution of chemical compositions based on molecular masses in tissue sections. Our radiochemical analysis revealed that most of the radioactivity in tumours existed as low-molecular-weight compounds with unknown chemical formulas, unlike observations made with conventional views, suggesting that the radioactivity distribution primarily reflected that of these unknown substances. The IMS analysis indicated that FMISO and its reductive metabolites were nonspecifically distributed in the tumour in patterns not corresponding to the radioactivity distribution. Our IMS search found an unknown low-molecular-weight metabolite whose distribution pattern corresponded to that of both the radioactivity and the hypoxia marker pimonidazole. This metabolite was identified as the glutathione conjugate of amino-FMISO. We showed that the glutathione conjugate of amino-FMISO is involved in FMISO accumulation in hypoxic tumour tissues, in addition to the conventional mechanism of FMISO covalent binding to macromolecules.

Temperature-Dependent Kinetic Prediction for Reactions Described by Isothermal Mathematics

DOE PAGES

Dinh, L. N.; Sun, T. C.; McLean, W.

2016-09-12

Most kinetic models are expressed in isothermal mathematics. In addition, this may lead unaware scientists either to the misconception that classical isothermal kinetic models cannot be used for any chemical process in an environment with a time-dependent temperature profile or, even worse, to a misuse of them. In reality, classical isothermal models can be employed to make kinetic predictions for reactions in environments with time-dependent temperature profiles, provided that there is a continuity/conservation in the reaction extent at every temperature–time step. In this article, fundamental analyses, illustrations, guiding tables, and examples are given to help the interested readers using eithermore » conventional isothermal reacted fraction curves or rate equations to make proper kinetic predictions for chemical reactions in environments with temperature profiles that vary, even arbitrarily, with time simply by the requirement of continuity/conservation of reaction extent whenever there is an external temperature change.« less

Explaining global surface aerosol number concentrations in terms of primary emissions and particle formation

NASA Astrophysics Data System (ADS)

Spracklen, D. V.; Carslaw, K. S.; Merikanto, J.; Mann, G. W.; Reddington, C. L.; Pickering, S.; Ogren, J. A.; Andrews, E.; Baltensperger, U.; Weingartner, E.; Boy, M.; Kulmala, M.; Laakso, L.; Lihavainen, H.; Kivekäs, N.; Komppula, M.; Mihalopoulos, N.; Kouvarakis, G.; Jennings, S. G.; O'Dowd, C.; Birmili, W.; Wiedensohler, A.; Weller, R.; Gras, J.; Laj, P.; Sellegri, K.; Bonn, B.; Krejci, R.; Laaksonen, A.; Hamed, A.; Minikin, A.; Harrison, R. M.; Talbot, R.; Sun, J.

2010-05-01

We synthesised observations of total particle number (CN) concentration from 36 sites around the world. We found that annual mean CN concentrations are typically 300-2000 cm-3 in the marine boundary layer and free troposphere (FT) and 1000-10 000 cm-3 in the continental boundary layer (BL). Many sites exhibit pronounced seasonality with summer time concentrations a factor of 2-10 greater than wintertime concentrations. We used these CN observations to evaluate primary and secondary sources of particle number in a global aerosol microphysics model. We found that emissions of primary particles can reasonably reproduce the spatial pattern of observed CN concentration (R2=0.46) but fail to explain the observed seasonal cycle (R2=0.1). The modeled CN concentration in the FT was biased low (normalised mean bias, NMB=-88%) unless a secondary source of particles was included, for example from binary homogeneous nucleation of sulfuric acid and water (NMB=-25%). Simulated CN concentrations in the continental BL were also biased low (NMB=-74%) unless the number emission of anthropogenic primary particles was increased or a mechanism that results in particle formation in the BL was included. We ran a number of simulations where we included an empirical BL nucleation mechanism either using the activation-type mechanism (nucleation rate, J, proportional to gas-phase sulfuric acid concentration to the power one) or kinetic-type mechanism (J proportional to sulfuric acid to the power two) with a range of nucleation coefficients. We found that the seasonal CN cycle observed at continental BL sites was better simulated by BL particle formation (R2=0.3) than by increasing the number emission from primary anthropogenic sources (R2=0.18). The nucleation constants that resulted in best overall match between model and observed CN concentrations were consistent with values derived in previous studies from detailed case studies at individual sites. In our model, kinetic and activation-type nucleation parameterizations gave similar agreement with observed monthly mean CN concentrations.

A reduced mechanism for biodiesel surrogates with low temperature chemistry for compression ignition engine applications

NASA Astrophysics Data System (ADS)

Luo, Zhaoyu; Plomer, Max; Lu, Tianfeng; Som, Sibendu; Longman, Douglas E.

2012-04-01

Biodiesel is a promising alternative fuel for compression ignition (CI) engines. It is a renewable energy source that can be used in these engines without significant alteration in design. The detailed chemical kinetics of biodiesel is however highly complex. In the present study, a skeletal mechanism with 123 species and 394 reactions for a tri-component biodiesel surrogate, which consists of methyl decanoate, methyl 9-decanoate and n-heptane was developed for simulations of 3-D turbulent spray combustion under engine-like conditions. The reduction was based on an improved directed relation graph (DRG) method that is particularly suitable for mechanisms with many isomers, followed by isomer lumping and DRG-aided sensitivity analysis (DRGASA). The reduction was performed for pressures from 1 to 100 atm and equivalence ratios from 0.5 to 2 for both extinction and ignition applications. The initial temperatures for ignition were from 700 to 1800 K. The wide parameter range ensures the applicability of the skeletal mechanism under engine-like conditions. As such the skeletal mechanism is applicable for ignition at both low and high temperatures. Compared with the detailed mechanism that consists of 3299 species and 10806 reactions, the skeletal mechanism features a significant reduction in size while still retaining good accuracy and comprehensiveness. The validations of ignition delay time, flame lift-off length and important species profiles were also performed in 3-D engine simulations and compared with the experimental data from Sandia National Laboratories under CI engine conditions.

Modeling aerosol surface chemistry and gas-particle interaction kinetics with K2-SURF: PAH oxidation

NASA Astrophysics Data System (ADS)

Shiraiwa, M.; Garland, R.; Pöschl, U.

2009-04-01

Atmospheric aerosols are ubiquitous in the atmosphere. They have the ability to impact cloud properties, radiative balance and provide surfaces for heterogeneous reactions. The uptake of gaseous species on aerosol surfaces impacts both the aerosol particles and the atmospheric budget of trace gases. These subsequent changes to the aerosol can in turn impact the aerosol chemical and physical properties. However, this uptake, as well as the impact on the aerosol, is not fully understood. This uncertainty is due not only to limited measurement data, but also a dearth of comprehensive and applicable modeling formalizations used for the analysis, interpretation and description of these heterogeneous processes. Without a common model framework, comparing and extrapolating experimental data is difficult. In this study, a novel kinetic surface model (K2-SURF) [Ammann & Pöschl, 2007; Pöschl et al., 2007] was used to describe the oxidation of a variety of polycyclic aromatic hydrocarbons (PAHs). Integrated into this consistent and universally applicable kinetic and thermodynamic process model are the concepts, terminologies and mathematical formalizations essential to the description of atmospherically relevant physicochemical processes involving organic and mixed organic-inorganic aerosols. Within this process model framework, a detailed master mechanism, simplified mechanism and parameterizations of atmospheric aerosol chemistry are being developed and integrated in analogy to existing mechanisms and parameterizations of atmospheric gas-phase chemistry. One of the key aspects to this model is the defining of a clear distinction between various layers of the particle and surrounding gas phase. The processes occurring at each layer can be fully described using known fluxes and kinetic parameters. Using this system there is a clear separation of gas phase, gas-surface and surface bulk transport and reactions. The partitioning of compounds can be calculated using the flux values between the layers. By describing these layers unambiguously, the interactions of all species in the system can be appropriately modeled. In describing the oxidation of PAHs, the focus was on the interactions between the sorption layer and quasi-static surface layer. The results from a variety of published experimental studies [Pöschl et al., 2001; Kahan et al., 2006; Kwamena et al., 2004, 2006, 2007; Mmereki and Donaldson, 2003; Mmereki et al., 2004; Dubowski et al., 2004; Donaldson et al., 2005; Segal-Rosenheimer and Dubowski, 2007] were analyzed and compared utilizing K2-SURF. The heterogeneous reaction of PAH and O3 are found to follow a Langmuir-Hinshelwood mechanism, in which ozone first absorbs to the surface and then reacts with PAH. The Langmuir equilibrium constants and second-order-rate coefficients of surface reaction were estimated. In PAH/O3/solid substrate system, they showed similar reaction rate (×10), but large difference (×1000) in adsorption. The mean residence time and adsorption enthalpy were estimated for O3 at the surface of substrates, suggesting the chemisorption of O3 molecules or O atoms, respectively. Initial uptake coefficients of O3 under different conditions were also investigated. The observed dependence on gas-phase O3 concentration was well explained with K2-SURF model in five-order range. In addition, competitive adsorption of other gas phase species (NO2, H2O) was well described by the model. Possible mechanism of PAH degradation system and atmospheric implications are discussed.

The molecular mechanism of thermal noise in rod photoreceptors.

PubMed

Gozem, Samer; Schapiro, Igor; Ferré, Nicolas; Olivucci, Massimo

2012-09-07

Spontaneous electrical signals in the retina's photoreceptors impose a limit on visual sensitivity. Their origin is attributed to a thermal, rather than photochemical, activation of the transduction cascade. Although the mechanism of such a process is under debate, the observation of a relationship between the maximum absorption wavelength (λ(max)) and the thermal activation kinetic constant (k) of different visual pigments (the Barlow correlation) indicates that the thermal and photochemical activations are related. Here we show that a quantum chemical model of the bovine rod pigment provides a molecular-level understanding of the Barlow correlation. The transition state mediating thermal activation has the same electronic structure as the photoreceptor excited state, thus creating a direct link between λ(max) and k. Such a link appears to be the manifestation of intrinsic chromophore features associated with the existence of a conical intersection between its ground and excited states.

Time-Resolved Investigations of Heterobimetallic Cofactor Assembly in R2lox Reveal Distinct Mn/Fe Intermediates.

PubMed

Miller, Effie K; Trivelas, Nicholas E; Maugeri, Pearson T; Blaesi, Elizabeth J; Shafaat, Hannah S

2017-07-05

The assembly mechanism of the Mn/Fe ligand-binding oxidases (R2lox), a family of proteins that are homologous to the nonheme diiron carboxylate enzymes, has been investigated using time-resolved techniques. Multiple heterobimetallic intermediates that exhibit unique spectral features, including visible absorption bands and exceptionally broad electron paramagnetic resonance signatures, are observed through optical and magnetic resonance spectroscopies. On the basis of comparison to known diiron species and model compounds, the spectra have been attributed to (μ-peroxo)-Mn III /Fe III and high-valent Mn/Fe species. Global spectral analysis coupled with isotopic substitution and kinetic modeling reveals elementary rate constants for the assembly of Mn/Fe R2lox under aerobic conditions. A complete reaction mechanism for cofactor maturation that is consistent with experimental data has been developed. These results suggest that the Mn/Fe cofactor can perform direct C-H bond abstraction, demonstrating the potential for potent chemical reactivity that remains unexplored.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bell, L.; Castaldi, A.; Jones, C.

The ultimate goal of the project is to develop procedures, techniques, data and other information that will aid in the design of cost effective and energy efficient drying processes that produce high quality foods. This objective has been sought by performing studies to determine the pertinent properties of food products, by developing models to describe the fundamental phenomena of food drying and by testing the models at laboratory scale. Finally, this information is used to develop recommendations and strategies for improved dryer design and control. This volume emphasizes a detailed literature review and several extensive experimental studies. Since the basicmore » principle of food dehydration is the removal of water from food, the process of removing water causes quality changes which can be categorized as physical, chemical, and nutritional. These changes often have adverse effects on the quality of the resulting dehydrated food. In this work, the types of physical and chemical changes common in food drying and the important factors for them were reviewed. Pertinent kinetic models and kinetic data reported in literature were also collected and compiled as the results of review study. The overall objectives of this study were to identify major quality change in foods caused by drying process and to get the knowledge of the relationship between the quality change and factors known to affect them. The quality parameters reviewed included: browning, lipid oxidation, color loss, shrinkage, solubility, texture, aroma and flavor, vitamin and protein loss and microbiological concerns. 54 refs., 74 figs., 49 tabs.« less

Oscillations and patterns in a model of simultaneous CO and C2H2 oxidation and NO(x) reduction in a cross-flow reactor.

PubMed

Hadač, Otto; Kohout, Martin; Havlica, Jaromír; Schreiber, Igor

2015-03-07

A model describing simultaneous catalytic oxidation of CO and C2H2 and reduction of NOx in a cross-flow tubular reactor is explored with the aim of relating spatiotemporal patterns to specific pathways in the mechanism. For that purpose, a detailed mechanism proposed for three-way catalytic converters is split into two subsystems, (i) simultaneous oxidation of CO and C2H2, and (ii) oxidation of CO combined with NOx reduction. The ability of these two subsystems to display mechanism-specific dynamical effects is studied initially by neglecting transport phenomena and applying stoichiometric network and bifurcation analyses. We obtain inlet temperature - inlet oxygen concentration bifurcation diagrams, where each region possessing specific dynamics - oscillatory, bistable and excitable - is associated with a dominant reaction pathway. Next, the spatiotemporal behaviour due to reaction kinetics combined with transport processes is studied. The observed spatiotemporal patterns include phase waves, travelling fronts, pulse waves and spatiotemporal chaos. Although these types of pattern occur generally when the kinetic scheme possesses autocatalysis, we find that some of their properties depend on the underlying dominant reaction pathway. The relation of patterns to specific reaction pathways is discussed.

Thermogravimetric and model-free kinetic studies on CO2 gasification of low-quality, high-sulphur Indian coals

NASA Astrophysics Data System (ADS)

Das, Tonkeswar; Saikia, Ananya; Mahanta, Banashree; Choudhury, Rahul; Saikia, Binoy K.

2016-10-01

Coal gasification with CO2 has emerged as a cleaner and more efficient way for the production of energy, and it offers the advantages of CO2 mitigation policies through simultaneous CO2 sequestration. In the present investigation, a feasibility study on the gasification of three low-quality, high-sulphur coals from the north-eastern region (NER) of India in a CO2 atmosphere using thermogravimetric analysis (TGA-DTA) has been made in order to have a better understanding of the physical and chemical characteristics in the process of gasification of coal. Model-free kinetics was applied to determine the activation energies (E) and pre-exponential factors (A) of the CO2 gasification process of the coals. Multivariate non-linear regression analyses were performed to find out the formal mechanisms, kinetic model, and the corresponding kinetic triplets. The results revealed that coal gasification with CO2 mainly occurs in the temperature range of 800∘-1400∘C and a maximum of at around 1100∘C. The reaction mechanisms responsible for CO2 gasification of the coals were observed to be of the ` nth order with autocatalysis (CnB)' and ` nth order (Fn) mechanism'. The activation energy of the CO2 gasification was found to be in the range 129.07-146.81 kJ mol-1.

A Transient Kinetic Approach to Investigate Nucleoside Inhibitors of Mitochondrial DNA polymerase γ

PubMed Central

Anderson, Karen S.

2010-01-01

Nucleoside analogs play an essential role in treating human immunodeficiency virus (HIV) infection since the beginning of the AIDS epidemic and work by inhibition of HIV-1 reverse transcriptase (RT), a viral polymerase essential for DNA replication. Today, over 90% of all regimens for HIV treatment contain at least one nucleoside. Long-term use of nucleoside analogs has been associated with adverse effects including mitochondrial toxicity due to inhibition of the mitochondrial polymerase, DNA polymerase gamma (mtDNA pol ©). In this review, we describe our efforts to delineate the molecular mechanism of nucleoside inhibition of HIV-1 RT and mtDNA pol © based upon a transient kinetic approach using rapid chemical quench methodology. Using transient kinetic methods, the maximum rate of polymerization (kpol), the dissociation constant for the ground state binding (Kd), and the incorporation efficiency (kpol/Kd) can be determined for the nucleoside analogs and their natural substrates. This analysis allowed us to develop an understanding of the structure activity relationships that allow correlation between the structural and stereochemical features of the nucleoside analog drugs with their mechanistic behavior toward the viral polymerase, RT, and the host cell polymerase, mtDNA pol γ. An in-depth understanding of the mechanisms of inhibition of these enzymes is imperative in overcoming problems associated with toxicity. PMID:20573564

Reduced description of reactive flows with tabulation of chemistry

NASA Astrophysics Data System (ADS)

Ren, Zhuyin; Goldin, Graham M.; Hiremath, Varun; Pope, Stephen B.

2011-12-01

The direct use of large chemical mechanisms in multi-dimensional Computational Fluid Dynamics (CFD) is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. To meet this challenge, a reduced description of reactive flows in combination with chemistry tabulation is proposed to effectively reduce the computational cost. In the reduced description, the species are partitioned into represented species and unrepresented species; the reactive system is described in terms of a smaller number of represented species instead of the full set of chemical species in the mechanism; and the evolution equations are solved only for the represented species. When required, the unrepresented species are reconstructed assuming that they are in constrained chemical equilibrium. In situ adaptive tabulation (ISAT) is employed to speed the chemistry calculation through tabulating information of the reduced system. The proposed dimension-reduction / tabulation methodology determines and tabulates in situ the necessary information of the nr-dimensional reduced system based on the ns-species detailed mechanism. Compared to the full description with ISAT, the reduced descriptions achieve additional computational speed-up by solving fewer transport equations and faster ISAT retrieving. The approach is validated in both a methane/air premixed flame and a methane/air non-premixed flame. With the GRI 1.2 mechanism consisting of 31 species, the reduced descriptions (with 12 to 16 represented species) achieve a speed-up factor of up to three compared to the full description with ISAT, with a relatively moderate decrease in accuracy compared to the full description.

Adsorption of aluminum and lead from wastewater by chitosan-tannic acid modified biopolymers: Isotherms, kinetics, thermodynamics and process mechanism.

PubMed

Badawi, M A; Negm, N A; Abou Kana, M T H; Hefni, H H; Abdel Moneem, M M

2017-06-01

Chitosan was reacted by tannic acid to obtain three modified chitosan biopolymer. Their chemical structures were characterized by FTIR and elemental analysis. The prepared biopolymers were used to adsorb Al(III) and Pb(II) metal ions from industrial wastewater. The factors affecting the adsorption process were biosorbent amount, initial concentration of metal ion and pH of the medium. The adsorption efficiency increased considerably with the increase of the biosorbent amount and pH of the medium. The adsorption process of biosorbent on different metal ions was fitted by Freundlich adsorption model. The adsorption kinetics was followed Pseudo-second-order kinetic model. The adsorption process occurred according to diffusion mechanism which was confirmed by the interparticle diffusion model. The modified biopolymers were efficient biosorbents for removal of Pb(II) and Al(III) metal ions from the medium. Copyright © 2017 Elsevier B.V. All rights reserved.

Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study.

PubMed

Maia, Luisa B; Fonseca, Luis; Moura, Isabel; Moura, José J G

2016-07-20

Carbon dioxide accumulation is a major concern for the ecosystems, but its abundance and low cost make it an interesting source for the production of chemical feedstocks and fuels. However, the thermodynamic and kinetic stability of the carbon dioxide molecule makes its activation a challenging task. Studying the chemistry used by nature to functionalize carbon dioxide should be helpful for the development of new efficient (bio)catalysts for atmospheric carbon dioxide utilization. In this work, the ability of Desulfovibrio desulfuricans formate dehydrogenase (Dd FDH) to reduce carbon dioxide was kinetically and mechanistically characterized. The Dd FDH is suggested to be purified in an inactive form that has to be activated through a reduction-dependent mechanism. A kinetic model of a hysteretic enzyme is proposed to interpret and predict the progress curves of the Dd FDH-catalyzed reactions (initial lag phase and subsequent faster phase). Once activated, Dd FDH is able to efficiently catalyze, not only the formate oxidation (kcat of 543 s(-1), Km of 57.1 μM), but also the carbon dioxide reduction (kcat of 46.6 s(-1), Km of 15.7 μM), in an overall reaction that is thermodynamically and kinetically reversible. Noteworthy, both Dd FDH-catalyzed formate oxidation and carbon dioxide reduction are completely inactivated by cyanide. Current FDH reaction mechanistic proposals are discussed and a different mechanism is here suggested: formate oxidation and carbon dioxide reduction are proposed to proceed through hydride transfer and the sulfo group of the oxidized and reduced molybdenum center, Mo(6+)═S and Mo(4+)-SH, are suggested to be the direct hydride acceptor and donor, respectively.

Adsorption removal of tannic acid from aqueous solution by polyaniline: Analysis of operating parameters and mechanism.

PubMed

Sun, Chencheng; Xiong, Bowen; Pan, Yang; Cui, Hao

2017-02-01

Polyaniline (PANI) prepared by chemical oxidation was studied for adsorption removal of tannic acid (TA) from aqueous solution. Batch adsorption studies were carried out under different adsorbent dosages, pH, ionic strength, initial TA concentration and coexisting anions. Solution pH had an important impact on TA adsorption onto PANI with optimal removal in the pH range of 8-11. TA adsorption on PANI at three ionic strength levels (0.02, 0.2 and 2molL -1 NaCl) could be well described by Langmuir model (monolayer adsorption process) and the maximum adsorption capacity was 230, 223 and 1023mgg -1 , respectively. Kinetic data showed that TA adsorption on PANI fitted well with pseudo-second-order model (controlled by chemical process). Among the coexisting anions tested, PO 4 3- significantly inhibited TA adsorption due to the enhancement of repulsive interaction. Continuous flow adsorption studies indicated good flexibility and adaptability of the PANI adsorbent under different flow rates and influent TA concentrations. The mechanism controlling TA adsorption onto PANI under different operating conditions was analyzed with the combination of electrostatic interactions, hydrogen bonding, π-π interactions and Van der Waals interactions. Copyright © 2016 Elsevier Inc. All rights reserved.

Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

NASA Astrophysics Data System (ADS)

Koledina, K. F.; Gubaidullin, I. M.

2016-05-01

The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

Quantum Chemical Molecular Dynamics Simulations of 1,3-Dichloropropene Combustion.

PubMed

Ahubelem, Nwakamma; Shah, Kalpit; Moghtaderi, Behdad; Page, Alister J

2015-09-03

Oxidative decomposition of 1,3-dichloropropene was investigated using quantum chemical molecular dynamics (QM/MD) at 1500 and 3000 K. Thermal oxidation of 1,3-dichloropropene was initiated by (1) abstraction of allylic H/Cl by O2 and (2) intra-annular C-Cl bond scission and elimination of allylic Cl. A kinetic analysis shows that (2) is the more dominant initiation pathway, in agreement with QM/MD results. These QM/MD simulations reveal new routes to the formation of major products (H2O, CO, HCl, CO2), which are propagated primarily by the chloroperoxy (ClO2), OH, and 1,3-dichloropropene derived radicals. In particular, intra-annular C-C/C-H bond dissociation reactions of intermediate aldehydes/ketones are shown to play a dominant role in the formation of CO and CO2. Our simulations demonstrate that both combustion temperature and radical concentration can influence the product yield, however not the combustion mechanism.

Nuclear quantum effects and kinetic isotope effects in enzyme reactions.

PubMed

Vardi-Kilshtain, Alexandra; Nitoker, Neta; Major, Dan Thomas

2015-09-15

Enzymes are extraordinarily effective catalysts evolved to perform well-defined and highly specific chemical transformations. Studying the nature of rate enhancements and the mechanistic strategies in enzymes is very important, both from a basic scientific point of view, as well as in order to improve rational design of biomimetics. Kinetic isotope effect (KIE) is a very important tool in the study of chemical reactions and has been used extensively in the field of enzymology. Theoretically, the prediction of KIEs in condensed phase environments such as enzymes is challenging due to the need to include nuclear quantum effects (NQEs). Herein we describe recent progress in our group in the development of multi-scale simulation methods for the calculation of NQEs and accurate computation of KIEs. We also describe their application to several enzyme systems. In particular we describe the use of combined quantum mechanics/molecular mechanics (QM/MM) methods in classical and quantum simulations. The development of various novel path-integral methods is reviewed. These methods are tailor suited to enzyme systems, where only a few degrees of freedom involved in the chemistry need to be quantized. The application of the hybrid QM/MM quantum-classical simulation approach to three case studies is presented. The first case involves the proton transfer in alanine racemase. The second case presented involves orotidine 5'-monophosphate decarboxylase where multidimensional free energy simulations together with kinetic isotope effects are combined in the study of the reaction mechanism. Finally, we discuss the proton transfer in nitroalkane oxidase, where the enzyme employs tunneling as a catalytic fine-tuning tool. Copyright © 2015 Elsevier Inc. All rights reserved.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Operando MAS NMR Reaction Studies at High Temperatures and Pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walter, Eric D.; Qi, Long; Chamas, Ali

Operando MAS-NMR studies provide unique insights into the details of chemical reactions; comprehensive information about temperature- and time-dependent changes in chemical species is accompanied by similarly rich information about changes in phase and chemical environment. Here we describe a new MAS-NMR rotor (the WHiMS rotor) capable of achieving internal pressures up to 400 bar at 20 °C or 225 bar at 250 °C, a range which includes many reactions of interest. The MAS-NMR spectroscopy enabled by these rotors is ideal for studying the behavior of mixed-phase systems, such as reactions involving solid catalysts and volatile liquids, with the potential tomore » add gases at high pressure. The versatile operation of the new rotors is demonstrated by collecting operando 1H and 13C spectra during the hydrogenolysis of benzyl phenyl ether, catalyzed by Ni/-Al2O3 at ca. 250 ºC, both with and without H2 (g) supplied to the rotor. The 2-propanol solvent, which exists in the supercritical phase under these reaction conditions, serves as an internal source of H2. The NMR spectra provide detailed kinetic profiles for the formation of the primary products toluene and phenol, as well as secondary hydrogenation and etherification products.« less

Enzymatic oxidation of rutin by horseradish peroxidase: kinetic mechanism and identification of a dimeric product by LC-Orbitrap mass spectrometry.

PubMed

Savic, Sasa; Vojinovic, Katarina; Milenkovic, Sanja; Smelcerovic, Andrija; Lamshoeft, Marc; Petronijevic, Zivomir

2013-12-15

Flavonoid oxidation is important issue in food processing and quality. The kinetic mechanism of enzymatic oxidation of rutin by horseradish peroxidase (HRP) was studied. Rutin oxidation reaction was followed by recording of spectral changes over the time at 360 nm. The studied oxidation is mostly enzymatic and less part non-enzymatic. The reaction with HRP has a higher rate compared with the reaction without of HRP, whereby is part of non-enzymatic reaction about 10% of the total reaction. Kinetic parameters were determined from graphics of linear Michaelis-Menten equation, and it was found that investigated reactions of rutin oxidation by HRP take place in a ping-pong kinetic mechanism. High resolution HPLC-MS analysis of the mixture of oxidized products of rutin revealed the presence of rutin dimer. Because of widely distribution of rutin as well as presence of peroxidases and hydrogen peroxide in fresh foods identification of this enzymatic modification product can be beneficial for foods quality and safety. Copyright © 2013 Elsevier Ltd. All rights reserved.

The effect of carbon surface chemical composition on the adsorption of acetanilide.

PubMed

Terzyk, Artur P

2004-04-01

The study of acetanilide adsorption-desorption performed at three temperatures (300, 310, and 320 K) and at two pH levels (7.0 and 1.5) on the series of D43/1 carbons (initial and modified with HNO3, fuming H2SO4, and gaseous NH3) is reported. Sorption data are additionally supplemented with the results of thermal analysis and calorimetric and kinetic measurements. It is shown that, generally, acetanilide adsorption at the neutral pH level is reversible (only on the more acidic carbons and at the lowest temperature does hysteresis occur due to the formation of hydrogen bonds with surface OH groups), and it decreases for the chemically modified carbons. In contrast, at the acidic pH level acetanilide adsorption is irreversible. A mechanism of irreversibility is proposed and it is shown that hysteresis is caused by the chemical reaction between the nucleophile (carbon) and the protonized acetanilide molecules. For all studied carbons, at the acidic pH level, adsorption increases and this is caused by the weakly basic character of acetanilide molecule. Adsorption results are described applying adsorbability and Dubinin-Astakhov, quasi-Freundlich and solution analogue of the Toth adsorption isotherm equations. Using the kinetic data, the effective diffusion coefficients and the energy of diffusion are calculated. It is shown that the diffusion is mainly a surface process, and the contribution of the pore diffusion increases with the rise in temperature. By applying different correlations between the parameters obtained from the theoretical description of experimental data and those characterizing the chemical composition of the studied carbons, the role of the latter in the adsorption and kinetics of acetanilide adsorption is determined.

Global reduced mechanisms for methane and hydrogen combustion with nitric oxide formation constructed with CSP data

NASA Astrophysics Data System (ADS)

Massias, A.; Diamantis, D.; Mastorakos, E.; Goussis, D. A.

1999-06-01

Reduced mechanisms for methane-air and hydrogen-air combustion including NO formation have been constructed with the computational singular perturbation (CSP) method using the fully automated algorithm described by Massias et al. The analysis was performed on solutions of unstrained adiabatic premixed flames with detailed chemical kinetics described by GRI 2.11 for methane and a 71-reaction mechanism for hydrogen including NOx formation. A 10-step reduced mechanism for methane has been constructed which reproduces accurately laminar burning velocities, flame temperatures and mass fraction distributions of major species for the whole flammability range. Many steady-state species are also predicted satisfactorily. This mechanism is an improvement over the seven-step set of Massias et al, especially for rich flames, because the use of HCNO, HCN and C2H2 as major species results in a better calculation of prompt NO. The present 10-step mechanism may thus also be applicable to diffusion flames. A five-step mechanism for lean and hydrogen-rich combustion has also been constructed based on a detailed mechanism including thermal NO. This mechanism is accurate for a wide range of the equivalence ratio and for pressures as high as 40 bar. For both fuels, the CSP algorithm automatically pointed to the same steady-state species as those identified by laborious analysis or intuition in the literature and the global reactions were similar to well established previous methane-reduced mechanisms. This implies that the method is very well suited for the study of complex mechanisms for heavy hydrocarbon combustion.

Direct Numerical Simulation of a Cavity-Stabilized Ethylene/Air Premixed Flame

NASA Astrophysics Data System (ADS)

Chen, Jacqueline; Konduri, Aditya; Kolla, Hemanth; Rauch, Andreas; Chelliah, Harsha

2016-11-01

Cavity flame holders have been shown to be important for flame stabilization in scramjet combustors. In the present study the stabilization of a lean premixed ethylene/air flame in a rectangular cavity at thermo-chemical conditions relevant to scramjet combustors is simulated using a compressible reacting multi-block direct numerical simulation solver, S3D, incorporating a 22 species ethylene-air reduced chemical model. The fuel is premixed with air to an equivalence ratio of 0.4 and enters the computational domain at Mach numbers between 0.3 and 0.6. An auxiliary inert channel flow simulation is used to provide the turbulent velocity profile at the inlet for the reacting flow simulation. The detailed interaction between intense turbulence, nonequilibrium concentrations of radical species formed in the cavity and mixing with the premixed main stream under density variations due to heat release rate and compressibility effects is quantified. The mechanism for flame stabilization is quantified in terms of relevant non-dimensional parameters, and detailed analysis of the flame and turbulence structure will be presented. We acknowledge the sponsorship of the AFOSR-NSF Joint Effort on Turbulent Combustion Model Assumptions and the DOE Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

Kinetic recognition of the retinoblastoma tumor suppressor by a specific protein target.

PubMed

Chemes, Lucía B; Sánchez, Ignacio E; de Prat-Gay, Gonzalo

2011-09-16

The retinoblastoma tumor suppressor (Rb) plays a key role in cell cycle control and is linked to various types of human cancer. Rb binds to the LxCxE motif, present in a number of cellular and viral proteins such as AdE1A, SV40 large T-antigen and human papillomavirus (HPV) E7, all instrumental in revealing fundamental mechanisms of tumor suppression, cell cycle control and gene expression. A detailed kinetic study of RbAB binding to the HPV E7 oncoprotein shows that an LxCxE-containing E7 fragment binds through a fast two-state reaction strongly favored by electrostatic interactions. Conversely, full-length E7 binds through a multistep process involving a pre-equilibrium between E7 conformers, a fast electrostatically driven association step guided by the LxCxE motif and a slow conformational rearrangement. This kinetic complexity arises from the conformational plasticity and intrinsically disordered nature of E7 and from multiple interaction surfaces present in both proteins. Affinity differences between E7N domains from high- and low-risk types are explained by their dissociation rates. In fact, since Rb is at the center of a large protein interaction network, fast and tight recognition provides an advantage for disruption by the viral proteins, where the balance of physiological and pathological interactions is dictated by kinetic ligand competition. The localization of the LxCxE motif within an intrinsically disordered domain provides the fast, diffusion-controlled interaction that allows viral proteins to outcompete physiological targets. We describe the interaction mechanism of Rb with a protein ligand, at the same time an LxCxE-containing model target, and a paradigmatic intrinsically disordered viral oncoprotein. Copyright © 2011 Elsevier Ltd. All rights reserved.

Biochemical and kinetic analysis of the GH3 family beta-xylosidase from Aspergillus awamori X-100.

PubMed

Eneyskaya, Elena V; Ivanen, Dina R; Bobrov, Kirill S; Isaeva-Ivanova, Lyudmila S; Shabalin, Konstantin A; Savel'ev, Andrew N; Golubev, Alexander M; Kulminskaya, Anna A

2007-01-15

The beta-xylosidase from Aspergillus awamori X-100 belonging to the family 3 glycoside hydrolase revealed a distinctive transglycosylating ability to produce xylooligosaccharides with degree of polymerization more than 7. In order to explain this fact, the enzyme has been subjected to the detailed biochemical study. The enzymatic hydrolysis of p-nitrophenyl beta-D-xylopyranoside was found to occur with overall retention of substrate anomeric configuration suggesting cleavage of xylosidic bonds through a double-displacement mechanism. Kinetic study with aryl beta-xylopyranosides substrates, in which leaving group pK(a)s were in the range of 3.96-10.32, revealed monotonic function of log(k(cat)) and no correlation of log(k(cat)/Km) versus pKa values indicating deglycosylation as a rate-limiting step for the enzymatic hydrolysis. The classical bell-shaped pH dependence of k(cat)/Km indicated two ionizable groups in the beta-xylosidase active site with apparent pKa values of 2.2 and 6.4. The kinetic parameters of hydrolysis, Km and k(cat), of p-nitrophenyl beta-D-1,4-xylooligosaccharides were very close to those for hydrolysis of p-nitrophenyl-beta-D-xylopyranoside. Increase of p-nitrophenyl-beta-D-xylopyranoside concentration up to 80 mM led to increasing of the reaction velocity resulting in k(cat)(app)=81 s(-1). Addition of alpha-methyl D-xylopyranoside to the reaction mixture at high concentration of p-nitrophenyl-beta-D-xylopyranoside (50 mM) caused an acceleration of the beta-xylosidase-catalyzed reactions and appearance of a new transglycosylation product, alpha-methyl D-xylopyranosyl-1,4-beta-D-xylopyranoside, that was identified by 1H NMR spectroscopy. The kinetic model suggested for the enzymatic reaction was consistent with the results obtained.

Methane Activation by 5 d Transition Metals: Energetics, Mechanisms, and Periodic Trends.

PubMed

Armentrout, Peter B

2017-01-01

Although it has been known for almost three decades that several 5d transition-metal cations will activate methane at room temperature, a more detailed examination of these reactions across the periodic table has only recently been completed. In this Minireview, we compare and contrast studies of the kinetic energy dependence of these reactions as studied using guided-ion-beam tandem mass spectrometry. Thermochemistry for the various products observed (MH + , MH 2 + , MC + , MCH + , MCH 2 + , and MCH 3 + ) are collected and periodic trends evaluated and discussed. The mechanisms for the reactions as elucidated by synergistic quantum chemical calculations are also reviewed. Recent spectroscopic evidence for the structures of the MCH 2 + dehydrogenation products are discussed as well. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase: a unique bifunctional enzyme from Plasmodium falciparum.

PubMed

Jortzik, Esther; Mailu, Boniface M; Preuss, Janina; Fischer, Marina; Bode, Lars; Rahlfs, Stefan; Becker, Katja

2011-06-15

The survival of malaria parasites in human RBCs (red blood cells) depends on the pentose phosphate pathway, both in Plasmodium falciparum and its human host. G6PD (glucose-6-phosphate dehydrogenase) deficiency, the most common human enzyme deficiency, leads to a lack of NADPH in erythrocytes, and protects from malaria. In P. falciparum, G6PD is combined with the second enzyme of the pentose phosphate pathway to create a unique bifunctional enzyme named GluPho (glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase). In the present paper, we report for the first time the cloning, heterologous overexpression, purification and kinetic characterization of both enzymatic activities of full-length PfGluPho (P. falciparum GluPho), and demonstrate striking structural and functional differences with the human enzymes. Detailed kinetic analyses indicate that PfGluPho functions on the basis of a rapid equilibrium random Bi Bi mechanism, where the binding of the second substrate depends on the first substrate. We furthermore show that PfGluPho is inhibited by S-glutathionylation. The availability of recombinant PfGluPho and the major differences to hG6PD (human G6PD) facilitate studies on PfGluPho as an excellent drug target candidate in the search for new antimalarial drugs.

Second generation biofuels: Thermochemistry of glucose and fructose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osmont, A.; Catoire, L.; C.N.R.S. - I.N.S.I.S., I.C.A.R.E., 1C, Avenue de la Recherche Scientifique, 45071 Orleans Cedex 2

2010-06-15

The energetic conversion of biomass into syngas or biogas is a more and more important topic. In the framework of these studies, improved understanding of glucose and fructose thermal decomposition and oxidation appears crucial. For this task, thermodynamic data are needed to make possible, for instance, the building of a detailed chemical kinetic model of glucose and fructose reactivity at high temperature. A semitheoretical protocol, presented elsewhere, is used for the estimation of the thermodynamic data of glucose and fructose in the gas phase. Five isomers of glucose and five isomers of fructose are considered and the lowest-energy conformers aremore » found to be {beta}-D-glucopyranose for glucose and {beta}-D-fructopyranose for fructose. The data for all 10 isomers are provided in the CHEMKIN-NASA format. (author)« less

Solid state amorphization kinetic of alpha lactose upon mechanical milling.

PubMed

Caron, Vincent; Willart, Jean-François; Lefort, Ronan; Derollez, Patrick; Danède, Florence; Descamps, Marc

2011-11-29

It has been previously reported that α-lactose could be totally amorphized by ball milling. In this paper we report a detailed investigation of the structural and microstructural changes by which this solid state amorphization takes place. The investigations have been performed by Powder X-ray Diffraction, Solid State Nuclear Magnetic Resonance ((13)C CP-MAS) and Differential Scanning Calorimetry. The results reveal the structural complexity of the material in the course of its amorphization so that it cannot be considered as a simple mixture made of a decreasing crystalline fraction and an increasing amorphous fraction. Heating this complexity can give rise to a fully nano-crystalline material. The results also show that chemical degradations upon heating are strongly connected to the melting process. Copyright © 2011 Elsevier Ltd. All rights reserved.

Mesoscale Thermodynamically motivated Statistical Mechanics based Kinetic Model for Sintering monoliths

NASA Astrophysics Data System (ADS)

Mohan, Nisha

Modeling the evolution of microstructure during sintering is a persistent challenge in ceramics science, although needed as the microstructure impacts properties of an engineered material. Bridging the gap between microscopic and continuum models, kinetic Monte Carlo (kMC) methods provide a stochastic approach towards sintering and microstructure evolution. These kMC models work at the mesoscale, with length and time-scales between those of atomistic and continuum approaches. We develop a sintering/compacting model for the two-phase sintering of boron nitride ceramics and allotropes alike. Our formulation includes mechanisms for phase transformation between h-BN and c-BN and takes into account thermodynamics of pressure and temperature on interaction energies and mechanism rates. In addition to replicating the micro-structure evolution observed in experiments, it also captures the phase diagram of Boron Nitride materials. Results have been analyzed in terms of phase diagrams and crystal growth. It also serves with insights to guide the choice of additives and conditions for the sintering process.While detailed time and spatial resolutions are lost in any MC, the progression of stochastic events still captures plausible local energy minima and long-time temporal developments. DARPA.

A new methodology to determine kinetic parameters for one- and two-step chemical models

NASA Technical Reports Server (NTRS)

Mantel, T.; Egolfopoulos, F. N.; Bowman, C. T.

1996-01-01

In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.

Maximizing the efficiency of multienzyme process by stoichiometry optimization.

PubMed

Dvorak, Pavel; Kurumbang, Nagendra P; Bendl, Jaroslav; Brezovsky, Jan; Prokop, Zbynek; Damborsky, Jiri

2014-09-05

Multienzyme processes represent an important area of biocatalysis. Their efficiency can be enhanced by optimization of the stoichiometry of the biocatalysts. Here we present a workflow for maximizing the efficiency of a three-enzyme system catalyzing a five-step chemical conversion. Kinetic models of pathways with wild-type or engineered enzymes were built, and the enzyme stoichiometry of each pathway was optimized. Mathematical modeling and one-pot multienzyme experiments provided detailed insights into pathway dynamics, enabled the selection of a suitable engineered enzyme, and afforded high efficiency while minimizing biocatalyst loadings. Optimizing the stoichiometry in a pathway with an engineered enzyme reduced the total biocatalyst load by an impressive 56 %. Our new workflow represents a broadly applicable strategy for optimizing multienzyme processes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanism of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutase from rabbit muscle

PubMed Central

Britton, H. G.; Clarke, J. B.

1972-01-01

1. The properties and kinetics of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutases are discussed. There are at least three possible mechanisms for the reaction: (i) a phosphoenzyme (Ping Pong) mechanism; (ii) an intermolecular transfer of phosphate from 2,3-diphosphoglycerate to the substrates (sequential mechanism); (iii) an intramolecular transfer of phosphate. It is concluded that these mechanisms cannot be distinguished by conventional kinetic measurements. 2. The fluxes for the different mechanisms are calculated and it is shown that it should be possible to distinguish between the mechanisms by appropriate induced-transport tests and by comparing the fluxes of 32P- and 14C-labelled substrates at chemical equilibrium. 3. With 14C-labelled substrates no induced transport was found over a wide concentration range, and with 32P-labelled substrates co-transport occurred that was independent of concentration over a twofold range. 14C-labelled substrates exchange at twice the rate of 32P-labelled substrates at chemical equilibrium. The results were completely in accord with a phosphoenzyme mechanism and indicated a rate constant for the isomerization of the phosphoenzyme of not less than 4×106s−1. The intramolecular transfer of phosphate (and intermolecular transfer between two or more molecules of substrate) were completely excluded. The intermolecular transfer of phosphate from 2,3-diphosphoglycerate would have been compatible with the results only if the Km for 2-phosphoglycerate had been over 7.5-fold smaller than the observed value and if an isomerization of the enzyme-2,3-diphosphoglycerate complex had been the major rate-limiting step in the reaction. 4. The very rapid isomerization of the phosphoenzyme that the experiments demonstrate suggests a mechanism that does not involve a formal isomerization. According to this new scheme the enzyme is closely related mechanistically and perhaps evolutionarily to a 2,3-diphosphoglycerate diphosphatase. PMID:4677138

MISTRA mechanism development: A new mechanism focused on marine environments

NASA Astrophysics Data System (ADS)

Bräuer, Peter; Sommariva, Roberto; von Glasow, Roland

2015-04-01

The tropospheric multiphase chemistry of halogen compounds plays a key role in marine environments. Moreover, halogen compounds have an impact on the tropospheric oxidation capacity and climate. With more than two thirds of the Earth's surface covered with oceans, effects are of global importance. Various conditions are found in marine environments ranging from pristine regions to polluted regimes in the continental outflow. Furthermore, there are important sources for halogen compounds over land, such as volcanoes, salt lakes, or emissions from industrial processes. To assess the impact of halogen chemistry with numerical models under these distinct conditions, a multiphase mechanism has been developed in the last decades and applied successfully in numerous box and 1D model studies. Contributions from these model studies helped to identify important chemical cycles affecting the composition and chemistry of the troposphere. However, several discrepancies between model results and field measurements remain. Therefore, a major revision of the chemical mechanism has been performed including an update of the kinetic data and the addition of new reaction cycles. The extended mechansims have been evaluated in several model studies with the 1D model MISTRA. Current work focuses at the identification of the most important reaction cycles, which led to significant changes in the concentration-time profiles of several halogen species. Subsequently, the mechanism will be reduced to the most imporatant reactions, which are currently investigated. As regional and global model studies become more important to identify the importance of tropospheric halogen multiphase chemistry, the goal is to derive parameterisations for the most important halogen chemistry cycles, which can than be implemented in regional and global 3D models. In the reduction process, the extented MISTRA version will serve as a benchmark to assess the quality and accuracy of the reduced mechansim versions.

Purified reconstituted lac carrier protein from Escherichia coli is fully functional.

PubMed

Viitanen, P; Garcia, M L; Kaback, H R

1984-03-01

Proteoliposomes reconstituted with lac carrier protein purified from the plasma membrane of Escherichia coli catalyze each of the translocation reactions typical of the beta-galactoside transport system (i.e., active transport, counterflow, facilitated influx and efflux) with turnover numbers and apparent Km values comparable to those observed in right-side-out membrane vesicles. Furthermore, detailed kinetic studies show that the reconstituted system exhibits properties analogous to those observed in membrane vesicles. Imposition of a membrane potential (delta psi, interior negative) causes a marked decrease in apparent Km (by a factor of 7 to 10) with a smaller increase in Vmax (approximately equal to 3-fold). At submaximal values of delta psi, the reconstituted carrier exhibits biphasic kinetics, with one component manifesting the kinetic parameters of active transport and the other exhibiting the characteristics of facilitated diffusion. Finally, at low lactose concentrations, the initial velocity of influx varies linearly with the square of the proton electro-chemical gradient. The results provide quantitative support for the contention that a single polypeptide species, the product of the lac y gene, is responsible for each of the transport reactions typical of the beta-galactoside transport system.

Influence of Solar-Geomagnetic Disturbances on SABER Measurements of 4.3 Micrometer Emission and the Retrieval of Kinetic Temperature and Carbon Dioxide

NASA Technical Reports Server (NTRS)

Mertens, Christopher J.; Winick, Jeremy R.; Picard, Richard H.; Evans, David S.; Lopez-Puertas, Manuel; Wintersteiner, Peter P.; Xu, Xiaojing; Mlynczak, Martin G.; Russell, James M., III

2008-01-01

Thermospheric infrared radiance at 4.3 micrometers is susceptible to the influence of solar-geomagnetic disturbances. Ionization processes followed by ion-neutral chemical reactions lead to vibrationally excited NO(+) (i.e., NO(+)(v)) and subsequent 4.3 micrometer emission in the ionospheric E-region. Large enhancements of nighttime 4.3 m emission were observed by the TIMED/SABER instrument during the April 2002 and October-November 2003 solar storms. Global measurements of infrared 4.3 micrometer emission provide an excellent proxy to observe the nighttime E-region response to auroral dosing and to conduct a detailed study of E-region ion-neutral chemistry and energy transfer mechanisms. Furthermore, we find that photoionization processes followed by ion-neutral reactions during quiescent, daytime conditions increase the NO(+) concentration enough to introduce biases in the TIMED/SABER operational processing of kinetic temperature and CO2 data, with the largest effect at summer solstice. In this paper, we discuss solar storm enhancements of 4.3 micrometer emission observed from SABER and assess the impact of NO(+)(v) 4.3 micrometer emission on quiescent, daytime retrievals of Tk/CO2 from the SABER instrument.

Electron acceleration and kinetic energy tailoring via ultrafast terahertz fields.

PubMed

Greig, S R; Elezzabi, A Y

2014-11-17

We propose a mechanism for tuning the kinetic energy of surface plasmon generated electron pulses through control of the time delay between a pair of externally applied terahertz pulses. Varying the time delay results in translation, compression, and broadening of the kinetic energy spectrum of the generated electron pulse. We also observe that the electrons' kinetic energy dependence on the carrier envelope phase of the surface plasmon is preserved under the influence of a terahertz electric field.

Morphological evolution and characterization of GaN pyramid arrays fabricated by photo-assisted chemical etching

NASA Astrophysics Data System (ADS)

Zhang, Shiying; Xiu, Xiangqian; Xu, Qingjun; Li, Yuewen; Hua, Xuemei; Chen, Peng; Xie, Zili; Liu, Bin; Zhou, Yugang; Han, Ping; Zhang, Rong; Zheng, Youdou

2016-12-01

GaN pyramid arrays have been successfully synthesized by selective photo-assisted chemical etching in a K2S2O8/KOH solution. A detailed analysis of time evolution of surface morphology has been conducted, which describes an etching process of GaN pyramids. Room temperature cathodoluminescence images indicate that these pyramids are composed of crystalline GaN surrounding dislocations, which is caused by the greater recombination rate of electrons and holes at dislocation than that of crystalline GaN. The Raman results show a stress relaxation in GaN pyramids compared with unetched GaN. The optical property of both unetched GaN and GaN pyramids has been studied by photoluminescence. The formation mechanism and feature of GaN pyramids are also rationally explained.

Energy harvesting concepts for small electric unmanned systems

NASA Astrophysics Data System (ADS)

Qidwai, Muhammad A.; Thomas, James P.; Kellogg, James C.; Baucom, Jared N.

2004-07-01

In this study, we identify and survey energy harvesting technologies for small electrically powered unmanned systems designed for long-term (>1 day) time-on-station missions. An environmental energy harvesting scheme will provide long-term, energy additions to the on-board energy source. We have identified four technologies that cover a broad array of available energy sources: solar, kinetic (wind) flow, autophagous structure-power (both combustible and metal air-battery systems) and electromagnetic (EM) energy scavenging. We present existing conceptual designs, critical system components, performance, constraints and state-of-readiness for each technology. We have concluded that the solar and autophagous technologies are relatively matured for small-scale applications and are capable of moderate power output levels (>1 W). We have identified key components and possible multifunctionalities in each technology. The kinetic flow and EM energy scavenging technologies will require more in-depth study before they can be considered for implementation. We have also realized that all of the harvesting systems require design and integration of various electrical, mechanical and chemical components, which will require modeling and optimization using hybrid mechatronics-circuit simulation tools. This study provides a starting point for detailed investigation into the proposed technologies for unmanned system applications under current development.

Universal bound on the efficiency of molecular motors

NASA Astrophysics Data System (ADS)

Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

2016-12-01

The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a molecular motor running against an external force or torque, we show that the thermodynamic efficiency of such motors is universally bounded by an expression involving only experimentally accessible quantities. For motors pulling cargo through a viscous fluid, a universal bound for the corresponding Stokes efficiency follows as a variant. A similar result holds if mechanical force is used to synthesize molecules of high chemical potential. Crucially, no knowledge of the detailed underlying mechano-chemical mechanism is required for applying these bounds.

Structural and kinetic studies of metal hydride hydrogen storage materials using thin film deposition and characterization techniques

NASA Astrophysics Data System (ADS)

Kelly, Stephen Thomas

Hydrogen makes an attractive energy carrier for many reasons. It is an abundant chemical fuel that can be produced from a wide variety of sources and stored for very long periods of time. When used in a fuel cell, hydrogen emits only water at the point of use, making it very attractive for mobile applications such as in an automobile. Metal hydrides are promising candidates for on-board reversible hydrogen storage in mobile applications due to their very high volumetric storage capacities---in most cases exceeding even that of liquid hydrogen. The United States Department of Energy (DOE) has set fuel system targets for an automotive hydrogen storage system, but as of yet no single material meets all the requirements. In particular, slow reaction kinetics and/or inappropriate thermodynamics plague many metal hydride hydrogen storage materials. In order to engineer a practical material that meets the DOE targets, we need a detailed understanding of the kinetic and thermodynamic properties of these materials during the phase change. In this work I employed sputter deposited thin films as a platform to study materials with highly controlled chemistry, microstructure and catalyst placement using thin film characterization techniques such as in situ x-ray diffraction (XRD) and neutron reflectivity. I observed kinetic limitations in the destabilized Mg2Si system due to the slow diffusion of the host Mg and Si atoms while forming separate MgH2 and Si phases. Conversely, I observed that the presence of Al in the Mg/Al system inhibits hydrogen diffusion while the host Mg and Al atoms interdiffuse readily, allowing the material to fall into a kinetic and/or thermodynamic trap by forming intermetallic compounds such as Mg17Al 12. By using in situ XRD to analyze epitaxial Mg films grown on (001) oriented Al2O3 substrates I observed hydride growth consistent with a model of a planar hydride layer growing into an existing metal layer. Subsequent film cycling changes the hydrogen absorption and desorption kinetics and degrades the material texture. Cycling the films to greater hydrogen loading accelerates the changes to the kinetics and material texture. In addition to in situ XRD experiments, in situ neutron reflectivity experiments on epitaxial Mg films exposed to hydrogen gas reveal details about the microstructural development of the growing hydride layer as the film absorbs and releases hydrogen. Small (10 wt%) additions of Ti to epitaxial Mg films during growth result in metastable solid solution films of Ti in Mg that deposit epitaxially on (001) Al2O3 substrates with epitaxy similar to the pure Mg films. These metastable alloy films absorb hydrogen faster than pure Mg films under identical conditions. Subsequent film cycling results in altered reaction kinetics and a transition to a different kinetic mechanism during desorption than for pure Mg films.

A Detailed Derivation of Gaussian Orbital-Based Matrix Elements in Electron Structure Calculations

ERIC Educational Resources Information Center

Petersson, T.; Hellsing, B.

2010-01-01

A detailed derivation of analytic solutions is presented for overlap, kinetic, nuclear attraction and electron repulsion integrals involving Cartesian Gaussian-type orbitals. It is demonstrated how s-type orbitals can be used to evaluate integrals with higher angular momentum via the properties of Hermite polynomials and differentiation with…

Mechanism of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutase from rabbit muscle.

PubMed

Britton, H G; Clarke, J B

1972-11-01

1. The properties and kinetics of the 2,3-diphosphoglycerate-dependent phosphoglycerate mutases are discussed. There are at least three possible mechanisms for the reaction: (i) a phosphoenzyme (Ping Pong) mechanism; (ii) an intermolecular transfer of phosphate from 2,3-diphosphoglycerate to the substrates (sequential mechanism); (iii) an intramolecular transfer of phosphate. It is concluded that these mechanisms cannot be distinguished by conventional kinetic measurements. 2. The fluxes for the different mechanisms are calculated and it is shown that it should be possible to distinguish between the mechanisms by appropriate induced-transport tests and by comparing the fluxes of (32)P- and (14)C-labelled substrates at chemical equilibrium. 3. With (14)C-labelled substrates no induced transport was found over a wide concentration range, and with (32)P-labelled substrates co-transport occurred that was independent of concentration over a twofold range. (14)C-labelled substrates exchange at twice the rate of (32)P-labelled substrates at chemical equilibrium. The results were completely in accord with a phosphoenzyme mechanism and indicated a rate constant for the isomerization of the phosphoenzyme of not less than 4x10(6)s(-1). The intramolecular transfer of phosphate (and intermolecular transfer between two or more molecules of substrate) were completely excluded. The intermolecular transfer of phosphate from 2,3-diphosphoglycerate would have been compatible with the results only if the K(m) for 2-phosphoglycerate had been over 7.5-fold smaller than the observed value and if an isomerization of the enzyme-2,3-diphosphoglycerate complex had been the major rate-limiting step in the reaction. 4. The very rapid isomerization of the phosphoenzyme that the experiments demonstrate suggests a mechanism that does not involve a formal isomerization. According to this new scheme the enzyme is closely related mechanistically and perhaps evolutionarily to a 2,3-diphosphoglycerate diphosphatase.

A Reduced-order NLTE Kinetic Model for Radiating Plasmas of Outer Envelopes of Stellar Atmospheres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munafò, Alessandro; Mansour, Nagi N.; Panesi, Marco, E-mail: munafo@illinois.edu, E-mail: nagi.n.mansour@nasa.gov, E-mail: m.panesi@illinois.edu

The present work proposes a self-consistent reduced-order NLTE kinetic model for radiating plasmas found in the outer layers of stellar atmospheres. A detailed collisional-radiative kinetic mechanism is constructed by leveraging the most up-to-date set of ab initio and experimental data available in the literature. This constitutes the starting point for the derivation of a reduced-order model, obtained by lumping the bound energy states into groups. In order to determine the needed thermo-physical group properties, uniform and Maxwell–Boltzmann energy distributions are used to reconstruct the energy population of each group. Finally, the reduced set of governing equations for the material gasmore » and the radiation field is obtained based on the moment method. Applications consider the steady flow across a shock wave in partially ionized hydrogen. The results clearly demonstrate that adopting a Maxwell–Boltzmann grouping allows, on the one hand, for a substantial reduction of the number of unknowns and, on the other, to maintain accuracy for both gas and radiation quantities. Also, it is observed that, when neglecting line radiation, the use of two groups already leads to a very accurate resolution of the photo-ionization precursor, internal relaxation, and radiative cooling regions. The inclusion of line radiation requires adopting just one additional group to account for optically thin losses in the α , β , and γ lines of the Balmer and Paschen series. This trend has been observed for a wide range of shock wave velocities.« less

How Do Nutritional Antioxidants Really Work: Nucleophilic Tone and Para-Hormesis Versus Free Radical Scavenging in vivo

PubMed Central

Forman, Henry Jay; Davies, Kelvin J. A.; Ursini, Fulvio

2013-01-01

We present arguments for an evolution in our understanding of how antioxidants in fruits and vegetables exert their health-protective effects. There is much epidemiological evidence for disease prevention by dietary antioxidants and chemical evidence that such compounds react in one-electron reactions with free radicals in vitro. Nonetheless, kinetic constraints indicate that in vivo scavenging of radicals is ineffective in antioxidant defense. Instead, enzymatic removal of non-radical electrophiles, such as hydroperoxides, in two-electron redox reactions is the major antioxidant mechanism. Furthermore, we propose that a major mechanism of action for nutritional antioxidants is the paradoxical oxidative activation of the Nrf2 (NF-E2-related factor 2) signaling pathway, which maintains protective oxidoreductases and their nucleophilic substrates. This maintenance of ‘Nucleophilic Tone,’ by a mechanism that can be called ‘Para-Hormesis,’ provides a means for regulating physiological non-toxic concentrations of the non-radical oxidant electrophiles that boost antioxidant enzymes, and damage removal and repair systems (for proteins, lipids, and DNA), at the optimal levels consistent with good health. PMID:23747930

Modeling of uncertainties in biochemical reactions.

PubMed

Mišković, Ljubiša; Hatzimanikatis, Vassily

2011-02-01

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual reactions. However, kinetic data acquired from experimental observations bring along uncertainties due to various experimental conditions and measurement methods. In this contribution, we propose a novel way to model the uncertainty in the enzyme kinetics and to predict quantitatively the responses of metabolic reactions to the changes in enzyme activities under uncertainty. The proposed methodology accounts explicitly for mechanistic properties of enzymes and physico-chemical and thermodynamic constraints, and is based on formalism from systems theory and metabolic control analysis. We achieve this by observing that kinetic responses of metabolic reactions depend: (i) on the distribution of the enzymes among their free form and all reactive states; (ii) on the equilibrium displacements of the overall reaction and that of the individual enzymatic steps; and (iii) on the net fluxes through the enzyme. Relying on this observation, we develop a novel, efficient Monte Carlo sampling procedure to generate all states within a metabolic reaction that satisfy imposed constrains. Thus, we derive the statistics of the expected responses of the metabolic reactions to changes in enzyme levels and activities, in the levels of metabolites, and in the values of the kinetic parameters. We present aspects of the proposed framework through an example of the fundamental three-step reversible enzymatic reaction mechanism. We demonstrate that the equilibrium displacements of the individual enzymatic steps have an important influence on kinetic responses of the enzyme. Furthermore, we derive the conditions that must be satisfied by a reversible three-step enzymatic reaction operating far away from the equilibrium in order to respond to changes in metabolite levels according to the irreversible Michelis-Menten kinetics. The efficient sampling procedure allows easy, scalable, implementation of this methodology to modeling of large-scale biochemical networks. © 2010 Wiley Periodicals, Inc.

On the equilibrium between proton kappa distribution and compressible kinetic Alfvenic fluctuations

NASA Astrophysics Data System (ADS)

Yoon, P. H.

2017-12-01

Protons with a quasi inverse power law energetic population featuring the property f v-α, with α close to 5, are pervasively observed in the heliosphere. While many theoretical attempts have been made in order to describe such a feature, the so-called pump acceleration mechanism put forth by Fisk & Gloeckler is one of the most prominent theories. Their mechanism involves the low-frequency compressional fluctuations accelerating the protons. This presentation aims to reformulate the problem from the perspective of the steady state solution of the self-consistent plasma kinetic theory involving compressible kinetic Alfvenic fluctuations. By considering the steady state proton particle kinetic equation and quasi-linear wave kinetic for the kinetic Alfvenic turbulence we seek to obtain concomitant solutions for both proton velocity distribution function and the spectral intensity for kinetic Alfvenic fluctuation. It is found that the kappa distribution for the protons is a legitimate, if not unique, solution. The steady state spectrum of kinetic Alfvenic fluctuation is also obtained. The present investigation demonstrates that the kappa distribution for the protons featuring energetic tail population characterized by f v-2κ-2, where κ is the parameter for kappa distribution, may represent the background population of the protons in the heliosphere. However, it is speculated that in order to uniquely determine the value of κ, which must be close to 1.5 for asymptotic behavior of f v-5, one must have an additional constraint that involves the balance of nonlinear mode coupling terms in the wave kinetic equation.

From minerals to hillslopes: Towards an integrated framework for interpreting chemical and physical erosion

NASA Astrophysics Data System (ADS)

Hahm, W.; Riebe, C. S.; Ferrier, K.; Kirchner, J. W.

2011-12-01

Traditional frameworks for conceptualizing hillslope denudation distinguish between the movement of mass in solution (chemical erosion) and mass moved via mechanical processes (physical erosion). At the hillslope scale, physical and chemical erosion rates can be quantified by combining measurements of regolith chemistry with cosmogenic nuclide concentrations in bedrock and sediment, while basin-scale rates are often inferred from riverine solute and sediment loads. These techniques integrate the effects of numerous weathering and erosion mechanisms and do not provide prima facie information about the precise nature and scale of those mechanisms. For insight into erosional process, physical erosion has been considered in terms of two limiting regimes. When physical erosion outpaces weathering front advance, regolith is mobilized downslope as soon as it is sufficiently loosened by weathering, and physical erosion rates are limited by rates of mobile regolith production. This is commonly termed weathering-limited erosion. Conversely, when weathering front advance outpaces erosion, the mobile regolith layer grows thicker over time, and physical erosion rates are limited by the efficiency of downslope transport processes. This is termed transport-limited erosion. This terminology brings the description of hillslope evolution closer to the realm of essential realism, to the extent that measurable quantities from the field can be cast in a process-based framework. An analogous process-limitation framework describes chemical erosion. In supply-limited chemical erosion, chemical weathering depletes regolith of its reactive phases during residence on a hillslope, and chemical erosion rates are limited by the supply of fresh minerals to the weathering zone. Alternatively, hillslopes may exhibit kinetic-limited chemical erosion, where physical erosion transports regolith downslope before weatherable phases are completely removed by chemical erosion. We show how supply- and kinetic-limited chemical erosion can be distinguished from one another using data from a global compilation of physical and chemical erosion rates. As a step towards understanding these rates at the level of essential realism, we explore how the hillslope-scale regimes of supply- and kinetic-limited chemical erosion relate to existing conceptual frameworks that interpret weathering rates in terms of transport- and kinetic-limitation at the mineral scale.

What can we learn from relaxation measurements of a laser-perturbed atmosphere? A modeling study

NASA Technical Reports Server (NTRS)

Clericetti, Agostino; Vandenbergh, Hubert; Rossi, Michel J.

1994-01-01

The chemical kinetic aspects of a transient increase in OH and HO2 by several orders of magnitude are explored in three model tropospheres. This chemical kinetic modeling effort was undertaken to support the operation of a pump-and-probe LIDAR instrument. A powerful excimer laser pulse perturbs the troposphere after which its relaxation back to steady state is examined by remote sensing, for example by DIAL or LIF. Instead of probing ambient levels of key free radicals, a study of the relaxation kinetics in real time enables chemical mechanistic studies in situ.

Chemical kinetics on extrasolar planets.

PubMed

Moses, Julianne I

2014-04-28

Chemical kinetics plays an important role in controlling the atmospheric composition of all planetary atmospheres, including those of extrasolar planets. For the hottest exoplanets, the composition can closely follow thermochemical-equilibrium predictions, at least in the visible and infrared photosphere at dayside (eclipse) conditions. However, for atmospheric temperatures approximately <2000K, and in the uppermost atmosphere at any temperature, chemical kinetics matters. The two key mechanisms by which kinetic processes drive an exoplanet atmosphere out of equilibrium are photochemistry and transport-induced quenching. I review these disequilibrium processes in detail, discuss observational consequences and examine some of the current evidence for kinetic processes on extrasolar planets.

Computational Analyses of Complex Flows with Chemical Reactions

NASA Astrophysics Data System (ADS)

Bae, Kang-Sik

The heat and mass transfer phenomena in micro-scale for the mass transfer phenomena on drug in cylindrical matrix system, the simulation of oxygen/drug diffusion in a three dimensional capillary network, and a reduced chemical kinetic modeling of gas turbine combustion for Jet propellant-10 have been studied numerically. For the numerical analysis of the mass transfer phenomena on drug in cylindrical matrix system, the governing equations are derived from the cylindrical matrix systems, Krogh cylinder model, which modeling system is comprised of a capillary to a surrounding cylinder tissue along with the arterial distance to veins. ADI (Alternative Direction Implicit) scheme and Thomas algorithm are applied to solve the nonlinear partial differential equations (PDEs). This study shows that the important factors which have an effect on the drug penetration depth to the tissue are the mass diffusivity and the consumption of relevant species during the time allowed for diffusion to the brain tissue. Also, a computational fluid dynamics (CFD) model has been developed to simulate the blood flow and oxygen/drug diffusion in a three dimensional capillary network, which are satisfied in the physiological range of a typical capillary. A three dimensional geometry has been constructed to replicate the one studied by Secomb et al. (2000), and the computational framework features a non-Newtonian viscosity model for blood, the oxygen transport model including in oxygen-hemoglobin dissociation and wall flux due to tissue absorption, as well as an ability to study the diffusion of drugs and other materials in the capillary streams. Finally, a chemical kinetic mechanism of JP-10 has been compiled and validated for a wide range of combustion regimes, covering pressures of 1atm to 40atm with temperature ranges of 1,200 K--1,700 K, which is being studied as a possible Jet propellant for the Pulse Detonation Engine (PDE) and other high-speed flight applications such as hypersonic missiles. The comprehensive skeletal mechanism consists of 58 species and 315 reactions including in CPD, Benzene formation process by the theory for polycyclic aromatic hydrocarbons (PAH) and soot formation process on the constant volume combustor, premixed flame characteristics.

Examinations of the Chemical Step in Enzyme Catalysis.

PubMed

Singh, P; Islam, Z; Kohen, A

2016-01-01

Advances in computational and experimental methods in enzymology have aided comprehension of enzyme-catalyzed chemical reactions. The main difficulty in comparing computational findings to rate measurements is that the first examines a single energy barrier, while the second frequently reflects a combination of many microscopic barriers. We present here intrinsic kinetic isotope effects and their temperature dependence as a useful experimental probe of a single chemical step in a complex kinetic cascade. Computational predictions are tested by this method for two model enzymes: dihydrofolate reductase and thymidylate synthase. The description highlights the significance of collaboration between experimentalists and theoreticians to develop a better understanding of enzyme-catalyzed chemical conversions. © 2016 Elsevier Inc. All rights reserved.

A hybrid computer program for rapidly solving flowing or static chemical kinetic problems involving many chemical species

NASA Technical Reports Server (NTRS)

Mclain, A. G.; Rao, C. S. R.

1976-01-01

A hybrid chemical kinetic computer program was assembled which provides a rapid solution to problems involving flowing or static, chemically reacting, gas mixtures. The computer program uses existing subroutines for problem setup, initialization, and preliminary calculations and incorporates a stiff ordinary differential equation solution technique. A number of check cases were recomputed with the hybrid program and the results were almost identical to those previously obtained. The computational time saving was demonstrated with a propane-oxygen-argon shock tube combustion problem involving 31 chemical species and 64 reactions. Information is presented to enable potential users to prepare an input data deck for the calculation of a problem.

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.

Recently, Zr-based metal organic frameworks (MOFs) were shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. Here, we report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. Our experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE PAGES

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.; ...

2016-12-30

Recently, Zr-based metal organic frameworks (MOFs) were shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. Here, we report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. Our experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

In Situ Probes of Capture and Decomposition of Chemical Warfare Agent Simulants by Zr-Based Metal Organic Frameworks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plonka, Anna M.; Wang, Qi; Gordon, Wesley O.

Zr-based metal organic frameworks (MOFs) have been recently shown to be among the fastest catalysts of nerve-agent hydrolysis in solution. We report a detailed study of the adsorption and decomposition of a nerve-agent simulant, dimethyl methylphosphonate (DMMP), on UiO-66, UiO-67, MOF-808, and NU-1000 using synchrotron-based X-ray powder diffraction, X-ray absorption, and infrared spectroscopy, which reveals key aspects of the reaction mechanism. The diffraction measurements indicate that all four MOFs adsorb DMMP (introduced at atmospheric pressures through a flow of helium or air) within the pore space. In addition, the combination of X-ray absorption and infrared spectra suggests direct coordination ofmore » DMMP to the Zr6 cores of all MOFs, which ultimately leads to decomposition to phosphonate products. These experimental probes into the mechanism of adsorption and decomposition of chemical warfare agent simulants on Zr-based MOFs open new opportunities in rational design of new and superior decontamination materials.« less

Theoretical modeling of PEB procedure on EUV resist using FDM formulation

NASA Astrophysics Data System (ADS)

Kim, Muyoung; Moon, Junghwan; Choi, Joonmyung; Lee, Byunghoon; Jeong, Changyoung; Kim, Heebom; Cho, Maenghyo

2018-03-01

Semiconductor manufacturing industry has reduced the size of wafer for enhanced productivity and performance, and Extreme Ultraviolet (EUV) light source is considered as a promising solution for downsizing. A series of EUV lithography procedures contain complex photo-chemical reaction on photoresist, and it causes technical difficulties on constructing theoretical framework which facilitates rigorous investigation of underlying mechanism. Thus, we formulated finite difference method (FDM) model of post exposure bake (PEB) process on positive chemically amplified resist (CAR), and it involved acid diffusion coupled-deprotection reaction. The model is based on Fick's second law and first-order chemical reaction rate law for diffusion and deprotection, respectively. Two kinetic parameters, diffusion coefficient of acid and rate constant of deprotection, which were obtained by experiment and atomic scale simulation were applied to the model. As a result, we obtained time evolutional protecting ratio of each functional group in resist monomer which can be used to predict resulting polymer morphology after overall chemical reactions. This achievement will be the cornerstone of multiscale modeling which provides fundamental understanding on important factors for EUV performance and rational design of the next-generation photoresist.

Fast microwave-assisted green synthesis of xanthan gum grafted acrylic acid for enhanced methylene blue dye removal from aqueous solution.

PubMed

Makhado, Edwin; Pandey, Sadanand; Nomngongo, Philiswa N; Ramontja, James

2017-11-15

In the present project, graft polymerization was employed to synthesis a novel adsorbent using acrylic acid (AA) and xanthan gum (XG) for cationic methylene dye (MB + ) removal from aqueous solution. The XG was rapidly grafted with acrylic acid (CH 2 =CHCOOH) under microwave heating. Fourier-transform infrared spectroscopy (FTIR), Proton Nuclear magnetic resonance spectroscopy ( 1 H NMR), scanning electron microscopy (SEM), X-ray diffraction (XRD) and Thermal gravimetric analysis (TGA) techniques were used to verify the adsorbent formed under optimized reaction conditions. Optimum reaction conditions [AA (0.4M), APS (0.05M), XG (2gL -1 ), MW power (100%), MW time (80s)] offer maximum %G and %GE of 484 and 78.3, respectively. The removal ratio of adsorbent to MB + reached to 92.8% at 100mgL -1 . Equilibrium and kinetic adsorptions of dyes were better explained by the Langmuir isotherm and pseudo second-order kinetic model respectively. The results demonstrate xanthan gum grafted polyacrylic acid (mw XG-g-PAA) absorbent had the universality for removal of dyes through the chemical adsorption mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rates and mechanism of fluoride and water exchange in UO(2)F(5)(3-) and [UO(2)F(4)(H(2)O)](2-) studied by NMR spectroscopy and wave function based methods.

PubMed

Vallet, Valérie; Wahlgren, Ulf; Szabó, Zoltán; Grenthe, Ingmar

2002-10-21

The reaction mechanism for the exchange of fluoride in UO(2)F(5)(3-) and UO(2)F(4)(H(2)O)(2-) has been investigated experimentally using (19)F NMR spectroscopy at -5 degrees C, by studying the line broadening of the free fluoride, UO(2)F(4)(2-)(aq) and UO(2)F(5)(3-), and theoretically using quantum chemical methods to calculate the activation energy for different pathways. The new experimental data allowed us to make a more detailed study of chemical equilibria and exchange mechanisms than in previous studies. From the integrals of the different individual peaks in the new NMR spectra, we obtained the stepwise stability constant K(5) = 0.60 +/- 0.05 M(-1) for UO(2)F(5)(3-). The theoretical results indicate that the fluoride exchange pathway of lowest activation energy, 71 kJ/mol, in UO(2)F(5)(3-) is water assisted. The pure dissociative pathway has an activation energy of 75 kJ/mol, while the associative mechanism can be excluded as there is no stable UO(2)F(6)(4-) intermediate. The quantum chemical calculations have been made at the SCF/MP2 levels, using a conductor-like polarizable continuum model (CPCM) to describe the solvent. The effects of different model assumptions on the activation energy have been studied. The activation energy is not strongly dependent on the cavity size or on interactions between the complex and Na(+) counterions. However, the solvation of the complex and the leaving fluoride results in substantial changes in the activation energy. The mechanism for water exchange in UO(2)F(4)(H(2)O)(2-) has also been studied. We could eliminate the associative mechanism, the dissociative mechanism had the lowest activation energy, 39 kJ/mol, while the interchange mechanism has an activation energy that is approximately 50 kJ/mol higher.

Development of a reduced tri-propylene glycol monomethyl ether– n -hexadecane–poly-aromatic hydrocarbon mechanism and its application for soot prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Seunghyun; Ra, Youngchul; Reitz, Rolf D.

A reduced chemical kinetic mechanism for Tri-Propylene Glycol Monomethyl Ether (TPGME) has been developed and applied to computational fluid dynamics (CFD) calculations for predicting combustion and soot formation processes. The reduced TPGME mechanism was combined with a reduced n-hexadecane mechanism and a Poly-Aromatic Hydrocarbon (PAH) mechanism to investigate the effect of fuel oxygenation on combustion and soot emissions. The final version of the TPGME-n-hexadecane-PAH mechanism consists of 144 species and 730 reactions and was validated with experiments in shock tubes as well as in a constant volume spray combustion vessel (CVCV) from the Engine Combustion Network (ECN). The effects ofmore » ambient temperature, varying oxygen content in the tested fuels on ignition delay, spray liftoff length and soot formation under diesel-like conditions were analyzed and addressed using multidimensional reacting flow simulations and the reduced mechanism. Here, the results show that the present reduced mechanism gives reliable predictions of the combustion characteristics and soot formation processes. In the CVCV simulations, two important trends were identified. First, increasing the initial temperature in the CVCV shortens the ignition delay and lift-off length, reduces the fuel-air mixing, thereby increasing the soot levels. Secondly, fuel oxygenation introduces more oxygen into the central region of a fuel jet and reduces residence times of fuel rich area in active soot forming regions, thereby reducing soot levels.« less

A Multicomponent Blend as a Diesel Fuel Surrogate for Compression Ignition Engine Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pei, Yuanjiang; Mehl, Marco; Liu, Wei

A mixture of n-dodecane and m-xylene is investigated as a diesel fuel surrogate for compression ignition engine applications. Compared to neat n-dodecane, this binary mixture is more representative of diesel fuel because it contains an alkyl-benzene which represents an important chemical class present in diesel fuels. A detailed multi-component mechanism for n-dodecane and m-xylene was developed by combining a previously developed n-dodecane mechanism with a recently developed mechanism for xylenes. The xylene mechanism is shown to reproduce experimental ignition data from a rapid compression machine and shock tube, speciation data from the jet stirred reactor and flame speed data. Thismore » combined mechanism was validated by comparing predictions from the model with experimental data for ignition in shock tubes and for reactivity in a flow reactor. The combined mechanism, consisting of 2885 species and 11754 reactions, was reduced to a skeletal mechanism consisting 163 species and 887 reactions for 3D diesel engine simulations. The mechanism reduction was performed using directed relation graph (DRG) with expert knowledge (DRG-X) and DRG-aided sensitivity analysis (DRGASA) at a fixed fuel composition of 77% of n-dodecane and 23% m-xylene by volume. The sample space for the reduction covered pressure of 1 – 80 bar, equivalence ratio of 0.5 – 2.0, and initial temperature of 700 – 1600 K for ignition. The skeletal mechanism was compared with the detailed mechanism for ignition and flow reactor predictions. Finally, the skeletal mechanism was validated against a spray flame dataset under diesel engine conditions documented on the Engine Combustion Network (ECN) website. These multi-dimensional simulations were performed using a Representative Interactive Flame (RIF) turbulent combustion model. Encouraging results were obtained compared to the experiments with regards to the predictions of ignition delay and lift-off length at different ambient temperatures.« less

What Is Chemical Stoichiometry?

ERIC Educational Resources Information Center

Smith, William R.; Missen, Ronald W.

1979-01-01

Chemical stoichiometry is discussed free from kinetic or thermodynamic considerations. The means for determining the following are presented: the number of stoichiometric degrees of freedom, the number of components, a permissible set of chemical equations, and a permissible set of components, for a closed system undergoing chemical reaction.…