Science.gov

Sample records for activity kinetic analysis

  1. Kinetic analysis of a general model of activation of aspartic proteinase zymogens involving a reversible inhibitor. I. Kinetic analysis.

    PubMed

    Muñoz-López, A; Sotos-Lomas, A; Arribas, E; Masia-Perez, J; Garcia-Molina, F; García-Moreno, M; Varon, R

    2007-04-01

    Starting from a simple general reaction mechanism of activation of aspartic proteinases zymogens involving a uni- and a bimolecular simultaneous activation route and a reversible inhibition step, the time course equation of the zymogen, inhibitor and activated enzyme concentrations have been derived. Likewise, expressions for the time required for any reaction progress and the corresponding mean activation rates as well as the half-life of the global zymogen activation have been derived. An experimental design and kinetic data analysis is suggested to estimate the kinetic parameters involved in the reaction mechanism proposed.

  2. [Kinetic analysis of additive effect on desulfurization activity].

    PubMed

    Han, Kui-hua; Zhao, Jian-li; Lu, Chun-mei; Wang, Yong-zheng; Zhao, Gai-ju; Cheng, Shi-qing

    2006-02-01

    The additive effects of A12O3, Fe2O3 and MnCO3 on CaO sulfation kinetics were investigated by thermogravimetic analysis method and modified grain model. The activation energy (Ea) and the pre-exponential factor (k0) of surface reaction, the activation energy (Ep) and the pre-exponential factor (D0) of product layer diffusion reaction were calculated according to the model. Additions of MnCO3 can enhance the initial reaction rate, product layer diffusion and the final CaO conversion of sorbents, the effect mechanism of which is similar to that of Fe2O3. The method based isokinetic temperature Ts and activation energy can not estimate the contribution of additive to the sulfation reactivity, the rate constant of the surface reaction (k), and the effective diffusivity of reactant in the product layer (Ds) under certain experimental conditions can reflect the effect of additives on the activation. Unstoichiometric metal oxide may catalyze the surface reaction and promote the diffusivity of reactant in the product layer by the crystal defect and distinct diffusion of cation and anion. According to the mechanism and effect of additive on the sulfation, the effective temperature and the stoichiometric relation of reaction, it is possible to improve the utilization of sorbent by compounding more additives to the calcium-based sorbent.

  3. Kinetic analysis of a general model of activation of aspartic proteinase zymogens.

    PubMed

    Varón, R; García-Moreno, M; Valera-Ruipérez, D; García-Molina, F; García-Cánovas, F; Ladrón-de Guevara, R G; Masiá-Pérez, J; Havsteen, B H

    2006-10-07

    Starting from a simple general reaction mechanism of activation of aspartic proteinase zymogens involving an uni- and a bimolecular simultaneous route, the time course equation of the concentration of the zymogen and of the activated enzyme have been derived. From these equations, an analysis quantifying the relative contribution to the global process of the two routes has been carried out for the first time. This analysis suggests a way to predict the time course of the relative contribution as well as the effect of the initial zymogen and activating enzyme concentrations, on the relative weight. An experimental design and kinetic data analysis is suggested to estimate the kinetic parameters involved in the reaction mechanism proposed. Finally, we apply some of our results to experimental data obtained by other authors in experimental studies of the activation of some aspartic proteinase zymogens.

  4. Branched pore kinetic model analysis of geosmin adsorption on super-powdered activated carbon.

    PubMed

    Matsui, Yoshihiko; Ando, Naoya; Sasaki, Hiroshi; Matsushita, Taku; Ohno, Koichi

    2009-07-01

    Super-powdered activated carbon (S-PAC) is activated carbon of much finer particle size than powdered activated carbon (PAC). Geosmin is a naturally occurring taste and odor compound that impairs aesthetic quality in drinking water. Experiments on geosmin adsorption on S-PAC and PAC were conducted, and the results using adsorption kinetic models were analyzed. PAC pulverization, which produced the S-PAC, did not change geosmin adsorption capacity, and geosmin adsorption capacities did not differ between S-PAC and PAC. Geosmin adsorption kinetics, however, were much higher on S-PAC than on PAC. A solution to the branched pore kinetic model (BPKM) was developed, and experimental adsorption kinetic data were analyzed by BPKM and by a homogeneous surface diffusion model (HSDM). The HSDM describing the adsorption behavior of geosmin required different surface diffusivity values for S-PAC and PAC, which indicated a decrease in surface diffusivity apparently associated with activated carbon particle size. The BPKM, consisting of macropore diffusion followed by mass transfer from macropore to micropore, successfully described the batch adsorption kinetics on S-PAC and PAC with the same set of model parameter values, including surface diffusivity. The BPKM simulation clearly showed geosmin removal was improved as activated carbon particle size decreased. The simulation also implied that the rate-determining step in overall mass transfer shifted from intraparticle radial diffusion in macropores to local mass transfer from macropore to micropore. Sensitivity analysis showed that adsorptive removal of geosmin improved with decrease in activated carbon particle size down to 1microm, but further particle size reduction produced little improvement.

  5. Neutron activation analysis via nuclear decay kinetics using gamma-ray spectroscopy at SFU

    NASA Astrophysics Data System (ADS)

    Domingo, Thomas; Chester, Aaron; Starosta, Krzysztof; Williams, Jonathan

    2016-09-01

    Gamma-ray spectroscopy is a powerful tool used in a variety of fields including nuclear and analytical chemistry, environmental science, and health risk management. At SFU, the Germanium detector for Elemental Analysis and Radiation Studies (GEARS), a low-background shielded high-purity germanium gamma-ray detector, has been used recently in all of the above fields. The current project aims to expand upon the number of applications for which GEARS can be used while enhancing its current functionality. A recent addition to the SFU Nuclear Science laboratory is the Thermo Scientific P 385 neutron generator. This device provides a nominal yield of 3 ×108 neutrons/s providing the capacity for neutron activation analysis, opening a major avenue of research at SFU which was previously unavailable. The isotopes created via neutron activation have a wide range of half-lives. To measure and study isotopes with half-lives above a second, a new analogue data acquisition system has been installed on GEARS allowing accurate measurements of decay kinetics. This new functionality enables identification and quantification of the products of neutron activation. Results from the neutron activation analysis of pure metals will be presented.

  6. Simultaneous Kinetic Analysis of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Activities 1

    PubMed Central

    Kent, Samuel S.; Young, Joseph D.

    1980-01-01

    An assay was developed for simultaneous kinetic analysis of the activities of the bifunctional plant enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase [EC 4.1.1.39]. [1-14C,5-3H]Ribulose 1,5-bisphosphate (RuBP) was used as the labeled substrate. Tritium enrichment of the doubly labeled 3-phosphoglycerate (3-PGA) product, common to both enzyme activities, may be used to calculate Vc/Vo ratios from the expression A/(B-A) where A and B represent the 3H/14C isotope ratios of doubly labeled RuBP and 3-PGA, and Vc and Vo represent the activities of carboxylase and oxygenase, respectively. Doubly labeled substrate was synthesized from [2-14C]glucose and [6-3H]glucose using the enzymes of the pentose phosphate pathway coupled with phosphoribulokinase. The kinetic properties of a commercial preparation of fully activated spinach carboxylase were studied under approximated physiological conditions of 20% O2 (252 micromolar), 295 μl/l CO2 (10 micromolar), 25 C, and pH 8.19. The Vc/Vo ratio was, within experimental error, constant at 30 seconds and 1 minute. This double label assay method may be used to calculate Vc/Vo ratios for the Laing-Ogren-Hageman equation, Vc/Vo = (VcKo/VoKc) ([CO2]/[O2]) where Vc and Vo represent Vmax, and Kc and Ko represent Michaelis constants for the carboxylase and oxygenase activities, respectively. PMID:16661214

  7. In vivo control of soluble guanylate cyclase activation by nitric oxide: a kinetic analysis.

    PubMed Central

    Condorelli, P; George, S C

    2001-01-01

    Free nitric oxide (NO) activates soluble guanylate cyclase (sGC), an enzyme, within both pulmonary and vascular smooth muscle. sGC catalyzes the cyclization of guanosine 5'-triphosphate to guanosine 3',5'-cyclic monophosphate (cGMP). Binding rates of NO to the ferrous heme(s) of sGC have been measured in vitro. However, a missing link in our understanding of the control mechanism of sGC by NO is a comprehensive in vivo kinetic analysis. Available literature data suggests that NO dissociation from the heme center of sGC is accelerated by its interaction with one or more cofactors in vivo. We present a working model for sGC activation and NO consumption in vivo. Our model predicts that NO influences the cGMP formation rate over a concentration range of approximately 5-100 nM (apparent Michaelis constant approximately 23 nM), with Hill coefficients between 1.1 and 1.5. The apparent reaction order for NO consumption by sGC is dependent on NO concentration, and varies between 0 and 1.5. Finally, the activation of sGC (half-life approximately 1-2 s) is much more rapid than deactivation (approximately 50 s). We conclude that control of sGC in vivo is most likely ultra-sensitive, and that activation in vivo occurs at lower NO concentrations than previously reported. PMID:11325714

  8. Kinetic parameters from thermogravimetric analysis

    NASA Technical Reports Server (NTRS)

    Kiefer, Richard L.

    1993-01-01

    High performance polymeric materials are finding increased use in aerospace applications. Proposed high speed aircraft will require materials to withstand high temperatures in an oxidative atmosphere for long periods of time. It is essential that accurate estimates be made of the performance of these materials at the given conditions of temperature and time. Temperatures of 350 F (177 C) and times of 60,000 to 100,000 hours are anticipated. In order to survey a large number of high performance polymeric materials on a reasonable time scale, some form of accelerated testing must be performed. A knowledge of the rate of a process can be used to predict the lifetime of that process. Thermogravimetric analysis (TGA) has frequently been used to determine kinetic information for degradation reactions in polymeric materials. Flynn and Wall studied a number of methods for using TGA experiments to determine kinetic information in polymer reactions. Kinetic parameters, such as the apparent activation energy and the frequency factor, can be determined in such experiments. Recently, researchers at the McDonnell Douglas Research Laboratory suggested that a graph of the logarithm of the frequency factor against the apparent activation energy can be used to predict long-term thermo-oxidative stability for polymeric materials. Such a graph has been called a kinetic map. In this study, thermogravimetric analyses were performed in air to study the thermo-oxidative degradation of several high performance polymers and to plot their kinetic parameters on a kinetic map.

  9. Integrated Analysis of Contractile Kinetics, Force Generation, and Electrical Activity in Single Human Stem Cell-Derived Cardiomyocytes.

    PubMed

    Kijlstra, Jan David; Hu, Dongjian; Mittal, Nikhil; Kausel, Eduardo; van der Meer, Peter; Garakani, Arman; Domian, Ibrahim J

    2015-12-08

    The quantitative analysis of cardiomyocyte function is essential for stem cell-based approaches for the in vitro study of human cardiac physiology and pathophysiology. We present a method to comprehensively assess the function of single human pluripotent stem cell-derived cardiomyocyte (hPSC-CMs) through simultaneous quantitative analysis of contraction kinetics, force generation, and electrical activity. We demonstrate that statistical analysis of movies of contracting hPSC-CMs can be used to quantify changes in cellular morphology over time and compute contractile kinetics. Using a biomechanical model that incorporates substrate stiffness, we calculate cardiomyocyte force generation at single-cell resolution and validate this approach with conventional traction force microscopy. The addition of fluorescent calcium indicators or membrane potential dyes allows the simultaneous analysis of contractility and calcium handling or action potential morphology. Accordingly, our approach has the potential for broad application in the study of cardiac disease, drug discovery, and cardiotoxicity screening.

  10. Integrated Analysis of Contractile Kinetics, Force Generation, and Electrical Activity in Single Human Stem Cell-Derived Cardiomyocytes

    PubMed Central

    Kijlstra, Jan David; Hu, Dongjian; Mittal, Nikhil; Kausel, Eduardo; van der Meer, Peter; Garakani, Arman; Domian, Ibrahim J.

    2015-01-01

    Summary The quantitative analysis of cardiomyocyte function is essential for stem cell-based approaches for the in vitro study of human cardiac physiology and pathophysiology. We present a method to comprehensively assess the function of single human pluripotent stem cell-derived cardiomyocyte (hPSC-CMs) through simultaneous quantitative analysis of contraction kinetics, force generation, and electrical activity. We demonstrate that statistical analysis of movies of contracting hPSC-CMs can be used to quantify changes in cellular morphology over time and compute contractile kinetics. Using a biomechanical model that incorporates substrate stiffness, we calculate cardiomyocyte force generation at single-cell resolution and validate this approach with conventional traction force microscopy. The addition of fluorescent calcium indicators or membrane potential dyes allows the simultaneous analysis of contractility and calcium handling or action potential morphology. Accordingly, our approach has the potential for broad application in the study of cardiac disease, drug discovery, and cardiotoxicity screening. PMID:26626178

  11. Aerobic composting of waste activated sludge: Kinetic analysis for microbiological reaction and oxygen consumption

    SciTech Connect

    Yamada, Y.; Kawase, Y. . E-mail: bckawase@mail.eng.toyo.ac.jp

    2006-07-01

    In order to examine the optimal design and operating parameters, kinetics for microbiological reaction and oxygen consumption in composting of waste activated sludge were quantitatively examined. A series of experiments was conducted to discuss the optimal operating parameters for aerobic composting of waste activated sludge obtained from Kawagoe City Wastewater Treatment Plant (Saitama, Japan) using 4 and 20 L laboratory scale bioreactors. Aeration rate, compositions of compost mixture and height of compost pile were investigated as main design and operating parameters. The optimal aerobic composting of waste activated sludge was found at the aeration rate of 2.0 L/min/kg (initial composting mixture dry weight). A compost pile up to 0.5 m could be operated effectively. A simple model for composting of waste activated sludge in a composting reactor was developed by assuming that a solid phase of compost mixture is well mixed and the kinetics for microbiological reaction is represented by a Monod-type equation. The model predictions could fit the experimental data for decomposition of waste activated sludge with an average deviation of 2.14%. Oxygen consumption during composting was also examined using a simplified model in which the oxygen consumption was represented by a Monod-type equation and the axial distribution of oxygen concentration in the composting pile was described by a plug-flow model. The predictions could satisfactorily simulate the experiment results for the average maximum oxygen consumption rate during aerobic composting with an average deviation of 7.4%.

  12. The effect of salinity on waste activated sludge alkaline fermentation and kinetic analysis.

    PubMed

    Jin, Baodan; Wang, Shuying; Xing, Liqun; Li, Baikun; Peng, Yongzhen

    2016-05-01

    The effect of salinity on sludge alkaline fermentation at low temperature (20°C) was investigated, and a kinetic analysis was performed. Different doses of sodium chloride (NaCl, 0-25g/L) were added into the fermentation system. The batch-mode results showed that the soluble chemical oxygen demand (SCOD) increased with salinity. The hydrolysate (soluble protein, polysaccharide) and the acidification products (short chain fatty acids (SCFAs), NH4(+)-N, and PO4(3-)-P) increased with salinity initially, but slightly declined respectively at higher level salinity (20g/L or 20-25g/L). However, the hydrolytic acidification performance increased in the presence of salt compared to that without salt. Furthermore, the results of Haldane inhibition kinetics analysis showed that the salt enhanced the hydrolysis rate of particulate organic matter from sludge particulate and the specific utilization of hydrolysate, and decreased the specific utilization of SCFAs. Pearson correlation coefficient analysis indicated that the importance of polysaccharide on the accumulation of SCFAs was reduced with salt addition, but the importance of protein and NH4(+)-N on SCFA accumulation was increased.

  13. Analysis of Crystallization Kinetics

    NASA Technical Reports Server (NTRS)

    Kelton, Kenneth F.

    1997-01-01

    A realistic computer model for polymorphic crystallization (i.e., initial and final phases with identical compositions), which includes time-dependent nucleation and cluster-size-dependent growth rates, is developed and tested by fits to experimental data. Model calculations are used to assess the validity of two of the more common approaches for the analysis of crystallization data. The effects of particle size on transformation kinetics, important for the crystallization of many systems of limited dimension including thin films, fine powders, and nanoparticles, are examined.

  14. Kinetic analysis of a general model of activation of aspartic proteinase zymogens involving a reversible inhibitor. II. Contribution of the uni- and bimolecular activation routes.

    PubMed

    Muñoz-López, A; Sotos-Lomas, A; Arribas, E; Escribano, J; Masia-Perez, J; Muñoz-Muñoz, J L; Varon, R

    2007-04-01

    From the kinetic study carried out in part I of this series (preceding article) an analysis quantifying the relative contribution to the global process of the uni- and bimolecular routes has been carried out. This analysis suggests a way to predict the time course of the relative contribution as well as the effect on this relative weight of the initial zymogen, inhibitor and activating enzyme concentrations.

  15. Thermogravimetric and Kinetic Analysis of Melon (Citrullus colocynthis L.) Seed Husk Using the Distributed Activation Energy Model

    NASA Astrophysics Data System (ADS)

    Nyakuma, Bemgba Bevan

    2015-12-01

    This study seeks to characterize the thermochemical fuel properties of melon seed husk (MSH) as a potential biomass feedstock for clean energy and power generation. It examined the ultimate analysis, proximate analysis, FTIR spectroscopy and thermal decomposition of MSH. Thermogravimetric (TG) analysis was examined at 5, 10, 20 °C/min from 30-800 °C under nitrogen atmosphere. Subsequently, the Distributed Activation Energy Model (DAEM) was applied to determine the activation energy, E, and frequency factor, A. The results revealed that thermal decomposition of MSH occurs in three (3) stages; drying (30-150 °C), devolatization (150-400 °C) and char degradation (400-800 °C). Kinetic analysis revealed that the E values fluctuated from 145.44-300 kJ/mol (Average E = 193 kJ/mol) while A ranged from 2.64 × 1010 to 9.18 × 1020 min-1 (Average E = 9.18 × 1019 min-1) highlighting the complexity of MSH pyrolysis. The fuel characterization and kinetics of MSH showed it is an environmentally friendly solid biofuel for future thermal biomass conversion.

  16. Inhibition of α-amylase activity by cellulose: Kinetic analysis and nutritional implications.

    PubMed

    Dhital, Sushil; Gidley, Michael J; Warren, Frederick J

    2015-06-05

    We report on inhibition of α-amylase activity by cellulose based on in vitro experiments. The presence of cellulose in the hydrolysing medium reduced the initial velocity of starch hydrolysis in a concentration dependent manner. α-Amylase adsorption to cellulose was reversible, attaining equilibrium within 30min of incubation, and showed a higher affinity at 37°C compared to 20 and 0°C. The adsorption was almost unchanged in the presence of maltose (2.5-20mM) but was hindered in the presence of excess protein, suggesting non-specific adsorption of α-amylase to cellulose. Kinetic analyses of α-amylase hydrolysis of maize starch in the presence of cellulose showed that the inhibition is of a mixed type. The dissociation constant (Kic) of the EI complex was found to be ca. 3mg/mL. The observed inhibition of α-amylase activity suggests that cellulose in the diet can potentially attenuate starch hydrolysis.

  17. Kinetic analysis of microbe opsonification based on stimulated polymorphonuclear leukocyte oxygenation activity.

    PubMed

    Allen, R C; Lieberman, M M

    1984-08-01

    With Pseudomonas aeruginosa as the target microbes and polymorphonuclear leukocytes (PMNL) as effector phagocytes, the microbe-specific, immunoglobulin G (IgG)-dependent opsonic capacities of preimmune and immune sera were measured as the rate of stimulated PMNL dioxygenation of luminol yielding chemiluminescence (CL). When the reactants other than opsonin are present in concentrations that are not rate limiting, the information-effector relationship linking specific opsonin concentration to effector PMNL stimulation is described by the rate equation: L' = k'[IgG]i, where L' is the peak CL velocity (photons per minute), k' is the proportionality constant, [IgG] is the concentration of specific opsonin, and the exponent i is the order of the reaction with respect to opsonin. Since the specific opsonins were polyclonal IgG of unknown absolute serum concentration, the reciprocal rate expression, L' = k'D-i, was employed for data presentation; D is the serum dilution (final volume/initial serum volume), and the sign of i is changed to negative. The relationships of integral, first-derivative, and second-derivative expressions of the CL response to opsonin concentration are illustrated with experimentally obtained data. Based on peak CL velocity or peak CL acceleration measurements taken over different time intervals of testing, the estimated order with respect to opsonin is highest, and probably most accurate, using the shortest test interval allowing reasonably good precision of measurement. As an alternative temporal approach, microbe opsonification kinetics are analyzed based on nodal time (Tn) measurements. The Tn is the time point separating the acceleration and deceleration phases of the PMNL oxygenation response to stimulation and as such satisfies the criterion of a selected condition of PMNL activation.

  18. Kinetic analysis of acid orange 7 degradation by pulsed discharge plasma combined with activated carbon and the synergistic mechanism exploration.

    PubMed

    Guo, He; Wang, Huijuan; Wu, Qiangshun; Zhou, Guangshun; Yi, Chengwu

    2016-09-01

    The synergistic technique of pulsed discharge plasma (PDP) and activated carbon (AC) was built to investigate the kinetics of acid orange 7 (AO7) degradation under different conditions of AC addition, electrode gap, initial pH value of solution, gas variety and gas flow rate. Emission spectra of OH and O, UV-vis absorption spectra of the AO7 solution and TOC removal were measured to illustrate the synergistic mechanism of the PDP and the AC. The obtained results indicated that the kinetic constant of AO7 degradation increased from 0.00947 min(-1) to 0.01419 min(-1) when 4 g AC was added into the PDP system; AO7 degradation was higher in the case of alkaline solution when oxygen was used as the flow gas in the PDP/AC system, 2 L/min oxygen flow was more favorable for the degradation. Results of the relative emission intensities of OH and O indicated the catalytic effect of the AC on the active species formation as well as the important role of the two radicals for the AO7 degradation. There was no new peaks appeared by the UV-vis analysis of the AO7 solution after 60 min treatment. The highest TOC removal in the PDP/AC system was 30.3%, which was achieved under the condition of 4 L/min air flow rate and 3 initial pH value.

  19. Kinetic activation-relaxation technique.

    PubMed

    Béland, Laurent Karim; Brommer, Peter; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-10-01

    We present a detailed description of the kinetic activation-relaxation technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si (crystalline silicon), self-interstitial diffusion in Fe, and structural relaxation in a-Si (amorphous silicon).

  20. Kinetic activation-relaxation technique

    NASA Astrophysics Data System (ADS)

    Béland, Laurent Karim; Brommer, Peter; El-Mellouhi, Fedwa; Joly, Jean-François; Mousseau, Normand

    2011-10-01

    We present a detailed description of the kinetic activation-relaxation technique (k-ART), an off-lattice, self-learning kinetic Monte Carlo (KMC) algorithm with on-the-fly event search. Combining a topological classification for local environments and event generation with ART nouveau, an efficient unbiased sampling method for finding transition states, k-ART can be applied to complex materials with atoms in off-lattice positions or with elastic deformations that cannot be handled with standard KMC approaches. In addition to presenting the various elements of the algorithm, we demonstrate the general character of k-ART by applying the algorithm to three challenging systems: self-defect annihilation in c-Si (crystalline silicon), self-interstitial diffusion in Fe, and structural relaxation in a-Si (amorphous silicon).

  1. Effect of anaerobic digestion on sequential pyrolysis kinetics of organic solid wastes using thermogravimetric analysis and distributed activation energy model.

    PubMed

    Li, Xiaowei; Mei, Qingqing; Dai, Xiaohu; Ding, Guoji

    2017-03-01

    Thermogravimetric analysis, Gaussian-fit-peak model (GFPM), and distributed activation energy model (DAEM) were firstly used to explore the effect of anaerobic digestion on sequential pyrolysis kinetic of four organic solid wastes (OSW). Results showed that the OSW weight loss mainly occurred in the second pyrolysis stage relating to organic matter decomposition. Compared with raw substrate, the weight loss of corresponding digestate was lower in the range of 180-550°C, but was higher in 550-900°C. GFPM analysis revealed that organic components volatized at peak temperatures of 188-263, 373-401 and 420-462°C had a faster degradation rate than those at 274-327°C during anaerobic digestion. DAEM analysis showed that anaerobic digestion had discrepant effects on activation energy for four OSW pyrolysis, possibly because of their different organic composition. It requires further investigation for the special organic matter, i.e., protein-like and carbohydrate-like groups, to confirm the assumption.

  2. An Inducible Reconstitution System for the Real-Time Kinetic Analysis of Protease Activity and Inhibition Inside the Membrane.

    PubMed

    Baker, R P; Urban, S

    2017-01-01

    Intramembrane proteases are an ancient and diverse group of multispanning membrane proteins that cleave transmembrane substrates inside the membrane to effect a wide range of biological processes. As proteases, a clear understanding of their function requires kinetic dissection of their catalytic mechanism, but this is difficult to achieve for membrane proteins. Kinetic measurements in detergent systems are complicated by micelle fusion/exchange, which introduces an additional kinetic step and imposes system-specific behaviors (e.g., cooperativity). Conversely, kinetic analysis in proteoliposomes is hindered by premature substrate cleavage during coreconstitution, and lack of methods to quantify proteolysis in membranes in real time. In this chapter, we describe a method for the real-time kinetic analysis of intramembrane proteolysis in model liposomes. Our assay is inducible, because the enzyme is held inactive by low pH during reconstitution, and fluorogenic, since fluorescence emission from the substrate is quenched near lipids but restored upon proteolytic release from the membrane. The precise measurement of initial reaction velocities continuously in real time facilitates accurate steady-state kinetic analysis of intramembrane proteolysis and its inhibition inside the membrane environment. Using real data we describe a step-by-step strategy to implement this assay for essentially any intramembrane protease.

  3. Kinetic and product distribution analysis of NO* reductase activity in Nitrosomonas europaea hydroxylamine oxidoreductase.

    PubMed

    Kostera, Joshua; Youngblut, Matthew D; Slosarczyk, Jeffrey M; Pacheco, A Andrew

    2008-09-01

    Hydroxylamine oxidoreductase (HAO) from the ammonia-oxidizing bacterium Nitrosomonas europaea normally catalyzes the four-electron oxidation of hydroxylamine to nitrite, which is the second step in ammonia-dependent respiration. Here we show that, in the presence of methyl viologen monocation radical (MV(red)), HAO can catalyze the reduction of nitric oxide to ammonia. The process is analogous to that catalyzed by cytochrome c nitrite reductase, an enzyme found in some bacteria that use nitrite as a terminal electron acceptor during anaerobic respiration. The availability of a reduction pathway to ammonia is an important factor to consider when designing in vitro studies of HAO, and may also have some physiological relevance. The reduction of nitric oxide to ammonia proceeds in two kinetically distinct steps: nitric oxide is first reduced to hydroxylamine, and then hydroxylamine is reduced to ammonia at a tenfold slower rate. The second step was investigated independently in solutions initially containing hydroxylamine, MV(red), and HAO. Both steps show first-order dependence on nitric oxide and HAO concentrations, and zero-order dependence on MV(red) concentration. The rate constants governing each reduction step were found to have values of (4.7 +/- 0.3) x 10(5) and (2.06 +/- 0.04) x 10(4) M(-1) s(-1), respectively. A second reduction pathway, with second-order dependence on nitric oxide, may become available as the concentration of nitric oxide is increased. Such a pathway might lead to production of nitrous oxide. We estimate a maximum value of (1.5 +/- 0.05) x 10(10) M(-2) s(-1) for the rate constant of the alternative pathway, which is small and suggests that the pathway is not physiologically important.

  4. Enhanced Lipid and Biodiesel Production from Glucose-Fed Activated Sludge: Kinetics an Microbial Community Analysis

    EPA Science Inventory

    An innovative approach to increase biofuel feedstock lipid yields from municipal sewage sludge via manipulation of carbon:nitrogen (C:N) ratio and glucose loading in activated sludge bioreactors was investigated. Sludge lipid and fatty acid methyl ester (biodiesel) yields (% cel...

  5. A century of enzyme kinetic analysis, 1913 to 2013.

    PubMed

    Johnson, Kenneth A

    2013-09-02

    This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function.

  6. Structural and kinetic analysis of the COP9-Signalosome activation and the cullin-RING ubiquitin ligase deneddylation cycle

    PubMed Central

    Mosadeghi, Ruzbeh; Reichermeier, Kurt M; Winkler, Martin; Schreiber, Anne; Reitsma, Justin M; Zhang, Yaru; Stengel, Florian; Cao, Junyue; Kim, Minsoo; Sweredoski, Michael J; Hess, Sonja; Leitner, Alexander; Aebersold, Ruedi; Peter, Matthias; Deshaies, Raymond J; Enchev, Radoslav I

    2016-01-01

    The COP9-Signalosome (CSN) regulates cullin–RING ubiquitin ligase (CRL) activity and assembly by cleaving Nedd8 from cullins. Free CSN is autoinhibited, and it remains unclear how it becomes activated. We combine structural and kinetic analyses to identify mechanisms that contribute to CSN activation and Nedd8 deconjugation. Both CSN and neddylated substrate undergo large conformational changes upon binding, with important roles played by the N-terminal domains of Csn2 and Csn4 and the RING domain of Rbx1 in enabling formation of a high affinity, fully active complex. The RING domain is crucial for deneddylation, and works in part through conformational changes involving insert-2 of Csn6. Nedd8 deconjugation and re-engagement of the active site zinc by the autoinhibitory Csn5 glutamate-104 diminish affinity for Cul1/Rbx1 by ~100-fold, resulting in its rapid ejection from the active site. Together, these mechanisms enable a dynamic deneddylation-disassembly cycle that promotes rapid remodeling of the cellular CRL network. DOI: http://dx.doi.org/10.7554/eLife.12102.001 PMID:27031283

  7. Analysis of Flow Cytometry DNA Damage Response Protein Activation Kinetics Following X-rays and High Energy Iron Nuclei Exposure

    SciTech Connect

    Universities Space Research Association; Chappell, Lori J.; Whalen, Mary K.; Gurai, Sheena; Ponomarev, Artem; Cucinotta, Francis A.; Pluth, Janice M.

    2010-12-15

    We developed a mathematical method to analyze flow cytometry data to describe the kinetics of {gamma}H2AX and pATF2 phosphorylations ensuing various qualities of low dose radiation in normal human fibroblast cells. Previously reported flow cytometry kinetic results for these DSB repair phospho-proteins revealed that distributions of intensity were highly skewed, severely limiting the detection of differences in the very low dose range. Distributional analysis reveals significant differences between control and low dose samples when distributions are compared using the Kolmogorov-Smirnov test. Radiation quality differences are found in the distribution shapes and when a nonlinear model is used to relate dose and time to the decay of the mean ratio of phosphoprotein intensities of irradiated samples to controls. We analyzed cell cycle phase and radiation quality dependent characteristic repair times and residual phospho-protein levels with these methods. Characteristic repair times for {gamma}H2AX were higher following Fe nuclei as compared to X-rays in G1 cells (4.5 {+-} 0.46 h vs 3.26 {+-} 0.76 h, respectively), and in S/G2 cells (5.51 {+-} 2.94 h vs 2.87 {+-} 0.45 h, respectively). The RBE in G1 cells for Fe nuclei relative to X-rays for {gamma}H2AX was 2.05 {+-} 0.61 and 5.02 {+-} 3.47, at 2 h and 24-h postirradiation, respectively. For pATF2, a saturation effect is observed with reduced expression at high doses, especially for Fe nuclei, with much slower characteristic repair times (>7 h) compared to X-rays. RBEs for pATF2 were 0.66 {+-} 0.13 and 1.66 {+-} 0.46 at 2 h and 24 h, respectively. Significant differences in {gamma}H2AX and pATF2 levels comparing irradiated samples to control were noted even at the lowest dose analyzed (0.05 Gy) using these methods of analysis. These results reveal that mathematical models can be applied to flow cytometry data to uncover important and subtle differences following exposure to various qualities of low dose radiation.

  8. The change of activation energy in microchannel laminar flow as demonstrated by kinetic analysis of the DNA duplex-coil equilibrium.

    PubMed

    Yamashita, Kenichi; Miyazaki, Masaya; Yamaguchi, Yoshiko; Nakamura, Hiroyuki; Maeda, Hideaki

    2008-07-01

    This paper presents the capability of changing the activation energy of chemical reactions using microchannel laminar flow. Kinetic parameters of the duplex-coil equilibrium of DNA oligomers were studied by measuring the hysteresis between denaturation-renaturation curves using an in-house temperature-controllable microchannel-type flow cell. For this study, DNA oligomers were used because they allow physicochemical analysis and theoretical discussion. Kinetic parameters of the duplex-coil equilibrium of DNA oligomers were obtained by measuring the denaturation-renaturation hysteresis curves. Both cooling and heating curves were shifted to the high-temperature side at higher flow rates. The renaturation reaction was influenced by a slower flow rate. The effect of the slower flow rate was more pronounced for renaturation than denaturation reactions. The magnitude of the activation energies of association decreased as the flow rate increased, but that of the activation energies of the dissociation increased as the flow rate increased. Overall, these results suggest that chemical reactions' change of activation energy depends on the flow rate and the DNA molecular size.

  9. Kinetic and thermal analysis of polymeric materials

    NASA Astrophysics Data System (ADS)

    Peterson, Jeffery David

    2002-09-01

    Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques have been used to study the thermal degradation of polymeric materials. These polymers were subjected to a variety of heating programs as well as numerous types of atmospheric conditions. The results from these analyses were then used to determine activation energies as a function of an extent of reaction variable, alpha. This technique, known as the model-free isoconversional method, allows for changes in energies to occur as decomposition pathways change. This produces a more realistic means of observing complex kinetic schemes and is a better representation of kinetic analysis. Chapters 1 and 2 provide introductory backgrounds into both polymer chemistry and the isoconversional analysis technique, respectively. A brief description of the research goals and motivations is also discussed. Thermal analysis of pure polystyrene (PS), polyethylene (PE), and polypropylene (PP) samples are presented in Chapter 3. The obtained activation energy dependencies are interpreted in terms of degradation mechanisms. These mechanisms vary greatly according to the gaseous environment in which they were analyzed. The thermal degradation of poly(methyl methacrylate) (PMMA) in both pure nitrogen and in various oxygen-containing atmospheres is discussed in Chapter 4. It was observed that oxygen exhibits a stabilizing effect on PMMA decomposition. Activation energies for these processes, and their mechanistic interpretations, will also be presented. Chapter 5 builds off the understanding gained in Chapter 4 by investigating the char-forming effects of silica gel and potassium carbonate additives on PMMA. These additives are known for their fire-resistant properties when combined in a 3:1 silica gel to potassium carbonate ratio. The effects of these additives, and their respective ratio amounts, on PMMA char formation are reported. Chapters 6 and 7 conclude the dissertation by looking at the thermal

  10. CURRENT AND KINETIC HELICITY OF LONG-LIVED ACTIVITY COMPLEXES

    SciTech Connect

    Komm, Rudolf; Gosain, Sanjay

    2015-01-01

    We study long-lived activity complexes and their current helicity at the solar surface and their kinetic helicity below the surface. The current helicity has been determined from synoptic vector magnetograms from the NSO/SOLIS facility, and the kinetic helicity of subsurface flows has been determined with ring-diagram analysis applied to full-disk Dopplergrams from NSO/GONG and SDO/HMI. Current and kinetic helicity of activity complexes follow the hemispheric helicity rule with mainly positive values (78%; 78%, respectively, with a 95% confidence level of 31%) in the southern hemisphere and negative ones (80%; 93%, respectively, with a 95% confidence level of 22% and 14%, respectively) in the northern hemisphere. The locations with the dominant sign of kinetic helicity derived from Global Oscillation Network Group (GONG) and SDO/HMI data are more organized than those of the secondary sign even if they are not part of an activity complex, while locations with the secondary sign are more fragmented. This is the case for both hemispheres even for the northern one where it is not as obvious visually due to the large amount of magnetic activity present as compared to the southern hemisphere. The current helicity shows a similar behavior. The dominant sign of current helicity is the same as that of kinetic helicity for the majority of the activity complexes (83% with a 95% confidence level of 15%). During the 24 Carrington rotations analyzed here, there is at least one longitude in each hemisphere where activity complexes occur repeatedly throughout the epoch. These ''active'' longitudes are identifiable as locations of strong current and kinetic helicity of the same sign.

  11. Kinetic modeling of active plasma resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Oberrath, Jens

    2016-09-01

    The term ``active plasma resonance spectroscopy'' (APRS) refers to a plasma diagnostic method which employs the natural ability of plasmas to resonate close to the plasma frequency. Essential for this method is an appropriate model to determine the relation between the resonance parameters and demanded plasma parameters. Measurements with these probes in plasmas of a few Pa typically show a broadening of the spectrum that cannot be predicted by a fluid model. Thus, a kinetic model is necessary. A general kinetic model of APRS probes, which can be described in electorstatic approximation, valid for all pressures has been presented. This model is used to analyze the dynamic behavior of such probes by means of functional analytic methods. One of the main results is, that the system response function Y (ω) is given in terms of the matrix elements of the resolvent of the dynamic operator evaluated for values on the imaginary axis. The spectrum of this operator is continuous which implies a new phenomenon related to anomalous or non-collisional dissipation. Based on the scalar product, which is motivated by the kinetic free energy, the non-collisional damping can be interpreted: In a periodic state, the probe constantly emits plasma waves which propagate to ``infinity''. The free energy simply leaves the ``observation range'' of the probe which is recorded as damping. The kinetic damping, which depends on the mean kinetic energy of the electrons, is responsible for the broadening of a resonance peak in the measured spectrum of APRS probes. The ultimate goal is to determine explicit formulas for the relation between the broadening of the resonance peak and the ``equivalent electron temperature'', especially in the case of the spherical Impedance Probe and the Multipole Resonance Probe. Gratitude is expressed to the internal funding of Leuphana University, the BMBF via PluTO+, the DFG via Collaborative Research Center TR 87, and the Ruhr University Research School.

  12. Kinetic Analysis of a Mammalian Phospholipase D

    PubMed Central

    Henage, Lee G.; Exton, John H.; Brown, H. Alex

    2013-01-01

    In mammalian cells, phospholipase D activity is tightly regulated by diverse cellular signals, including hormones, neurotransmitters, and growth factors. Multiple signaling pathways converge upon phospholipase D to modulate cellular actions, such as cell growth, shape, and secretion. We examined the kinetics of protein kinase C and G-protein regulation of mammalian phospholipase D1 (PLD1) in order to better understand interactions between PLD1 and its regulators. Activation by Arf-1, RhoA, Rac1, Cdc42, protein kinase Cα, and phosphatidylinositol 4,5-bisphosphate displayed surface dilution kinetics, but these effectors modulated different kinetic parameters. PKCα activation of PLD1 involves N- and C-terminal PLD domains. Rho GTPases were binding activators, enhancing the catalytic efficiency of a purified PLD1 catalytic domain via effects on Km. Arf-1, a catalytic activator, stimulated PLD1 by enhancing the catalytic constant, kcat. A kinetic description of PLD1 activation by multiple modulators reveals a mechanism for apparent synergy between activators. Synergy was observed only when PLD1 was simultaneously stimulated by a binding activator and a catalytic activator. Surprisingly, synergistic activation was steeply dependent on phosphatidylinositol 4,5-bisphosphate and phosphatidylcholine. Together, these findings suggest a role for PLD1 as a signaling node, in which integration of convergent signals occurs within discrete locales of the cellular membrane. PMID:16339153

  13. Active biopolymers confer fast reorganization kinetics.

    PubMed

    Swanson, Douglas; Wingreen, Ned S

    2011-11-18

    Many cytoskeletal biopolymers are "active," consuming energy in large quantities. In this Letter, we identify a fundamental difference between active polymers and passive, equilibrium polymers: for equal mean lengths, active polymers can reorganize faster than equilibrium polymers. We show that equilibrium polymers are intrinsically limited to linear scaling between mean lifetime (or mean first-passage time, or MFPT) and mean length, MFPT∼, by analogy to 1D Potts models. By contrast, we present a simple active-polymer model that improves upon this scaling, such that MFPT∼(1/2). Since, to be biologically useful, structural biopolymers must typically be many monomers long yet respond dynamically to the needs of the cell, the difference in reorganization kinetics may help to justify the active polymers' greater energy cost.

  14. Kinetic analysis of Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase, wild type and mutants, reveals roles of active site amino acids.

    PubMed

    Richard, Stéphane B; Lillo, Antonietta M; Tetzlaff, Charles N; Bowman, Marianne E; Noel, Joseph P; Cane, David E

    2004-09-28

    Escherichia coli 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase (YgbP or IspD) catalyzes the conversion of 2-C-methyl-D-erythritol 4-phosphate (MEP) and cytidine triphosphate (CTP) to 4-diphosphocytidyl-2-C-methylerythritol (CDPME). Pulse chase experiments established that the reaction involves an ordered sequential mechanism with mandatory initial binding of CTP. On the basis of analysis of the previously reported crystal structures of apo-YgbP as well as YgbP complexed with both CTP.Mg(2+) and CDPME.Mg(2+) [Richard, S. B., Bowman, M. E., Kwiatkowski, W., Kang, I., Chow, C., Lillo, A. M., Cane, D. E., and Noel, J. P. (2001) Nat. Struct. Biol. 8, 641-648], a group of active site residues were selected for site-directed mutagenesis and steady-state kinetic analysis. Both Lys27 and Lys213 were shown to be essential to catalytic activity, consistent with their proposed role in stabilization of a pentacoordinate phosphate transition state resulting from in-line attack of the MEP phosphate on the alpha-phosphate of CTP. In addition, Thr140, Arg109, Asp106, and Thr165 were all shown to play critical roles in the binding and proper orientation of the MEP substrate.

  15. A Kinetic Model of Active Extensile Bundles

    NASA Astrophysics Data System (ADS)

    Goldstein, Daniel; Chakraborty, Bulbul; Baskaran, Aparna

    Recent experiments in active filament networks reveal interesting rheological properties (Dan Chen: APS March Meeting 2015 D49.00001). This system consumes ATP to produce an extensile motion in bundles of microtubules. This extension then leads to self generated stresses and spontaneous flows. We propose a minimal model where the activity is modeled by self-extending bundles that are part of a cross linked network. This network can reorganize itself through buckling of extending filaments and merging events that alter the topology of the network. We numerically simulate this minimal kinetic model and examine the emergent rheological properties and determine how stresses are generated by the extensile activity. We will present results that focus on the effects of confinement and network connectivity of the bundles on stress fluctuations and response of an active gel.

  16. Kinetic model of excess activated sludge thermohydrolysis.

    PubMed

    Imbierowicz, Mirosław; Chacuk, Andrzej

    2012-11-01

    Thermal hydrolysis of excess activated sludge suspensions was carried at temperatures ranging from 423 K to 523 K and under pressure 0.2-4.0 MPa. Changes of total organic carbon (TOC) concentration in a solid and liquid phase were measured during these studies. At the temperature 423 K, after 2 h of the process, TOC concentration in the reaction mixture decreased by 15-18% of the initial value. At 473 K total organic carbon removal from activated sludge suspension increased to 30%. It was also found that the solubilisation of particulate organic matter strongly depended on the process temperature. At 423 K the transfer of TOC from solid particles into liquid phase after 1 h of the process reached 25% of the initial value, however, at the temperature of 523 K the conversion degree of 'solid' TOC attained 50% just after 15 min of the process. In the article a lumped kinetic model of the process of activated sludge thermohydrolysis has been proposed. It was assumed that during heating of the activated sludge suspension to a temperature in the range of 423-523 K two parallel reactions occurred. One, connected with thermal destruction of activated sludge particles, caused solubilisation of organic carbon and an increase of dissolved organic carbon concentration in the liquid phase (hydrolysate). The parallel reaction led to a new kind of unsolvable solid phase, which was further decomposed into gaseous products (CO(2)). The collected experimental data were used to identify unknown parameters of the model, i.e. activation energies and pre-exponential factors of elementary reactions. The mathematical model of activated sludge thermohydrolysis appropriately describes the kinetics of reactions occurring in the studied system.

  17. Kinetic behaviour of zymogen activation processes in the presence of an inhibitor.

    PubMed Central

    Varón, R; Manjabacas, M C; García-Moreno, M; Valero, E; Garcia-Canovas, F

    1993-01-01

    A global kinetic analysis of a general zymogen activation model, where not only the activating but also the activated enzyme suffer an irreversible inhibition is presented. A reaction in which the enzyme acts upon a substrate is coupled to monitor the process. In addition, we determined the corresponding kinetic equations for a number of particular cases of the general model studied. Finally, a kinetic data analysis and a procedure to discriminate among the different mechanisms considered, which are based on the kinetic equations obtained, are suggested. PMID:8452535

  18. Fluidization and Active Thinning by Molecular Kinetics in Active Gels.

    PubMed

    Oriola, David; Alert, Ricard; Casademunt, Jaume

    2017-02-24

    We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity-active thinning-of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.

  19. Fluidization and Active Thinning by Molecular Kinetics in Active Gels

    NASA Astrophysics Data System (ADS)

    Oriola, David; Alert, Ricard; Casademunt, Jaume

    2017-02-01

    We derive the constitutive equations of an active polar gel from a model for the dynamics of elastic molecules that link polar elements. Molecular binding kinetics induces the fluidization of the material, giving rise to Maxwell viscoelasticity and, provided that detailed balance is broken, to the generation of active stresses. We give explicit expressions for the transport coefficients of active gels in terms of molecular properties, including nonlinear contributions on the departure from equilibrium. In particular, when activity favors linker unbinding, we predict a decrease of viscosity with activity—active thinning—of kinetic origin, which could explain some experimental results on the cell cortex. By bridging the molecular and hydrodynamic scales, our results could help understand the interplay between molecular perturbations and the mechanics of cells and tissues.

  20. Pyrolysis kinetics of hazelnut husk using thermogravimetric analysis.

    PubMed

    Ceylan, Selim; Topçu, Yıldıray

    2014-03-01

    This study aims at investigating physicochemical properties and pyrolysis kinetics of hazelnut husk, an abundant agricultural waste in Turkey. The physicochemical properties were determined by bomb calorimeter, elemental analysis and FT-IR spectroscopy. Physicochemical analysis results showed that hazelnut husk has a high calorimetric value and high volatile matter content. Pyrolysis experiments were carried out in a thermogravimetric analyzer under inert conditions and operated at different heating rates (5, 10, 20°C/min). Three different kinetic models, the iso-conversional Kissinger-Akahira-Sunose (KAS) and Ozawa-Flynn-Wall (OFW) models and Coats-Redfern method were applied on TGA data of hazelnut husk to calculate the kinetic parameters including activation energy, pre-exponential factor and reaction order. Simulation of hazelnut husk pyrolysis using data obtained from TGA analysis showed good agreement with experimental data. Combining with physicochemical properties, it was concluded that this biomass can become useful source of energy or chemicals.

  1. Influence of activated-carbon-supported transition metals on the decomposition of polychlorobiphenyls. Part I: Catalytic decomposition and kinetic analysis.

    PubMed

    Sun, Yifei; Tao, Fei; Liu, Lina; Zeng, Xiaolan; Wang, Wei

    2016-09-01

    In this study, the synergism between activated carbon (AC) as a catalyst support and transition metals (TMs) is used to destroy low concentrations of PCBs. AC-supported TM catalysts were prepared according to two different methods: impregnation and ion exchange. Thermal reactions between 2,2',4,4',5,5'-hexachlorobiphenyl (PCB-153) and catalysts generated using AC-supported Ni or Cu ion exchange were conducted under a N2 atmosphere and resulted in a decomposition efficiency > 99.0%. Decomposition efficiency of PCB-153, the residual PCB-153 distribution, and the fingerprint characteristics of the decomposition products are investigated. Important findings include: (i) establishing a ranking of TM reactivities with respect to PCB decomposition of: Ni > Cu > Zn > Fe, (ii) PCB degradation reactions proceed via adsorption, reaction, and desorption, (iii) for ion-exchange-type catalysts, the activation energy order was IRNi-C < IRCu-C < IRZn-C < IRFe-C, which matches the order of the catalytic effects of the catalyst.

  2. Center for Environmental Kinetics Analysis

    SciTech Connect

    Bandstra, Joel Z.; Burgos, William D.; Peyton, Brent M.

    2006-04-05

    Over the past two decades, numerous studies have produced high quality information on the rates at which bacteria can reduce metal oxides. The prototypical study--such as the one depicted to the right--focuses on only a few of the myriad variables affecting the rate. This approach allows for effective dissection of the mechanisms underlying DMRB activity, but, it also produces disjoint information that must be synthesized if we hope to predict the behavior of bacteria at the systems level.

  3. Quantitative full time course analysis of nonlinear enzyme cycling kinetics.

    PubMed

    Cao, Wenxiang; De La Cruz, Enrique M

    2013-01-01

    Enzyme inhibition due to the reversible binding of reaction products is common and underlies the origins of negative feedback inhibition in many metabolic and signaling pathways. Product inhibition generates non-linearity in steady-state time courses of enzyme activity, which limits the utility of well-established enzymology approaches developed under the assumption of irreversible product release. For more than a century, numerous attempts to find a mathematical solution for analysis of kinetic time courses with product inhibition have been put forth. However, no practical general method capable of extracting common enzymatic parameters from such non-linear time courses has been successfully developed. Here we present a simple and practical method of analysis capable of efficiently extracting steady-state enzyme kinetic parameters and product binding constants from non-linear kinetic time courses with product inhibition and/or substrate depletion. The method is general and applicable to all enzyme systems, independent of reaction schemes and pathways.

  4. Adsorption studies of molasse's wastewaters on activated carbon: modelling with a new fractal kinetic equation and evaluation of kinetic models.

    PubMed

    Figaro, S; Avril, J P; Brouers, F; Ouensanga, A; Gaspard, S

    2009-01-30

    Adsorption kinetic of molasses wastewaters after anaerobic digestion (MSWD) and melanoidin respectively on activated carbon was studied at different pH. The kinetic parameters could be determined using classical kinetic equations and a recently published fractal kinetic equation. A linear form of this equation can also be used to fit adsorption data. Even with lower correlation coefficients the fractal kinetic equation gives lower normalized standard deviation values than the pseudo-second order model generally used to fit adsorption kinetic data, indicating that the fractal kinetic model is much more accurate for describing the kinetic adsorption data than the pseudo-second order kinetic model.

  5. Mathematics analysis of polymerase chain reaction kinetic curves.

    PubMed

    Sochivko, D G; Fedorov, A A; Varlamov, D A; Kurochkin, V E; Petrov, R V

    2016-01-01

    The paper reviews different approaches to the mathematical analysis of polymerase chain reaction (PCR) kinetic curves. The basic principles of PCR mathematical analysis are presented. Approximation of PCR kinetic curves and PCR efficiency curves by various functions is described. Several PCR models based on chemical kinetics equations are suggested. Decision criteria for an optimal function to describe PCR efficiency are proposed.

  6. Kinetic Analysis of δ Ribozyme Cleavage†

    PubMed Central

    Mercure, Stéphane; Lafontaine, Daniel; Ananvoranich, Sirinart; Perreault, Jean-Pierre

    2010-01-01

    The ability of δ ribozyme to catalyze the cleavage of an 11-mer RNA substrate was examined under both single- and multiple-turnover conditions. In both cases only small differences in the kinetic parameters were observed in the presence of either magnesium or calcium as cofactor. Under multiple-turnover conditions, the catalytic efficiency of the ribozyme (kcat/KM) was higher at 37 °C than at 56 °C. The cleavage reaction seems to be limited by the product release step at 37 °C and by the chemical cleavage step at 56 °C. We observed substrate inhibition at high concentrations of the 11-mer substrate. Cleavage rate constants were determined with a structural derivative characterized by an ultrastable L4 tetraloop. The kinetic parameters (kcat and KM) and dissociation constant (Kd) were almost identical for both ribozymes, suggesting that the stability of the L4 loop has a negligible impact on the catalytic activities of the examined ribozymes. Various cleavage inhibition and gel-shift assays with analogues, substrate, and both active and inactive ribozymes were performed. The 2′-hydroxyl group adjacent to the scissile phosphate was shown to be involved in binding with the ribozyme, while the essential cytosine residue of the J4/2 junction was shown to contribute to substrate association. We clearly show that substrate binding to the δ ribozyme is not restricted to the formation of a helix located downstream of the cleavage site. Using these results, we postulate a kinetic pathway involving a conformational transition step essential for the formation of the active ribozyme/substrate complex. PMID:9836591

  7. Reaction kinetic analysis of reactor surveillance data

    NASA Astrophysics Data System (ADS)

    Yoshiie, T.; Kinomura, A.; Nagai, Y.

    2017-02-01

    In the reactor pressure vessel surveillance data of a European-type pressurized water reactor (low-Cu steel), it was found that the concentration of matrix defects was very high, and a large number of precipitates existed. In this study, defect structure evolution obtained from surveillance data was simulated by reaction kinetic analysis using 15 rate equations. The saturation of precipitation and the growth of loops were simulated, but it was not possible to explain the increase in DBTT on the basis of the defect structures. The sub-grain boundary segregation of solutes was discussed for the origin of the DBTT increase.

  8. Kinetic analysis of interactions of different sarin and tabun analogues with human acetylcholinesterase and oximes: is there a structure-activity relationship?

    PubMed

    Aurbek, Nadine; Herkert, Nadja M; Koller, Marianne; Thiermann, Horst; Worek, Franz

    2010-09-06

    The repeated misuse of highly toxic organophosphorus compound (OP) based chemical warfare agents in military conflicts and terrorist attacks poses a continuous threat to the military and civilian sector. The toxic symptomatology of OP poisoning is mainly caused by inhibition of acetylcholinesterase (AChE, E.C. 3.1.1.7) resulting in generalized cholinergic crisis due to accumulation of the neurotransmitter acetylcholine (ACh) in synaptic clefts. Beside atropine as competitive antagonist of ACh at muscarinic ACh receptors oximes as reactivators of OP-inhibited AChE are a mainstay of standard antidotal treatment. However, human AChE inhibited by certain OP is rather resistant to oxime-induced reactivation. The development of more effective oxime-based reactivators may fill the gaps. To get more insight into a potential structure-activity relationship between human AChE, OPs and oximes in vitro studies were conducted to investigate interactions of different tabun and sarin analogues with human AChE and the oximes obidoxime and HI 6 by determination of various kinetic constants. Rate constants for the inhibition of human AChE by OPs, spontaneous dealkylation and reactivation as well as reactivation by obidoxime and HI 6 of OP-inhibited human AChE were determined. The recorded kinetic data did not allow a general statement concerning a structure-activity relationship between human AChE, OP and oximes.

  9. A pre-steady state and steady state kinetic analysis of the N-ribosyl hydrolase activity of hCD157.

    PubMed

    Preugschat, Frank; Carter, Luke H; Boros, Eric E; Porter, David J T; Stewart, Eugene L; Shewchuk, Lisa M

    2014-12-15

    hCD157 catalyzes the hydrolysis of nicotinamide riboside (NR) and nicotinic acid riboside (NAR). The release of nicotinamide or nicotinic acid from NR or NAR was confirmed by spectrophotometric, HPLC and NMR analyses. hCD157 is inactivated by a mechanism-based inhibitor, 2'-deoxy-2'-fluoro-nicotinamide arabinoside (fNR). Modification of the enzyme during the catalytic cycle by NR, NAR, or fNR increased the intrinsic protein fluorescence by approximately 50%. Pre-steady state and steady state data were used to derive a minimal kinetic scheme for the hydrolysis of NR. After initial complex formation a reversible step (360 and 30s(-1)) is followed by a slow irreversible step (0.1s(-1)) that defined the rate limiting step, or kcat. The calculated KMapp value for NR in the hydrolytic reaction is 6nM. The values of the kinetic constants suggest that one biological function of cell-surface hCD157 is to bind and slowly hydrolyze NR, possibly converting it to a ligand-activated receptor. Differences in substrate preference between hCD157 and hCD38 were rationalized through a comparison of the crystal structures of the two proteins. This comparison identified several residues in hCD157 (F108 and F173) that can potentially hinder the binding of dinucleotide substrates (NAD+).

  10. Kinetics of small particle activation in supersaturated vapors

    SciTech Connect

    McGraw, R.; Wang, J.

    2010-08-29

    We examine the nucleated (with barrier) activation of perfectly wetting (zero contact angle) particles ranging from bulk size down to one nanometer. Thermodynamic properties of the particles, coated with liquid layers of varying thickness and surrounded by vapor, are analyzed. Nano-size particles are predicted to activate at relative humidity below the Kelvin curve on crossing a nucleation barrier, located at a critical liquid layer thickness such that the total particle size (core + liquid layer) equals the Kelvin radius (Fig. 1). This barrier vanishes precisely as the critical layer thickness approaches the thin layer limit and the Kelvin radius equals the radius of the particle itself. These considerations are similar to those included in Fletcher's theory (Fletcher, 1958) however the present analysis differs in several important respects. Firstly, where Fletcher used the classical prefactor-exponent form for the nucleation rate, requiring separate estimation of the kinetic prefactor, we solve a diffusion-drift equation that is equivalent to including the full Becker-Doering (BD) multi-state kinetics of condensation/evaporation along the growth coordinate. We also determine the mean first passage time (MFPT) for barrier crossing (Wedekind et al., 2007), which is shown to provide a generalization of BD nucleation kinetics especially useful for barrier heights that are considerably lower than those typically encountered in homogeneous vapor-liquid nucleation, and make explicit comparisons between the MFPT and BD kinetic models. Barrier heights for heterogeneous nucleation are computed by a thermo-dynamic area construction introduced recently to model deliquescence and efflorescence of small particles (McGraw and Lewis, 2009). In addition to providing a graphical representation of the activation process that offers new insights, the area construction provides a molecular approach that avoids explicit use of the interfacial tension. Typical barrier profiles for

  11. Kinetic Analysis of tRNA Methylfransferases

    PubMed Central

    Hou, Ya-Ming; Masuda, Isao

    2016-01-01

    Transfer RNA (tRNA) molecules contain many chemical modifications that are introduced after transcription. A major form of these modifications is methyl transfer to bases and backbone groups, using S-adenosyl methionine (AdoMet) as the methyl donor. Each methylation confers a specific advantage to tRNA in structure or in function. A remarkable methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA, which suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. This chapter summarizes the kinetic assays that are used to reveal the distinction between TrmD and Trm5. Three types of assays are described, the steady-state, the pre-steady-state, and the single turnover assays, which collectively provide the basis for mechanistic investigation of AdoMet-dependent methyl transfer reactions. PMID:26253967

  12. Updated Chemical Kinetics and Sensitivity Analysis Code

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan

    2005-01-01

    An updated version of the General Chemical Kinetics and Sensitivity Analysis (LSENS) computer code has become available. A prior version of LSENS was described in "Program Helps to Determine Chemical-Reaction Mechanisms" (LEW-15758), NASA Tech Briefs, Vol. 19, No. 5 (May 1995), page 66. To recapitulate: LSENS solves complex, homogeneous, gas-phase, chemical-kinetics problems (e.g., combustion of fuels) that are represented by sets of many coupled, nonlinear, first-order ordinary differential equations. LSENS has been designed for flexibility, convenience, and computational efficiency. The present version of LSENS incorporates mathematical models for (1) a static system; (2) steady, one-dimensional inviscid flow; (3) reaction behind an incident shock wave, including boundary layer correction; (4) a perfectly stirred reactor; and (5) a perfectly stirred reactor followed by a plug-flow reactor. In addition, LSENS can compute equilibrium properties for the following assigned states: enthalpy and pressure, temperature and pressure, internal energy and volume, and temperature and volume. For static and one-dimensional-flow problems, including those behind an incident shock wave and following a perfectly stirred reactor calculation, LSENS can compute sensitivity coefficients of dependent variables and their derivatives, with respect to the initial values of dependent variables and/or the rate-coefficient parameters of the chemical reactions.

  13. Geosmin and 2-methylisoborneol removal using superfine powdered activated carbon: shell adsorption and branched-pore kinetic model analysis and optimal particle size.

    PubMed

    Matsui, Yoshihiko; Nakao, Soichi; Taniguchi, Takuma; Matsushita, Taku

    2013-05-15

    2-Methylisoborneol (MIB) and geosmin are naturally occurring compounds responsible for musty-earthy taste and odor in public drinking-water supplies, a severe problem faced by many utilities throughout the world. In this study, we investigated adsorptive removal of these compounds by superfine powdered activation carbon (SPAC, particle size <1 μm) produced by novel micro-grinding of powdered activated carbon; we also discuss the optimization of carbon particle size to efficiently enhance the adsorptive removal. After grinding, the absorptive capacity remained unchanged for a 2007 carbon sample and was increased for a 2010 carbon sample; the capacity increase was quantitatively described by the shell adsorption model, in which MIB and geosmin adsorbed more in the exterior of a carbon particle than in the center. The extremely high uptake rates of MIB and geosmin by SPAC were simulated well by a combination of the branched-pore kinetic model and the shell adsorption model, in which intraparticle diffusion through macropores was followed by diffusion from macropore to micropore. Simulations suggested that D40 was on the whole the best characteristic diameter to represent a size-disperse group of adsorbent particles; D40 is the diameter through which 40% of the particles by volume pass. Therefore, D40 can be used as an index for evaluating the improvement of adsorptive removal that resulted from pulverization. The dose required for a certain percentage removal of MIB or geosmin decreased linearly with carbon particle size (D40), but the dose reduction became less effective as the activated carbon was ground down to smaller sizes around a critical value of D40. For a 60-min contact time, critical D40 was 2-2.5 μm for MIB and 0.4-0.5 μm for geosmin. The smaller critical D40 was when the shorter the carbon-water contact time was or the slower the intraparticle mass transfer rate of an adsorbate was.

  14. Analysis of flow cytometry DNA damage response protein activation kinetics after exposure to x rays and high-energy iron nuclei.

    PubMed

    Chappell, Lori J; Whalen, Mary K; Gurai, Sheena; Ponomarev, Artem; Cucinotta, Francis A; Pluth, Janice M

    2010-12-01

    We developed a mathematical method to analyze flow cytometry data to describe the kinetics of γ-H2AX and pATF2 phosphorylation in normal human fibroblast cells after exposure to various qualities of low-dose radiation. Previously reported flow cytometry kinetics for these DSB repair phospho-proteins revealed that distributions of intensity were highly skewed, severely limiting the detection of differences in the very low-dose range. Distributional analysis revealed significant differences between control and low-dose samples when distributions were compared using the Kolmogorov-Smirnov test. Differences in radiation quality were found in the distribution shapes and when a nonlinear model was used to relate dose and time to the decay of the mean ratio of phospho-protein intensities of irradiated samples to controls. We analyzed cell cycle phase- and radiation quality-dependent characteristic repair times and residual phospho-protein levels with these methods. Characteristic repair times for γ-H2AX were higher after exposure to iron nuclei compared to X rays in G(1) cells and in S/G(2) cells. The RBE in G(1) cells for iron nuclei relative to X rays for γ-H2AX was 2.1 ± 0.6 and 5.0 ± 3.5 at 2 and 24 h after irradiation, respectively. For pATF2, a saturation effect was observed with reduced expression at high doses, especially for iron nuclei, with much slower characteristic repair times (>7 h) compared to X rays. RBEs for pATF2 were 0.7 ± 0.1 and 1.7 ± 0.5 at 2 and 24 h, respectively. Significant differences in γ-H2AX and pATF2 levels when irradiated samples were compared to controls were noted even at the lowest dose analyzed (0.05 Gy). These results show that mathematical models can be applied to flow cytometry data to identify important and subtle differences after exposure to various qualities of low-dose radiation.

  15. Cloud condensation nuclei activity and droplet activation kinetics of wet processed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2011-08-01

    This study reports laboratory measurements of particle size distributions, cloud condensation nuclei (CCN) activity, and droplet activation kinetics of wet generated aerosols from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. The dependence of critical supersaturation, sc, on particle dry diameter, Ddry, is used to characterize particle-water interactions and assess the ability of Frenkel-Halsey-Hill adsorption activation theory (FHH-AT) and Köhler theory (KT) to describe the CCN activity of the considered samples. Wet generated regional dust samples produce unimodal size distributions with particle sizes as small as 40 nm, CCN activation consistent with KT, and exhibit hygroscopicity similar to inorganic salts. Wet generated clays and minerals produce a bimodal size distribution; the CCN activity of the smaller mode is consistent with KT, while the larger mode is less hydrophilic, follows activation by FHH-AT, and displays almost identical CCN activity to dry generated dust. Ion Chromatography (IC) analysis performed on regional dust samples indicates a soluble fraction that cannot explain the CCN activity of dry or wet generated dust. A mass balance and hygroscopicity closure suggests that the small amount of ions (from low solubility compounds like calcite) present in the dry dust dissolve in the aqueous suspension during the wet generation process and give rise to the observed small hygroscopic mode. Overall these results identify an artifact that may question the atmospheric relevance of dust CCN activity studies using the wet generation method. Based on the method of threshold droplet growth analysis, wet generated mineral aerosols display similar activation kinetics compared to ammonium sulfate calibration aerosol. Finally, a unified CCN activity framework that accounts for concurrent effects of solute and adsorption is developed to describe the CCN activity of aged or hygroscopic dusts.

  16. Kinetic approach for evaluation of total antioxidant activity.

    PubMed

    Karyakina, Elena E; Vokhmyanina, Darya V; Sizova, Natalya V; Sabitov, Aytugan N; Borisova, Anastasiya V; Sazontova, Tatyana G; Arkhipenko, Yury V; Tkachuk, Vsevolod A; Zolotov, Yury A; Karyakin, Arkady A

    2009-12-15

    We propose a novel approach for assessment of total antioxidant activity by monitoring kinetics of hydrogen peroxide (H(2)O(2)) scavenging after its injection into liquid sample under study. H(2)O(2) is known to be the strongest oxidant, really presented in human body in contrast to the majority of the model oxidative systems used for evaluation of antioxidant activity. In addition, kinetic approach, being more informative than the commonly used determination of the final product, obviously provides better discrimination of potential antioxidants. Prussian Blue based sensor due to its high sensitivity and operational stability allowed to monitor kinetics of hydrogen peroxide consumption in turbid and colored samples. The pseudo-first order kinetic constants of hydrogen peroxide scavenging in the presence of different food additives correlated with total antioxidant activity of these samples evaluated via standard procedure based on lipid peroxidation. However, in contrast to the standard method, the proposed kinetic approach is expressed and does not require fresh biological tissues.

  17. Evaluation of proton activity in microemulsions by a kinetic probe.

    PubMed

    Peñacoba, Indalecio A; García, Begoña; Navarro, Ana M; Hoyuelos, F Javier; Leal, José M

    2010-12-15

    The decomposition reaction of the purple dye murexide in acidic media is used as a probe indicator for protons in nonionic microemulsions. The reaction kinetics primarily rely on the proton concentration and permit assessment of the proton activity in the nonionic microemulsions of water/cyclohexane/Igepal and water/heptane/Igepal. The experiments performed in the two microemulsions covered a wide range of water-to-oil mass fraction for the two systems. The kinetic runs were monitored under pseudo-first order conditions by the stopped-flow technique. The equilibrium constants for the formation of purpuric acid and the kinetic constants for the ensuing decomposition reaction fulfill a trend consistent with the micro compartmentalized nature of the multicomponent medium, and support the use of murexide as an indicator of the proton activity in microemulsions.

  18. Kinetic discrimination in T-cell activation.

    PubMed Central

    Rabinowitz, J D; Beeson, C; Lyons, D S; Davis, M M; McConnell, H M

    1996-01-01

    We propose a quantitative model for T-cell activation in which the rate of dissociation of ligand from T-cell receptors determines the agonist and antagonist properties of the ligand. The ligands are molecular complexes between antigenic peptides and proteins of the major histocompatibility complex on the surfaces of antigen-presenting cells. Binding of ligand to receptor triggers a series of biochemical reactions in the T cell. If the ligand dissociates after these reactions are complete, the T cell receives a positive activation signal. However, dissociation of ligand after completion of the first reaction but prior to generation of the final products results in partial T-cell activation, which acts to suppress a positive response. Such a negative signal is brought about by T-cell ligands containing the variants of antigenic peptides referred to as T-cell receptor antagonists. Results of recent experiments with altered peptide ligands compare favorably with T-cell responses predicted by this model. PMID:8643643

  19. Pyrolysis characteristics and kinetics of Arundo donax using thermogravimetric analysis.

    PubMed

    Jeguirim, Mejdi; Trouvé, Gwenaelle

    2009-09-01

    The increase of the price of fossil means, as well as their programmed disappearing, contributed to increase among appliances based on biomass and energy crops. The thermal behavior of Arundo donax by thermogravimetric analysis was studied under inert atmosphere at heating rates ranging from 5 to 20 degrees C min(-1) from room temperature to 750 degrees C. Gaseous emissions as CO(2), CO and volatile organic compounds (VOC) were measured and global kinetic parameters were determined during pyrolysis with the study of the influence of the heating rate. The thermal process describes two main phases. The first phase named active zone, characterizes the degradation of hemicellulose and cellulose polymers. It started at low temperature (200 degrees C) comparatively to wood samples and was finished at 350 degrees C. The pyrolysis of the lignin polymer occurred during the second phase from 350 to 750 degrees C, named passive zone. Carbon oxides are emitted during the active zone whereas VOC are mainly formed during the passive zone. Mass losses, mass loss rates and emission factors were strongly affected by the variation of the heating rate in the active zone. It was found that the global pyrolysis of A. donax can be satisfactorily described using global independent reactions model for hemicellulose and cellulose in the active zone. The activation energy for hemicellulose was not affected by a variation of the heating rate with a value close to 110 kJ mol(-1) and presented a reaction order close to 0.5. An increase of the heating rate decreased the activation energy of the cellulose. However, a first reaction order was observed for cellulose decomposition. The experimental results and kinetic parameters may provide useful data for the design of pyrolytic processing system using A. donax as feedstock.

  20. 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.

  1. Kinetics of nucleotide entry into RNA polymerase active site provides mechanism for efficiency and fidelity.

    PubMed

    Wang, Beibei; Sexton, Rachel E; Feig, Michael

    2017-04-01

    During transcription, RNA polymerase II elongates RNA by adding nucleotide triphosphates (NTPs) complementary to a DNA template. Structural studies have suggested that NTPs enter and exit the active site via the narrow secondary pore but details have remained unclear. A kinetic model is presented that integrates molecular dynamics simulations with experimental data. Previous simulations of trigger loop dynamics and the dynamics of matched and mismatched NTPs in and near the active site were combined with new simulations describing NTP exit from the active site via the secondary pore. Markov state analysis was applied to identify major states and estimate kinetic rates for transitions between those states. The kinetic model predicts elongation and misincorporation rates in close agreement with experiment and provides mechanistic hypotheses for how NTP entry and exit via the secondary pore is feasible and a key feature for achieving high elongation and low misincorporation rates during RNA elongation.

  2. The roles of active-site residues in the catalytic mechanism of trans-3-chloroacrylic acid dehalogenase: a kinetic, NMR, and mutational analysis.

    PubMed

    Azurmendi, Hugo F; Wang, Susan C; Massiah, Michael A; Poelarends, Gerrit J; Whitman, Christian P; Mildvan, Albert S

    2004-04-13

    (G)) disappeared in the spectrum of the inactive alphaR8A mutant (deltaH = 7.48 ppm, deltaN = 89.6 ppm), thereby assigning these resonances to alphaArg-11NepsilonH, and alphaArg-8NepsilonH, respectively. (1)H-(15)N-HSQC titration of the enzyme with the substrate analogue 3-chloro-2-butenoic acid (3-CBA), a competitive inhibitor (K(I)(slope) = 0.35 +/- 0.06 mM), resulted in progressive downfield shifts of the alphaArg-8Nepsilon resonance yielding a K(D) = 0.77 +/- 0.44 mM, comparable to the (K(I)(slope), suggestive of active site binding. Increasing the pH of free CaaD to 8.9 at 5 degrees C resulted in the disappearance of all nine Arg-NepsilonH resonances due to base-catalyzed NepsilonH exchange. Saturating the enzyme with 3-CBA (16 mM) induced the reappearance of two NepsilonH signals, those of alphaArg-8 and alphaArg-11, indicating that the binding of the substrate analogue 3-CBA selectively slows the NepsilonH exchange rates of these two arginine residues. The kinetic and NMR data thus indicate that betaPro-1 is the acid catalyst, alphaGlu-52 is a reasonable candidate for the general base, and alphaArg-8 and alphaArg-11 participate in substrate binding and in stabilizing the aci-carboxylate intermediate in a Michael addition mechanism.

  3. Co-combustion of different sewage sludge and coal: a non-isothermal thermogravimetric kinetic analysis.

    PubMed

    Otero, M; Calvo, L F; Gil, M V; García, A I; Morán, A

    2008-09-01

    The kinetics of the combustion of coal, two different sewage sludge and their blends (containing different dried weight percentages of sewage sludge) was studied by simultaneous thermogravimetric analysis. Once the weight percentage of sludge in the blend was 10%, the effects on the combustion of coal were hardly noticeable in terms of weight loss. The Arrhenius activation energy corresponding to the co-combustion of the blends was evaluated by non-isothermal kinetic analysis. This showed that, though differences between coal and sewage sludge, the combustion of their blends kept kinetically alike to that of the coal. This work illustrates how thermogravimetric analysis may be used as an easy rapid tool to asses, not only mass loss, but also kinetics of the co-combustion of sewage sludge and coal blends.

  4. Norepinephrine metabolism in humans. Kinetic analysis and model

    SciTech Connect

    Linares, O.A.; Jacquez, J.A.; Zech, L.A.; Smith, M.J.; Sanfield, J.A.; Morrow, L.A.; Rosen, S.G.; Halter, J.B.

    1987-11-01

    The present study was undertaken to quantify more precisely and to begin to address the problem of heterogeneity of the kinetics of distribution and metabolism of norepinephrine (NE) in humans, by using compartmental analysis. Steady-state NE specific activity in arterialized plasma during (/sup 3/H)NE infusion and postinfusion plasma disappearance of (/sup 3/H)NE were measured in eight healthy subjects in the supine and upright positions. Two exponentials were clearly identified in the plasma (/sup 3/H)NE disappearance curves of each subject studied in the supine (r = 0.94-1.00, all P less than 0.01) and upright (r = 0.90-0.98, all P less than 0.01) positions. A two-compartment model was the minimal model necessary to simultaneously describe the kinetics of NE in the supine and upright positions. The NE input rate into the extravascular compartment 2, estimated with the minimal model, increased with upright posture (1.87 +/- 0.08 vs. 3.25 +/- 0.2 micrograms/min per m2, P less than 0.001). Upright posture was associated with a fall in the volume of distribution of NE in compartment 1 (7.5 +/- 0.6 vs. 4.7 +/- 0.3 liters, P less than 0.001), and as a result of that, there was a fall in the metabolic clearance rate of NE from compartment 1 (1.80 +/- 0.11 vs. 1.21 +/- 0.08 liters/min per m2, P less than 0.001). We conclude that a two-compartment model is the minimal model that can accurately describe the kinetics of distribution and metabolism of NE in humans.

  5. Activity Level-Dependent Synapse-Specific AMPA Receptor Trafficking Regulates Transmission Kinetics

    PubMed Central

    Zhu, J. Julius

    2009-01-01

    Central glutamatergic synapses may express AMPA-sensitive glutamate receptors (AMPA-Rs) with distinct gating properties and exhibit different transmission dynamics, which are important for computing various synaptic inputs received at different populations of synapses. However, how glutamatergic synapses acquire AMPA-Rs with distinct kinetics to influence synaptic integration remains poorly understood. Here I report synapse-specific trafficking of distinct AMPA-Rs in rat cortical layer 4 stellate and layer 5 pyramidal neurons. The analysis indicates that in single layer 4 stellate neurons thalamocortical synapses generate faster synaptic responses than intracortical synapses. Moreover, GluR1-containing AMPA-Rs traffic selectively into intracortical synapses, and this process requires sensory experience-dependent activity and slows down transmission kinetics. GluR4-containing AMPA-Rs traffic more heavily into thalamocortical synapses than intracortical synapses, and this process requires spontaneous synaptic activity and speeds up transmission kinetics. GluR2-containing AMPA-Rs traffic equally into both thalamocortical and intracortical synapses, and this process requires no synaptic activity and resets transmission kinetics. Notably, synaptic trafficking of distinct AMPA-Rs differentially regulates synaptic integration. Thus, synapse-specific AMPA-R trafficking coarsely sets and synaptic activity finely tunes transmission kinetics and integration properties at different synapses in central neurons. PMID:19439609

  6. Pyrolysis kinetic and product analysis of different microalgal biomass by distributed activation energy model and pyrolysis-gas chromatography-mass spectrometry.

    PubMed

    Yang, Xuewei; Zhang, Rui; Fu, Juan; Geng, Shu; Cheng, Jay Jiayang; Sun, Yuan

    2014-07-01

    To assess the energy potential of different microalgae, Chlorella sorokiniana and Monoraphidium were selected for studying the pyrolytic behavior at different heating rates with the analytical method of thermogravimetric analysis (TG), distributed activation energy model (DAEM) and pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS). Results presented that Monoraphidium 3s35 showed superiority for pyrolysis at low heating rate. Calculated by DAEM, during the conversion rate range from 0.1 to 0.7, the activation energies of C. sorokiniana 21 were much lower than that of Monoraphidium 3s35. Both C. sorokiniana 21 and Monoraphidium 3s35 can produce certain amount (up to 20.50%) of alkane compounds, with 9-Octadecyne (C18H34) as the primary compound. Short-chain alkanes (C7-C13) with unsaturated carbon can be released in the pyrolysis at 500°C for both microalgal biomass. It was also observed that the pyrolysis of C. sorokiniana 21 released more alcohol compounds, while Monoraphidium 3s35 produced more saccharides.

  7. Kinetic analysis of manure pyrolysis and combustion processes.

    PubMed

    Fernandez-Lopez, M; Pedrosa-Castro, G J; Valverde, J L; Sanchez-Silva, L

    2016-12-01

    Due to the depletion of fossil fuel reserves and the environmental issues derived from their use, biomass seems to be an excellent source of renewable energy. In this work, the kinetics of the pyrolysis and combustion of three different biomass waste samples (two dairy manure samples before (Pre) and after (Dig R) anaerobic digestion and one swine manure sample (SW)) was studied by means of thermogravimetric analysis. In this work, three iso-conversional methods (Friedman, Flynn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS)) were compared with the Coats-Redfern method. The Ea values of devolatilization stages were in the range of 152-170kJ/mol, 148-178kJ/mol and 156-209kJ/mol for samples Pre, Dig R and SW, respectively. Concerning combustion process, char oxidation stages showed lower Ea values than that obtained for the combustion devolatilization stage, being in the range of 140-175kJ/mol, 178-199kJ/mol and 122-144kJ/mol for samples Pre, Dig R and SW, respectively. These results were practically the same for samples Pre and Dig R, which means that the kinetics of the thermochemical processes were not affected by anaerobic digestion. Finally, the distributed activation energy model (DAEM) and the pseudo-multi component stage model (PMSM) were applied to predict the weight loss curves of pyrolysis and combustion. DAEM was the best model that fitted the experimental data.

  8. Antioxidant activity and kinetics studies of eugenol and 6-bromoeugenol.

    PubMed

    Mahboub, Radia; Memmou, Faiza

    2015-01-01

    In this work, we report the antioxidant and free radical scavenging activity of 6-bromoeugenol and eugenol. EC50, the concentration providing 50% inhibition, is calculated and the antioxidant activity index (AAI) is evaluated. The antioxidant activity was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging method. EC50 values of 6-bromoeugenol, ascorbic acid and eugenol were 34.270 μg/mL, 54.888 μg/mL and 130.485 μg/mL, respectively. 6-Bromoeugenol showed higher AAI value (1.122) followed by ascorbic acid (0.700), then by eugenol (0.295). We also investigate the kinetics of DPPH radical scavenging activity of our products to determine the useful parameter TEC50 to evaluate their antiradical efficiency (ARE). Our results have shown high ARE. This study has provided the following ARE ( × 10(-3)) order for the tested antioxidants: ascorbic acid (70.119)>6-bromoeugenol (34.842) > eugenol (21.313). Finally, we classify ascorbic acid and eugenol as fast kinetics reaction (TEC50 8.82 and 11.38 min, respectively) and 6-bromoeugenol as medium kinetics reaction (TEC50 39.24 min).

  9. Joint factor and kinetic analysis of dynamic FDOPA PET scans of brain cancer patients.

    PubMed

    Dowson, N; Bourgeat, P; Rose, S; Daglish, M; Smith, J; Fay, M; Coulthard, A; Winter, C; MacFarlane, D; Thomas, P; Crozier, S; Salvado, O

    2010-01-01

    Kinetic analysis is an essential tool of Positron Emission Tomography image analysis. However it requires a pure tissue time activity curve (TAC) in order to calculate the system parameters. Pure tissue TACs are particularly difficult to obtain in the brain as the low resolution of PET means almost all voxels are a mixture of tissues. Factor analysis explicitly accounts for mixing but is an underdetermined problem that can give arbitrary results. A joint factor and kinetic analysis is proposed whereby factor analysis explicitly accounts for mixing of tissues. Hence, more meaningful parameters are obtained by the kinetic models, which also ensure a less ambiguous solution to the factor analysis. The method was tested using a cylindrical phantom and the 18F-DOPA data of a brain cancer patient.

  10. Oxidation kinetics of ferrous sulfate over active carbon

    SciTech Connect

    Roennholm, M.R.; Waernaa, J.; Salmi, T.; Turunen, I.; Luoma, M.

    1999-07-01

    Catalyzed oxidation kinetics of dissolved Fe{sup 2+} ions to Fe{sup 3+} over active carbon in concentrated H{sub 2}SO{sub 4}-FeSO{sub 4} solutions was studied with isothermal and isobaric experiments carried out in a laboratory-scale pressurized autoclave. The experiments were performed at temperatures between 60 and 130 C, and the pressure of oxygen (O{sub 2}) was varied between 4 and 10 bar. The kinetic results revealed that the oxidation rate was enhanced by increasing the temperature and pressure and that the catalytic and noncatalytic oxidations proceed as parallel processes. A rate equation was obtained for the catalytic oxidation process, based on the assumption that the oxidation of Fe{sup 2+} with adsorbed oxygen is rate determining. The total oxidation rate was simulated by including a previously determined rate equation for the noncatalytic oxidation into the global model, from which the kinetic parameters of the catalytic oxidation rate were determined. A comparison of the model fit with the experimental data revealed that the proposed rate equation is applicable for the prediction of the Fe{sup 2+} oxidation kinetics in acidic ferrous sulfate solutions.

  11. Kinetic analysis of dynamic PET data

    SciTech Connect

    Knittel, B.

    1983-12-01

    Our goal is to quantify regional physiological processes such as blood flow and metabolism by means of tracer kinetic modeling and positron emission tomography (PET). Compartmental models are one way of characterizing the behavior of tracers in physiological systems. This paper describes a general method of estimating compartmental model rate constants from measurements of the concentration of tracers in blood and tissue, taken at multiple time intervals. A computer program which applies the method is described, and examples are shown for simulated and actual data acquired from the Donner 280-Crystal Positron Tomograph.

  12. Spectrum Analysis of Some Kinetic Equations

    NASA Astrophysics Data System (ADS)

    Yang, Tong; Yu, Hongjun

    2016-11-01

    We analyze the spectrum structure of some kinetic equations qualitatively by using semigroup theory and linear operator perturbation theory. The models include the classical Boltzmann equation for hard potentials with or without angular cutoff and the Landau equation with {γ≥q-2}. As an application, we show that the solutions to these two fundamental equations are asymptotically equivalent (mod time decay rate {t^{-5/4}}) as {tto∞} to that of the compressible Navier-Stokes equations for initial data around an equilibrium state.

  13. 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.

  14. Visual evaluation of kinetic characteristics of PET probe for neuroreceptors using a two-phase graphic plot analysis.

    PubMed

    Ito, Hiroshi; Ikoma, Yoko; Seki, Chie; Kimura, Yasuyuki; Kawaguchi, Hiroshi; Takuwa, Hiroyuki; Ichise, Masanori; Suhara, Tetsuya; Kanno, Iwao

    2017-02-08

    Objectives In PET studies for neuroreceptors, tracer kinetics are described by the two-tissue compartment model (2-TCM), and binding parameters, including the total distribution volume (V T), non-displaceable distribution volume (V ND), and binding potential (BPND), can be determined from model parameters estimated by kinetic analysis. The stability of binding parameter estimates depends on the kinetic characteristics of radioligands. To describe these kinetic characteristics, we previously developed a two-phase graphic plot analysis in which V ND and V T can be estimated from the x-intercept of regression lines for early and delayed phases, respectively. In this study, we applied this graphic plot analysis to visual evaluation of the kinetic characteristics of radioligands for neuroreceptors, and investigated a relationship between the shape of these graphic plots and the stability of binding parameters estimated by the kinetic analysis with 2-TCM in simulated brain tissue time-activity curves (TACs) with various binding parameters. Methods 90-min TACs were generated with the arterial input function and assumed kinetic parameters according to 2-TCM. Graphic plot analysis was applied to these simulated TACs, and the curvature of the plot for each TAC was evaluated visually. TACs with several noise levels were also generated with various kinetic parameters, and the bias and variation of binding parameters estimated by kinetic analysis were calculated in each TAC. These bias and variation were compared with the shape of graphic plots. Results The graphic plots showed larger curvature for TACs with higher specific binding and slower dissociation of specific binding. The quartile deviations of V ND and BPND determined by kinetic analysis were smaller for radioligands with slow dissociation. Conclusions The larger curvature of graphic plots for radioligands with slow dissociation might indicate a stable determination of V ND and BPND by kinetic analysis. For

  15. Kinetic compartmental analysis of carnitine metabolism in the dog

    SciTech Connect

    Rebouche, C.J.; Engel, A.G.

    1983-01-01

    This study was undertaken to quantitate the dynamic parameters of carnitine metabolism in the dog. Six mongrel dogs were given intravenous injections of L-(methyl-3H)carnitine and the specific radioactivity of carnitine was followed in plasma and urine for 19-28 days. The data were analyzed by kinetic compartmental analysis. A three-compartment, open-system model ((a) extracellular fluid, (b) cardiac and skeletal muscle, (c) other tissues, particularly liver and kidney) was adopted and kinetic parameters (carnitine flux, pool sizes, kinetic constants) were derived. In four of six dogs the size of the muscle carnitine pool obtained by kinetic compartmental analysis agreed (+/- 5%) with estimates based on measurement of carnitine concentrations in different muscles. In three of six dogs carnitine excretion rates derived from kinetic compartmental analysis agreed (+/- 9%) with experimentally measured values, but in three dogs the rates by kinetic compartmental analysis were significantly higher than the corresponding rates measured directly. Appropriate chromatographic analyses revealed no radioactive metabolites in muscle or urine of any of the dogs. Turnover times for carnitine were (mean +/- SEM): 0.44 +/- 0.05 h for extracellular fluid, 232 +/- 22 h for muscle, and 7.9 +/- 1.1 h for other tissues. The estimated flux of carnitine in muscle was 210 pmol/min/g of tissue. Whole-body turnover time for carnitine was 62.9 +/- 5.6 days (mean +/- SEM). Estimated carnitine biosynthesis ranged from 2.9 to 28 mumol/kg body wt/day. Results of this study indicate that kinetic compartmental analysis may be applicable to study of human carnitine metabolism.

  16. 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

  17. Continuum Theory of Phase Separation Kinetics for Active Brownian Particles

    NASA Astrophysics Data System (ADS)

    Stenhammar, Joakim; Tiribocchi, Adriano; Allen, Rosalind J.; Marenduzzo, Davide; Cates, Michael E.

    2013-10-01

    Active Brownian particles (ABPs), when subject to purely repulsive interactions, are known to undergo activity-induced phase separation broadly resembling an equilibrium (attraction-induced) gas-liquid coexistence. Here we present an accurate continuum theory for the dynamics of phase-separating ABPs, derived by direct coarse graining, capturing leading-order density gradient terms alongside an effective bulk free energy. Such gradient terms do not obey detailed balance; yet we find coarsening dynamics closely resembling that of equilibrium phase separation. Our continuum theory is numerically compared to large-scale direct simulations of ABPs and accurately accounts for domain growth kinetics, domain topologies, and coexistence densities.

  18. Adsorption of chromium onto activated alumina: kinetics and thermodynamics studies.

    PubMed

    Marzouk, Ikhlass; Dammak, Lassaad; Hamrouni, Béchir

    2013-02-01

    In this study, the removal of chromium (VI) by adsorption on activated alumina was investigated and the results were fitted to Langmuir, Freundlich, Dubinin-Redushkevich, and Temkin adsorption models at various temperatures. The constants of each model were evaluated depending on temperature. Thermodynamic parameters for the adsorption system were determined at 10, 25 and 40 degrees C. (deltaH degrees = -21.18 kJ x mol(-1); deltaG degrees = -8.75 to -7.43 kJ x mol(-1) and deltaS degrees = -0.043 kJ x K(-1) x mol(-1)). The obtained values showed that chromium (VI) adsorption is a spontaneous and exothermic process. The kinetic process was evaluated by first-order, second-order and Elovich kinetic models.

  19. Kinetics of enzyme action on surface-attached substrates: a practical guide to progress curve analysis in any kinetic situation.

    PubMed

    Anne, Agnès; Demaille, Christophe

    2012-10-16

    In the present work, exact kinetic equations describing the action of an enzyme in solution on a substrate attached to a surface have been derived in the framework of the Michaelis-Menten mechanism but without resorting to the often-used steady-state approximation. The here-derived kinetic equations are cast in a workable format, allowing us to introduce a simple and universal procedure for the quantitative analysis of enzyme surface kinetics that is valid for any kinetic situation. The results presented here should allow experimentalists studying the kinetics of enzyme action on immobilized substrates to analyze their data in a perfectly rigorous way.

  20. Rethinking growth and decay kinetics in activated sludge - towards a new adaptive kinetics approach.

    PubMed

    Friedrich, Michael; Jimenez, Jose; Pruden, Amy; Miller, Jennifer H; Metch, Jacob; Takács, Imre

    2017-02-01

    Growth kinetics in activated sludge modelling (ASM) are typically assumed to be the result of intrinsic growth and decay properties and thus process parameters are deemed to be constant. The activity change in a microbial population is expressed in terms of variance of the active biomass fraction and not actual shifts in bacterial cellular activities. This approach is limited, in that it does not recognise the reality that active biomass is highly physiologically adaptive. Here, a strong correlation between maximum specific growth rate (μmax) and decay rate (be) of ordinary heterotrophic organisms was revealed in both low solids retention times (SRT) and high SRT activated sludge systems. This relationship is indicative of physiological adaptation either for growth (high μmax and be) or survival optimization (low μmax and be). Further, the nitrifier decay process was investigated using molecular techniques to measure decay rates of ammonia oxidizing bacteria and nitrite oxidizing bacteria over a range of temperatures. This approach revealed decay rates 10-12% lower than values previously accepted and used in ASM. These findings highlight potential benefits of incorporating physiological adaptation of heterotrophic and nitrifying populations in future ASM.

  1. Triacylglycerol kinetics in endotoxic rats with suppressed lipoprotein lipase activity

    SciTech Connect

    Bagby, G.J.; Corll, C.B.; Martinez, R.R.

    1987-07-01

    Hypertriglyceridemia observed in animals after bacterial endotoxin administration and some forms of sepsis can result from increased hepatic triacylglycerol (TG) output or decreased TG clearance by extrahepatic tissues. To differentiate between these two possibilities, TG and free fatty acid (FFA) kinetics were determined in control and endotoxin-injected rats 18 h after treatment. Plasma TG and FFA kinetics were assessed by a constant intravenous infusion with (9,10-/sup 3/H)palmitate-labeled very low-density lipoprotein and (1-/sup 14/C)palmitate bound to albumin, respectively. In addition, lipoprotein lipase (LPL) activity was determined in heart, skeletal muscle, and adipose tissue as well as in postheparin plasma of functionally hepatectomized, adrenalectomized, and gonadectomized rats. Plasma FFA acid concentrations were slightly increased in endotoxin-treated rats but their turnover did not differ from control. Endotoxin-treated rats had a threefold increase in plasma TG concentrations and decreased heart, skeletal muscle, and post-heparin plasma LPL activity. Plasma TG turnover was decreased, indicating that hypertriglyceridemia was not due to an increased TG output by the liver. Instead, the endotoxin-induced increase in plasma TG concentration was consequence of the 80% reduction in TG metabolic clearance rate. Thus, suppression of LPL activity in endotoxic animals impairs TG clearance resulting in hypertriglyceridemia. Furthermore, endotoxin administration reduced the delivery of TG-FFA to extrahepatic tissues because hepatic synthesis and secretion of TG from plasma FFA was decreased and LPL activity was suppressed.

  2. Comparative evaluation of adsorption kinetics of diclofenac and isoproturon by activated carbon.

    PubMed

    Torrellas, Silvia A; Rodriguez, Araceli R; Escudero, Gabriel O; Martín, José María G; Rodriguez, Juan G

    2015-01-01

    Adsorption mechanism of diclofenac and isoproturon onto activated carbon has been proposed using Langmuir and Freundlich isotherms. Adsorption capacity and optimum adsorption isotherms were predicted by nonlinear regression method. Different kinetic equations, pseudo-first-order, pseudo-second-order, intraparticle diffusion model and Bangham kinetic model, were applied to study the adsorption kinetics of emerging contaminants on activated carbon in two aqueous matrices.

  3. Kinetic, Mutational, and Structural Analysis of Malonate Semialdehyde Decarboxylase from Coryneform bacterium strain FG41: Mechanistic Implications for the Decarboxylase and Hydratase Activities

    PubMed Central

    Guo, Youzhong; Serrano, Hector; Poelarends, Gerrit J.; Johnson, William H.; Hackert, Marvin L.; Whitman, Christian P.

    2013-01-01

    Malonate semialdehyde decarboxylase from Pseudomonas pavonaceae 170 (designated Pp MSAD) is in a bacterial catabolic pathway for the nematicide 1,3-dichloropropene. MSAD has two known activities: it catalyzes the metal-ion independent decarboxylation of malonate semialdehyde to produce acetaldehyde and carbon dioxide, as well as a low-level hydration of 2-oxo-3-pentynoate to yield acetopyruvate. The latter activity is not known to be biologically relevant. Previous studies identified Pro-1, Asp-37, and a pair of arginines (Arg-73 and Arg-75) as critical residues in these activities. MSAD from Coryneform bacterium strain FG41 (designated FG41 MSAD) shares 38% pairwise sequence identity with the Pseudomonas enzyme including Pro-1 and Asp-37. However, Gln-73 replaces Arg-73, and the second arginine is shifted to Arg-76 by the insertion of a glycine. In order to determine how these changes relate to the activities of FG41 MSAD, the gene was cloned and the enzyme expressed and characterized. The enzyme has a comparable decarboxylase activity, but a significantly reduced hydratase activity. Mutagenesis along with crystal structures of the native enzyme (2.0 Å resolution) and the enzyme modified by a 3-oxopropanoate moiety (resulting from the incubation of enzyme and 3-bromopropiolate) (2.2 Å resolution) provided a structural basis. The roles of Pro-1 and Asp-37 are likely the same as those proposed for MSAD. However, the side chains of Thr-72, Gln-73, and Tyr-123 replace those of Arg-73 and Arg-75 in the mechanism and play a role in binding and catalysis. The structures also show that Arg-76 is likely too distant to play a direct role in the mechanism. FG41 MSAD is the second functionally annotated homologue in the MSAD family of the tautomerase superfamily and could represent a new subfamily. PMID:23781927

  4. [Calmodulin can induce and control damping oscillations in the plasma membrane Ca2+ -ATPase activity: a kinetic model].

    PubMed

    Gol'dshtein, B N; Aksirov, A M; Zakrzhevskaia, D T

    2007-01-01

    Plasma membrane Ca2+-ATPase is the calcium pump that extrudes calcium ions from cells using ATP hydrolisis for the maintenance of low Ca2+ concentrations in the cell. Calmodulin stimulates Ca2+-ATPase by binding to the autoinhibitory enzyme domain, which allows the access of cytoplasmic ATP and Ca2+ to the active and transport cites. Our kinetic model predicts damped oscillations in the enzyme activity and interprets the known nonmonotonous kinetic behavior of the enzyme in the presence of calmodulin. For the parameters close to the experimental ones, the kinetic model explains the changes in frequency and damping factor of the oscillatory enzyme activity, as dependent on calmodulin concentration. The calculated pre-steady-state curves fit well the known experimental data. The kinetic analysis allows us to assign Ca2+-ATPase to the hysteretic enzymes exhibiting activity oscillations in open systems.

  5. A KINETIC ANALYSIS OF THE CONFORMATIONAL FLEXIBILITY OF STEROID HORMONES

    EPA Science Inventory

    For a set of 10 androgen steroids and estradiol (E2), the kinetic feasibility of conformation flexibility of the cyclic moieties was studied under the constraint of maintaining the B/C trans and C/D trans ring fusion of the natural and biologically active enantiomer. To this end,...

  6. Investigation kinetics mechanisms of adsorption malachite green onto activated carbon.

    PubMed

    Onal, Y; Akmil-Başar, C; Sarici-Ozdemir, C

    2007-07-19

    Lignite was used to prepare activated carbon (T3K618) by chemical activation with KOH. Pore properties of the activated carbon such as BET surface area, pore volume, pore size distribution, and pore diameter were characterized by t-plot based on N2 adsorption isotherm. BET surface area of activated carbon is determined as 1000 m2/g. Adsorption capacity of malachite green (MG) onto T3K618 activated carbon was investigated in a batch system by considering the effects of various parameters like initial concentration (100, 150 and 200 mg/L) and temperature (25, 40 and 50 degrees C). The adsorption process was relatively fast and equilibrium was reached after about 20 min for 100, 150 mg/L at all adsorption temperature. Equilibrium time for 200 mg/L was determined as 20 min and 40 min at 298, 313 and 323 K, respectively. Simple mass and kinetic models were applied to the experimental data to examine the mechanisms of adsorption and potential rate controlling steps such as external mass transfer, intraparticle diffusion. Pseudo second-order model was found to explain the kinetics of MG adsorption most effectively. It was found that both mass transfer and pore diffusion are important in determining the adsorption rates. The intraparticle diffusion rate constant, external mass transfer coefficient, film and pore diffusion coefficient at various temperatures were evaluated. The activation energy (Ea) was determined as 48.56, 63.16, 67.93 kJ/mol for 100, 150, 200 mg/L, respectively. The Langmiur and Freundlich isotherm were used to describe the adsorption equilibrium studies at different temperatures. Langmiur isotherm shows better fit than Freundlich isotherm in the temperature range studied. The thermodynamic parameters, such as DeltaG degrees, DeltaS and DeltaH degrees were calculated. The thermodynamics of dyes-T3K618 system indicates endothermic process.

  7. Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity.

    PubMed

    Breit, Marc; Netzer, Michael; Weinberger, Klaus M; Baumgartner, Christian

    2015-08-01

    The objectives of this work were the classification of dynamic metabolic biomarker candidates and the modeling and characterization of kinetic regulatory mechanisms in human metabolism with response to external perturbations by physical activity. Longitudinal metabolic concentration data of 47 individuals from 4 different groups were examined, obtained from a cycle ergometry cohort study. In total, 110 metabolites (within the classes of acylcarnitines, amino acids, and sugars) were measured through a targeted metabolomics approach, combining tandem mass spectrometry (MS/MS) with the concept of stable isotope dilution (SID) for metabolite quantitation. Biomarker candidates were selected by combined analysis of maximum fold changes (MFCs) in concentrations and P-values resulting from statistical hypothesis testing. Characteristic kinetic signatures were identified through a mathematical modeling approach utilizing polynomial fitting. Modeled kinetic signatures were analyzed for groups with similar behavior by applying hierarchical cluster analysis. Kinetic shape templates were characterized, defining different forms of basic kinetic response patterns, such as sustained, early, late, and other forms, that can be used for metabolite classification. Acetylcarnitine (C2), showing a late response pattern and having the highest values in MFC and statistical significance, was classified as late marker and ranked as strong predictor (MFC = 1.97, P < 0.001). In the class of amino acids, highest values were shown for alanine (MFC = 1.42, P < 0.001), classified as late marker and strong predictor. Glucose yields a delayed response pattern, similar to a hockey stick function, being classified as delayed marker and ranked as moderate predictor (MFC = 1.32, P < 0.001). These findings coincide with existing knowledge on central metabolic pathways affected in exercise physiology, such as β-oxidation of fatty acids, glycolysis, and glycogenolysis. The presented modeling approach

  8. Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity

    PubMed Central

    Breit, Marc; Netzer, Michael

    2015-01-01

    The objectives of this work were the classification of dynamic metabolic biomarker candidates and the modeling and characterization of kinetic regulatory mechanisms in human metabolism with response to external perturbations by physical activity. Longitudinal metabolic concentration data of 47 individuals from 4 different groups were examined, obtained from a cycle ergometry cohort study. In total, 110 metabolites (within the classes of acylcarnitines, amino acids, and sugars) were measured through a targeted metabolomics approach, combining tandem mass spectrometry (MS/MS) with the concept of stable isotope dilution (SID) for metabolite quantitation. Biomarker candidates were selected by combined analysis of maximum fold changes (MFCs) in concentrations and P-values resulting from statistical hypothesis testing. Characteristic kinetic signatures were identified through a mathematical modeling approach utilizing polynomial fitting. Modeled kinetic signatures were analyzed for groups with similar behavior by applying hierarchical cluster analysis. Kinetic shape templates were characterized, defining different forms of basic kinetic response patterns, such as sustained, early, late, and other forms, that can be used for metabolite classification. Acetylcarnitine (C2), showing a late response pattern and having the highest values in MFC and statistical significance, was classified as late marker and ranked as strong predictor (MFC = 1.97, P < 0.001). In the class of amino acids, highest values were shown for alanine (MFC = 1.42, P < 0.001), classified as late marker and strong predictor. Glucose yields a delayed response pattern, similar to a hockey stick function, being classified as delayed marker and ranked as moderate predictor (MFC = 1.32, P < 0.001). These findings coincide with existing knowledge on central metabolic pathways affected in exercise physiology, such as β-oxidation of fatty acids, glycolysis, and glycogenolysis. The presented modeling approach

  9. Kinetic analysis of complex metabolic networks

    SciTech Connect

    Stephanopoulos, G.

    1996-12-31

    A new methodology is presented for the analysis of complex metabolic networks with the goal of metabolite overproduction. The objective is to locate a small number of reaction steps in a network that have maximum impact on network flux amplification and whose rate can also be increased without functional network derangement. This method extends the concepts of Metabolic Control Analysis to groups of reactions and offers the means for calculating group control coefficients as measures of the control exercised by groups of reactions on the overall network fluxes and intracellular metabolite pools. It is further demonstrated that the optimal strategy for the effective increase of network fluxes, while maintaining an uninterrupted supply of intermediate metabolites, is through the coordinated amplification of multiple (as opposed to a single) reaction steps. Satisfying this requirement invokes the concept of the concentration control to coefficient, which emerges as a critical parameter in the identification of feasible enzymatic modifications with maximal impact on the network flux. A case study of aromatic aminoacid production is provided to illustrate these concepts.

  10. Kinetic Analysis of Membrane Potential Dye Response to NaV1.7 Channel Activation Identifies Antagonists with Pharmacological Selectivity against NaV1.5.

    PubMed

    Finley, Michael; Cassaday, Jason; Kreamer, Tony; Li, Xinnian; Solly, Kelli; O'Donnell, Greg; Clements, Michelle; Converso, Antonella; Cook, Sean; Daley, Chris; Kraus, Richard; Lai, Ming-Tain; Layton, Mark; Lemaire, Wei; Staas, Donnette; Wang, Jixin

    2016-06-01

    The NaV1.7 voltage-gated sodium channel is a highly valued target for the treatment of neuropathic pain due to its expression in pain-sensing neurons and human genetic mutations in the gene encoding NaV1.7, resulting in either loss-of-function (e.g., congenital analgesia) or gain-of-function (e.g., paroxysmal extreme pain disorder) pain phenotypes. We exploited existing technologies in a novel manner to identify selective antagonists of NaV1.7. A full-deck high-throughput screen was developed for both NaV1.7 and cardiac NaV1.5 channels using a cell-based membrane potential dye FLIPR assay. In assay development, known local anesthetic site inhibitors produced a decrease in maximal response; however, a subset of compounds exhibited a concentration-dependent delay in the onset of the response with little change in the peak of the response at any concentration. Therefore, two methods of analysis were employed for the screen: one to measure peak response and another to measure area under the curve, which would capture the delay-to-onset phenotype. Although a number of compounds were identified by a selective reduction in peak response in NaV1.7 relative to 1.5, the AUC measurement and a subsequent refinement of this measurement were able to differentiate compounds with NaV1.7 pharmacological selectivity over NaV1.5 as confirmed in electrophysiology.

  11. Quantifying a pathway: kinetic analysis of actin dendritic nucleation.

    PubMed

    Kraikivski, Pavel; Slepchenko, Boris M

    2010-08-04

    Progress in uncovering the reaction networks that underlie important cell functions is laying the groundwork for quantitative identification of protein-interaction pathways. Since direct measurement of rate constants is not always feasible, the parameters are often inferred from multiple pieces of data using kinetic analyses based on appropriate mathematical models. The success of this approach relies on the sufficiency of available experimental data for a unique parameterization of the network. The concept of a rate-limiting step is applied to the analysis of experimental data that are usually used to quantify a pathway of actin dendritic nucleation, the Arp2/3-mediated mechanism that enables rapid changes of cell shape in response to external cues. The method yields analytical descriptions of the dynamics of polymerized actin and provides insights into how the experimental curves should be analyzed. It is shown that dynamics measured by pyrene-labeled actin assays with varying Arp2/3 concentrations are equally well described by two different rate-limiting steps: 1), binding of a nucleating complex to the side of a preexisting filament; or 2), its subsequent activation. To distinguish between the alternatives, we propose experiments with varying concentrations of actin monomers, taking advantage of the fact that the number of branches in the two cases depends differently on the initial monomer concentration. The idea is tested by simulating the proposed experiments with the use of spatial stochastic modeling.

  12. Thermal Decomposition of Thermoelectric Material CoSb3: A Thermogravimetry Kinetic Analysis

    NASA Astrophysics Data System (ADS)

    Wu, Fang; He, Qingli; Hu, Dinxu; Gao, Feng; Song, Hongzhang; Jia, Jianfeng; Hu, Xing

    2013-08-01

    The thermal decomposition of the thermoelectric CoSb3 alloy was investigated using thermogravimetry (TG). TG curves obtained in inert gas flow with different heating rates were used to perform kinetic analysis based on the Arrhenius equation. Kinetic parameters, such as the effective activation energy, the pre-exponential factor, and the kinetic model function f(α ) , were obtained using the Freeman-Carroll method, the multiheating rates method, and the Coats-Redfern equation. The activation energy was found to be around 200 kJ/mol, and the reaction mechanism for the decomposition of CoSb3 alloy mostly obeys the second-order chemical decomposition process f(α ) = (1 - α )2.

  13. Physiological adaptation of growth kinetics in activated sludge.

    PubMed

    Friedrich, M; Takács, I; Tränckner, J

    2015-11-15

    Physiological adaptation as it occurs in bacterial cells at variable environmental conditions influences characteristic properties of growth kinetics significantly. However, physiological adaptation to growth related parameters in activated sludge modelling is not yet recognised. Consequently these parameters are regarded to be constant. To investigate physiological adaptation in activated sludge the endogenous respiration in an aerobic degradation batch experiment and simultaneous to that the maximum possible respiration in an aerobic growth batch experiment was measured. The activated sludge samples were taken from full scale wastewater treatment plants with different sludge retention times (SRTs). It could be shown that the low SRT sludge adapts by growth optimisation (high maximum growth rate and high decay rate) to its particular environment where a high SRT sludge adapts by survival optimization (low maximum growth rate and low decay rate). Thereby, both the maximum specific growth rate and the decay rate vary in the same pattern and are strongly correlated to each other. To describe the physiological state of mixed cultures like activated sludge quantitatively a physiological state factor (PSF) is proposed as the ratio of the maximum specific growth rate and the decay rate. The PSF can be expressed as an exponential function with respect to the SRT.

  14. 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

  15. Active colloids in the context of chemical kinetics

    NASA Astrophysics Data System (ADS)

    Oshanin, G.; Popescu, M. N.; Dietrich, S.

    2017-03-01

    We study a mesoscopic model of a chemically active colloidal particle which on certain parts of its surface promotes chemical reactions in the surrounding solution. For reasons of simplicity and conceptual clarity, we focus on the case in which only electrically neutral species are present in the solution and on chemical reactions which are described by first order kinetics. Within a self-consistent approach we explicitly determine the steady state product and reactant number density fields around the colloid as functionals of the interaction potentials of the various molecular species in solution with the colloid. By using a reciprocal theorem, this allows us to compute and to interpret—in a transparent way in terms of the classical Smoluchowski theory of chemical kinetics—the external force needed to keep such a catalytically active colloid at rest (stall force) or, equivalently, the corresponding velocity of the colloid if it is free to move. We use the particular case of triangular-well interaction potentials as a benchmark example for applying the general theoretical framework developed here. For this latter case, we derive explicit expressions for the dependences of the quantities of interest on the diffusion coefficients of the chemical species, the reaction rate constant, the coverage by catalyst, the size of the colloid, as well as on the parameters of the interaction potentials. These expressions provide a detailed picture of the phenomenology associated with catalytically-active colloids and self-diffusiophoresis.

  16. Comparative kinetic analysis of silent and ultrasound-assisted catalytic wet peroxide oxidation of phenol.

    PubMed

    Rokhina, Ekaterina V; Repo, Eveliina; Virkutyte, Jurate

    2010-03-01

    The kinetic study of silent and ultrasound-assisted catalytic wet peroxide oxidation of phenol in water was performed to qualitatively assess the effect of ultrasound on the process kinetics. Various kinetic parameters such as the apparent kinetic rate constants, the surface utilization coefficient and activation energy of phenol oxidation over RuI(3) catalyst were investigated. Comparative analysis revealed that the use of ultrasound irradiation reduced the energy barrier of the reaction but had no impact on the reaction pathway. The activation energy for the oxidation of phenol over RuI(3) catalyst in the presence of ultrasound was found to be 13kJmol(-1), which was four times smaller in comparison to the silent oxidation process (57kJmol(-1)). Finally, 'figures-of-merit' was utilized to assess different experimental strategies such as sonolysis alone, H(2)O(2)-enhanced sonolysis and sono-catalytic oxidation of phenol in order to estimate the electric energy consumption based on the kinetic rate constants of the oxidation process.

  17. Kinetic analysis of the multistep aggregation mechanism of monoclonal antibodies.

    PubMed

    Nicoud, Lucrèce; Arosio, Paolo; Sozo, Margaux; Yates, Andrew; Norrant, Edith; Morbidelli, Massimo

    2014-09-11

    We investigate by kinetic analysis the aggregation mechanism of two monoclonal antibodies belonging to the IgG1 and IgG2 subclass under thermal stress. For each IgG, we apply a combination of size exclusion chromatography and light scattering techniques to resolve the time evolution of the monomer, dimer, and trimer concentrations, as well as the average molecular weight and the average hydrodynamic radius of the aggregate distribution. By combining the detailed experimental characterization with a theoretical kinetic model based on population balance equations, we extract relevant information on the contribution of the individual elementary steps on the global aggregation process. The analysis shows that the two molecules follow different aggregation pathways under the same operating conditions. In particular, while the monomer depletion of the IgG1 is found to be rate-limited by monomeric conformational changes, bimolecular collision is identified as the rate-limiting step in the IgG2 aggregation process. The measurement of the microscopic rate constants by kinetic analysis allows the quantification of the protein-protein interaction potentials expressed in terms of the Fuchs stability ratio (W). It is found that the antibody solutions exhibit large W values, which are several orders of magnitude larger than the values computed in the frame of the DLVO theory. This indicates that, besides net electrostatic repulsion, additional effects delay the aggregation kinetics of the antibody solutions with respect to diffusion-limited conditions. These effects likely include the limited efficiency of the collision events due to the presence of a limited number of specific aggregation-prone patches on the heterogeneous protein surface, and the contribution of additional repulsive non-DLVO forces to the protein-protein interaction potential, such as hydration forces.

  18. Measurements of cloud condensation nuclei activity and droplet activation kinetics of wet processed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2011-04-01

    This study reports laboratory measurements of particle size distributions, cloud condensation nuclei (CCN) activity, and droplet activation kinetics of wet generated aerosols from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. The dependence of critical supersaturation, sc, on particle dry diameter, Ddry, is used to characterize particle-water interactions and assess the ability of Frenkel-Halsey-Hill adsorption activation theory (FHH-AT) and Köhler theory (KT) to describe the CCN activity of the considered samples. Regional dust samples produce unimodal size distributions with particle sizes as small as 40 nm, CCN activation consistent with KT, and exhibit hygroscopicity similar to inorganic salts. Clays and minerals produce a bimodal size distribution; the CCN activity of the smaller mode is consistent with KT, while the larger mode is less hydrophilic, follows activation by FHH-AT, and displays almost identical CCN activity to dry generated dust. Ion Chromatography (IC) analysis performed on regional dust samples indicates a soluble fraction that cannot explain the CCN activity of dry or wet generated dust. A mass balance and hygroscopicity closure suggests that the small amount of ions (of low solubility compounds like calcite) present in the dry dust dissolve in the aqueous suspension during the wet generation process and give rise to the observed small hygroscopic mode. Overall these results identify an artifact that may question the atmospheric relevance of dust CCN activity studies using the wet generation method. Based on a threshold droplet growth analysis, wet generated mineral aerosols display similar activation kinetics compared to ammonium sulfate calibration aerosol. Finally, a unified CCN activity framework that accounts for concurrent effects of solute and adsorption is developed to describe the CCN activity of aged or hygroscopic dusts.

  19. LSENS, The NASA Lewis Kinetics and Sensitivity Analysis Code

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, K.

    2000-01-01

    A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS (the NASA Lewis kinetics and sensitivity analysis code), are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include: static system; steady, one-dimensional, inviscid flow; incident-shock initiated reaction in a shock tube; and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method (LSODE, the Livermore Solver for Ordinary Differential Equations), which works efficiently for the extremes of very fast and very slow reactions, is used to solve the "stiff" ordinary differential equation systems that arise in chemical kinetics. For static reactions, the code uses the decoupled direct method to calculate sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters. Solution methods for the equilibrium and post-shock conditions and for perfectly stirred reactor problems are either adapted from or based on the procedures built into the NASA code CEA (Chemical Equilibrium and Applications).

  20. NMR analysis of staphylococcal nuclease thermal quench refolding kinetics.

    PubMed

    Kautz, R A; Fox, R O

    1993-05-01

    Thermally unfolded staphylococcal nuclease has been rapidly quenched to temperatures near 0 degree C and the refolding behavior examined using an NMR kinetic experiment. Unfolded protein, exhibiting random coil chemical shifts, persists following the quench and refolds in two distinct kinetic phases. A protein folding intermediate with a trans Lys 116-Pro 117 peptide bond is transiently overpopulated and relaxes to the predominantly cis native cis-trans equilibrium. The rate of trans-->cis isomerization in the native-like nuclease intermediate is approximately 100-fold faster than that observed in a Lys-Pro model peptide. The activation enthalpy of 20 kcal/mol observed for the nuclease Lys 116-Pro 117 peptide bond is comparable to that observed for other X-Pro isomerizations.

  1. Kinetic phosphorescence analysis to quantify europium and terbium

    SciTech Connect

    Beck, Chelsie; Seiner, Brienne; Smith, Steven; Bowen, James; Finch, Zach; Friese, Judah

    2015-09-04

    The ability to measure europium and terbium may be confounded by the presence of other lanthanides when using spectroscopic techniques such as optical emission spectroscopy, especially at trace levels. Kinetic Phosphorescence Analysis (KPA) offers a method to avoid these interferences during trace level measurements. This study examined analysis parameters for Eu and Tb by testing the effects of different acids, molarities, and the use of a complexing agent to determine the ideal conditions and limits of detection for each analyte in samples containing various mixtures of lanthanides.

  2. Fluctuation Analysis: Dissecting Transcriptional Kinetics with Signal Theory.

    PubMed

    Coulon, A; Larson, D R

    2016-01-01

    Recent live-cell microscopy techniques now allow the visualization in multiple colors of RNAs as they are transcribed on genes of interest. Following the number of nascent RNAs over time at a single locus reveals complex fluctuations originating from the underlying transcriptional kinetics. We present here a technique based on concepts from signal theory-called fluctuation analysis-to analyze and interpret multicolor transcriptional time traces and extract the temporal signatures of the underlying mechanisms. The principle is to generate, from the time traces, a set of functions called correlation functions. We explain how to compute these functions practically from a set of experimental traces and how to interpret them through different theoretical and computational means. We also present the major difficulties and pitfalls one might encounter with this technique. This approach is capable of extracting mechanistic information hidden in transcriptional fluctuations at multiple timescales and has broad applications for understanding transcriptional kinetics.

  3. Towards a quantitative kinetic theory of polar active matter

    NASA Astrophysics Data System (ADS)

    Ihle, T.

    2014-06-01

    A recent kinetic approach for Vicsek-like models of active particles is reviewed. The theory is based on an exact Chapman- Kolmogorov equation in phase space. It can handle discrete time dynamics and "exotic" multi-particle interactions. A nonlocal mean-field theory for the one-particle distribution function is obtained by assuming molecular chaos. The Boltzmann approach of Bertin, et al., Phys. Rev. E 74, 022101 (2006) and J. Phys. A 42, 445001 (2009), is critically assessed and compared to the current approach. In Boltzmann theory, a collision starts when two particles enter each others action spheres and is finished when their distance exceeds the interaction radius. The average duration of such a collision, τ0, is measured for the Vicsek model with continuous time-evolution. If the noise is chosen to be close to the flocking threshold, the average time between collisions is found to be roughly equal to τ0 at low densities. Thus, the continuous-time Vicsek-model near the flocking threshold cannot be accurately described by a Boltzmann equation, even at very small density because collisions take so long that typically other particles join in, rendering Boltzmann's binary collision assumption invalid. Hydrodynamic equations for the phase space approach are derived by means of a Chapman-Enskog expansion. The equations are compared to the Toner-Tu theory of polar active matter. New terms, absent in the Toner-Tu theory, are highlighted. Convergence problems of Chapman-Enskog and similar gradient expansions are discussed.

  4. Measurements of cloud condensation nuclei activity and droplet activation kinetics of fresh unprocessed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2010-12-01

    This study reports laboratory measurements of cloud condensation nuclei (CCN) activity and droplet activation kinetics of aerosols dry-generated from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. Based on the observed dependence of critical supersaturation, sc, with particle dry diameter, Ddry, we find that FHH adsorption activation theory is a far more suitable framework for describing fresh dust CCN activity than Köhler theory. One set of FHH parameters (AFFH ~ 2.25 ± 0.75, BFFH ~ 1.20 ± 0.10) can adequately reproduce the measured CCN activity for all species considered, and also explains the large range of hygroscopicities reported in the literature. Based on threshold droplet growth analysis, mineral dust aerosols were found to display retarded activation kinetics compared to ammonium sulfate. Comprehensive simulations of mineral dust activation and growth in the CCN instrument suggest that this retardation is equivalent to a reduction of the water vapor uptake coefficient (relative to that for calibration ammonium sulfate aerosol) by 30-80%. These results suggest that dust particles do not require deliquescent material to act as CCN in the atmosphere.

  5. Measurements of cloud condensation nuclei activity and droplet activation kinetics of fresh unprocessed regional dust samples and minerals

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Sokolik, I. N.; Nenes, A.

    2011-04-01

    This study reports laboratory measurements of cloud condensation nuclei (CCN) activity and droplet activation kinetics of aerosols dry generated from clays, calcite, quartz, and desert soil samples from Northern Africa, East Asia/China, and Northern America. Based on the observed dependence of critical supersaturation, sc, with particle dry diameter, Ddry, we found that FHH (Frenkel, Halsey and Hill) adsorption activation theory is a far more suitable framework for describing fresh dust CCN activity than Köhler theory. One set of FHH parameters (AFHH ∼ 2.25 ± 0.75, BFHH ∼ 1.20 ± 0.10) can adequately reproduce the measured CCN activity for all species considered, and also explains the large range of hygroscopicities reported in the literature. Based on a threshold droplet growth analysis, mineral dust aerosols were found to display retarded activation kinetics compared to ammonium sulfate. Comprehensive simulations of mineral dust activation and growth in the CCN instrument suggest that this retardation is equivalent to a reduction of the water vapor uptake coefficient (relative to that for calibration ammonium sulfate aerosol) by 30-80%. These results suggest that dust particles do not require deliquescent material to act as CCN in the atmosphere.

  6. Kinetic analysis of supine stepping for early rehabilitation of walking.

    PubMed

    Fang, Juan; Galen, Sujay; Vuckovic, Aleksandra; Conway, Bernard A; Hunt, Kenneth J

    2014-05-01

    In order to promote gait restoration in patients who cannot maintain an upright position in the early post-injury phase, a Gait Orthosis for Early Rehabilitation was proposed for supine stepping. Although supine stepping can generate lower-limb joint trajectories which are close to normal gait, the inter-segmental dynamics of supine stepping are believed to be different from those of upright walking. Furthermore, training in a supine position requires a certain loading on the foot to mimic the ground reaction forces, where different loading amplitudes influence the joint dynamics. This work analysed the kinetics of supine stepping with variable loading and investigated structural modifications for the Gait Orthosis for Early Rehabilitation system to address this kinetic difference. Three able-bodied subjects walked overground while their walking performance was recorded. Based on the experimental data, a leg-linkage model was developed to simulate the dynamics of upright walking. This model was then rotated by 90° with different foot loadings to investigate the kinetics of supine stepping. Compared to upright walking, supine stepping had a large kinetic difference at the hip joint due to the supine leg position. The ankle joint during supine stepping was sensitive to the force amplitude simulated on the foot. Thus, the Gait Orthosis for Early Rehabilitation system requires a leg frame to compensate the position change and a shoe platform to activate the leg muscles, especially at the ankle joint. This study provided important structural information for the further development of the Gait Orthosis for Early Rehabilitation system.

  7. Platelet-activating factor-induced increases in glucose kinetics

    SciTech Connect

    Lang, C.H.; Dobrescu, C.; Hargrove, D.M.; Bagby, G.J.; Spitzer, J.J. )

    1988-02-01

    Platelet-activating factor (PAF) is a postulated mediator of many of the early hemodynamic effects of endotoxin. The aim of the present study was to determine whether in vivo administration of PAF could produce alterations in whole-body glucose metabolism that would mimic those seen during endotoxemia. Glucose kinetics were assessed in chronically catheterized conscious rats by the constant infusion of (6-{sup 3}H)- and (U-{sup 14}C)glucose before and for 4 h after either a bolus injection or a constant infusion of PAF. The bolus injection of PAF elevated the rate of glucose appearance (R{sub a}; 44%) for 1.5 h. The lower PAF infusion rate decreased blood pressure 11% to 104 mmHg, whereas the higher infusion rate decreased pressure 34% to 77 mmHg. Both PAF infusion rates produced elevations in plasma glucose and glucose R{sub a} throughout the 4-h infusion period in a dose-related manner. The PAF infusions also induced dose-related increases in plasma glucagon and catecholamine levels throughout the infusion period. Because the constant infusion of PAF did stimulate many of the hemodynamic and metabolic alterations produced by endotoxin, this study provides additional support for the potential importance of PAF as a mediator of the early hemodynamic and metabolic sequela of endotoxin shock. Furthermore, the PAF-induced changes in glucose metabolism appear to be mediated by the resultant elevation in plasma catecholamines.

  8. Kinetic analysis of barium currents in chick cochlear hair cells.

    PubMed Central

    Zidanic, M; Fuchs, P A

    1995-01-01

    Inward barium current (IBa) through voltage-gated calcium channels was recorded from chick cochlear hair cells using the whole-cell clamp technique. IBa was sensitive to dihydropyridines and insensitive to the peptide toxins omega-agatoxin IVa, omega-conotoxin GVIa, and omega-conotoxin MVIIC. Changing the holding potential over a -40 to -80 mV range had no effect on the time course or magnitude of IBa nor did it reveal any inactivating inward currents. The activation of IBa was modeled with Hodgkin-Huxley m2 kinetics. The time constant of activation, tau m, was 550 microseconds at -30 mV and gradually decreased to 100 microseconds at +50 mV. A Boltzmann fit to the activation curve, m infinity, yielded a half activation voltage of -15 mV and a steepness factor of 7.8 mV. Opening and closing rate constants, alpha m and beta m, were calculated from tau m and m infinity, then fit with modified exponential functions. The H-H model derived by evaluating the exponential functions for alpha m and beta m not only provided an excellent fit to the time course of IBa activation, but was predictive of the time course and magnitude of the IBa tail current. No differences in kinetics or voltage dependence of activation of IBa were found between tall and short hair cells. We conclude that both tall and short hair cells of the chick cochlea predominantly, if not exclusively, express noninactivating L-type calcium channels. These channels are therefore responsible for processes requiring voltage-dependent calcium entry through the basolateral cell membrane, such as transmitter release and activation of Ca(2+)-dependent K+ channels. PMID:7787021

  9. Kinetic analysis of two dimensional metallic grating Cerenkov maser

    SciTech Connect

    Zhao Ding

    2011-08-15

    The dispersion relation of two dimensional metallic grating Cerenkov maser has been given by using kinetic analysis, in which the influence of electron movement is directly considered without using an equivalent dielectric medium assumption. The effects of structural parameters and beam state on the interaction gain and synchronous frequency have also been investigated in detail by numerical calculations. To an illustrative case, the quantitative relations produced from varying the gap distance between electron beam and metallic grating, beam current, electron transverse to axial velocity ratio, and electron axial velocity spread have been obtained. The developed method can be used to predict the real interaction system performances.

  10. Kinetics of the Factor XIa catalyzed activation of human blood coagulation Factor IX

    SciTech Connect

    Walsh, P.N.; Bradford, H.; Sinha, D.; Piperno, J.R.; Tuszynski, G.P.

    1984-05-01

    The kinetics of activation of human Factor IX by human Factor XIa was studied by measuring the release of a trichloroacetic acid-soluble tritium-labeled activation peptide from Factor IX. Initial rates of trichloroacetic acid-soluble /sup 3/H-release were linear over 10-30 min of incubation of Factor IX (88 nM) with CaCl/sub 2/ (5 mM) and with pure (greater than 98%) Factor XIa (0.06-1.3 nM), which was prepared by incubating human Factor XI with bovine Factor XIIa. Release of /sup 3/H preceded the appearance of Factor IXa activity, and the percentage of /sup 3/H released remained constant when the mole fraction of /sup 3/H-labeled and unlabeled Factor IX was varied and the total Factor IX concentration remained constant. A linear correlation (r greater than 0.98, P less than 0.001) was observed between initial rates of /sup 3/H-release and the concentration of Factor XIa, measured by chromogenic assay and by radioimmunoassay and added at a Factor IX:Factor XIa molar ratio of 70-5,600. Kinetic parameters, determined by Lineweaver-Burk analysis, include K/sub m/ (0.49 microM) of about five- to sixfold higher than the plasma Factor IX concentration, which could therefore regulate the reaction. The catalytic constant (k/sub cat/) (7.7/s) is approximately 20-50 times higher than that reported by Zur and Nemerson for Factor IX activation by Factor VIIa plus tissue factor. Therefore, depending on the relative amounts of Factor XIa and Factor VIIa generated in vivo and other factors which may influence reaction rates, these kinetic parameters provide part of the information required for assessing the relative contributions of the intrinsic and extrinsic pathways to Factor IX activation, and suggest that the Factor XIa catalyzed reaction is physiologically significant.

  11. Interactions of xanthines with activated carbon. I. Kinetics of the adsorption process

    NASA Astrophysics Data System (ADS)

    Navarrete Casas, R.; García Rodriguez, A.; Rey Bueno, F.; Espínola Lara, A.; Valenzuela Calahorro, C.; Navarrete Guijosa, A.

    2006-06-01

    Because of their pharmaceutical and industrial applications, we have studied the adsorption of xanthine derivates (caffeine and theophylline) by activated carbon. To this end, we examined kinetic, equilibrium and thermodynamic aspects of the process. This paper reports the kinetics results. The experimental results indicate that the process was first order in C and the overall process was assumed to involve a single, reversible adsorption-desorption process obeying a kinetic law postulated by us.

  12. Kinetic study of solid waste pyrolysis using distributed activation energy model.

    PubMed

    Bhavanam, Anjireddy; Sastry, R C

    2015-02-01

    The pyrolysis characteristics of municipal solid waste, agricultural residues such as ground nut shell, cotton husk and their blends are investigated using non-isothermal thermogravimetric analysis (TGA) with in a temperature range of 30-900 °C at different heating rates of 10 °C, 30 °C and 50 °C/min in inert atmosphere. From the thermograms obtained from TGA, it is observed that the maximum rate of degradation occurred in the second stage of the pyrolysis process for all the solid wastes. The distributed activation energy model (DAEM) is used to study the pyrolysis kinetics of the solid wastes. The kinetic parameters E (activation energy), k0 (frequency factor) are calculated from this model. It is found that the range of activation energies for agricultural residues are lower than the municipal solid waste. The activation energies for the municipal solid waste pyrolysis process drastically decreased with addition of agricultural residues. The proposed DAEM is successfully validated with TGA experimental data.

  13. A thermogravimetric analysis of the combustion kinetics of karanja (Pongamia pinnata) fruit hulls char.

    PubMed

    Islam, Md Azharul; Auta, M; Kabir, G; Hameed, B H

    2016-01-01

    The combustion characteristics of Karanj fruit hulls char (KFH-char) was investigated with thermogravimetry analysis (TGA). The TGA outlined the char combustion thermographs at a different heating rate and isoconversional methods expressed the combustion kinetics. The Kissinger-Akahira-Sunose (KAS) and Flynn-Wall-Ozawa (FWO) methods authenticated the char average activation energy at 62.13 and 68.53kJ/mol respectively, enough to derive the char to burnout. However, the Coats-Redfern method verified the char combustion via complex multi-step mechanism; the second stage mechanism has 135kJ/mol average activation energy. The TGA thermographs and kinetic parameters revealed the adequacy of the KFH-char as fuel substrate than its precursor, Karanj fruit hulls (KFH).

  14. Dissecting the Catalytic Mechanism of Trypanosoma brucei Trypanothione Synthetase by Kinetic Analysis and Computational Modeling*

    PubMed Central

    Leroux, Alejandro E.; Haanstra, Jurgen R.; Bakker, Barbara M.; Krauth-Siegel, R. Luise

    2013-01-01

    In pathogenic trypanosomes, trypanothione synthetase (TryS) catalyzes the synthesis of both glutathionylspermidine (Gsp) and trypanothione (bis(glutathionyl)spermidine (T(SH)2)). Here we present a thorough kinetic analysis of Trypanosoma brucei TryS in a newly developed phosphate buffer system at pH 7.0 and 37 °C, mimicking the physiological environment of the enzyme in the cytosol of bloodstream parasites. Under these conditions, TryS displays Km values for GSH, ATP, spermidine, and Gsp of 34, 18, 687, and 32 μm, respectively, as well as Ki values for GSH and T(SH)2 of 1 mm and 360 μm, respectively. As Gsp hydrolysis has a Km value of 5.6 mm, the in vivo amidase activity is probably negligible. To obtain deeper insight in the molecular mechanism of TryS, we have formulated alternative kinetic models, with elementary reaction steps represented by linear kinetic equations. The model parameters were fitted to the extensive matrix of steady-state data obtained for different substrate/product combinations under the in vivo-like conditions. The best model describes the full kinetic profile and is able to predict time course data that were not used for fitting. This system's biology approach to enzyme kinetics led us to conclude that (i) TryS follows a ter-reactant mechanism, (ii) the intermediate Gsp dissociates from the enzyme between the two catalytic steps, and (iii) T(SH)2 inhibits the enzyme by remaining bound at its product site and, as does the inhibitory GSH, by binding to the activated enzyme complex. The newly detected concerted substrate and product inhibition suggests that TryS activity is tightly regulated. PMID:23814051

  15. 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

  16. Adaptive approach for nonlinear sensitivity analysis of reaction kinetics.

    PubMed

    Horenko, Illia; Lorenz, Sönke; Schütte, Christof; Huisinga, Wilhelm

    2005-07-15

    We present a unified approach for linear and nonlinear sensitivity analysis for models of reaction kinetics that are stated in terms of systems of ordinary differential equations (ODEs). The approach is based on the reformulation of the ODE problem as a density transport problem described by a Fokker-Planck equation. The resulting multidimensional partial differential equation is herein solved by extending the TRAIL algorithm originally introduced by Horenko and Weiser in the context of molecular dynamics (J. Comp. Chem. 2003, 24, 1921) and discussed it in comparison with Monte Carlo techniques. The extended TRAIL approach is fully adaptive and easily allows to study the influence of nonlinear dynamical effects. We illustrate the scheme in application to an enzyme-substrate model problem for sensitivity analysis w.r.t. to initial concentrations and parameter values.

  17. Evaluation of kinetic phosphorescence analysis for the determination of uranium

    SciTech Connect

    Croatto, P.V.; Frank, I.W.; Johnson, K.D.; Mason, P.B.; Smith, M.M.

    1997-12-01

    In the past, New Brunswick Laboratory (NBL) has used a fluorometric method for the determination of sub-microgram quantities of uranium. In its continuing effort to upgrade and improve measurement technology, NBL has evaluated the commercially-available KPA-11 kinetic phosphorescence analyzer (Chemchek, Richland, WA). The Chemchek KPA-11 is a bench-top instrument which performs single-measurement, quench-corrected analyses for trace uranium. It incorporates patented kinetic phosphorimetry techniques to measure and analyze sample phosphorescence as a function of time. With laser excitation and time-corrected photon counting, the KPA-11 has a lower detection limit than conventional fluorometric methods. Operated with a personal computer, the state-of-the-art KPA-11 offers extensive time resolution and phosphorescence lifetime capabilities for additional specificity. Interferences are thereby avoided while obtaining precise measurements. Routine analyses can be easily and effectively accomplished, with the accuracy and precision equivalent to the pulsed-laser fluorometric method presently performed at NBL, without the need for internal standards. Applications of kinetic phosphorimetry at NBL include the measurement of trace level uranium in retention tank, waste samples, and low-level samples. It has also been used to support other experimental activities at NBL by the measuring of nanogram amounts of uranium contamination (in blanks) in isotopic sample preparations, and the determining of elution curves of different ion exchange resins used for uranium purification. In many cases, no pretreatment of samples was necessary except to fume them with nitric acid, and then to redissolve and dilute them to an appropriate concentration with 1 M HNO{sub 3} before measurement. Concentrations were determined on a mass basis ({micro}g U/g of solution), but no density corrections were needed since all the samples (including the samples used for calibration) were in the same

  18. A Simple and Fast Kinetic Assay for the Determination of Fructan Exohydrolase Activity in Perennial Ryegrass (Lolium perenne L.).

    PubMed

    Gasperl, Anna; Morvan-Bertrand, Annette; Prud'homme, Marie-Pascale; van der Graaff, Eric; Roitsch, Thomas

    2015-01-01

    Despite the fact that fructans are the main constituent of water-soluble carbohydrates in forage grasses and cereal crops of temperate climates, little knowledge is available on the regulation of the enzymes involved in fructan metabolism. The analysis of enzyme activities involved in this process has been hampered by the low affinity of the fructan enzymes for sucrose and fructans used as fructosyl donor. Further, the analysis of fructan composition and enzyme activities is restricted to specialized labs with access to suited HPLC equipment and appropriate fructan standards. The degradation of fructan polymers with high degree of polymerization (DP) by fructan exohydrolases (FEHs) to fructosyloligomers is important to liberate energy in the form of fructan, but also under conditions where the generation of low DP polymers is required. Based on published protocols employing enzyme coupled endpoint reactions in single cuvettes, we developed a simple and fast kinetic 1-FEH assay. This assay can be performed in multi-well plate format using plate readers to determine the activity of 1-FEH against 1-kestotriose, resulting in a significant time reduction. Kinetic assays allow an optimal and more precise determination of enzyme activities compared to endpoint assays, and enable to check the quality of any reaction with respect to linearity of the assay. The enzyme coupled kinetic 1-FEH assay was validated in a case study showing the expected increase in 1-FEH activity during cold treatment. This assay is cost effective and could be performed by any lab with access to a plate reader suited for kinetic measurements and readings at 340 nm, and is highly suited to assess temporal changes and relative differences in 1-FEH activities. Thus, this enzyme coupled kinetic 1-FEH assay is of high importance both to the field of basic fructan research and plant breeding.

  19. A Simple and Fast Kinetic Assay for the Determination of Fructan Exohydrolase Activity in Perennial Ryegrass (Lolium perenne L.)

    PubMed Central

    Gasperl, Anna; Morvan-Bertrand, Annette; Prud’homme, Marie-Pascale; Roitsch, Thomas

    2015-01-01

    Despite the fact that fructans are the main constituent of water-soluble carbohydrates in forage grasses and cereal crops of temperate climates, little knowledge is available on the regulation of the enzymes involved in fructan metabolism. The analysis of enzyme activities involved in this process has been hampered by the low affinity of the fructan enzymes for sucrose and fructans used as fructosyl donor. Further, the analysis of fructan composition and enzyme activities is restricted to specialized labs with access to suited HPLC equipment and appropriate fructan standards. The degradation of fructan polymers with high degree of polymerization (DP) by fructan exohydrolases (FEHs) to fructosyloligomers is important to liberate energy in the form of fructan, but also under conditions where the generation of low DP polymers is required. Based on published protocols employing enzyme coupled endpoint reactions in single cuvettes, we developed a simple and fast kinetic 1-FEH assay. This assay can be performed in multi-well plate format using plate readers to determine the activity of 1-FEH against 1-kestotriose, resulting in a significant time reduction. Kinetic assays allow an optimal and more precise determination of enzyme activities compared to endpoint assays, and enable to check the quality of any reaction with respect to linearity of the assay. The enzyme coupled kinetic 1-FEH assay was validated in a case study showing the expected increase in 1-FEH activity during cold treatment. This assay is cost effective and could be performed by any lab with access to a plate reader suited for kinetic measurements and readings at 340 nm, and is highly suited to assess temporal changes and relative differences in 1-FEH activities. Thus, this enzyme coupled kinetic 1-FEH assay is of high importance both to the field of basic fructan research and plant breeding. PMID:26734049

  20. Fluctuation analysis of motor protein movement and single enzyme kinetics.

    PubMed Central

    Svoboda, K; Mitra, P P; Block, S M

    1994-01-01

    We studied fluctuations in the displacement of silica beads driven by single molecules of the motor protein kinesin, moving under low mechanical loads at saturating ATP concentrations. The variance in position was significantly smaller than expected for the case of stepwise movement along a regular lattice of positions with exponentially distributed intervals. The small variance suggests that two or more sequential processes with comparable reaction rates dominate the biochemical cycle. The low value is inconsistent with certain recently proposed thermal ratchet models for motor movement as well as with scenarios where the hydrolysis of a single ATP molecule leads to a cluster of several steps. Fluctuation analysis is a potential powerful tool for studying kinetic behavior whenever the output of a single enzyme can be monitored. PMID:7991536

  1. An integral turbulent kinetic energy analysis of free shear flows

    NASA Technical Reports Server (NTRS)

    Peters, C. E.; Phares, W. J.

    1973-01-01

    Mixing of coaxial streams is analyzed by application of integral techniques. An integrated turbulent kinetic energy (TKE) equation is solved simultaneously with the integral equations for the mean flow. Normalized TKE profile shapes are obtained from incompressible jet and shear layer experiments and are assumed to be applicable to all free turbulent flows. The shear stress at the midpoint of the mixing zone is assumed to be directly proportional to the local TKE, and dissipation is treated with a generalization of the model developed for isotropic turbulence. Although the analysis was developed for ducted flows, constant-pressure flows were approximated with the duct much larger than the jet. The axisymmetric flows under consideration were predicted with reasonable accuracy. Fairly good results were also obtained for the fully developed two-dimensional shear layers, which were computed as thin layers at the boundary of a large circular jet.

  2. Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics

    PubMed Central

    Prescott, Aaron M.; McCollough, Forest W.; Eldreth, Bryan L.; Binder, Brad M.; Abel, Steven M.

    2016-01-01

    Most models for ethylene signaling involve a linear pathway. However, measurements of seedling growth kinetics when ethylene is applied and removed have resulted in more complex network models that include coherent feedforward, negative feedback, and positive feedback motifs. The dynamical responses of the proposed networks have not been explored in a quantitative manner. Here, we explore (i) whether any of the proposed models are capable of producing growth-response behaviors consistent with experimental observations and (ii) what mechanistic roles various parts of the network topologies play in ethylene signaling. To address this, we used computational methods to explore two general network topologies: The first contains a coherent feedforward loop that inhibits growth and a negative feedback from growth onto itself (CFF/NFB). In the second, ethylene promotes the cleavage of EIN2, with the product of the cleavage inhibiting growth and promoting the production of EIN2 through a positive feedback loop (PFB). Since few network parameters for ethylene signaling are known in detail, we used an evolutionary algorithm to explore sets of parameters that produce behaviors similar to experimental growth response kinetics of both wildtype and mutant seedlings. We generated a library of parameter sets by independently running the evolutionary algorithm many times. Both network topologies produce behavior consistent with experimental observations, and analysis of the parameter sets allows us to identify important network interactions and parameter constraints. We additionally screened these parameter sets for growth recovery in the presence of sub-saturating ethylene doses, which is an experimentally-observed property that emerges in some of the evolved parameter sets. Finally, we probed simplified networks maintaining key features of the CFF/NFB and PFB topologies. From this, we verified observations drawn from the larger networks about mechanisms underlying ethylene

  3. Piezoresistive microcantilever aptasensor for ricin detection and kinetic analysis

    NASA Astrophysics Data System (ADS)

    Liu, Zhi-Wei; Tong, Zhao-Yang; Liu, Bing; Hao, Lan-Qun; Mu, Xi-Hui; Zhang, Jin-Ping; Gao, Chuan

    2015-04-01

    Up to now, there has been no report on target molecules detection by a piezoresistive microcantilever aptasensor. In order to evaluate the test performance and investigate the response dynamic characteristics of a piezoresistive microcantilever aptasensor, a novel method for ricin detection and kinetic analysis based on a piezoresistive microcantilever aptasensor was proposed, where ricin aptamer was immobilised on the microcantilever surface by biotin-avidin binding system. Results showed that the detection limit of ricin was 0.04μg L-1 (S/N ≥ 3). A linear relationship between the response voltage and the concentration of ricin in the range of 0.2μg L-1-40μg L-1 was obtained, with the linear regression equation of ΔUe = 0.904C + 5.852 (n = 5, R = 0.991, p < 0.001). The sensor showed no response for abrin, BSA, and could overcome the influence of complex environmental disruptors, indicating high specificity and good selectivity. Recovery and reproducibility in the result of simulated samples (simulated water, soil, and flour sample) determination met the analysis requirements, which was 90.5˜95.5% and 7.85%˜9.39%, respectively. On this basis, a reaction kinetic model based on ligand-receptor binding and the relationship with response voltage was established. The model could well reflect the dynamic response of the sensor. The correlation coefficient (R) was greater than or equal to 0.9456 (p < 0.001). Response voltage (ΔUe) and response time (t0) obtained from the fitting equation on different concentrations of ricin fitted well with the measured values.

  4. [Kinetics of in vitro bactericidal activity of the antiseptic biseptine combining 3 active principles].

    PubMed

    Reverdy, M E; Rougier, M; Fleurette, J

    1996-09-01

    Biseptine, is an association of chlorhexidine digluconate, benzalkonium chloride and benzylic alcohol. Little is known, in literature, on this antiseptic, used for cutaneous antisepsis. We studied killing kinetic of Biseptine, at different concentrations, on 4 AFNOR bacterial strains. Killing curves were studied at antiseptic concentration of 90 to 0.1% in 10 ml of distilled water. Bacterial counts were determined after neutralization in liquid medium. Synergy of chlorhexidine and benzalkonium chloride in Biseptine, allowed to obtain similar bactericidal activity than Hibitane champ with chlorhexidine concentrations 2 fold less. At 90, 50, 25, 10 and 5% concentrations, bactericidal activity (5 log10 reduction of the initial bacterial count) was effective in one minute. After 5 to 15 minutes, activity persisted at 1 and 0.5% concentrations. The 0.1% solution was inefficacious. This report disclosed an important security margin in antiseptic activity.

  5. Bioregeneration of activated carbon and activated rice husk loaded with phenolic compounds: Kinetic modeling.

    PubMed

    Ng, S L; Seng, C E; Lim, P E

    2010-01-01

    A kinetic model consisting of first-order desorption and biodegradation processes was developed to describe the bioregeneration of phenol- and p-nitrophenol-loaded powdered activated carbon (PAC) and pyrolyzed rice husk (PRH), respectively. Different dosages of PAC and PRH were loaded with phenol or p-nitrophenol by contacting with the respective phenolic compound at various concentrations. The kinetic model was used to fit the phenol or p-nitrophenol concentration data in the bulk solution during the bioregeneration process to determine the rate constants of desorption, k(d), and biodegradation, k. The results showed that the kinetic model fitted relatively well (R(2)>0.9) to the experimental data for the phenol- and p-nitrophenol-loaded PAC as well as p-nitrophenol-loaded PRH. Comparison of the values of k(d) and k shows that k is much greater than k(d). This indicates clearly that the desorption process is the rate-determining step in bioregeneration and k(d) can be used to characterize the rate of bioregeneration. The trend of the variation of the k(d) values with the dosages of PAC or PRH used suggests that higher rate of bioregeneration can be achieved under non-excess adsorbent dosage condition.

  6. Modeling high adsorption capacity and kinetics of organic macromolecules on super-powdered activated carbon.

    PubMed

    Matsui, Yoshihiko; Ando, Naoya; Yoshida, Tomoaki; Kurotobi, Ryuji; Matsushita, Taku; Ohno, Koichi

    2011-02-01

    The capacity to adsorb natural organic matter (NOM) and polystyrene sulfonates (PSSs) on small particle-size activated carbon (super-powdered activated carbon, SPAC) is higher than that on larger particle-size activated carbon (powdered-activated carbon, PAC). Increased adsorption capacity is likely attributable to the larger external surface area because the NOM and PSS molecules do not completely penetrate the adsorbent particle; they preferentially adsorb near the outer surface of the particle. In this study, we propose a new isotherm equation, the Shell Adsorption Model (SAM), to explain the higher adsorption capacity on smaller adsorbent particles and to describe quantitatively adsorption isotherms of activated carbons of different particle sizes: PAC and SPAC. The SAM was verified with the experimental data of PSS adsorption kinetics as well as equilibrium. SAM successfully characterized PSS adsorption isotherm data for SPACs and PAC simultaneously with the same model parameters. When SAM was incorporated into an adsorption kinetic model, kinetic decay curves for PSSs adsorbing onto activated carbons of different particle sizes could be simultaneously described with a single kinetics parameter value. On the other hand, when SAM was not incorporated into such an adsorption kinetic model and instead isotherms were described by the Freundlich model, the kinetic decay curves were not well described. The success of the SAM further supports the adsorption mechanism of PSSs preferentially adsorbing near the outer surface of activated carbon particles.

  7. Bioleaching kinetics and multivariate analysis of spent petroleum catalyst dissolution using two acidophiles.

    PubMed

    Pradhan, Debabrata; Mishra, Debaraj; Kim, Dong J; Ahn, Jong G; Chaudhury, G Roy; Lee, Seoung W

    2010-03-15

    Bioleaching studies were conducted to evaluate the recovery of metal values from waste petroleum catalyst using two different acidophilic microorganisms, Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans. Various leaching parameters such as contact time, pH, oxidant concentration, pulp densities, particle size, and temperature were studied in detail. Activation energy was evaluated from Arrhenius equation and values for Ni, V and Mo were calculated in case of both the acidophiles. In both cases, the dissolution kinetics of Mo was lower than those of V and Ni. The lower dissolution kinetics may have been due to the formation of a sulfur product layer, refractoriness of MoS(2) or both. Multivariate statistical data were presented to interpret the leaching data in the present case. The significance of the leaching parameters was derived through principle component analysis and multi linear regression analyses for both iron and sulfur oxidizing bacteria.

  8. Anion exchange kinetics of nanodimensional layered metal hydroxides: use of isoconversional analysis.

    PubMed

    Majoni, Stephen; Hossenlopp, Jeanne M

    2010-12-16

    Anion exchange reactions of nanodimensional layered metal hydroxide compounds are utilized to create materials with targeted physical and chemical properties and also as a means for controlled release of intercalated anions. The kinetics of this important class of reaction are generally characterized by model-based approaches. In this work, a different approach based on isothermal, isoconversional analysis was utilized to determine effective activation energies with respect to extent of reaction. Two different layered metal hydroxide materials were chosen for reaction with chloride anions, using a temperature range of 30-60 °C. The concentrations of anions released into solution and the changes in polycrystalline solid phases were evaluated using model-based (Avrami-Erofe'ev nucleation-growth model) and model-free (integral isoconversional) methods. The results demonstrate the utility of the isoconversional approach for identifying when fitting to a single model is not appropriate, particularly for characterizing the temperature dependence of the reaction kinetics.

  9. Color changes in wood during heating: kinetic analysis by applying a time-temperature superposition method

    NASA Astrophysics Data System (ADS)

    Matsuo, Miyuki; Yokoyama, Misao; Umemura, Kenji; Gril, Joseph; Yano, Ken'ichiro; Kawai, Shuichi

    2010-04-01

    This paper deals with the kinetics of the color properties of hinoki ( Chamaecyparis obtusa Endl.) wood. Specimens cut from the wood were heated at 90-180°C as accelerated aging treatment. The specimens completely dried and heated in the presence of oxygen allowed us to evaluate the effects of thermal oxidation on wood color change. Color properties measured by a spectrophotometer showed similar behavior irrespective of the treatment temperature with each time scale. Kinetic analysis using the time-temperature superposition principle, which uses the whole data set, was successfully applied to the color changes. The calculated values of the apparent activation energy in terms of L *, a *, b *, and Δ E^{*}_{ab} were 117, 95, 114, and 113 kJ/mol, respectively, which are similar to the values of the literature obtained for other properties such as the physical and mechanical properties of wood.

  10. Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

    PubMed

    Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

    2017-01-25

    This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

  11. Thermogravimetric analysis and kinetic study of bamboo waste treated by Echinodontium taxodii using a modified three-parallel-reactions model.

    PubMed

    Yu, Hongbo; Liu, Fang; Ke, Ming; Zhang, Xiaoyu

    2015-06-01

    In this study, the effect of pretreatment with Echinodontium taxodii on thermal decomposition characteristics and kinetics of bamboo wastes was investigated by thermogravimetric analysis. The results showed fungal pretreatment can enhance the thermal degradation of bamboo. The negative effect of extractives in bamboo on the thermal decomposition can be decreased by the pretreatment. A modified three-parallel-reactions model based on isolated lignin was firstly proposed to study pyrolysis kinetics of bamboo lignocellulose. Kinetic analysis showed that with increasing pretreatment time fungal delignification was enhanced to transform the lignin component with high activation energy into that with low activation energy and raise the cellulose content in bamboo, making the thermal decomposition easier. These results demonstrated fungal pretreatment provided a potential way to improve thermal conversion efficiency of bamboo.

  12. Kinetic modeling and sensitivity analysis of plasma-assisted combustion

    NASA Astrophysics Data System (ADS)

    Togai, Kuninori

    Plasma-assisted combustion (PAC) is a promising combustion enhancement technique that shows great potential for applications to a number of different practical combustion systems. In this dissertation, the chemical kinetics associated with PAC are investigated numerically with a newly developed model that describes the chemical processes induced by plasma. To support the model development, experiments were performed using a plasma flow reactor in which the fuel oxidation proceeds with the aid of plasma discharges below and above the self-ignition thermal limit of the reactive mixtures. The mixtures used were heavily diluted with Ar in order to study the reactions with temperature-controlled environments by suppressing the temperature changes due to chemical reactions. The temperature of the reactor was varied from 420 K to 1250 K and the pressure was fixed at 1 atm. Simulations were performed for the conditions corresponding to the experiments and the results are compared against each other. Important reaction paths were identified through path flux and sensitivity analyses. Reaction systems studied in this work are oxidation of hydrogen, ethylene, and methane, as well as the kinetics of NOx in plasma. In the fuel oxidation studies, reaction schemes that control the fuel oxidation are analyzed and discussed. With all the fuels studied, the oxidation reactions were extended to lower temperatures with plasma discharges compared to the cases without plasma. The analyses showed that radicals produced by dissociation of the reactants in plasma plays an important role of initiating the reaction sequence. At low temperatures where the system exhibits a chain-terminating nature, reactions of HO2 were found to play important roles on overall fuel oxidation. The effectiveness of HO2 as a chain terminator was weakened in the ethylene oxidation system, because the reactions of C 2H4 + O that have low activation energies deflects the flux of O atoms away from HO2. For the

  13. Kinetic Activation-Relaxation Technique and Self-Evolving Atomistic Kinetic Monte Carlo: Comparison of on-the-fly kinetic Monte Carlo algorithms

    DOE PAGES

    Beland, Laurent Karim; Osetskiy, Yury N.; Stoller, Roger E.; ...

    2015-02-07

    Here, we present a comparison of the Kinetic Activation–Relaxation Technique (k-ART) and the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC), two off-lattice, on-the-fly Kinetic Monte Carlo (KMC) techniques that were recently used to solve several materials science problems. We show that if the initial displacements are localized the dimer method and the Activation–Relaxation Technique nouveau provide similar performance. We also show that k-ART and SEAKMC, although based on different approximations, are in agreement with each other, as demonstrated by the examples of 50 vacancies in a 1950-atom Fe box and of interstitial loops in 16,000-atom boxes. Generally speaking, k-ART’s treatment ofmore » geometry and flickers is more flexible, e.g. it can handle amorphous systems, and rigorous than SEAKMC’s, while the later’s concept of active volumes permits a significant speedup of simulations for the systems under consideration and therefore allows investigations of processes requiring large systems that are not accessible if not localizing calculations.« less

  14. Kinetic Activation-Relaxation Technique and Self-Evolving Atomistic Kinetic Monte Carlo: Comparison of on-the-fly kinetic Monte Carlo algorithms

    SciTech Connect

    Beland, Laurent Karim; Osetskiy, Yury N.; Stoller, Roger E.; Xu, Haixuan

    2015-02-07

    Here, we present a comparison of the Kinetic Activation–Relaxation Technique (k-ART) and the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC), two off-lattice, on-the-fly Kinetic Monte Carlo (KMC) techniques that were recently used to solve several materials science problems. We show that if the initial displacements are localized the dimer method and the Activation–Relaxation Technique nouveau provide similar performance. We also show that k-ART and SEAKMC, although based on different approximations, are in agreement with each other, as demonstrated by the examples of 50 vacancies in a 1950-atom Fe box and of interstitial loops in 16,000-atom boxes. Generally speaking, k-ART’s treatment of geometry and flickers is more flexible, e.g. it can handle amorphous systems, and rigorous than SEAKMC’s, while the later’s concept of active volumes permits a significant speedup of simulations for the systems under consideration and therefore allows investigations of processes requiring large systems that are not accessible if not localizing calculations.

  15. Iso-conversional kinetic analysis of quaternary glass re-crystallization.

    PubMed

    Srivastava, Ankita; Chandel, Namrata; Mehta, Neeraj

    2017-02-01

    Iso-conversional kinetic analysis is popular in scientific community for analyzing solid-state reactions (e.g., glass/amorphous and amorphous/crystal phase transformations, re-crystallization etc). It is a recognized significant tool to achieve useful outcomes for the solid state reaction under consideration. Present work is devoted to explore some insights of thermally activated crystallization using various heating rates (VHR) method. We have examined the correlation between iso-conversional activation energy and iso-conversional rate of crystal growth. In fact, we have observed the compensation law and iso-kinetic relationship using two different approaches for the study of crystallization phenomenon that drives thermally in an Arrhenian manner. Moreover, we found that the estimated intercepts and gradients (i.e., Meyer-Neldel energy and Meyer-Neldel pre-factor respectively) for both approaches also vary linearly and both sets are remarkably identical. These results approach to an inference for ensuring the equivalence of compensation law and iso-kinetic relationship and provide an understanding of various advanced materials in physical chemistry, materials sciences and solid-state physics.

  16. Physico-Geometrical Kinetics of Solid-State Reactions in an Undergraduate Thermal Analysis Laboratory

    ERIC Educational Resources Information Center

    Koga, Nobuyoshi; Goshi, Yuri; Yoshikawa, Masahiro; Tatsuoka, Tomoyuki

    2014-01-01

    An undergraduate kinetic experiment of the thermal decomposition of solids by microscopic observation and thermal analysis was developed by investigating a suitable reaction, applicable techniques of thermal analysis and microscopic observation, and a reliable kinetic calculation method. The thermal decomposition of sodium hydrogen carbonate is…

  17. Immobilization of enzymes using non-ionic colloidal liquid aphrons (CLAs): Activity kinetics, conformation, and energetics.

    PubMed

    Ward, Keeran; Xi, Jingshu; Stuckey, David C

    2016-05-01

    This study seeks to examine the ability of non-ionic/non-polar Colloidial Liquid Aphrons (CLAs) to preserve enzyme functionality upon immobilization and release. CLAs consisting of micron-sized oil droplets surrounded by a thin aqueous layer stabilized by a mixture of surfactants, were formulated by direct addition (pre-manufacture addition) using 1% Tween 80/mineral oil and 1% Tween 20 and the enzymes lipase, aprotinin and α-chymotrypsin. The results of activity assays for both lipase and α-chymotrypsin showed that kinetic activity increased upon immobilization by factors of 7 and 5.5, respectively, while aprotinin retained approximately 85% of its native activity. The conformation of the enzymes released through desorption showed no significant alterations compared to their native state. Changes in pH and temperature showed that optimum conditions did not change after immobilization, while analysis of activation energy for the immobilized enzyme showed an increase in activity at higher temperatures. Furthermore, the effect of bound water within the aphron structure allowed for some degree of enzyme hydration, and this hydration was needed for an active conformation with results showing a decrease in ΔH* for the immobilized system compared to its native counterpart.

  18. Analysis and Interpretation of Single Molecule Protein Unfolding Kinetics

    NASA Astrophysics Data System (ADS)

    Lannon, Herbert; Brujic, Jasna

    2012-02-01

    The kinetics of protein unfolding under a stretching force has been extensively studied by atomic force microscopy (AFM) over the past decade [1]. Experimental artifacts at the single molecule level introduce uncertainties in the data analysis that have led to several competing physical models for the unfolding process. For example, the unfolding dynamics of the protein ubiquitin under constant force has been described by probability distributions as diverse as exponential [2,3], a sum of exponentials, log-normal [4], and more recently a function describing static disorder in the Arrhenius model [5]. A new method for data analysis is presented that utilizes maximum likelihood estimation (MLE) combined with other traditional statistical tests to unambiguously rank the consistency of these and other models with the experimental data. These techniques applied to the ubiquitin unfolding data shows that the probability of unfolding is best fit with a stretched exponential distribution, with important implications on the complexity of the mechanism of protein unfolding. [4pt] [1] Carrion-Vazquez, et. al. Springer Series in Biophys. 2006 [0pt] [2] Fernandez et. al. Science 2004 [0pt] [3] Brujic et. al. Nat. Phys 2006 [0pt] [4] Garcia-Manyes et. al. Biophys. J. 2007 [0pt] [5] Kuo et. al. PNAS 2010

  19. Polymeric brushes as functional templates for immobilizing ribonuclease A: study of binding kinetics and activity.

    PubMed

    Cullen, Sean P; Liu, Xiaosong; Mandel, Ian C; Himpsel, Franz J; Gopalan, Padma

    2008-02-05

    The ability to immobilize proteins with high binding capacities on surfaces while maintaining their activity is critical for protein microarrays and other biotechnological applications. We employed poly(acrylic acid) (PAA) brushes as templates to immobilize ribonuclease A (RNase A), which is commonly used to remove RNA from plasmid DNA preparations. The brushes are grown by surface-anchored atom-transfer radical polymerization (ATRP) initiators. RNase A was immobilized by both covalent esterification and a high binding capacity metal-ion complexation method to PAA brushes. The polymer brushes immobilized 30 times more enzyme compared to self-assembled monolayers. As the thickness of the brush increases, the surface density of the RNase A increases monotonically. The immobilization was investigated by ellipsometry, X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), and near-edge X-ray absorption fine structure spectroscopy (NEXAFS). The activity of the immobilized RNase A was determined using UV absorbance. As much as 11.0 microg/cm(2) of RNase A was bound to PAA brushes by metal-ion complexation compared to 5.8 microg/cm(2) by covalent immobilization which is 30 and 16 times the estimated mass bound in a monolayer. The calculated diffusion coefficient D was 0.63 x 10(-14) cm(2)/s for metal-ion complexation and 0.71 x 10(-14) cm(2)/s for covalent immobilization. Similar values of D indicate that the binding kinetics is similar, but the thermodynamic equilibrium coverage varies with the binding chemistry. Immobilization kinetics and thermodynamics were characterized by ellipsometry for both methods. A maximum relative activity of 0.70-0.80 was reached between five and nine monolayers of the immobilized enzyme. However, the relative activity for covalent immobilization was greater than that of metal-ion complexation. Covalent esterification resulted in similar temperature dependence as free enzyme, whereas metal-ion complexation showed no

  20. Adsorptive removal of acrylonitrile by commercial grade activated carbon: kinetics, equilibrium and thermodynamics.

    PubMed

    Kumar, Arvind; Prasad, B; Mishra, I M

    2008-04-01

    The potential of activated carbons--powdered (PAC) and granular (GAC), for the adsorption of acrylonitrile (AN) at different initial AN concentrations (50analysis also confirmed the efficacy of the R-P isotherm to best fit the experimental data. The pseudo-second order kinetic model best represents the kinetics of the adsorption of AN onto PAC and GAC. Maximum adsorption capacity of PAC and GAC at optimum conditions of AN removal (adsorbent dose approximately 20 g/l of solution, and equilibrium time approximately 5 h) was found to be 51.72 and 46.63 mg/g, respectively.

  1. In vitro comparative kinetic analysis of the chloroplast Toc GTPases.

    PubMed

    Reddick, L Evan; Vaughn, Michael D; Wright, Sarah J; Campbell, Ian M; Bruce, Barry D

    2007-04-13

    A unique aspect of protein transport into plastids is the coordinate involvement of two GTPases in the translocon of the outer chloroplast membrane (Toc). There are two subfamilies in Arabidopsis, the small GTPases (Toc33 and Toc34) and the large acidic GTPases (Toc90, Toc120, Toc132, and Toc159). In chloroplasts, Toc34 and Toc159 are implicated in precursor binding, yet mechanistic details are poorly understood. How the GTPase cycle is modulated by precursor binding is complex and in need of careful dissection. To this end, we have developed novel in vitro assays to quantitate nucleotide binding and hydrolysis of the Toc GTPases. Here we present the first systematic kinetic characterization of four Toc GTPases (cytosolic domains of atToc33, atToc34, psToc34, and the GTPase domain of atToc159) to permit their direct comparison. We report the KM, Vmax, and Ea values for GTP hydrolysis and the Kd value for nucleotide binding for each protein. We demonstrate that GTP hydrolysis by psToc34 is stimulated by chloroplast transit peptides; however, this activity is not stimulated by homodimerization and is abolished by the R133A mutation. Furthermore, we show peptide stimulation of hydrolytic rates are not because of accelerated nucleotide exchange, indicating that transit peptides function as GTPase-activating proteins and not guanine nucleotide exchange factors in modulating the activity of psToc34. Finally, by using the psToc34 structure, we have developed molecular models for atToc33, atToc34, and atToc159G. By combining these models with the measured enzymatic properties of the Toc GTPases, we provide new insights of how the chloroplast protein import cycle may be regulated.

  2. Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions

    SciTech Connect

    Crichlow, G.; Lubetsky, J; Leng, L; Bucala, R; Lolis, E

    2009-01-01

    Macrophage migration inhibitory factor (MIF) is a secreted protein expressed in numerous cell types that counters the antiinflammatory effects of glucocorticoids and has been implicated in sepsis, cancer, and certain autoimmune diseases. Interestingly, the structure of MIF contains a catalytic site resembling the tautomerase/isomerase sites of microbial enzymes. While bona fide physiological substrates remain unknown, model substrates have been identified. Selected compounds that bind in the tautomerase active site also inhibit biological functions of MIF. It had previously been shown that the acetaminophen metabolite, N-acetyl-p-benzoquinone imine (NAPQI), covalently binds to the active site of MIF. In this study, kinetic data indicate that NAPQI inhibits MIF both covalently and noncovalently. The structure of MIF cocrystallized with NAPQI reveals that the NAPQI has undergone a chemical alteration forming an acetaminophen dimer (bi-APAP) and binds noncovalently to MIF at the mouth of the active site. We also find that the commonly used protease inhibitor, phenylmethylsulfonyl fluoride (PMSF), forms a covalent complex with MIF and inhibits the tautomerase activity. Crystallographic analysis reveals the formation of a stable, novel covalent bond for PMSF between the catalytic nitrogen of the N-terminal proline and the sulfur of PMSF with complete, well-defined electron density in all three active sites of the MIF homotrimer. Conclusions are drawn from the structures of these two MIF-inhibitor complexes regarding the design of novel compounds that may provide more potent reversible and irreversible inhibition of MIF.

  3. In situ X-ray pair distribution function analysis of geopolymer gel nanostructure formation kinetics.

    PubMed

    White, Claire E; Provis, John L; Bloomer, Breaunnah; Henson, Neil J; Page, Katharine

    2013-06-14

    With the ever-increasing environmentally-driven demand for technologically advanced structural materials, geopolymer cement is fast becoming a viable alternative to traditional cements due to its proven engineering characteristics and the reduction in CO2 emitted during manufacturing (as much as 80% less CO2 emitted in manufacture, compared to ordinary Portland cement). Nevertheless, much remains unknown regarding the kinetics of reaction responsible for nanostructural evolution during the geopolymerisation process. Here, in situ X-ray total scattering measurements and pair distribution function (PDF) analysis are used to quantify the extent of reaction as a function of time for alkali-activated metakaolin/slag geopolymer binders, including the impact of various activators (alkali hydroxide/silicate) on the kinetics of the geopolymerisation reaction. Quantifying the reaction process in situ from X-ray PDF data collected during the initial ten hours can provide an estimate of the total reaction extent, but when combined with data obtained at longer times (128 days here) enables more accurate determination of the overall rate of reaction. To further assess the initial stages of the geopolymerisation reaction process, a pseudo-single step first order rate equation is fitted to the extent of reaction data, which reveals important mechanistic information regarding the role of free silica in the activators in the evolution of the binder systems. Hence, it is shown that in situ X-ray PDF analysis is an ideal experimental local structure tool to probe the reaction kinetics of complex reacting systems involving transitions between disordered/amorphous phases, of which geopolymerisation is an important example.

  4. Kinetic analysis of Legionella inactivation using ozone in wastewater.

    PubMed

    Li, Jun; Li, Kunquan; Zhou, Yan; Li, Xuebin; Tao, Tao

    2017-02-01

    Legionella inactivation using ozone was studied in wastewater using kinetic analysis and modeling. The experimental results indicate that the relationship between the ozone concentration, germ concentration, and chemical oxygen demand (COD) can be used to predict variations in germ and COD concentrations. The ozone reaction with COD and inactivation of Legionella occurred simultaneously, but the reaction with COD likely occurred at a higher rate than the inactivation, as COD is more easily oxidized by ozone than Legionella. Higher initial COD concentrations resulted in a lower inactivation rate and higher lnN/N0. Higher temperature led to a higher inactivation efficiency. The relationship of the initial O3 concentration and Legionella inactivation rate was not linear, and thus, the Ct value required for a 99.99% reduction was not constant. The initial O3 concentration was more important than the contact time, and a reduction of the initial O3 concentration could not be compensated by increasing the contact time. The Ct values were compared over a narrow range of initial concentrations; the Ct values could only be contrasted when the initial O3 concentrations were very similar. A higher initial O3 concentration led to a higher inflection point value for the lnN/N0 vs C0t curve. Energy consumption using a plasma corona was lower than when using boron-doped diamond electrodes.

  5. A model for the interfacial kinetics of phospholipase D activity on long-chain lipids.

    PubMed

    Majd, Sheereen; Yusko, Erik C; Yang, Jerry; Sept, David; Mayer, Michael

    2013-07-02

    The membrane-active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a critical role in cell signaling. This catalytic reaction proceeds on lipid-water interfaces and is an example of heterogeneous catalysis in biology. Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial catalytic reactions under well-defined experimental conditions with chemical and electrical access to both sides of the lipid membrane. Employing an assay that relies on the conductance of the pore-forming peptide gramicidin A to monitor PLD activity, the work presented here reveals the kinetics of hydrolysis of long-chain phosphatidylcholine lipids in situ. We have developed an extension of a basic kinetic model for interfacial catalysis that includes product activation and substrate depletion. This model describes the kinetic behavior very well and reveals two kinetic parameters, the specificity constant and the interfacial quality constant. This approach results in a simple and general model to account for product accumulation in interfacial enzyme kinetics.

  6. Adsorption of methylene blue onto bamboo-based activated carbon: kinetics and equilibrium studies.

    PubMed

    Hameed, B H; Din, A T M; Ahmad, A L

    2007-03-22

    Bamboo, an abundant and inexpensive natural resource in Malaysia was used to prepare activated carbon by physiochemical activation with potassium hydroxide (KOH) and carbon dioxide (CO(2)) as the activating agents at 850 degrees C for 2h. The adsorption equilibrium and kinetics of methylene blue dye on such carbon were then examined at 30 degrees C. Adsorption isotherm of the methylene blue (MB) on the activated carbon was determined and correlated with common isotherm equations. The equilibrium data for methylene blue adsorption well fitted to the Langmuir equation, with maximum monolayer adsorption capacity of 454.2mg/g. Two simplified kinetic models including pseudo-first-order and pseudo-second-order equation were selected to follow the adsorption processes. The adsorption of methylene blue could be best described by the pseudo-second-order equation. The kinetic parameters of this best-fit model were calculated and discussed.

  7. Kinetic Monte Carlo simulations of boron activation in implanted Si under laser thermal annealing

    NASA Astrophysics Data System (ADS)

    Fisicaro, Giuseppe; Pelaz, Lourdes; Aboy, Maria; Lopez, Pedro; Italia, Markus; Huet, Karim; Cristiano, Filadelfo; Essa, Zahi; Yang, Qui; Bedel-Pereira, Elena; Quillec, Maurice; La Magna, Antonino

    2014-02-01

    We investigate the correlation between dopant activation and damage evolution in boron-implanted silicon under excimer laser irradiation. The dopant activation efficiency in the solid phase was measured under a wide range of irradiation conditions and simulated using coupled phase-field and kinetic Monte Carlo models. With the inclusion of dopant atoms, the presented code extends the capabilities of a previous version, allowing its definitive validation by means of detailed comparisons with experimental data. The stochastic method predicts the post-implant kinetics of the defect-dopant system in the far-from-equilibrium conditions caused by laser irradiation. The simulations explain the dopant activation dynamics and demonstrate that the competitive dopant-defect kinetics during the first laser annealing treatment dominates the activation phenomenon, stabilizing the system against additional laser irradiation steps.

  8. Kinetic parameter estimation model for anaerobic co-digestion of waste activated sludge and microalgae.

    PubMed

    Lee, Eunyoung; Cumberbatch, Jewel; Wang, Meng; Zhang, Qiong

    2017-03-01

    Anaerobic co-digestion has a potential to improve biogas production, but limited kinetic information is available for co-digestion. This study introduced regression-based models to estimate the kinetic parameters for the co-digestion of microalgae and Waste Activated Sludge (WAS). The models were developed using the ratios of co-substrates and the kinetic parameters for the single substrate as indicators. The models were applied to the modified first-order kinetics and Monod model to determine the rate of hydrolysis and methanogenesis for the co-digestion. The results showed that the model using a hyperbola function was better for the estimation of the first-order kinetic coefficients, while the model using inverse tangent function closely estimated the Monod kinetic parameters. The models can be used for estimating kinetic parameters for not only microalgae-WAS co-digestion but also other substrates' co-digestion such as microalgae-swine manure and WAS-aquatic plants.

  9. Kinetics and activation thermodynamics of methane monooxygenase compound Q formation and reaction with substrates.

    PubMed

    Brazeau, B J; Lipscomb, J D

    2000-11-07

    The transient kinetics of formation and decay of the reaction cycle intermediates of the Methylosinus trichosporium OB3b methane monooxygenase (MMO) catalytic cycle are studied as a function of temperature and substrate type and deuteration. Kinetic evidence is presented for the existence of three intermediates termed compounds O, P, and P forming after the addition of O(2) to diferrous MMO hydroxylase (H(r)) and before the formation of the reactive intermediate compound Q. The Arrhenius plots for these reactions are linear and independent of substrate concentration and type, showing that substrate does not participate directly in the oxygen activation phase of the catalytic cycle. Analysis of the transient kinetic data revealed only small changes relative to the weak optical spectrum of H(r) for any of these intermediates. In contrast, large changes in the 430 nm spectral region are associated with the formation of Q. The decay reaction of Q exhibits an apparent first-order concentration dependence for all substrates tested, and the observed rate constant depends on the substrate type. The kinetics of the decay reaction of Q yield a nonlinear Arrhenius plot when methane is the substrate, and the rates in both segments of the plot increase linearly with methane concentration. Together these observations suggest that at least two reactions with a methane concentration dependence, and perhaps two methane molecules, are involved in the decay process. When CD(4) is used as the substrate, a large isotope effect and a linear Arrhenius plot are observed. Analogous plots for all other MMO substrates tested (e.g., ethane) are linear, and no isotope effect for deuterated analogues is observed. This demonstrates that a step other than C-H bond breaking is rate limiting for alternative MMO substrates. A two step Q decay mechanism is proposed that provides an explanation for the lack of an isotope effect for alternative MMO substrates and the fact that rate of oxidation of

  10. Kinetic analysis of pre-ribosome structure in vivo

    PubMed Central

    Swiatkowska, Agata; Wlotzka, Wiebke; Tuck, Alex; Barrass, J. David; Beggs, Jean D.; Tollervey, David

    2012-01-01

    Pre-ribosomal particles undergo numerous structural changes during maturation, but their high complexity and short lifetimes make these changes very difficult to follow in vivo. In consequence, pre-ribosome structure and composition have largely been inferred from purified particles and analyzed in vitro. Here we describe techniques for kinetic analyses of the changes in pre-ribosome structure in living cells of Saccharomyces cerevisiae. To allow this, in vivo structure probing by DMS modification was combined with affinity purification of newly synthesized 20S pre-rRNA over a time course of metabolic labeling with 4-thiouracil. To demonstrate that this approach is generally applicable, we initially analyzed the accessibility of the region surrounding cleavage site D site at the 3′ end of the mature 18S rRNA region of the pre-rRNA. This revealed a remarkably flexible structure throughout 40S subunit biogenesis, with little stable RNA–protein interaction apparent. Analysis of folding in the region of the 18S central pseudoknot was consistent with previous data showing U3 snoRNA–18S rRNA interactions. Dynamic changes in the structure of the hinge between helix 28 (H28) and H44 of pre-18S rRNA were consistent with recently reported interactions with the 3′ guide region of U3 snoRNA. Finally, analysis of the H18 region indicates that the RNA structure matures early, but additional protection appears subsequently, presumably reflecting protein binding. The structural analyses described here were performed on total, affinity-purified, newly synthesized RNA, so many classes of RNA and RNA–protein complex are potentially amenable to this approach. PMID:23093724

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

    SciTech Connect

    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 accounting 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.

  12. Study of kinetics of degradation of cyclohexane carboxylic acid by acclimated activated sludge.

    PubMed

    Wang, Chunhua; Shi, Shuian; Chen, Hongyan

    2016-01-01

    Activated sludge contains complex microorganisms, which are highly effective biodegrading agents. In this study, the kinetics of biodegradation of cyclohexane carboxylic acid (CHCA) by an acclimated aerobic activated sludge were investigated. The results showed that after 180 days of acclimation, the activated sludge could steadily degrade >90% of the CHCA in 120 h. The degradation of CHCA by the acclimated activated sludge could be modeled using a first-order kinetics equation. The equations for the degradation kinetics for different initial CHCA concentrations were also obtained. The kinetics constant, kd, decreased with an increase in the CHCA concentration, indicating that, at high concentrations, CHCA had an inhibiting effect on the microorganisms in the activated sludge. The effects of pH on the degradation kinetics of CHCA were also investigated. The results showed that a pH of 10 afforded the highest degradation rate, indicating that basic conditions significantly promoted the degradation of CHCA. Moreover, it was found that the degradation efficiency for CHCA increased with an increase in temperature and concentration of dissolved oxygen under the experimental conditions.

  13. Kinetics of adsorption with granular, powdered, and fibrous activated carbon

    SciTech Connect

    Shmidt, J.L.; Pimenov, A.V.; Lieberman, A.I.; Cheh, H.Y.

    1997-08-01

    The properties of three different types of activated carbon, fibrous, powdered, and granular, were investigated theoretically and experimentally. The adsorption rate of the activated carbon fiber was found to be two orders of magnitude higher than that of the granular activated carbon, and one order of magnitude higher than that of the powdered activated carbon. Diffusion coefficients of methylene blue in the fibrous, powdered, and granular activated carbons were determined experimentally. A new method for estimating the meso- and macropore surface areas in these carbons was proposed.

  14. Kinetic analysis of microbial respiratory response to substrate addition

    NASA Astrophysics Data System (ADS)

    Blagodatskaya, Evgenia; Blagodatsky, Sergey; Yuyukina, Tatayna; Kuzyakov, Yakov

    2010-05-01

    Heterotrophic component of CO2 emitted from soil is mainly due to the respiratory activity of soil microorganisms. Field measurements of microbial respiration can be used for estimation of C-budget in soil, while laboratory estimation of respiration kinetics allows the elucidation of mechanisms of soil C sequestration. Physiological approaches based on 1) time-dependent or 2) substrate-dependent respiratory response of soil microorganisms decomposing the organic substrates allow to relate the functional properties of soil microbial community with decomposition rates of soil organic matter. We used a novel methodology combining (i) microbial growth kinetics and (ii) enzymes affinity to the substrate to show the shift in functional properties of the soil microbial community after amendments with substrates of contrasting availability. We combined the application of 14C labeled glucose as easily available C source to soil with natural isotope labeling of old and young soil SOM. The possible contribution of two processes: isotopic fractionation and preferential substrate utilization to the shifts in δ13C during SOM decomposition in soil after C3-C4 vegetation change was evaluated. Specific growth rate (µ) of soil microorganisms was estimated by fitting the parameters of the equation v(t) = A + B * exp(µ*t), to the measured CO2 evolution rate (v(t)) after glucose addition, and where A is the initial rate of non-growth respiration, B - initial rate of the growing fraction of total respiration. Maximal mineralization rate (Vmax), substrate affinity of microbial enzymes (Ks) and substrate availability (Sn) were determined by Michaelis-Menten kinetics. To study the effect of plant originated C on δ13C signature of SOM we compared the changes in isotopic composition of different C pools in C3 soil under grassland with C3-C4 soil where C4 plant Miscanthus giganteus was grown for 12 years on the plot after grassland. The shift in 13δ C caused by planting of M. giganteus

  15. TChem - A Software Toolkit for the Analysis of Complex Kinetic Models

    SciTech Connect

    Safta, Cosmin; Najm, Habib N.; Knio, Omar

    2011-05-01

    The TChem toolkit is a software library that enables numerical simulations using complex chemistry and facilitates the analysis of detailed kinetic models. The toolkit provide capabilities for thermodynamic properties based on NASA polynomials and species production/consumption rates. It incorporates methods that can selectively modify reaction parameters for sensitivity analysis. The library contains several functions that provide analytically computed Jacobian matrices necessary for the efficient time advancement and analysis of detailed kinetic models.

  16. [Adsorption kinetic and thermodynamic studies of lead onto activated carbons from cotton stalk].

    PubMed

    Li, Kun-quan; Zheng, Zheng; Jiang, Jian-chun; Zhang, Ji-biao

    2010-05-01

    Low-cost high surface area microporous carbons were prepared from cotton stalk and cotton stalk fiber by H3PO4 activation. The adsorption of lead ions on the carbons was investigated by conducting a series of batch adsorption experiments. The influence of solution pH value, contact time and temperature was investigated. The adsorption kinetics, thermodynamic behavior and mechanism were also discussed. The surface area and pore structure of the activated carbons were analyzed by BET equation, BJH method and H-K method according to the data from nitrogen adsorption at 77K. Boehm titration, Fourier transform infrared spectroscopy (FTIR), the point of zero charge (pH(PZC)) measurement and elemental analysis were used to characterize the surface properties. The results show that the carbons from cotton stalk and cotton stalk fiber have high surface area of 1570 and 1731 m2 x g(-1), and high content of oxygen-containing functional groups of 1.43 and 0.83 mmol x g(-1). The adsorption experiments show that the carbons have high adsorption capacity for lead, and the maximum adsorption equilibrium amount was found to be 120 mg x g(-1). The adsorption amount increased with contact time, and almost 80% of the adsorption occurred in the first 5 min. The pseudo-second-order model describes the adsorption kinetics most effectively. The Freundlich isotherm was found to the best explanation for experimental data. The negative change in free energy (delta G0) and positive change in enthalpy (delta H0) indicate that the adsorption is a spontaneous and endothermic process, and the adsorption of lead ions onto the carbons might be involved in an ion-exchange mechanism.

  17. Interaction and kinetic analysis for coal and biomass co-gasification by TG-FTIR.

    PubMed

    Xu, Chaofen; Hu, Song; Xiang, Jun; Zhang, Liqi; Sun, Lushi; Shuai, Chao; Chen, Qindong; He, Limo; Edreis, Elbager M A

    2014-02-01

    This study aims to investigate the interaction and kinetic behavior of CO2 gasification of coal, biomass and their blends by thermogravimetry analysis (TG). The gas products evolved from gasification were measured online with Fourier Transform Infrared Spectroscopy (FTIR) coupled with TG. Firstly, TG experiments indicated that interaction between the coals and biomasses mainly occurred during co-gasification process. The most significant synergistic interaction occurred for LN with SD at the blending mass ratio 4:1. Furthermore, thermal kinetic analysis indicated that the activation energy involved in co-gasification decreased as the SD content increased until the blending ratio of SD with coal reached 4:1. The rise of the frequency factor indicated that the increase of SD content favored their synergistic interaction. Finally, FTIR analysis of co-gasification of SD with LN indicated that except for CO, most gases including CH3COOH, C6H5OH, H2O, etc., were detected at around 50-700°C.

  18. Sorption kinetics of polycyclic aromatic hydrocarbons removal using granular activated carbon: intraparticle diffusion coefficients.

    PubMed

    Valderrama, C; Gamisans, X; de las Heras, X; Farrán, A; Cortina, J L

    2008-09-15

    Granular activated carbon (GAC) was evaluated as a suitable sorbent for polycyclic aromatic hydrocarbons (PAHs) removal from aqueous solutions. For this purpose, kinetic measurements on the extraction of a family of six PAHs were taken. A morphology study was performed by means of a scanning electron microscopy (SEM) analysis of GAC samples. Analyses of the batch rate data for each PAH were carried out using two kinetic models: the homogenous particle diffusion model (HPDM) and the shell progressive model (SPM). The process was controlled by diffusion rate the solutes (PAHs) that penetrated the reacted layer at PAH concentrations in the range of 0.2-10 mg L(-1). The effective particle diffusion coefficients (D(eff)) derived from the two models were determined from the batch rate data. The Weber and Morris intraparticle diffusion model made a double contribution to the surface and pore diffusivities in the sorption process. The D(eff) values derived from both the HPMD and SPM equations varied from 1.1 x 10(-13) to 6.0 x 10(-14) m(2) s(-1). The simplest model, the pore diffusion model, was applied first for data analysis. The model of the next level of complexity, the surface diffusion model, was applied in order to gain a deeper understanding of the diffusion process. This model is able to explain the data, and the apparent surface diffusivities are in the same order of magnitude as the values for the sorption of functionalized aromatic hydrocarbons (phenols and sulphonates) that are described in the literature.

  19. Kinetic analysis and mechanistic aspects of autoxidation of catechins.

    PubMed

    Mochizuki, Manabu; Yamazaki, Shin-ichi; Kano, Kenji; Ikeda, Tokuji

    2002-01-15

    A peroxidase-based bioelectrochemical sensor of hydrogen peroxide (H(2)O(2)) and a Clark-type oxygen electrode were applied to continuous monitoring and kinetic analysis of the autoxidation of catechins. Four major catechins in green tea, (-)-epicatechin, (-)-epicatechin gallate, (-)-epigallocatechin, and (-)-epigallocatechin gallate, were used as model compounds. It was found that dioxygen (O(2)) is quantitatively reduced to H(2)O(2). The initial rate of autoxidation is suppressed by superoxide dismutase and H(+), but is independent of buffer capacity. Based on these results, a mechanism of autoxidation is proposed; the initial step is the one-electron oxidation of the B ring of catechins by O(2) to generate a superoxide anion (O(2)(*-)) and a semiquinone radical, as supported in part by electron spin resonance measurements. O(2)(*-) works as a stronger one-electron oxidant than O(2) against catechins and is reduced to H(2)O(2). The semiquinone radical is more susceptible to oxidation with O(2) than fully reduced catechins. The autoxidation rate increases with pH. This behavior can be interpreted in terms of the increase in the stability of O(2)(*-) and the semiquinone radical with increasing pH, rather than the acid dissociation of phenolic groups. Cupric ion enhances autoxidation; most probably it functions as a catalyst of the initial oxidation step of catechins. The product cuprous ion can trigger a Fenton reaction to generate hydroxyl radical. On the other hand, borate ion suppresses autoxidation drastically, due to the strong complex formation with catechins. The biological significance of autoxidation and its effectors are also discussed.

  20. Non-equilibrium thermodynamics analysis of transcriptional regulation kinetics

    NASA Astrophysics Data System (ADS)

    Hernández-Lemus, Enrique; Tovar, Hugo; Mejía, Carmen

    2014-12-01

    Gene expression in eukaryotic cells is an extremely complex and interesting phenomenon whose dynamics are controlled by a large number of subtle physicochemical processes commonly described by means of gene regulatory networks. Such networks consist in a series of coupled chemical reactions, conformational changes, and other biomolecular processes involving the interaction of the DNA molecule itself with a number of proteins usually called transcription factors as well as enzymes and other components. The kinetics behind the functioning of such gene regulatory networks are largely unknown, though its description in terms of non-equilibrium thermodynamics has been discussed recently. In this work we will derive general kinetic equations for a gene regulatory network from a non-equilibrium thermodynamical description and discuss its use in understanding the free energy constrains imposed in the network structure. We also will discuss explicit expressions for the kinetics of a simple model of gene regulation and show that the kinetic role of mRNA decay during the RNA synthesis stage (or transcription) is somehow limited due to the comparatively low values of decay rates. At the level discussed here, this implies a decoupling of the kinetics of mRNA synthesis and degradation a fact that may become quite useful when modeling gene regulatory networks from experimental data on whole genome gene expression.

  1. Penicillin V acylase from Pectobacterium atrosepticum exhibits high specific activity and unique kinetics.

    PubMed

    Avinash, V S; Ramasamy, Sureshkumar; Suresh, C G; Pundle, Archana

    2015-08-01

    Penicillin V acylases (PVAs, E.C.3.5.11) belong to the Ntn hydrolase super family of enzymes that catalyze the deacylation of the side chain from phenoxymethyl penicillin (penicillin V). Penicillin acylases find use in the pharmaceutical industry for the production of semi-synthetic antibiotics. PVAs employ the N-terminal cysteine residue as catalytic nucleophile and are structurally and evolutionarily related to bile salt hydrolases (BSHs). Here, we report the cloning and characterization of a PVA enzyme from the Gram-negative plant pathogen, Pectobacterium atrosepticum (PaPVA). The enzyme was cloned and expressed in Escherichia coli attaining a very high yield (250 mg/l) and a comparatively high specific activity (430 IU/mg). The enzyme showed marginally better pH and thermo-stability over PVAs characterized from Gram-positive bacteria. The enzyme also showed enhanced activity in presence of organic solvents and detergents. The enzyme kinetics turned out to be significantly different from that of previously reported PVAs, displaying positive cooperativity and substrate inhibition. The presence of bile salts had a modulating effect on PaPVA activity. Sequence analysis and characterization reveal the distinctive nature of these enzymes and underscore the need to study PVAs from Gram-negative bacteria.

  2. Kinetics of Detergent-Induced Activation and Inhibition of a Minimal Lipase.

    PubMed

    Kübler, Daniel; Bergmann, Anna; Weger, Lukas; Ingenbosch, Kim N; Hoffmann-Jacobsen, Kerstin

    2017-02-16

    Detergents are commonly applied in lipase assays to solubilize sparingly soluble model substrates. However, detergents affect lipases as well as substrates in multiple ways. The effect of detergents on lipase activity is commonly attributed to conformational changes in the lid region. This study deals with the effect of the nonionic detergent, poly(ethylene glycol) dodecyl ether, on a lipase that does not contain a lid sequence, lipase A from Bacillus subtilis (BSLA). We show that BSLA activity depends strongly on the detergent concentration and the dependency profile changes with pH. The interaction of BSLA with detergent monomers and micelles is studied using fluorescence correlation spectroscopy, time-resolved anisotropy decay, and temperature-induced unfolding. Detergent-dependent hydrolysis kinetics of two different substrates at two pH values are fitted with a microkinetic model. This analysis shows that the mechanism of interfacial lipase catalysis is strongly affected by the detergent. It reveals an activation mechanism by monomeric detergent that does not result from structural changes of the lipase. Instead, we propose that interfacial diffusion of the lipase is enhanced by detergent binding.

  3. Osteoclast spreading kinetics are correlated with an oscillatory activation of a calcium-dependent potassium current.

    PubMed

    Espinosa, Leon; Paret, Laurent; Ojeda, Carlos; Tourneur, Yves; Delmas, Pierre D; Chenu, Chantal

    2002-10-01

    Cell movement and spreading involve calcium-dependent processes and ionic channel activation. During bone resorption, osteoclasts alternate between spread, motile and resorptive phases. We investigated whether the electrical membrane properties of osteoclasts were linked to their membrane morphological changes. Rabbit osteoclasts were recorded by time-lapse videomicroscopy performed simultaneously with patch-clamp whole cell and single channel recordings. Original image analysis methods were developed and used to demonstrate for the first time an oscillatory activation of a spontaneous membrane current in osteoclasts, which is directly correlated to the membrane movement rate. This current was identified as a calcium-dependent potassium current (IK(Ca)) that is sensitive to both charybdotoxin and apamin and was generated by a channel with unitary conductance of approximately 25+/-2 pS. Blockade of this current also decreased osteoclast spreading and inhibited bone resorption in vitro, demonstrating a physiological role for this current in osteoclast activity. These results establish for the first time a temporal correlation between lamellipodia formation kinetics and spontaneous peaks of IK(Ca), which are both involved in the control of osteoclast spreading and bone resorption.

  4. CCN Activity, Hygroscopicity, and Droplet Activation Kinetics of Secondary Organic Aerosol Resulting from the 2010 Gulf Oil Spill

    NASA Astrophysics Data System (ADS)

    Moore, R.; Lathem, T. L.; Cerully, K.; Bahreini, R.; Brock, C. A.; Langridge, J. M.; Middlebrook, A. M.; Nenes, A.; Calnex Science Team

    2010-12-01

    We present an analysis of the hygroscopicity and droplet activation kinetics of cloud condensation nuclei (CCN) sampled onboard the National Oceanic and Atmospheric Administration WP-3D aircraft downwind of the Deepwater Horizon oil spill site on June 8th and 10th, 2010. This set of measurements provides a unique case study for assessing in-situ the impact of fresh, hydrocarbonlike aerosols, which are expected to be formed via gas-to-particle conversion of the semi-volatile vapors released from oil evaporation. Similar hydrocarbon-rich aerosols constitute an important local emissions source in urban areas, but often coexist as an external/partially-internal mixture with more-oxidized, aged organic and sulfate aerosol. The DWH site provides the means to study the hygroscopic properties of these less-oxidized organic aerosols above a cleaner environmental background typical of marine environments in order to better discern their contribution to CCN activity and droplet growth. Measurements were performed with a Droplet Measurement Technologies Streamwise, Thermal-Gradient CCN counter, operating both as a counter (s=0.3%) and as a spectrometer (s=0.2-0.6%) using the newly-developed Scanning Flow CCN Analysis (SFCA) technique [1]. The instrument measures both the number concentration of particles able to nucleate droplets and also their resulting droplet sizes. The measured size information combined with a comprehensive computational fluid dynamics instrument model enables us to determine the rate of water uptake onto the particles and parameterize it in terms of an effective mass transfer coefficient [2], a key parameter needed to predict the number of activated droplets in ambient clouds. Non-refractory aerosol chemical composition was measured with an Aerodyne compact time-of-flight aerosol mass spectrometer. It was observed that the aerosols sampled downwind of the site on both days were composed predominantly of organics with a low degree of oxidation and low

  5. Effect of temperature on Candida antartica lipase B activity in the kinetic resolution of acebutolol

    NASA Astrophysics Data System (ADS)

    Rajin, Mariani; Kamaruddin, A. H.

    2016-06-01

    Thermodynamic studies of free Candida antartica lipase B in kinetic resolution of acebutolol have been carried out to characterize the temperature effects towards enzyme stability and activity. A decreased in reaction rate was observed in temperature above 40oC. Thermodynamic studies on lipase deactivation exhibited a first-order kinetic pattern. The activation and deactivation energies were 39.63 kJ/mol and 54.90 kJ/mol, respectively. The enthalpy and entropy of the lipase deactivation were found to be 52.12 kJ/mol and -0.18 kJ/mol, respectively.

  6. Kinetics of adsorption of dyes from aqueous solution using activated carbon prepared from waste apricot.

    PubMed

    Onal, Yunus

    2006-10-11

    Adsorbent (WA11Zn5) has been prepared from waste apricot by chemical activation with ZnCl(2). Pore properties of the activated carbon such as BET surface area, pore volume, pore size distribution, and pore diameter were characterized by N(2) adsorption and DFT plus software. Adsorption of three dyes, namely, Methylene Blue (MB), Malachite Green (MG), Crystal Violet (CV), onto activated carbon in aqueous solution was studied in a batch system with respect to contact time, temperature. The kinetics of adsorption of MB, MG and CV have been discussed using six kinetic models, i.e., the pseudo-first-order model, the pseudo-second-order model, the Elovich equation, the intraparticle diffusion model, the Bangham equation, the modified Freundlich equation. Kinetic parameters and correlation coefficients were determined. It was shown that the second-order kinetic equation could describe the adsorption kinetics for three dyes. The dyes uptake process was found to be controlled by external mass transfer at earlier stages (before 5 min) and by intraparticle diffusion at later stages (after 5 min). Thermodynamic parameters, such as DeltaG, DeltaH and DeltaS, have been calculated by using the thermodynamic equilibrium coefficient obtained at different temperatures and concentrations. The thermodynamics of dyes-WA11Zn5 system indicates endothermic process.

  7. NMR analysis of base-pair opening kinetics in DNA.

    PubMed

    Szulik, Marta W; Voehler, Markus; Stone, Michael P

    2014-12-12

    Base pairing in nucleic acids plays a crucial role in their structure and function. Differences in the base-pair opening and closing kinetics of individual double-stranded DNA sequences or between chemically modified base pairs provide insight into the recognition of these base pairs by DNA processing enzymes. This unit describes how to quantify the kinetics for localized base pairs by observing changes in the imino proton signals by nuclear magnetic resonance spectroscopy. The determination of all relevant parameters using state-of-the art techniques and NMR instrumentation, including cryoprobes, is discussed.

  8. Kinetic study of an enzymic cycling system coupled to an enzymic step: determination of alkaline phosphatase activity.

    PubMed Central

    Valero, E; Varón, R; García-Carmona, F

    1995-01-01

    A kinetic study is made of a system consisting of a specific enzymic cycling assay coupled to an enzymic reaction. A kinetic analysis of this system is presented, and the accumulation of chromophore involved in the cycle is seen to be parabolic, i.e. the rate of the reaction increases continuously with constant acceleration. The system is illustrated by the measurement of alkaline phosphatase activity using beta-NADP+ as substrate. The enzymes alcohol dehydrogenase and diaphorase are used to cycle beta-NAD+ in the presence of ethanol and p-Iodonitrotetrazolium Violet. During each turn of the cycle, one molecule of the tetrazolium salt is reduced to an intensely coloured formazan. A simple procedure for evaluating the kinetic parameters involved in the system and for optimizing this cycling assay is described. The method is applicable to the measurement of any enzyme, and its amplification capacity as well as the simplicity of determining kinetic parameters enable it to be employed in enzyme immunoassays to increase the magnitude of the measured response. PMID:7619054

  9. Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts.

    PubMed

    Park, Chang Shin; Schneider, Ian C; Haugh, Jason M

    2003-09-26

    Isoforms of the serine-threonine kinase Akt coordinate multiple cell survival pathways in response to stimuli such as platelet-derived growth factor (PDGF). Activation of Akt is a multistep process, which relies on the production of 3'-phosphorylated phosphoinositide (PI) lipids by PI 3-kinases. To quantitatively assess the kinetics of PDGF receptor/PI 3-kinase/Akt signaling in fibroblasts, a systematic study of this pathway was performed, and a mechanistic mathematical model that describes its operation was formulated. We find that PDGF receptor phosphorylation exhibits positive cooperativity with respect to PDGF concentration, and its kinetics are quantitatively consistent with a mechanism in which receptor dimerization is initially mediated by the association of two 1:1 PDGF/PDGF receptor complexes. Receptor phosphorylation is transient at high concentrations of PDGF, consistent with the loss of activated receptors upon endocytosis. By comparison, Akt activation responds to lower PDGF concentrations and exhibits more sustained kinetics. Further analysis and modeling suggest that the pathway is saturated at the level of PI 3-kinase activation, and that the p110alpha catalytic subunit of PI 3-kinase contributes most to PDGF-stimulated 3'-PI production. Thus, at high concentrations of PDGF the kinetics of 3'-PI production are limited by the turnover rate of these lipids, while the Akt response is additionally influenced by the rate of Akt deactivation.

  10. Analysis of “On/Off” Kinetics of a CETP Inhibitor Using a Mechanistic Model of Lipoprotein Metabolism and Kinetics

    PubMed Central

    Lu, J; Cleary, Y; Maugeais, C; Kiu Weber, CI; Mazer, NA

    2015-01-01

    RG7232 is a potent inhibitor of cholesteryl-ester transfer protein (CETP). Daily oral administration of RG7232 produces a dose- and time-dependent increase in high-density lipoprotein-cholesterol (HDL-C) and apolipoproteinA-I (ApoA-I) levels and a corresponding decrease in low-density lipoprotein-cholesterol (LDL-C) and apolipoproteinB (ApoB) levels. Due to its short plasma half-life (∼3 hours), RG7232 transiently inhibits CETP activity during each dosing interval (“on/off” kinetics), as reflected by the temporal effects on HDL-C and LDL-C. The influence of RG7232 on lipid-poor ApoA-I (i.e., pre-β1) levels and reverse cholesterol transport rates is unclear. To investigate this, a published model of lipoprotein metabolism and kinetics was combined with a pharmacokinetic model of RG7232. After calibration and validation of the combined model, the effect of RG7232 on pre-β1 levels was simulated. A dose-dependent oscillation of pre-β1, driven by the “on/off” kinetics of RG7232 was observed. The possible implications of these findings are discussed. PMID:26380155

  11. Single-cell analysis of transcription kinetics across the cell cycle.

    PubMed

    Skinner, Samuel O; Xu, Heng; Nagarkar-Jaiswal, Sonal; Freire, Pablo R; Zwaka, Thomas P; Golding, Ido

    2016-01-29

    Transcription is a highly stochastic process. To infer transcription kinetics for a gene-of-interest, researchers commonly compare the distribution of mRNA copy-number to the prediction of a theoretical model. However, the reliability of this procedure is limited because the measured mRNA numbers represent integration over the mRNA lifetime, contribution from multiple gene copies, and mixing of cells from different cell-cycle phases. We address these limitations by simultaneously quantifying nascent and mature mRNA in individual cells, and incorporating cell-cycle effects in the analysis of mRNA statistics. We demonstrate our approach on Oct4 and Nanog in mouse embryonic stem cells. Both genes follow similar two-state kinetics. However, Nanog exhibits slower ON/OFF switching, resulting in increased cell-to-cell variability in mRNA levels. Early in the cell cycle, the two copies of each gene exhibit independent activity. After gene replication, the probability of each gene copy to be active diminishes, resulting in dosage compensation.

  12. Single-cell analysis of transcription kinetics across the cell cycle

    PubMed Central

    Skinner, Samuel O; Xu, Heng; Nagarkar-Jaiswal, Sonal; Freire, Pablo R; Zwaka, Thomas P; Golding, Ido

    2016-01-01

    Transcription is a highly stochastic process. To infer transcription kinetics for a gene-of-interest, researchers commonly compare the distribution of mRNA copy-number to the prediction of a theoretical model. However, the reliability of this procedure is limited because the measured mRNA numbers represent integration over the mRNA lifetime, contribution from multiple gene copies, and mixing of cells from different cell-cycle phases. We address these limitations by simultaneously quantifying nascent and mature mRNA in individual cells, and incorporating cell-cycle effects in the analysis of mRNA statistics. We demonstrate our approach on Oct4 and Nanog in mouse embryonic stem cells. Both genes follow similar two-state kinetics. However, Nanog exhibits slower ON/OFF switching, resulting in increased cell-to-cell variability in mRNA levels. Early in the cell cycle, the two copies of each gene exhibit independent activity. After gene replication, the probability of each gene copy to be active diminishes, resulting in dosage compensation. DOI: http://dx.doi.org/10.7554/eLife.12175.001 PMID:26824388

  13. Multisubstrate kinetics of PAH mixture biodegradation: analysis in the double-logarithmic plot.

    PubMed

    Baboshin, Mikhail; Golovleva, Ludmila

    2011-02-01

    The proposed method of kinetic analysis of aqueous-phase biodegradation of polycyclic aromatic hydrocarbons (PAH) mixture presupposes representation of kinetic curves for each pair of mixture components, S(x) and S(y), in double-logarithmic coordinates (ln S(x); ln S(y)). If PAH mixture conversion corresponds to the multisubstrate model with a common active site, then the graphs in double-logarithmic coordinates are straight lines with the angular coefficients equal to the ratio of respective first-order rate constants k(y)(x)= V(y)K(x)/K(y)V(x), where K(x) and K(y) are half-saturation constants, V(x) and V( y ) are the maximum conversion rates for substrates S(x) and S(y); the graph slope does not depend on any concentrations and remains constant during the change of reaction rates as a result of inhibition, induction/inactivation of enzymes or biomass growth. The formulated method has been used to analyze PAH mixture conversion by the culture of Sphingomonas sp. VKM B-2434. It has been shown that this process does not satisfy the multisubstrate model with a single active site. The results suggest that the strain VKM B-2434 contains at least two dioxygenases of different substrate specificity: one enzyme converts phenanthrene and fluoranthene and the other converts acenaphthene and acenaphthylene. The ratios of first-order rate constants have been obtained for these pairs of substrates.

  14. Kinetic analysis for formation of Cd1-xZnxSe solid-solution nanocrystals.

    PubMed

    Sung, Yun-Mo; Lee, Yong-Ji; Park, Kyung-Soo

    2006-07-19

    Kinetic analysis on the nanocrystal solid-solution formation was performed by heat treating CdSe/ZnSe core/shell nanocrystals, synthesized via a typical TOP/TOPO approach, at different temperatures for different time periods. X-ray diffraction (XRD) peak shifts in Cd1-xZnxSe cores according to the solid-solution treatments were monitored and used for the estimation of the lattice parameter change. The degree of solid-solution formation was determined considering the compositional variation in Cd1-xZnxSe cores, which was obtained from the Vegard's law. The degree of solid-solution formation (x) was applied to Jander analysis, and an Arrhenius-type plot was produced using the slopes of Jander plots. The activation energy for solid-solution formation was determined as approximately 152 kJ/mol, which evidently indicates that the diffusion of Zn2+ ions in the CdSe-ZnSe system is the governing mechanism for the Cd1-xZnxSe solid-solution formation. The Jander equation to predict the solid-solution formation kinetics for the CdSe/ZnSe core/shell systems was completed using the reaction rate constant (k).

  15. 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

  16. Combination Of Static And Dynami,C Stereophotogrammetry For The Kinetic Analysis Of Human Locomotion: Preliminary Results

    NASA Astrophysics Data System (ADS)

    Schaer, Alex R.; Sheffer, Daniel B.; Jones, D.; Meier, G.; Baumann, Juerg U.

    1989-04-01

    For a deeper understanding of the complexity of human walking movement not only a kinematic analysis , but also a comprehensive three-dimensional biomechanical model of the human body is required to detail the kinetic activities. This research combined static stereophotogrammetric determination of body segment mass parameters with three-dimensional gait analysis by cinephotography, direct linear transformation and two force plates. A method of combining the two independent analyses by defining the anatomical axes of each segment is shown. Practical problems arising in dynamic and stereometric analysis are demonstrated. Power spectra of a normal and a matched subject with spastic diplegia were calculated for a proper design of the kinematic analysis.

  17. Nonisothermal Analysis of Solution Kinetics by Spreadsheet Simulation

    ERIC Educational Resources Information Center

    de Levie, Robert

    2012-01-01

    A fast and generally applicable alternative solution to the problem of determining the useful shelf life of medicinal solutions is described. It illustrates the power and convenience of the combination of numerical simulation and nonlinear least squares with a practical pharmaceutical application of chemical kinetics and thermodynamics, validated…

  18. Growth of Listeria monocytogenes in Salmon Roe - a kinetic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to investigate the growth kinetics of Listeria monocytogenes in unsalted and salted (3%) salmon roe. Growth curves, developed using inoculated samples incubated at constant temperatures between 5 and 30 degrees C, were analyzed by curve-fitting to the Huang and Baran...

  19. Kinetic Analysis of Haloacetonitrile Stability in Drinking Waters.

    PubMed

    Yu, Yun; Reckhow, David A

    2015-09-15

    Haloacetonitriles (HANs) are an important class of drinking water disinfection byproducts (DBPs) that are reactive and can undergo considerable transformation on time scales relevant to system distribution (i.e., from a few hours to a week or more). The stability of seven mono-, di-, and trihaloacetonitriles was examined under a variety of conditions including different pH levels and disinfectant doses that are typical of drinking water distribution systems. Results indicated that hydroxide, hypochlorite, and their protonated forms could react with HANs via nucleophilic attack on the nitrile carbon, forming the corresponding haloacetamides (HAMs) and haloacetic acids (HAAs) as major reaction intermediates and end products. Other stable intermediate products, such as the N-chloro-haloacetamides (N-chloro-HAMs), may form during the course of HAN chlorination. A scheme of pathways for the HAN reactions was proposed, and the rate constants for individual reactions were estimated. Under slightly basic conditions, hydroxide and hypochlorite are primary reactants and their associated second-order reaction rate constants were estimated to be 6 to 9 orders of magnitude higher than those of their protonated conjugates (i.e., neutral water and hypochlorous acid), which are much weaker but more predominant nucleophiles at neutral and acidic pHs. Developed using the estimated reaction rate constants, the linear free energy relationships (LFERs) summarized the nucleophilic nature of HAN reactions and demonstrated an activating effect of the electron withdrawing halogens on nitrile reactivity, leading to decreasing HAN stability with increasing degree of halogenation of the substituents, while subsequent shift from chlorine to bromine atoms has a contrary stabilizing effect on HANs. The chemical kinetic model together with the reaction rate constants that were determined in this work can be used for quantitative predictions of HAN concentrations depending on pH and free chlorine

  20. Kinetic isotope effects for RNA cleavage by 2'-O- transphosphorylation: Nucleophilic activation by specific base

    PubMed Central

    Harris, Michael E; Dai, Qing; Gu, Hong; Kellerman, Dan; Piccirilli, Joseph A; Anderson, Vernon E

    2010-01-01

    To better understand the interactions between catalysts and transition states during RNA strand cleavage, primary 18O kinetic isotope effects and solvent D2O isotope effects were measured to probe the mechanism of base-catalyzed 2'-O-transphosphorylation of the RNA dinucleotide 5'-UpG-3'. The observed 18O KIEs for the nucleophilic 2'-O and in the 5'-O leaving group at pH 14 are both large relative to reactions of phosphodiesters with good leaving groups, indicating that the reaction catalyzed by hydroxide has a transition state (TS) with advanced phosphorus-oxygen bond fission to the leaving group (18kLG = 1.034 ± 0.004) and phosphorous-nucleophile bond formation (18kNUC = 0.984 ± 0.004). A breakpoint in the pH dependence of the 2'-O-transphosphorylation rate to a pH independent phase above pH 13 has been attributed to the pKa of the 2'-OH nucleophile. A smaller nucleophile KIE is observed at pH 12 (18kNUC = 0.995 ± 0.004) that is interpreted as the combined effect of the equilibrium isotope effect (~1.02) on deprotonation of the 2′-hydroxyl nucleophile and the intrinsic KIE on the nucleophilic addition step (ca. 0.981). An alternative mechanism in which the hydroxide ion acts as a general base is considered unlikely given the lack of a solvent deuterium isotope effect above the breakpoint in the pH versus rate profile. These results represent the first direct analysis of the transition state for RNA strand cleavage. The primary 18O KIE results and the lack of a kinetic solvent deuterium isotope effect together provide strong evidence for a late transition state and 2'-O nucleophile activation by specific base catalysis. PMID:20669950

  1. Ciprofloxacin adsorption on graphene and granular activated carbon: kinetics, isotherms, and effects of solution chemistry.

    PubMed

    Zhu, Xuan; Tsang, Daniel C W; Chen, Feng; Li, Shiyu; Yang, Xin

    2015-01-01

    Ciprofloxacin (CIP) is a commonly used antibiotic and widely detected in wastewaters and farmlands nowadays. This study evaluated the efficacy of next-generation adsorbent (graphene) and conventional adsorbent (granular activated carbon, GAC) for CIP removal. Batch experiments and characterization tests were conducted to investigate the adsorption kinetics, equilibrium isotherms, thermodynamic properties, and the influences of solution chemistry (pH, ionic strength, natural organic matter (NOM), and water sources). Compared to GAC, graphene showed significantly faster adsorption and reached equilibrium within 3 min, confirming the rapid access of CIP into the macroporous network of high surface area of graphene as revealed by the Brunner-Emmet-Teller measurements analysis. The kinetics was better described by a pseudo-second-order model, suggesting the importance of the initial CIP concentration related to surface site availability of graphene. The adsorption isotherm on graphene followed Langmuir model with a maximum adsorption capacity of 323 mg/g, which was higher than other reported carbonaceous adsorbents. The CIP adsorption was thermodynamically favourable on graphene and primarily occurred through π - π interaction, according to the FTIR spectroscopy. While the adsorption capacity of graphene decreased with increasing solution pH due to the speciation change of CIP, the adverse effects of ionic strength (0.01-0.5 mol L(-1)), presence of NOM (5 mg L⁻¹), and different water sources (river water or drinking water) were less significant on graphene than GAC. These results indicated that graphene can serve as an alternative adsorbent for CIP removal in commonly encountered field conditions, if proper separation and recovery is available in place.

  2. An enzyme kinetics study of the pH dependence of chloride activation of oxygen evolution in photosystem II.

    PubMed

    Baranov, Sergei; Haddy, Alice

    2017-03-01

    Oxygen evolution by photosystem II (PSII) involves activation by Cl(-) ion, which is regulated by extrinsic subunits PsbQ and PsbP. In this study, the kinetics of chloride activation of oxygen evolution was studied in preparations of PSII depleted of the PsbQ and PsbP subunits (NaCl-washed and Na2SO4/pH 7.5-treated) over a pH range from 5.3 to 8.0. At low pH, activation by chloride was followed by inhibition at chloride concentrations >100 mM, whereas at high pH activation continued as the chloride concentration increased above 100 mM. Both activation and inhibition were more pronounced at lower pH, indicating that Cl(-) binding depended on protonation events in each case. The simplest kinetic model that could account for the complete data set included binding of Cl(-) at two sites, one for activation and one for inhibition, and four protonation steps. The intrinsic (pH-independent) dissociation constant for Cl(-) activation, K S, was found to be 0.9 ± 0.2 mM for both preparations, and three of the four pK as were determined, with the fourth falling below the pH range studied. The intrinsic inhibition constant, K I, was found to be 64 ± 2 and 103 ± 7 mM for the NaCl-washed and Na2SO4/pH7.5-treated preparations, respectively, and is considered in terms of the conditions likely to be present in the thylakoid lumen. This enzyme kinetics analysis provides a more complete characterization of chloride and pH dependence of O2 evolution activity than has been previously presented.

  3. Concept of variable activation energy and its validity in nonisothermal kinetics.

    PubMed

    Tan, Guanglei; Wang, Qi; Zheng, Hongxia; Zhao, Wei; Zhang, Song; Liu, Zhongsuo

    2011-06-09

    The concept of variable activation energy in solid-state kinetics under nonisothermal conditions has been suffering from doubt and controversy. Rate equations of nonisothermal kinetics of solid decomposition, which involve the factors of thermodynamics conditions, pressure of gaseous product, structure parameters of solid, and/or extent of conversion, are derived from the models of the interface reaction, the diffusion of gaseous product, and the nuclei growth of the solid product, respectively. The definition of the validity function in the rate equations represents the influence of the factors on the reaction rate. A function of variable activation energy depending on the validity function is also developed. The changing trend and degree of activation energy are extrapolated from the function of variable activation energy and based on the data of nonisothermal thermal decomposition of calcium carbonate. It is shown that the concept of variable activation energy is meaningfully applicable to solid-state reactions under nonisothermal conditions.

  4. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

  5. Antifungal activity, kinetics and molecular mechanism of action of garlic oil against Candida albicans

    PubMed Central

    Li, Wen-Ru; Shi, Qing-Shan; Dai, Huan-Qin; Liang, Qing; Xie, Xiao-Bao; Huang, Xiao-Mo; Zhao, Guang-Ze; Zhang, Li-Xin

    2016-01-01

    The antifungal activity, kinetics, and molecular mechanism of action of garlic oil against Candida albicans were investigated in this study using multiple methods. Using the poisoned food technique, we determined that the minimum inhibitory concentration of garlic oil was 0.35 μg/mL. Observation by transmission electron microscopy indicated that garlic oil could penetrate the cellular membrane of C. albicans as well as the membranes of organelles such as the mitochondria, resulting in organelle destruction and ultimately cell death. RNA sequencing analysis showed that garlic oil induced differential expression of critical genes including those involved in oxidation-reduction processes, pathogenesis, and cellular response to drugs and starvation. Moreover, the differentially expressed genes were mainly clustered in 19 KEGG pathways, representing vital cellular processes such as oxidative phosphorylation, the spliceosome, the cell cycle, and protein processing in the endoplasmic reticulum. In addition, four upregulated proteins selected after two-dimensional fluorescence difference in gel electrophoresis (2D-DIGE) analysis were identified with high probability by mass spectrometry as putative cytoplasmic adenylate kinase, pyruvate decarboxylase, hexokinase, and heat shock proteins. This is suggestive of a C. albicans stress responses to garlic oil treatment. On the other hand, a large number of proteins were downregulated, leading to significant disruption of the normal metabolism and physical functions of C. albicans. PMID:26948845

  6. Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

    DOE PAGES

    Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean -François; ...

    2015-06-16

    We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion pathsmore » and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. In conclusion, this study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.« less

  7. Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

    SciTech Connect

    Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean -François; Brommer, Peter; Mousseau, Normand

    2015-06-16

    We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion paths and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. In conclusion, this study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.

  8. Employing Magnetic Levitation to Monitor Reaction Kinetics and Measure Activation Energy

    ERIC Educational Resources Information Center

    Benz, Lauren; Cesafsky, Karen E.; Le, Tran; Park, Aileen; Malicky, David

    2012-01-01

    This article describes a simple and inexpensive undergraduate-level kinetics experiment that uses magnetic levitation to monitor the progress and determine the activation energy of a condensation reaction on a polymeric solid support. The method employs a cuvette filled with a paramagnetic solution positioned between two strong magnets. The…

  9. Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

    NASA Astrophysics Data System (ADS)

    Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean-François; Brommer, Peter; Mousseau, Normand

    2015-06-01

    We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion paths and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. This study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.

  10. Kinetic effect of Pd additions on the hydrogen uptake of chemically activated, ultramicroporous carbon

    SciTech Connect

    Bhat, Vinay V; Contescu, Cristian I; Gallego, Nidia C

    2010-01-01

    The effect of mixing chemically-activated ultramicroporous carbon (UMC) with Pd nanopowder is investigated. Results show that Pd addition doubles the rate of hydrogen uptake, but does not enhance the hydrogen capacity or improve desorption kinetics. The effect of Pd on the rate of hydrogen adsorption supports the occurrence of the hydrogen spillover mechanism in the Pd - UMC system.

  11. Denitrification kinetics in anoxic/aerobic activated sludge systems

    SciTech Connect

    Horne, G.M.

    1998-12-11

    Nitrogen removal needs at municipal wastewater treatment plants (WWTPs) have increased due to greater concerns about eutrophication and increased interest in reuse of treated municipal effluents. Biological processes are the most cost-effective method for nitrogen removal. Biological nitrogen removal is accomplished in two distinctly different processes by the conversion of nitrogen in the wastewater from organic nitrogen and ammonia to nitrate, followed by reduction of the nitrate to nitrogen gas. Nitrate production occurs in an aerobic activated sludge treatment zone during a process called nitrification. The nitrate is then converted through a series of intermediate steps to nitrogen gas in an anoxic zone (an anaerobic condition with nitrate present) during a process called denitrification, effectively removing the nitrogen from the wastewater. Many different WWTP designs have been developed to incorporate these two conditions for nitrogen removal.

  12. Kinetics of thermal activation of an ultraviolet cone pigment.

    PubMed

    Mooney, Victoria; Sekharan, Sivakumar; Liu, Jian; Guo, Ying; Batista, Victor S; Yan, Elsa C Y

    2015-01-14

    Visual pigments can be thermally activated via isomerization of the retinyl chromophore and hydrolysis of the Schiff base (SB) through which the retinyl chromophore is bound to the opsin protein. Here, we present the first combined experimental and theoretical study of the thermal activation of a Siberian hamster ultraviolet (SHUV) pigment. We measured the rates of thermal isomerization and hydrolysis in the SHUV pigment and bovine rhodopsin. We found that these rates were significantly faster in the UV pigment than in rhodopsin due to the difference in the structural and electrostatic effects surrounding the unprotonated Schiff base (USB) retinyl chromophore in the UV pigment. Theoretical (DFT-QM/MM) calculations of the cis-trans thermal isomerization revealed a barrier of ∼23 kcal/mol for the USB retinyl chromophore in SHUV compared to ∼40 kcal/mol for protonated Schiff base (PSB) chromophore in rhodopsin. The lower barrier for thermal isomerization in the SHUV pigment is attributed to the (i) lessening of the steric restraints near the β-ionone ring and SB ends of the chromophore, (ii) displacement of the transmembrane helix 6 (TM6) away from the binding pocket toward TM5 due to absence of the salt bridge between the USB and the protonated E113 residue, and (iii) change in orientation of the hydrogen-bonding networks (HBNs) in the extracellular loop 2 (EII). The results in comparing thermal stability of UV cone pigment and rhodopsin provide insight into molecular evolution of vertebrate visual pigments in achieving low discrete dark noise and high photosensitivity in rod pigments for dim-light vision.

  13. Multicompartmental Analysis of Calcium Kinetics in Normal Adult Males*

    PubMed Central

    Neer, R.; Berman, M.; Fisher, L.; Rosenberg, L. E.

    1967-01-01

    This report describes studies of calcium kinetics in ten normal young men. Serum, urinary, and fecal radioactivity was measured from 1 minute to 20 days after intravenous tracer 47Ca injection, and these results were analyzed jointly with data obtained from a simultaneous metabolic balance study, using digital computer techniques. Surface radioactivity measurements were also obtained to gain further insight into the anatomic correlates of the tracer distribution. The data were satisfied by a model with four exchanging compartments. Series, branching, and mammillary models were analyzed. Several parameters of physiologic interest were independent of the model, but two were dependent on the duration of the study. Individual and mean values for these kinetic analyses are presented with their statistical uncertainties. These studies present detailed analyses in a healthy, normal population and provide a reference for future studies of skeletal metabolism and serum calcium homeostasis. Images PMID:16695925

  14. Systems engineering analysis of kinetic energy weapon concepts

    SciTech Connect

    Senglaub, M.

    1996-06-01

    This study examines, from a systems engineering design perspective, the potential of kinetic energy weapons being used in the role of a conventional strategic weapon. Within the Department of Energy (DOE) complex, strategic weapon experience falls predominantly in the nuclear weapons arena. The techniques developed over the years may not be the most suitable methodologies for use in a new design/development arena. For this reason a more fundamental approach was pursued with the objective of developing an information base from which design decisions might be made concerning the conventional strategic weapon system concepts. The study examined (1) a number of generic missions, (2) the effects of a number of damage mechanisms from a physics perspective, (3) measures of effectiveness (MOE`s), and (4) a design envelope for kinetic energy weapon concepts. With the base of information a cut at developing a set of high-level system requirements was made, and a number of concepts were assessed against these requirements.

  15. Effect of heating rate and kinetic model selection on activation energy of nonisothermal crystallization of amorphous felodipine.

    PubMed

    Chattoraj, Sayantan; Bhugra, Chandan; Li, Zheng Jane; Sun, Changquan Calvin

    2014-12-01

    The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate.

  16. Kinetic and structural evaluation of selected active site mutants of the Aspergillus fumigatus KDNase (sialidase).

    PubMed

    Yeung, Juliana H F; Telford, Judith C; Shidmoossavee, Fahimeh S; Bennet, Andrew J; Taylor, Garry L; Moore, Margo M

    2013-12-23

    Aspergillus fumigatus is an airborne fungal pathogen. We previously cloned and characterized an exo-sialidase from A. fumigatus and showed that it preferred 2-keto-3-deoxynononic acid (KDN) as a substrate to N-acetylneuraminic acid (Neu5Ac). The purpose of this study was to investigate the structure-function relationships of critical catalytic site residues. Site-directed mutagenesis was used to create three mutant recombinant enzymes: the catalytic nucleophile (Y358H), the general acid/base catalyst (D84A), and an enlargement of the binding pocket to attempt to accommodate the N-acetyl group of Neu5Ac (R171L). Crystal structures for all enzymes were determined. The D84A mutation had an effect in decreasing the activity of AfKDNase that was stronger than that of the same mutation in the structurally similar sialidase from the bacterium Micromonospora viridifaciens. These data suggest that the catalytic acid is more important in the reaction of AfKDNase and that catalysis is less dependent on nucleophilic or electrostatic stabilization of the developing positive charge at the transition state for hydrolysis. Removal of the catalytic nucleophile (Y358H) significantly lowered the activity of the enzyme, but this mutant remained a retaining glycosidase as demonstrated by nuclear magnetic resonance spectroscopic analysis. This is a novel finding that has not been shown with other sialidases. Kinetic activity measured at pH 5.2 revealed that R171L had higher activity on a Neu5Ac-based substrate than wild-type KDNase; hence, leucine in place of arginine in the binding pocket improved catalysis toward Neu5Ac substrates. Hence, whether a sialidase is primarily a KDNase or a neuraminidase is due in part to the presence of an amino acid that creates a steric clash with the N-acetyl group.

  17. Stabilized leachates: ozone-activated carbon treatment and kinetics.

    PubMed

    Rivas, F Javier; Beltrán, Fernando; Gimeno, Olga; Acedo, Benito; Carvalho, Fátima

    2003-12-01

    Ozone has been used as a pre-oxidation step for the treatment of stabilized leachates. Given the refractory nature of this type of effluents, the conversion of some wastewater quality parameters has been moderate after 1 h of ozonation (i.e. 30% chemical oxygen demand (COD) depletion). Ozone uptake was calculated in the interval 1.3-1.5 g of ozone per gram of COD degraded. An optimum dose of ozone has been experienced in terms of biodegradability of the processed effluent (60 min of treatment, 1 x 10(-3) mol L(-1) ozone inlet feeding concentration and 50 L h(-1) gas flow-rate). pH and other typical hydroxyl radical generator systems exerted no influence on the efficiency of the process, suggesting the negligible role played by the indirect route of oxidation (generation of hydroxyl radicals). The ozonated effluent was thereafter treated in a second adsorption stage by using a commercial activated carbon. Removal levels up to 90% of COD in approximately 120 h were experienced for adsorbent dosages of 30 g L(-1). Both steps, the single ozonation and the adsorption stage have been modelled by using different pseudoempirical models.

  18. Novel three-stage kinetic model for aqueous benzene adsorption on activated carbon.

    PubMed

    Choi, Jae-Woo; Choi, Nag-Choul; Lee, Soon-Jae; Kim, Dong-Ju

    2007-10-15

    We propose a novel kinetic model for adsorption of aqueous benzene onto both granular activated carbon (GAC) and powdered activated carbon (PAC). The model is based on mass conservation of benzene coupled with three-stage adsorption: (1) the first portion for an instantaneous stage or external surface adsorption, (2) the second portion for a gradual stage with rate-limiting intraparticle diffusion, and (3) the third portion for a constant stage in which the aqueous phase no longer interacts with activated carbon. An analytical solution of the kinetic model was validated with the kinetic data obtained from aqueous benzene adsorption onto GAC and PAC in batch experiments with two different solution concentrations (C(0)=300 mg L(-1), 600 mg L(-1)). Experimental results revealed that benzene adsorption for the two concentrations followed three distinct stages for PAC but two stages for GAC. The analytical solution could successfully describe the kinetic adsorption of aqueous benzene in the batch reaction system, showing a fast instantaneous adsorption followed by a slow rate-limiting adsorption and a final long constant adsorption. Use of the two-stage model gave incorrect values of adsorption coefficients in the analytical solution due to inability to describe the third stage.

  19. Effect of electric current frequency on the activation kinetics of raw charcoal

    SciTech Connect

    Shevchenko, A.O.; Ivakhnyuk, G.K.; Fedorov, N.F.

    1993-12-10

    The effect of electric current frequency on the kinetics of raw charcoal activation with water vapor has been investigated. It was established that under the effect of alternating current the rate constant increases under otherwise equal conditions. A dependence of the reaction rate on the current frequency was found. It was discovered that under the effect of alternating current the activation energy of interaction with water vapor diminishes.

  20. Cytokine-release kinetics of platelet-rich plasma according to various activation protocols

    PubMed Central

    Roh, Y. H.; Kim, W.; Park, K. U.

    2016-01-01

    Objectives This study was conducted to evaluate the cytokine-release kinetics of platelet-rich plasma (PRP) according to different activation protocols. Methods Two manual preparation procedures (single-spin (SS) at 900 g for five minutes; double-spin (DS) at 900 g for five minutes and then 1500 g for 15 minutes) were performed for each of 14 healthy subjects. Both preparations were tested for platelet activation by one of three activation protocols: no activation, activation with calcium (Ca) only, or calcium with a low dose (50 IU per 1 ml PRP) of thrombin. Each preparation was divided into four aliquots and incubated for one hour, 24 hours, 72 hours, and seven days. The cytokine-release kinetics were evaluated by assessing PDGF, TGF, VEGF, FGF, IL-1, and MMP-9 concentrations with bead-based sandwich immunoassay. Results The concentration of cytokine released from PRP varied over time and was influenced by various activation protocols. Ca-only activation had a significant effect on the DS PRPs (where the VEGF, FGF, and IL-1 concentrations were sustained) while Ca/thrombin activation had effects on both SS and DS PRPs (where the PDGF and VEGF concentrations were sustained and the TGF and FGF concentrations were short). The IL-1 content showed a significant increase with Ca-only or Ca/thrombin activation while these activations did not increase the MMP-9 concentration. Conclusion The SS and DS methods differed in their effect on cytokine release, and this effect varied among the cytokines analysed. In addition, low dose of thrombin/calcium activation increased the overall cytokine release of the PRP preparations over seven days, relative to that with a calcium-only supplement or non-activation. Cite this article: Professor J. H. Oh. Cytokine-release kinetics of platelet-rich plasma according to various activation protocols. Bone Joint Res 2016;5:37–45. DOI: 10.1302/2046-3758.52.2000540 PMID:26862077

  1. Pyrolysis kinetics of raw and hydrothermally carbonized Karanj (Pongamia pinnata) fruit hulls via thermogravimetric analysis.

    PubMed

    Islam, Md Azharul; Asif, M; Hameed, B H

    2015-03-01

    The pyrolysis of karanj fruit hulls (KFH) and karanj fruit hull hydrothermal carbonization (KFH-HTC) hydrochar was thermogravimetrically investigated under a nitrogen environment at 5 °C/min, 10 °C/min, and 20 °C/min. The pyrolysis decomposition of KFH biomass was faster than that of KFH-HTC hydrochar because of the high volatility and fixed carbon of KFH biomass. Weight loss percentage was also affected by the heating rates. The kinetic data were evaluated with the Kissinger-Akahira-Sunose and Flynn-Wall-Ozawa methods. The activation energy values obtained with these two methods were 61.06 and 68.53 kJ/mol for KFH biomass and 130.49 and 135.87 kJ/mol for KFH-HTC hydrochar, respectively. The analysis of kinetic process mechanisms was verified with the Coats-Redfern method. KFH-HTC hydrochar may play a potential role in transforming biomass to energy-rich feedstock for thermochemical applications because of its high heating value, high fixed carbon, and low ash and sulfur contents.

  2. Reflectance spectroscopy in analysis of UO2 scale: derivation of a kinetic model of uranium oxidation.

    PubMed

    Chernia, Z

    2009-03-21

    In this study, we analyzed the development of a compact oxide scale built in course of Uranium surface oxidation. The process was monitored by an in-situ acquisition of the reflectance interference peaks in the NIR-MIR. Dielectric properties of the growing oxide scale were derived in accord to the oscillator model. We used effective media approach to simulate heterogeneous dielectric content in the oxide-metal interface. Following dielectric parameterization, structural properties (e.g., scale thickness) of the proposed multi-scale scheme were calculated. As scale's growth process quantified, a valid kinetic model was proposed. Analysis showed that oxidation dynamics is governed by a multi-parabolic, true diffusion-limited mechanism of activation energy conveniently equaling the known anion diffusion enthalpy of 26 kcal/mol. The applied kinetic model suggested a setup of two consecutive oxide scales, characterized by differing anion diffusion rates. Though mathematical formalism presented a similar to the paralinear, time-dependent solution, here, in contrast to the classic paralinear assumption, both scales consisted of a compact, diffusion limited oxide barriers. As a result, the difference in anion flow across the outer and inner scale barriers assigned the overall, pseudo-linear rate constant-kl, of a negative (in contrast to the paralinear approach) value. Next, Uranium oxidation has been studied in the post-elastic domain. Markedly, upon breakaway of the compact oxide scale, classic paralinear behavior was reestablished for scale thickness of > or = 0.5 microm.

  3. Kinetic analysis of the thermal stability of the photosynthetic reaction center from Rhodobacter sphaeroides.

    PubMed

    Hughes, Arwel V; Rees, Paul; Heathcote, Peter; Jones, Michael R

    2006-06-01

    The temperature-induced denaturation of the photosynthetic reaction center from Rhodobacter sphaeroides has been studied through the changes that occur in the absorption spectrum of the bound chromophores on heating. At elevated temperatures, the characteristic absorbance bands of the bacteriochlorins bound to the polypeptides within the reaction center are lost, and are replaced by features typical of unbound bacteriochlorophyll and bacteriopheophytin. The kinetics of the spectral changes cannot be explained by a direct conversion from the functional to the denatured form of the protein, and require the presence of at least one intermediate. Possible mechanisms for the transformation via an intermediate are examined using a global analysis of the kinetic data, and the most likely mechanism is shown to involve a reversible transformation between the native state and an off-pathway intermediate, coupled to an irreversible transformation to the denatured state. The activation energies for the transformations between the three components are calculated from the effect of temperature on the individual rate constants, and the likely structural changes of the protein during the temperature-induced transformation are discussed.

  4. Kinetic modeling and sensitivity analysis of acetone-butanol-ethanol production.

    PubMed

    Shinto, Hideaki; Tashiro, Yukihiro; Yamashita, Mayu; Kobayashi, Genta; Sekiguchi, Tatsuya; Hanai, Taizo; Kuriya, Yuki; Okamoto, Masahiro; Sonomoto, Kenji

    2007-08-01

    A kinetic simulation model of metabolic pathways that describes the dynamic behaviors of metabolites in acetone-butanol-ethanol (ABE) production by Clostridium saccharoperbutylacetonicum N1-4 was proposed using a novel simulator WinBEST-KIT. This model was validated by comparing with experimental time-course data of metabolites in batch cultures over a wide range of initial glucose concentrations (36.1-295 mM). By introducing substrate inhibition, product inhibition of butanol, activation of butyrate and considering the cessation of metabolic reactions in the case of insufficiency of energy after glucose exhaustion, the revised model showed 0.901 of squared correlation coefficient (r(2)) between experimental time-course of metabolites and calculated ones. Thus, the final revised model is assumed to be one of the best candidates for kinetic simulation describing dynamic behavior of metabolites in ABE production. Sensitivity analysis revealed that 5% increase in reaction of reverse pathway of butyrate production (R(17)) and 5% decrease in reaction of CoA transferase for butyrate (R(15)) highly contribute to high production of butanol. These system analyses should be effective in the elucidation which pathway is metabolic bottleneck for high production of butanol.

  5. Thermogravimetric Analysis and Kinetics on Reducing Low-Grade Manganese Dioxide Ore by Biomass

    NASA Astrophysics Data System (ADS)

    Zhang, Honglei; Zhu, Guocai; Yan, Hong; Li, Tiancheng; Feng, Xiujuan

    2013-08-01

    Nonisothermal thermogravimetric analysis (TGA) was applied to evaluate rice straw, sawdust, wheat stalk, maize straw, and bamboo to explore their potential for reduction of manganese dioxide ore. Results from the biomass pyrolysis experiments showed that wood-based biomass materials, such as sawdust and bamboo, could produce more reductive agents, while herb-based biomass materials, such as rice straw, wheat stalk, and maize straw, had lower reaction temperatures. The peak temperatures for biomass reduction tests were 20 K to 50 K (20 °C to 50 °C) higher compared with the pyrolysis tests, and a clear shoulder at around 523 K (250 °C) could be observed. The effects of heating rate, biomass/manganese dioxide ore ratio, and different components of biomass were also investigated. An independent parallel first-order reaction kinetic model was used to calculate the values of activation energy and frequency factor for biomass pyrolysis and reduction of manganese dioxide ore. For better understanding the reduction process, kinetic parameters of independent behavior of manganese dioxide ore were also calculated by simple mathematical treatment. Finally, the isokinetic temperature T i and the rate constant k 0 for reduction of manganese oxide ore by reductive volatiles of biomass were derived according to the Arrhenius equation, which were determined to be 603 K (330 °C) and 108.99 min-1, respectively.

  6. Kinetics of Alkaline Activation of Slag and Fly ash-Slag Systems

    NASA Astrophysics Data System (ADS)

    Chithiraputhiran, Sundara Raman

    Alkali-activated aluminosilicates, commonly known as "geopolymers", are being increasingly studied as a potential replacement for Portland cement. These binders use an alkaline activator, typically alkali silicates, alkali hydroxides or a combination of both along with a silica-and-alumina rich material, such as fly ash or slag, to form a final product with properties comparable to or better than those of ordinary Portland cement. The kinetics of alkali activation is highly dependent on the chemical composition of the binder material and the activator concentration. The influence of binder composition (slag, fly ash or both), different levels of alkalinity, expressed using the ratios of Na2O-to-binders (n) and activator SiO2-to-Na2O ratios (Ms), on the early age behavior in sodium silicate solution (waterglass) activated fly ash-slag blended systems is discussed in this thesis. Optimal binder composition and the n values are selected based on the setting times. Higher activator alkalinity (n value) is required when the amount of slag in the fly ash-slag blended mixtures is reduced. Isothermal calorimetry is performed to evaluate the early age hydration process and to understand the reaction kinetics of the alkali activated systems. The differences in the calorimetric signatures between waterglass activated slag and fly ash-slag blends facilitate an understanding of the impact of the binder composition on the reaction rates. Kinetic modeling is used to quantify the differences in reaction kinetics using the Exponential as well as the Knudsen method. The influence of temperature on the reaction kinetics of activated slag and fly ash-slag blends based on the hydration parameters are discussed. Very high compressive strengths can be obtained both at early ages as well as later ages (more than 70 MPa) with waterglass activated slag mortars. Compressive strength decreases with the increase in the fly ash content. A qualitative evidence of leaching is presented through

  7. Kinetics Analysis of Higher Temperature Salt Bath Nitriding for Aisi 1045 Steel

    NASA Astrophysics Data System (ADS)

    Dai, Mingyang; Chen, Yao; Chai, Yating; Hu, Jing

    2016-05-01

    Rapid salt bath nitriding was conducted at higher temperature above 600∘C instead of normally used 560∘C for AISI 1045 steel. Optical microscopy (OM), X-ray diffraction (XRD) and micro-hardness tester were employed to characterize the microstructure, phase constituents and micro-hardness of the treated specimens. The results showed that salt bath nitriding at higher temperature could significantly increase the compound layer thickness and higher cross-sectional hardness can be obtained. Kinetics analysis illustrated that the nitrogen atoms diffusion coefficient was obviously increased with temperature, and the activation energy of nitrogen atom diffusion was decreased from 220kJṡmol-1 to 142kJṡmol-1.

  8. Neutron activation analysis system

    DOEpatents

    Taylor, M.C.; Rhodes, J.R.

    1973-12-25

    A neutron activation analysis system for monitoring a generally fluid media, such as slurries, solutions, and fluidized powders, including two separate conduit loops for circulating fluid samples within the range of radiation sources and detectors is described. Associated with the first loop is a neutron source that emits s high flux of slow and thermal neutrons. The second loop employs a fast neutron source, the flux from which is substantially free of thermal neutrons. Adjacent to both loops are gamma counters for spectrographic determination of the fluid constituents. Other gsmma sources and detectors are arranged across a portion of each loop for deterMining the fluid density. (Official Gazette)

  9. Educational activities of CAREER: Crystallization Kinetics in Volcanology

    NASA Astrophysics Data System (ADS)

    Hammer, J. E.

    2011-12-01

    Professional development of teachers is recognized as critical for improving student learning outcomes. The major outreach initiative of my CAREER award was to develop a teacher professional development program for middle school (grades 6-8) teachers that would improve teacher's mastery of geoscience and basic science skills and practices and expose them to an authentic research environment. The explicit objectives of the Research Experience for Teachers in Volcano-Petrology (RET/V-P) were for teachers to (1) master technical skills for safe and productive laboratory work, (2) deepen understanding of science content, (3) develop scientific "habits of the mind" as outlined in the National Science Standards, and (4) hone science communication skills. Six teachers, one undergraduate, and two graduate students participated in the teacher professional development program during the summers of the CAREER award period. A subsequent EAR award now supports the program, and summer 2011 saw the participation of five additional teachers. The teachers span a wide range of educational backgrounds, prior exposure to geoscience, and teaching assignments at public and private schools. Each year, the program was modified using formative and summative evaluation tools to better serve the scheduling needs and content preferences. In general, the program has evolved from an emphasis on research exposure to an emphasis on imparting basic geoscience concepts. A myriad of approaches including field trips to local outcrops, lecture tutorials and lecture-based active engagement exercises (such as iclicker delivery of Geoscience Concept Inventory questions), with a taste of laboratory work (crystal growth experiments, optics primer), has emerged as the most successful means of achieving objectives 1-4, above. The first summer I advertised the RET/V-P, no teachers applied. (This challenge was overcome in subsequent years by targeting the solicitation using teacher list serves, the Hawaii

  10. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    PubMed Central

    Martí-Centelles, Vicente; Burguete, M. Isabel; Luis, Santiago V.

    2012-01-01

    Several kinetic models for the macrocyclization of a C2 pseudopeptide with a dihalide through a SN2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes. PMID:22666148

  11. Kinetic analysis for macrocyclizations involving anionic template at the transition state.

    PubMed

    Martí-Centelles, Vicente; Burguete, M Isabel; Luis, Santiago V

    2012-01-01

    Several kinetic models for the macrocyclization of a C₂ pseudopeptide with a dihalide through a S(N)2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  12. Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood

    PubMed Central

    Chatterjee, Manash S.; Denney, William S.; Jing, Huiyan; Diamond, Scott L.

    2010-01-01

    Blood function defines bleeding and clotting risks and dictates approaches for clinical intervention. Independent of adding exogenous tissue factor (TF), human blood treated in vitro with corn trypsin inhibitor (CTI, to block Factor XIIa) will generate thrombin after an initiation time (Ti) of 1 to 2 hours (depending on donor), while activation of platelets with the GPVI-activator convulxin reduces Ti to ∼20 minutes. Since current kinetic models fail to generate thrombin in the absence of added TF, we implemented a Platelet-Plasma ODE model accounting for: the Hockin-Mann protease reaction network, thrombin-dependent display of platelet phosphatidylserine, VIIa function on activated platelets, XIIa and XIa generation and function, competitive thrombin substrates (fluorogenic detector and fibrinogen), and thrombin consumption during fibrin polymerization. The kinetic model consisting of 76 ordinary differential equations (76 species, 57 reactions, 105 kinetic parameters) predicted the clotting of resting and convulxin-activated human blood as well as predicted Ti of human blood under 50 different initial conditions that titrated increasing levels of TF, Xa, Va, XIa, IXa, and VIIa. Experiments with combined anti-XI and anti-XII antibodies prevented thrombin production, demonstrating that a leak of XIIa past saturating amounts of CTI (and not “blood-borne TF” alone) was responsible for in vitro initiation without added TF. Clotting was not blocked by antibodies used individually against TF, VII/VIIa, P-selectin, GPIb, protein disulfide isomerase, cathepsin G, nor blocked by the ribosome inhibitor puromycin, the Clk1 kinase inhibitor Tg003, or inhibited VIIa (VIIai). This is the first model to predict the observed behavior of CTI-treated human blood, either resting or stimulated with platelet activators. CTI-treated human blood will clot in vitro due to the combined activity of XIIa and XIa, a process enhanced by platelet activators and which proceeds in the

  13. Kinetic Monte Carlo study of activated states and correlated shear-transformation-zone activity during the deformation of an amorphous metal

    NASA Astrophysics Data System (ADS)

    Homer, Eric R.; Rodney, David; Schuh, Christopher A.

    2010-02-01

    Shear transformation zone (STZ) dynamics simulations, which are based on the kinetic Monte Carlo algorithm, are used to model the mechanical response of amorphous metals and provide insight into the collective aspects of the microscopic events underlying deformation. The present analysis details the activated states of STZs in such a model, as well as the statistics of their activation and how these are affected by imposed conditions of stress and temperature. The analysis sheds light on the spatial and temporal correlations between the individual STZ activations that lead to different macroscopic modes of deformation. Three basic STZ correlation behaviors are observed: uncorrelated activity, nearest-neighbor correlation, and self-reactivating STZs. These three behaviors correspond well with the macroscopic deformation modes of homogeneous flow, inhomogeneous deformation, and elastic behavior, respectively. The effect of pre-existing stresses in the simulation cell is also studied and found to have a homogenizing effect on STZ correlations, suppressing the tendency for localization.

  14. Kinetic and phylogenetic analysis of plant polyamine uptake transporters.

    PubMed

    Mulangi, Vaishali; Chibucos, Marcus C; Phuntumart, Vipaporn; Morris, Paul F

    2012-10-01

    The rice gene Polyamine Uptake Transporter1 (PUT1) was originally identified based on its homology to the polyamine uptake transporters LmPOT1 and TcPAT12 in Leishmania major and Trypanosoma cruzi, respectively. Here we show that five additional transporters from rice and Arabidopsis that cluster in the same clade as PUT1 all function as high affinity spermidine uptake transporters. Yeast expression assays of these genes confirmed that uptake of spermidine was minimally affected by 166 fold or greater concentrations of amino acids. Characterized polyamine transporters from both Arabidopsis thaliana and Oryza sativa along with the two polyamine transporters from L. major and T. cruzi were aligned and used to generate a hidden Markov model. This model was used to identify significant matches to proteins in other angiosperms, bryophytes, chlorophyta, discicristates, excavates, stramenopiles and amoebozoa. No significant matches were identified in fungal or metazoan genomes. Phylogenic analysis showed that some sequences from the haptophyte, Emiliania huxleyi, as well as sequences from oomycetes and diatoms clustered closer to sequences from plant genomes than from a homologous sequence in the red algal genome Galdieria sulphuraria, consistent with the hypothesis that these polyamine transporters were acquired by horizontal transfer from green algae. Leishmania and Trypansosoma formed a separate cluster with genes from other Discicristates and two Entamoeba species. We surmise that the genes in Entamoeba species were acquired by phagotrophy of Discicristates. In summary, phylogenetic and functional analysis has identified two clades of genes that are predictive of polyamine transport activity.

  15. Determination of kinetic data for soot oxidation: Modeling of competition between oxygen diffusion and reaction during thermogravimetric analysis

    SciTech Connect

    Gilot, P.; Bonnefoy, F.; Marcuccilli, F.; Prado, G. . Lab. Gestion des Risques et Environnement)

    1993-10-01

    Kinetic data concerning carbon black oxidation in the temperature range between 600 and 900 C have been obtained using thermogravimetric analysis. Modeling of diffusion in a boundary layer above the pan and inside the porous medium coupled to oxygen reaction with carbon black is necessary to obtain kinetic constants as a function of temperature. These calculations require the knowledge of the oxidation rate at a given constant temperature as a function of the initial mass loading m[sub o]. This oxidation rate, expressed in milligrams of soot consumed per second and per milligram of initial soot loading, decreases when m[sub o] increases, in agreement with a reaction in an intermediary regime where the kinetics and the oxygen diffusion operate. The equivalent diffusivity of oxygen inside the porous medium is evaluated assuming two degrees of porosity: between soot aggregates and inside each aggregate. Below 700 C an activation energy of about 103 kJ/mol can be related to a combustion reaction probably kinetically controlled. Beyond 700 C the activation energy of about 20 kJ/ mol corresponds to a reaction essentially controlled by oxygen diffusion leading to a constant density oxidation with oxygen consumption at or near the particle surface. To validate these data, they are used in the modeling of a Diesel particulate trap regeneration. In this particular case, the oxidizing flux is forced across the carbon black deposit, oxygen diffusion being insignificant. A good agreement between experimental results and model predictions is obtained, proving the rate constants validity.

  16. Thermal and Kinetic Properties of Motions in a Prominence Activation and Nearby Loop

    NASA Technical Reports Server (NTRS)

    Kucera, Therese; Landi, E.

    2005-01-01

    We perform a quantitative analysis of the thermal properties of a prominence activation and motions in a nearby loop. In order to make measurements of the quickly moving features seen in prominences in the UV we use the SOHO/SUMER spectrograph to take a time series of exposures from a single pointing position, providing a measurement of spectral line properties as a function of time and position along the slit. The lines observed cover a broad range of temperatures from 80,000 - 1.6 million K. These measurements are combined with TRACE movies in transition region and coronal temperature bands to obtain more complete information concerning prominence structure and motions. The resulting observations allow us to analyze the thermal and kinetic energy of the moving sources as functions of time. The loop and prominence are most apparent in lines formed at temperatures below 250,000 K. We find that in most cases the temperature distribution of plasma in a moving feature changes relatively little over time periods of about 20 minutes.

  17. Single-molecule kinetics under force: probing protein folding and enzymatic activity with optical tweezers

    NASA Astrophysics Data System (ADS)

    Wong, Wesley

    2010-03-01

    Weak non-covalent bonds between and within single molecules govern many aspects of biological structure and function (e.g. DNA base-paring, receptor-ligand binding, protein folding, etc.) In living systems, these interactions are often subject to mechanical forces, which can greatly alter their kinetics and activity. My group develops and applies novel single-molecule manipulation techniques to explore and quantify these force-dependent kinetics. Using optical tweezers, we have quantified the force-dependent unfolding and refolding kinetics of different proteins, including the cytoskeletal protein spectrin in collaboration with E. Evans's group [1], and the A2 domain of the von Willebrand factor blood clotting protein in collaboration with T. Springer's group [2]. Furthermore, we have studied the kinetics of the ADAMTS13 enzyme acting on a single A2 domain, and have shown that physiolgical forces in the circulation can act as a cofactor for enzymatic cleavage, regulating hemostatic activity [2]. References: 1. E. Evans, K. Halvorsen, K. Kinoshita, and W.P. Wong, Handbook of Single Molecule Biophysics, P. Hinterdorfer, ed., Springer (2009). 2. X. Zhang, K. Halvorsen, C.-Z. Zhang, W.P. Wong, and T.A. Springer, Science 324 (5932), 1330-1334 (2009).

  18. Adsorption of cellulase Aspergillus niger on a commercial activated carbon: kinetics and equilibrium studies.

    PubMed

    Daoud, Fatima Boukraa-Oulad; Kaddour, Samia; Sadoun, Tahar

    2010-01-01

    The adsorption kinetics of cellulase Aspergillus niger on a commercial activated carbon has been performed using a batch-adsorption technique. The effect of various experimental parameters such as initial enzyme concentration, contact time and temperature were investigated. The pseudo-first-order and pseudo-second-order kinetic models were used to describe the kinetic data which shows that the adsorption of the enzyme followed the pseudo-second-order rate expression and the rate constants were evaluated. The Langmuir and Freundlich adsorption isotherm models were applied to describe the equilibrium isotherms, and the isotherm constants were determined. It was found that Langmuir model was more suitable for our data. The activation energy of adsorption was also evaluated for the adsorption of enzyme onto activated carbon. It was found 11.37 kJ mol(-1). Thermodynamic parameters Delta G(0), Delta H(0) and DeltaS(0) were calculated, indicating that this process can be spontaneous and endothermic. The adsorption enthalpy and entropy were found 11.12 kJ mol(-1) and 0.084 kJ mol(-1)K(-1), respectively. At 30 degrees C and at pH 4.8, 1g activated carbon adsorbed about 1565 mg of cellulase, with a retention of 70% of the native enzyme activity up to five cycles of repeated batch enzyme reactions.

  19. Units of analysis and kinetic structure of behavioral repertoires

    PubMed Central

    Thompson, Travis; Lubinski, David

    1986-01-01

    It is suggested that molar streams of behavior are constructed of various arrangements of three elementary constituents (elicited, evoked, and emitted response classes). An eight-cell taxonomy is elaborated as a framework for analyzing and synthesizing complex behavioral repertoires based on these functional units. It is proposed that the local force binding functional units into a smoothly articulated kinetic sequence arises from temporally arranged relative response probability relationships. Behavioral integration is thought to reflect the joint influence of the organism's hierarchy of relative response probabilities, fluctuating biological states, and the arrangement of environmental and behavioral events in time. PMID:16812461

  20. Kinetic analysis of the hydrolysis of methyl parathion using citrate-stabilized 10 nm gold nanoparticles.

    PubMed

    Nita, Rafaela; Trammell, Scott A; Ellis, Gregory A; Moore, Martin H; Soto, Carissa M; Leary, Dagmar H; Fontana, Jake; Talebzadeh, Somayeh F; Knight, D Andrew

    2016-02-01

    "Ligand-free" citrate-stabilized 10 nm gold nanoparticles (AuNPs) promote the hydrolysis of the thiophosphate ester methyl parathion (MeP) on the surface of gold as a function of pH and two temperature values. At 50 °C, the active surface gold atoms show catalytic turnover ∼4 times after 8 h and little turnover of gold surface atoms at 25 °C with only 40% of the total atoms being active. From Michaelis-Menten analysis, k(cat) increases between pH 8 and 9 and decreases above pH 9. A global analysis of the spectral changes confirmed the stoichiometric reaction at 25 °C and the catalytic reaction at 50 °C and mass spectrometry confirmed the identity of p-nitrophenolate (PNP) product. Additional decomposition pathways involving oxidation and hydrolysis independent of the formation of PNP were also seen at 50 °C for both catalyzed and un-catalyzed reactions. This work represents the first kinetic analysis of ligand-free AuNP catalyzed hydrolysis of a thiophosphate ester.

  1. Kinetic studies of elemental mercury adsorption in activated carbon fixed bed reactor.

    PubMed

    Skodras, G; Diamantopoulou, Ir; Pantoleontos, G; Sakellaropoulos, G P

    2008-10-01

    Activated carbons are suitable materials for Hg(0) adsorption in fixed bed operation or in injection process. The fixed bed tests provide good indication of activated carbons effectiveness and service lives, which depend on the rates of Hg(0) adsorption. In order to correlate fixed bed properties and operation conditions, with their adsorptive capacity and saturation time, Hg(0) adsorption tests were realized in a bench-scale unit, consisted of F400 activated carbon fixed bed reactor. Hg(0) adsorption tests were conducted at 50 degrees C, under 0.1 and 0.35 ng/cm(3) Hg(0) initial concentrations and with carbon particle sizes ranging between 75-106 and 150-250 microm. Based on the experimental breakthrough data, kinetic studies were performed to investigate the mechanism of adsorption and the rate controlling steps. Kinetic models evaluated include the Fick's intraparticle diffusion equation, the pseudo-first order model, the pseudo-second order model and Elovich kinetic equation. The obtained experimental results revealed that the increase in particle size resulted in significant decrease of breakthrough time and mercury adsorptive capacity, due to the enhanced internal diffusion limitations and smaller external mass transfer coefficients. Additionally, higher initial mercury concentrations resulted in increased breakthrough time and mercury uptake. From the kinetic studies results it was observed that all the examined models describes efficiently Hg(0) breakthrough curves, from breakpoint up to equilibrium time. The most accurate prediction of the experimental data was achieved by second order model, indicating that the chemisorption rate seems to be the controlling step in the procedure. However, the successful attempt to describe mercury uptake with Fick's diffusion model and the first order kinetic model, reveals that the adsorption mechanism studied was complex and followed both surface adsorption and particle diffusion.

  2. Preparation of steam activated carbon from rubberwood sawdust (Hevea brasiliensis) and its adsorption kinetics.

    PubMed

    Prakash Kumar, B G; Shivakamy, K; Miranda, Lima Rose; Velan, M

    2006-08-25

    Activated carbon was produced from a biowaste product, rubberwood sawdust (RWSD) using steam in a high temperature fluidized bed reactor. Experiments were carried out to investigate the influence of various process parameters such as activation time, activation temperature, particle size and fluidising velocity on the quality of the activated carbon. The activated carbon was characterized based on its iodine number, methylene blue number, Brauner Emmet Teller (BET) surface area and surface area obtained using the ethylene glycol mono ethyl ether (EGME) retention method. The best quality activated carbon was obtained at an activation time and temperature of 1h and 750 degrees C for an average particle size of 0.46 mm. The adsorption kinetics shows that pseudo-second-order rate fitted the adsorption kinetics better than pseudo-first-order rate equation. The adsorption capacity of carbon produced from RWSD was found to be 1250 mg g(-1) for the Bismark Brown dye. The rate constant and diffusion coefficient for intraparticle transport were determined for steam activated carbon. The characteristic of the prepared activated carbon was found comparable to the commercial activated carbon.

  3. A kinetic energy analysis of the meso beta-scale severe storm environment

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.; Printy, M. F.

    1984-01-01

    Analyses are performed of the meso beta-scale (20-200 km wavelengths and several hours to one-day periods) severe storm kinetic energy balance on the fifth day of the AVE SESAME campaign of May 1979. A 24-hr interval covering the antecedent, active and post-convective outbreak activity over Oklahoma are considered. Use is made of the kinetic energy budget equation (KEBE) for a finite volume in an isobaric coordinate system. Rawindsonde data with 75 km resolution were treated. The KEBE model covered changes in kinetic energy due to the cross contour flows, horizontal and vertical components of flux divergence, and volumic mass changes on synoptic and subsynoptic scales. The greatest variability was concentrated above 400 mb height and over the most intense storm activity. Energy was generated at the highest rates in divergence and decreased the most in convection. The meso beta-scale lacked sufficient resolution for analyzing mesoscale activity.

  4. Nonparametric analysis of nonexponential and multidimensional kinetics. I. Quantifying rate dispersion, rate heterogeneity, and exchange dynamics.

    PubMed

    Berg, Mark A; Kaur, Harveen

    2017-02-07

    The quantification of nonexponential (dispersed) kinetics has relied on empirical functions, which yield parameters that are neither unique nor easily related to the underlying mechanism. Multidimensional kinetics provide more information on dispersed processes, but a good approach to their analysis is even less clear than for standard, one-dimensional kinetics. This paper is the first in a series that analyzes kinetic data in one or many dimensions with a scheme that is nonparametric: it quantifies nonexponential decays without relying on a specific functional form. The quantities obtained are directly related to properties of the mechanism causing the rate dispersion. Log-moments of decays, which parallel the standard moments of distributions (mean, standard deviation, etc.), are introduced for both one- and multi-dimensional decays. Kinetic spectra are defined to visualize the data. The utility of this approach is demonstrated on a simple, but general, model of dispersed kinetics-a nonexponential homogeneous decay combined with slowly exchanging rate heterogeneity. The first log-moments give a geometric-mean relaxation time. Second log-moments quantify the magnitude of rate dispersion, the fraction of the dispersion due to heterogeneity, and the dynamics of exchange between different rate subensembles. A suitable combination of these moments isolates exchange dynamics from three-dimensional kinetics without contamination by the rate-filtering effects that were identified in a recent paper [M. A. Berg and J. R. Darvin, J. Chem. Phys. 145, 054119 (2016)].

  5. Kinetic analysis of enzyme systems with suicide substrate in the presence of a reversible competitive inhibitor, tested by simulated progress curves.

    PubMed

    Moruno-Dávila, M A; Garrido-del Solo, C; García-Moreno, M; Havsteen, B H; Garcia-Sevilla, F; Garcia-Cánovas, F; Varón, R

    2001-02-01

    The use of suicide substrates remains a very important and useful method in enzymology for studying enzyme mechanisms and designing potential drugs. Suicide substrates act as modified substrates for the target enzymes and bind to the active site. Therefore the presence of a competitive reversible inhibitor decreases the rate of substrate-induced inactivation and protects the enzyme from this inactivation. This lowering on the inactivation rate has evident physiological advantages, since it allows the easy acquisition of experimental data and facilitates kinetic data analysis by providing another variable (inhibitor concentration). However despite the importance of the simultaneous action of a suicide substrate and a competitive reversible inhibition, to date no corresponding kinetic analysis has been carried out. Therefore we present a general kinetic analysis of a Michaelis-Menten reaction mechanism with double inhibition caused by both, a suicide substrate and a competitive reversible inhibitor. We assume rapid equilibrium of the reversible reaction steps involved, while the time course equations for the reaction product have been derived with the assumption of a limiting enzyme. The goodness of the analytical solutions has been tested by comparison with the simulated curves obtained by numerical integration. A kinetic data analysis to determine the corresponding kinetic parameters from the time progress curve of the product is suggested. In conclusion, we present a complete kinetic analysis of an enzyme reaction mechanism as described above in an attempt to fill a gap in the theoretical treatment of this type of system.

  6. Determination of reaction kinetics of rice husks in air using thermogravimetric analysis

    SciTech Connect

    Mansaray, K.G.; Ghaly, A.E.

    1999-12-01

    Rice husk is produced in large quantities as a by-product of rice milling in rice-producing countries and has posed disposal problems in these countries. Disposal of or energy recovery from rice husk can be accomplished by thermochemical conversion processes (pyrolysis, combustion, and gasification). However, it appears that the kinetics of rice husk, which can contribute to the accurate modeling and design of thermochemical conversion processes, have not been studied extensively. In this paper the technique of thermogravimetric analysis (TGA) was used to study the thermochemical behavior of four varieties of rice husk (Lemont LG, ROK 14, CP 4, and Pa Potho). The thermal degradation of rice husk was studied in an air atmosphere (21% oxygen and 79% nitrogen) from ambient temperature to 700 C at the heating rate of 20 C/min. The thermograms showed two distinct reaction zones. The kinetic parameters (activation energy, preexponential factor, and order of reaction) were determined for the two reaction zones by applying thermoanalytical techniques to the reaction kinetics. Higher thermal degradation rates were observed in the first reaction zone due to rapid release of volatiles as compared to those in the second reaction zone. In the first reaction zone the activation energies ranged from 37.0 to 54.7 kJ/mol. Relatively lower activation energies (18.0--21.0 kJ/mol) were obtained in the second reaction zone. The preexponential factors were in the range of 4.3 x 10{sup 4} to 6.4 x 10{sup 6} min{sup {minus}1} in the first reaction zone and 4.5 x 10{sup 2} to 1.5 x 10{sup 3} min{sup {minus}1} in the second reaction zone. The orders of reaction were in the range of 1.2--1.6 and 0.4--0.5 for the first and second reaction zones, respectively. The predicted thermal degradations were in good agreement with the experimental data in both the first and second reaction zones.

  7. Kinetics and equilibrium adsorption study of p-nitrophenol onto activated carbon derived from walnut peel.

    PubMed

    Liu, Xiaohong; Wang, Fang; Bai, Song

    2015-01-01

    An original activated carbon prepared from walnut peel, which was activated by zinc chloride, was modified with ammonium hydroxide or sodium hydroxide in order to contrast the adsorption property of the three different activated carbons. The experiment used a static adsorption test for p-nitrophenol. The effects of parameters such as initial concentration, contact time and pH value on amount adsorbed and removal are discussed in depth. The thermodynamic data of adsorption were analyzed by Freundlich and Langmuir models. The kinetic data of adsorption were measured by the pseudo-first-order kinetics and the pseudo-second-order kinetics models. The results indicated that the alkalized carbon samples derived from walnut peel had a better performance than the original activated carbon treated with zinc chloride. It was found that adsorption equilibrium time was 6 h. The maximum removal rate of activated carbon treated with zinc chloride for p-nitrophenol was 87.3% at pH 3,whereas the maximum removal rate of the two modified activated carbon materials was found to be 90.8% (alkalized with ammonium hydroxide) and 92.0% (alkalized with sodium hydroxide) at the same pH. The adsorption data of the zinc chloride activated carbon were fitted to the Langmuir isotherm model. The two alkalized activated carbon samples were fitted well to the Freundlich model. The pseudo-second-order dynamics equation provided better explanation of the adsorption dynamics data of the three activated carbons than the pseudo-first-order dynamics equation.

  8. Kinetics of the creatine kinase reaction in neonatal rabbit heart: An empirical analysis of the rate equation

    SciTech Connect

    McAuliffe, J.J. ); Perry, S.B. ); Brooks, E.E. ); Ingwall, J.S. Harvard Medical School, Boston, MA )

    1991-03-12

    Here the authors define the kinetics of the creatine kinase (CK) reaction in an intact mammalian heart containing the full rnage of CK isoenzymes. Previously derived kinetic constants were refit for the reaction occurring at 37C. Steady-state metabolite concentrations from {sup 31}P NMR and standard biochemical techniques were determined. {sup 31}P magnetization transfer data were obtained to determine unidirectional creatine kinase fluxes in hearts with differing total creatine contents and differing mitochondrial CK activities during KCl arrest and isovolumic work for both the forward reaction (MgATP synthesis) and reverse reaction (phosphocreatine synthesis). The NMR kinetic data and substrate concentrations data were used in conjunction with a kinetic model based on MM-CK in solution to determine the applicability of the solution-based kinetic models to the CK kinetics of the intact heart. The results indicated that no single set of rate equation constants could describe both the KCl-arrested and working hearts. Analysis of the results indicated that the CK reaction is rate limited in the direction of ATP synthesis, the size of the guanidino substrate pool drives the measured CK flux in the intact heart, and during isovolumic work, the CK reaction operates under saturating conditions; that is, the substrate concentrations are at least 2-fold greater than the K{sub m} or K{sub im} for each substrate. However, during KCl arrest the reaction does not operate under saturating conditions and the CK reaction velocity is strongly influenced by the guanidino substrate pool size.

  9. Adsorption behavior of direct red 80 and congo red onto activated carbon/surfactant: process optimization, kinetics and equilibrium.

    PubMed

    Cheng, Zhengjun; Zhang, Lei; Guo, Xiao; Jiang, Xiaohui; Li, Tian

    2015-02-25

    Adsorptions of congo red and direct red 80 onto activated carbon/surfactant from aqueous solution were optimized. The Box-Behnken design (BBD) has been employed to analyze the effects of concentration of surfactant, temperature, pH, and initial concentration of the dye in the adsorption capacity. Their corresponding experimental data could be evaluated excellently by second order polynomial regression models and the two models were also examined based on the analysis of variance and t test statistics, respectively. The optimum conditions were obtained as follows: Cs=34.10 μM, T=50°C, pH=3.5, and CCR=160 mg/L for the congo red system, and Cs=34.10 μM, T=50°C, pH=6.1, and CDR80=110 mg/L for the direct red 80 system. And in these conditions, the measured experimental maximum adsorption capacities for the congo red and direct red 80 removals were 769.48 mg/g and 519.90 mg/g, which were consistent with their corresponding predicted values, with small relative errors of -2.81% and -0.67%, respectively. The adsorption equilibrium and kinetics for the two dye adsorptions onto AC/DDAC were also investigated. The experimental data were fitted by four isotherm models, and Langmuir model presented the best fit. The kinetic studies indicated that the kinetic data followed the pseudo-second-order model.

  10. Thermogravimetric analysis and kinetic study of formation of lithium titanate by solid state route

    NASA Astrophysics Data System (ADS)

    Sonak, Sagar; Jain, Uttam; Sahu, Ashok Kumar; Kumar, Sanjay; Krishnamurthy, Nagaiyar

    2015-02-01

    The kinetics of formation of lithium titanate from the solid state reaction of lithium carbonate and titanium oxide was studied using non-isothermal thermogravimetric technique. Thermogravimetric data for the reaction of lithium carbonate and titanium oxide was obtained at various heating rates. The methods such as Flynn-Wall-Ozawa and Kissinger-Akahira-Sunose were used to estimate the kinetic parameters from the obtained thermogravimetric data. The average activation energy for the formation of lithium titanate by solid state route was found to be 243 kJ/mol K. The reaction mechanism was determined by the method given by Malek. It was found that the three dimensional diffusion model best describes the reaction kinetics. A kinetic equation describing the reaction is proposed and reaction mechanism is discussed.

  11. Thermal degradation studies and kinetic modeling of cardoon (Cynara cardunculus) pyrolysis using thermogravimetric analysis (TGA).

    PubMed

    Damartzis, Th; Vamvuka, D; Sfakiotakis, S; Zabaniotou, A

    2011-05-01

    A key element in the design of sustainable pyrolysis processes is the thermal degradation kinetics of biomass. In this work, pyrolysis tests for cardoon (Cynara carduculus) stems and leaves were performed in a non-isothermal thermogravimetric analyzer (TGA) in order to determine the thermal degradation behavior of both stems and leaves. The kinetic parameters of the process were evaluated using three different kinetic models, the independent parallel reaction model, KAS and OFW iso-conversional model. Good agreement with the experimental TGA data was observed for all models, the best being with the independent parallel reaction model. A variance in the activation energy with conversion was observed when the KAS and OFW models were employed, which reveals that the pyrolysis of cardoon progresses through more complex and multi-step kinetics.

  12. The kinetic activation-relaxation technique: an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search

    NASA Astrophysics Data System (ADS)

    Mousseau, Nomand

    2012-02-01

    While kinetic Monte Carlo algorithm has been proposed almost 40 years ago, its application in materials science has been mostly limited to lattice-based motion due to the difficulties associated with identifying new events and building usable catalogs when atoms moved into off-lattice position. Here, I present the kinetic activation-relaxation technique (kinetic ART) is an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search [1]. It combines ART nouveau [2], a very efficient unbiased open-ended activated method for finding transition states, with a topological classification [3] that allows a discrete cataloguing of local environments in complex systems, including disordered materials. In kinetic ART, local topologies are first identified for all atoms in a system. ART nouveau event searches are then launched for new topologies, building an extensive catalog of barriers and events. Next, all low energy events are fully reconstructed and relaxed, allowing to take complete account of elastic effects in the system's kinetics. Using standard kinetic Monte Carlo, the clock is brought forward and an event is then selected and applied before a new search for topologies is launched. In addition to presenting the various elements of the algorithm, I will discuss three recent applications to ion-bombarded silicon, defect diffusion in Fe and structural relaxation in amorphous silicon.[4pt] This work was done in collaboration with Laurent Karim B'eland, Peter Brommer, Fedwa El-Mellouhi, Jean-Francois Joly and Laurent Lewis.[4pt] [1] F. El-Mellouhi, N. Mousseau and L.J. Lewis, Phys. Rev. B. 78, 153202 (2008); L.K. B'eland et al., Phys. Rev. E 84, 046704 (2011).[2] G.T. Barkema and N. Mousseau, Phys. Rev. Lett. 77, 4358 (1996); E. Machado-Charry et al., J. Chem Phys. 135, 034102, (2011).[3] B.D. McKay, Congressus Numerantium 30, 45 (1981).

  13. Kinetics studies of d-glucose hydrogenation over activated charcoal supported platinum catalyst

    NASA Astrophysics Data System (ADS)

    Ahmed, Muthanna J.

    2012-02-01

    The kinetics of the catalytic hydrogenation of d-glucose to produce d-sorbitol was studied in a three-phase laboratory scale reactor. The hydrogenation reactions were performed on activated charcoal supported platinum catalyst in the temperature range 25-65°C and in a constant pressure of 1 atm. The kinetic data were modeled by zero, first and second-order reaction equations. In the operating regimes studied, the results show that the hydrogenation reaction was of a first order with respect to d-glucose concentration. Also the activation energy of the reaction was determined, and found to be 12.33 kJ mole-1. A set of experiment was carried out to test the deactivation of the catalyst, and the results show that the deactivation is slow with the ability of using the catalyst for several times with a small decrease in product yield.

  14. Effects of oligomerization phenomenon on dissolved organic matter removal kinetics on novel activated carbons.

    PubMed

    Yan, Liang; Deeter, Valerie; Lalley, Jacob; Medellin, Oscar; Kupferle, Margaret J; Sorial, George A

    2014-08-15

    The overall objective of this research was to determine the effects of oxidative coupling (oligomerization) phenomenon on the adsorption kinetics of dissolved natural organic matter (DOM) on novel tailored activated carbons. A comparison of adsorption kinetics data collected in the presence and absence of phenolic compounds under both oxic (presence of molecular oxygen) and anoxic (absence of molecular oxygen) conditions showed that the adsorption rate of DOM was strongly affected by the oligomerization phenomenon. The diffusion rate of DOM is in inverse proportion to the critical oxidation potential of the phenolic compound. In addition, the roles of carbon physicochemical characteristics and DOM molecular weight distribution were also investigated. Tailored activated carbon impregnated with manganese oxide was found to play an important role in promoting complexation reactions between DOM and phenolic compounds. Meanwhile, Fulvic acid molecules (component of DOM) with molecular weight below 2000 Da appeared to have more potential to get influenced from oligomerization effects.

  15. Crystallization kinetics of poly-(lactic acid) with and without talc: Optical microscopy and calorimetric analysis

    NASA Astrophysics Data System (ADS)

    Refaa, Z.; Boutaous, M.; Rousset, F.; Fulchiron, R.; Zinet, M.; Xin, S.; Bourgin, P.

    2014-05-01

    Poly-(lactic acid) or PLA is a biodegradable polymer synthesized from renewable resources. Recently, the discovery of new polymerization routes has allowed increasing the produced volumes. As a consequence, PLA is becoming of great interest for reducing the dependence on petroleum-based plastics. Because of its interesting mechanical properties, PLA is seen as a potential substitute for some usual polymers. However, its relatively slow crystallization kinetics can be a disadvantage with regard to industrial applications. The crystallization kinetics of PLA can be enhanced by adding nucleating agents, which also influences on crystalline morphology and rheological behavior. In the present work, the isothermal quiescent crystallization kinetics of both neat PLA and PLA/talc composite (5 wt% talc) are investigated. The effects of talc on the overall crystallization kinetics and on the crystalline morphology are analyzed using both optical microscopy measurements and thermal analysis by differential scanning calorimetry.

  16. Elimination of "hook-effect" in two-site immunoradiometric assays by kinetic rate analysis.

    PubMed

    Hoffman, K L; Parsons, G H; Allerdt, L J; Brooks, J M; Miles, L E

    1984-09-01

    Two-site or sandwich immunoradiometric assays (IRMAs) offer theoretical advantages over competitive immunoassay systems for sensitivity, precision, and rapid incubation. The practical realization of these advantages has been limited by the phenomenon of the "high-dose hook effect," such that high concentrations of an analyte give similar responses to those of much lower concentrations. We have developed a kinetic rate monitoring IRMA system for use with the Kineti-Count 48TM, an automated kinetic radioassay analyzer, which eliminates "hook-effect" interference, thereby permitting optimal assay design for increasing sensitivity and reducing incubation time. Practical illustration of these concepts is demonstrated by a 10-min, automated, quantitative assay we developed for human choriogonadotropin. The assay can detect as little as 1.2 int. units/L and kinetically screens for the hook effect. Kinetic rate analysis of the two-site IRMA and potentially of nonisotopic counterparts permits improvements in the speed and reliability of these immunoassays.

  17. RETRAN-3D MOD003 Peach Bottom Turbine Trip 2 Multidimensional Kinetics Analysis Models and Results

    SciTech Connect

    Mori, Michitsugu; Ogura, Katsunori; Gose, Garry C.; Wu, J.-Y

    2003-04-15

    An analysis of the Peach Bottom Unit 2 Turbine Trip Test 2 (PB2/TT2) has been performed using RETRAN-3D MOD003. The purpose of the analysis was to investigate the PB2/TT2 overpressurization transient using the RETRAN-3D multidimensional kinetics model.

  18. Kinetic theory analysis of solar wind interaction with planetary objects

    NASA Technical Reports Server (NTRS)

    Wu, S. T.; Dryer, M.

    1973-01-01

    A purely kinetic treatment is proposed for the interaction of the solar wind with any small planetary object. Small refers to those cases where the solar wind proton's thermal gyroradius is arbitrarily taken to be greater than 0.1 radius of the object under investigation. The 'object' may possibly include an ionosphere or magnetosphere. The collisionless Boltzmann equation, neglecting the magnetic field, is used to calculate steady-state profiles of density and velocity around the obstacle. A low density plasma void in the umbral region and a compression in the penumbral region are clearly found. The present technique, despite its neglect of the interplanetary magnetic field, is proposed as an alternative zeroth order approach to the continuum, local magnetic anomaly, and guiding center approaches used by others for the particular case of moon. Some recent, potentially relevant, observations on and in front of the moon are discussed.

  19. Decoupled direct method for sensitivity analysis in combustion kinetics

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan

    1987-01-01

    An efficient, decoupled direct method for calculating the first order sensitivity coefficients of homogeneous, batch combustion kinetic rate equations is presented. In this method the ordinary differential equations for the sensitivity coefficients are solved separately from , but sequentially with, those describing the combustion chemistry. The ordinary differential equations for the thermochemical variables are solved using an efficient, implicit method (LSODE) that automatically selects the steplength and order for each solution step. The solution procedure for the sensitivity coefficients maintains accuracy and stability by using exactly the same steplengths and numerical approximations. The method computes sensitivity coefficients with respect to any combination of the initial values of the thermochemical variables and the three rate constant parameters for the chemical reactions. The method is illustrated by application to several simple problems and, where possible, comparisons are made with exact solutions and those obtained by other techniques.

  20. Kinetics of hydrophobic organic contaminant extraction from sediment by granular activated carbon.

    PubMed

    Rakowska, M I; Kupryianchyk, D; Smit, M P J; Koelmans, A A; Grotenhuis, J T C; Rijnaarts, H H M

    2014-03-15

    Ex situ solid phase extraction with granular activated carbon (GAC) is a promising technique to remediate contaminated sediments. The methods' efficiency depends on the rate by which contaminants are transferred from the sediment to the surface of GAC. Here, we derive kinetic parameters for extraction of polycyclic aromatic hydrocarbons (PAH) from sediment by GAC, using a first-order multi-compartment kinetic model. The parameters were obtained by modeling sediment-GAC exchange kinetic data following a tiered model calibration approach. First, parameters for PAH desorption from sediment were calibrated using data from systems with 50% (by weight) GAC acting as an infinite sink. Second, the estimated parameters were used as fixed input to obtain GAC uptake kinetic parameters in sediment slurries with 4% GAC, representing the ex situ remediation scenario. PAH uptake rate constants (kGAC) by GAC ranged from 0.44 to 0.0005 d(-1), whereas GAC sorption coefficients (KGAC) ranged from 10(5.57) to 10(8.57) L kg(-1). These values are the first provided for GAC in the presence of sediment and show that ex situ extraction with GAC is sufficiently fast and effective to reduce the risks of the most available PAHs among those studied, such as fluorene, phenanthrene and anthracene.

  1. QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

    PubMed

    Martí, Sergio; Moliner, Vincent; Tuñón, Iñaki; Williams, Ian H

    2003-02-07

    Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.

  2. Impacts of amount of impregnated iron in granular activated carbon on arsenate adsorption capacities and kinetics.

    PubMed

    Chang, Qigang; Lin, Wei; Ying, Wei-Chi

    2012-06-01

    Iron-impregnated granular activated carbons (Fe-GAC) can remove arsenic effectively from water. In this study, Fe-GACs with iron content of 1.64 to 28.90% were synthesized using a new multi-step procedure for the investigation of effects of iron amount on arsenic adsorption capacities and kinetics. Langmuir model satisfactorily fit arsenic adsorption on Fe-GACs. The maximum arsenic adsorption capacity (q(m)) increased significantly with iron impregnation and reached 1,867 to 1,912 microg/g with iron content of 9.96 to 13.59%. Further increase of iron content (> 13.59%) caused gradual decrease of q(m). It was found that the amount of impregnated iron showed little impact on the affinity for arsenate. Kinetic study showed that the amount of impregnated iron affected the arsenic intraparticle diffusion rate greatly. The pseudo-second-order kinetic model fit arsenic adsorption kinetics on Fe-GACs better than the pseudo-first-order model. The arsenic adsorption rate increased with increasing of iron content from 1.64% to 13.59%, and then decreased with more impregnated iron (13.59 to 28.90%).

  3. Kinetic analysis of several variations of push-ups.

    PubMed

    Ebben, William P; Wurm, Bradley; VanderZanden, Tyler L; Spadavecchia, Mark L; Durocher, John J; Bickham, Curtis T; Petushek, Erich J

    2011-10-01

    Push-ups are a common and practical exercise that is used to enhance fitness, including upper body strength or endurance. The kinetic characteristics of push-ups and its variations are yet to be quantified. Kinetic quantification is necessary to accurately evaluate the training load, and thus the nature of the training stimulus, for these exercise variations. This study assessed the peak vertical ground reaction forces (GRFs) of push-up variations including the regular push-up and those performed with flexed knee, feet elevated on a 30.48-cm box, and a 60.96-cm box, and hands elevated on a 30.48-cm box and a 60.96-cm box. Twenty-three recreationally fit individuals (14 men, 9 women) performed each of the 6 push-up variations in a randomized order. Peak GRF and peak GRF expressed as a coefficient of subject body mass were obtained with a force platform. Push-ups with the feet elevated produced a higher GRF than all other push-up variations (p ≤ 0.05). Push-ups with hands elevated and push-ups from the flexed knee position produced a lower GRF than all other push-up variations (p ≤ 0.05). No gender differences in response to these push-up variations were found (p > 0.05). Additionally, subject height was not related to the GRF for any of the push-up conditions (p > 0.05) other than the condition where hands were elevated on a 60.96-cm box (p ≤ 0.05; r = 0.63). These data can be used to progress the intensity of push-ups in a program and to quantify the training load as a percentage of body mass.

  4. Kinetic Evidence of an Apparent Negative Activation Enthalpy in an Organocatalytic Process

    PubMed Central

    Han, Xiao; Lee, Richmond; Chen, Tao; Luo, Jie; Lu, Yixin; Huang, Kuo-Wei

    2013-01-01

    A combined kinetic and computational study on our tryptophan-based bifunctional thiourea catalyzed asymmetric Mannich reactions reveals an apparent negative activation enthalpy. The formation of the pre-transition state complex has been unambiguously confirmed and these observations provide an experimental support for the formation of multiple hydrogen bonding network between the substrates and the catalyst. Such interactions allow the creation of a binding cavity, a key factor to install high enantioselectivity. PMID:23990028

  5. Non-isothermal kinetic analysis of thermal decomposition of the Ca-bentonite from Santai, China

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang-hui; He, Chuan; Wang, Ling; Li, Zhong-quan; Deng, Miao; Liu, Jing; Li, Hong-kui; Feng, Qian

    2015-06-01

    The thermal decompositions of Ca-bentonites (CaB) from Santai, Shichuan Province, China, over the temperature range of 30-1,100 °C were investigated by simultaneous thermal analyzer. Non-isothermal kinetic analysis was employed to study the thermal decomposition mechanism by using Netzsch Thermokinetics software. Flynn-Wall-Ozawa and Friedman isoconversional methods were used to calculate the activation energy and analyze the reaction steps. The probable mechanism and the corresponding kinetic parameters were determined by multivariate non-linear regression program. The results show that the thermal decomposition process of CaB over the temperature range of 30-800 °C is a kind of six-step, competitive reaction ( F 1 D 3 F n C 1E F n F n model). The dehydration reaction is controlled by two consecutive mechanisms, nucleation and growth, followed by a diffusion-controlled reaction ( F 1 D 3 model), the first step: E = 61.68 kJ mol-1, log A = 6.75 s-1; the second step: E = 50.73 kJ mol-1, log A = 3.11 s-1. The dehydroxylation reaction is controlled by three-step competitive mechanisms, an autocatalytically activated, initial reaction followed by n-order competitive reaction ( C 1E F n F n model), the first step: E = 124.74 kJ mol-1, log A = 5.67 s-1; the second step: E = 245.29 kJ mol-1, log A = 11.69 s-1; the third step : E = 261.73 kJ mol-1, log A = 11.23 s-1. A combination reaction of the dehydration and dehydroxylation is observed, and controlled by one n-order reaction ( F n model), E = 8.99 kJ mol-1, log A = -1.91 s-1.

  6. Kinetic Analysis of Lauric Acid Hydroxylation by Human Cytochrome P450 4A11

    PubMed Central

    2015-01-01

    Cytochrome P450 (P450) 4A11 is the only functionally active subfamily 4A P450 in humans. P450 4A11 catalyzes mainly ω-hydroxylation of fatty acids in liver and kidney; this process is not a major degradative pathway, but at least one product, 20-hydroxyeicosatetraenoic acid, has important signaling properties. We studied catalysis by P450 4A11 and the issue of rate-limiting steps using lauric acid ω-hydroxylation, a prototypic substrate for this enzyme. Some individual reaction steps were studied using pre-steady-state kinetic approaches. Substrate and product binding and release were much faster than overall rates of catalysis. Reduction of ferric P450 4A11 (to ferrous) was rapid and not rate-limiting. Deuterium kinetic isotope effect (KIE) experiments yielded low but reproducible values (1.2–2) for 12-hydroxylation with 12-2H-substituted lauric acid. However, considerable “metabolic switching” to 11-hydroxylation was observed with [12-2H3]lauric acid. Analysis of switching results [Jones, J. P., et al. (1986) J. Am. Chem. Soc.108, 7074–7078] and the use of tritium KIE analysis with [12-3H]lauric acid [Northrop, D. B. (1987) Methods Enzymol.87, 607–625] both indicated a high intrinsic KIE (>10). Cytochrome b5 (b5) stimulated steady-state lauric acid ω-hydroxylation ∼2-fold; the apoprotein was ineffective, indicating that electron transfer is involved in the b5 enhancement. The rate of b5 reoxidation was increased in the presence of ferrous P450 mixed with O2. Collectively, the results indicate that both the transfer of an electron to the ferrous·O2 complex and C–H bond-breaking limit the rate of P450 4A11 ω-oxidation. PMID:25203493

  7. Kinetic analysis of lauric acid hydroxylation by human cytochrome P450 4A11.

    PubMed

    Kim, Donghak; Cha, Gun-Su; Nagy, Leslie D; Yun, Chul-Ho; Guengerich, F Peter

    2014-10-07

    Cytochrome P450 (P450) 4A11 is the only functionally active subfamily 4A P450 in humans. P450 4A11 catalyzes mainly ω-hydroxylation of fatty acids in liver and kidney; this process is not a major degradative pathway, but at least one product, 20-hydroxyeicosatetraenoic acid, has important signaling properties. We studied catalysis by P450 4A11 and the issue of rate-limiting steps using lauric acid ω-hydroxylation, a prototypic substrate for this enzyme. Some individual reaction steps were studied using pre-steady-state kinetic approaches. Substrate and product binding and release were much faster than overall rates of catalysis. Reduction of ferric P450 4A11 (to ferrous) was rapid and not rate-limiting. Deuterium kinetic isotope effect (KIE) experiments yielded low but reproducible values (1.2-2) for 12-hydroxylation with 12-(2)H-substituted lauric acid. However, considerable "metabolic switching" to 11-hydroxylation was observed with [12-(2)H3]lauric acid. Analysis of switching results [Jones, J. P., et al. (1986) J. Am. Chem. Soc. 108, 7074-7078] and the use of tritium KIE analysis with [12-(3)H]lauric acid [Northrop, D. B. (1987) Methods Enzymol. 87, 607-625] both indicated a high intrinsic KIE (>10). Cytochrome b5 (b5) stimulated steady-state lauric acid ω-hydroxylation ∼2-fold; the apoprotein was ineffective, indicating that electron transfer is involved in the b5 enhancement. The rate of b5 reoxidation was increased in the presence of ferrous P450 mixed with O2. Collectively, the results indicate that both the transfer of an electron to the ferrous·O2 complex and C-H bond-breaking limit the rate of P450 4A11 ω-oxidation.

  8. Adsorption of leather dye onto activated carbon prepared from bottle gourd: equilibrium, kinetic and mechanism studies.

    PubMed

    Foletto, Edson Luiz; Weber, Caroline Trevisan; Paz, Diego Silva; Mazutti, Marcio Antonio; Meili, Lucas; Bassaco, Mariana Moro; Collazzo, Gabriela Carvalho

    2013-01-01

    Activated carbon prepared from bottle gourd has been used as adsorbent for removal of leather dye (Direct Black 38) from aqueous solution. The activated carbon obtained showed a mesoporous texture, with surface area of 556.16 m(2) g(-1), and a surface free of organic functional groups. The initial dye concentration, contact time and pH significantly influenced the adsorption capacity. In the acid region (pH 2.5) the adsorption of dye was more favorable. The adsorption equilibrium was attained after 60 min. Equilibrium data were analyzed by the Langmuir, Freundlich, Dubinin-Radushkevich and Temkin isotherm models. The equilibrium data were best described by the Langmuir isotherm, with maximum adsorption capacity of 94.9 mg g(-1). Adsorption kinetic data were fitted using the pseudo-first-order, pseudo-second-order, Elovich and intraparticle diffusion models. The adsorption kinetic was best described by the second-order kinetic equation. The adsorption process was controlled by both external mass transfer and intraparticle diffusion. Activated carbon prepared from bottle gourd was shown to be a promising material for adsorption of Direct Black 38 from aqueous solution.

  9. Combining an Optical Resonance Biosensor with Enzyme Activity Kinetics to Understand Protein Adsorption and Denaturation

    PubMed Central

    Wilson, Kerry A.; Finch, Craig A.; Anderson, Phillip; Vollmer, Frank; Hickman, James J.

    2014-01-01

    Understanding protein adsorption and resultant conformation changes on modified and unmodified silicon dioxide surfaces is a subject of keen interest in biosensors, microfluidic systems and for medical diagnostics. However, it has been proven difficult to investigate the kinetics of the adsorption process on these surfaces as well as understand the topic of the denaturation of proteins and its effect on enzyme activity. A highly sensitive optical whispering gallery mode (WGM) resonator was used to study a catalytic enzyme’s adsorption processes on different silane modified glass substrates (plain glass control, DETA, 13F, and SiPEG). The WGM sensor was able to obtain high resolution kinetic data of glucose oxidase (GO) adsorption with sensitivity of adsorption better than that possible with SPR. The kinetic data, in combination with a functional assay of the enzyme activity, was used to test hypotheses on adsorption mechanisms. By fitting numerical models to the WGM sensograms for protein adsorption, and by confirming numerical predictions of enzyme activity in a separate assay, we were able to identify mechanisms for GO adsorption on different alkylsilanes and infer information about the adsorption of protein on nanostructured surfaces. PMID:25453976

  10. Diffusion barriers in the kinetics of water vapor adsorption/desorption on activated carbons

    SciTech Connect

    Harding, A.W.; Foley, N.J.; Thomas, K.M.; Norman, P.R.; Francis, D.C.

    1998-07-07

    The adsorption of water vapor on a highly microporous coconut-shell-derived carbon and a mesoporous wood-derived carbon was studied. These carbons were chosen as they had markedly different porous structures. The adsorption and desorption characteristics of water vapor on the activated carbons were investigated over the relative pressure range p/p{degree} = 0--0.9 for temperatures in the range 285--313 K in a static water vapor system. The adsorption isotherms were analyzed using the Dubinin-Serpinski equation, and this provided an assessment of the polarity of the carbons. The kinetics of water vapor adsorption and desorption were studied with different amounts of preadsorbed water for set changes in pressure relative to the saturated vapor pressure (p/p{degree}). The adsorption kinetics for each relative pressure step were compared and used to calculate the activation energies for the vapor pressure increments. The kinetic results are discussed in relation to their relative position on the equilibrium isotherm and the adsorption mechanism of water vapor on activated carbons.

  11. Two-Dimensional Kinetic Analysis of Low Frequency Electromagnetic Instabilities in Tokamaks

    NASA Astrophysics Data System (ADS)

    Qin, H.; Tang, W. M.; Rewoldt, G.

    1996-11-01

    Previous studies of low-toroidal-mode-number microinstabilities in tokamaks have included two-dimensional (r and θ) fully-kinetic analysis(R. Marchand, W.M. Tang, and G. Rewoldt, Phys. Fluids 23), 1164 (1980); W.M. Tang and G. Rewoldt, Phys. Fluids B 5, 2451 (1993) of electrostatic instabilities such as the trapped-ion mode. Recently, this analysis was extended to include effects of sheared toroidal plasma rotation(M. Artun, W.M. Tang, and G. Rewoldt, Phys. Plasmas 2), 3384 (1995). In the present work, the electrostatic calculation, implemented in the KIN-2DES computer code, is being extended to the electromagnetic case, in the KIN-2DEM code. This will allow treatment of both electromagnetic effects on electrostatic instabilities, and of kinetic effects on low-n tokamak MHD instabilities such as kink and ballooning modes. In the latter cases, the analysis represents the first systematic kinetic treatment of low-n MHD modes.

  12. Progress curve analysis for enzyme and microbial kinetic reactions using explicit solutions based on the Lambert W function.

    PubMed

    Goudar, Chetan T; Harris, Steve K; McInerney, Michael J; Suflita, Joseph M

    2004-12-01

    We present a simple method for estimating kinetic parameters from progress curve analysis of biologically catalyzed reactions that reduce to forms analogous to the Michaelis-Menten equation. Specifically, the Lambert W function is used to obtain explicit, closed-form solutions to differential rate expressions that describe the dynamics of substrate depletion. The explicit nature of the new solutions greatly simplifies nonlinear estimation of the kinetic parameters since numerical techniques such as the Runge-Kutta and Newton-Raphson methods used to solve the differential and integral forms of the kinetic equations, respectively, are replaced with a simple algebraic expression. The applicability of this approach for estimating Vmax and Km in the Michaelis-Menten equation was verified using a combination of simulated and experimental progress curve data. For simulated data, final estimates of Vmax and Km were close to the actual values of 1 microM/h and 1 microM, respectively, while the standard errors for these parameter estimates were proportional to the error level in the simulated data sets. The method was also applied to hydrogen depletion experiments by mixed cultures of bacteria in activated sludge resulting in Vmax and Km estimates of 6.531 microM/h and 2.136 microM, respectively. The algebraic nature of this solution, coupled with its relatively high accuracy, makes it an attractive candidate for kinetic parameter estimation from progress curve data.

  13. Single-cell analysis of transcription kinetics across the cell cycle

    NASA Astrophysics Data System (ADS)

    Skinner, Samuel; Xu, Heng; Jaiswal, Sonal; Freire, Pablo; Zwaka, Thomas; Golding, Ido

    2015-03-01

    Transcription is a highly stochastic process. A common way of inferring transcription kinetics is to measure mRNA abundance in individual cells and compare the observed copy-number statistics to the prediction of a theoretical stochastic model. However, the reliability of this procedure is hampered by the fact that the measured mRNA numbers represent integration over the finite lifetime of mRNA, over multiple copies of the same gene, and the mixing of cells from different phases of the cell cycle. Here we address these limitations by simultaneously quantifying nascent and mature mRNA in individual cells, and incorporating gene-copy and cell-cycle effects in the analysis of mRNA statistics. We demonstrate this approach on Oct4 and Nanog, two key players in the mouse pluripotency network. We find that both genes are well described by a two-state stochastic model for transcription initiation. The difference in their expression characteristics is attributed to a 2.6-fold difference in the probability of switching to an active transcriptional state. Early in the cell cycle, the two copies of each gene exhibit independent activity. However, after gene replication, the probability of each gene copy to be active diminishes, resulting in dosage compensation.

  14. Dynamics of a lamellar system with diffusion and reaction: Scaling analysis and global kinetics

    NASA Astrophysics Data System (ADS)

    Muzzio, F. J.; Ottino, J. M.

    1989-12-01

    The evolution of a one-dimensional array of reactive lamellae with distributed striation thickness is studied by means of simulations, scaling analysis, and space-averaged kinetics. An infinitely fast, diffusion-controlled reaction A+B-->2P occurs at the interfaces between striations. As time increases, thin striations are eaten by thicker neighbors resulting in a modification of the striation thickness distribution (STD). Scaling analysis suggests that the STD evolves into a universal form and that the behavior of the system at short and long times is characterized by two different kinetic regimes. These predictions are confirmed by means of a novel numerical algorithm.

  15. Application of zeolite-activated carbon macrocomposite for the adsorption of Acid Orange 7: isotherm, kinetic and thermodynamic studies.

    PubMed

    Lim, Chi Kim; Bay, Hui Han; Neoh, Chin Hong; Aris, Azmi; Abdul Majid, Zaiton; Ibrahim, Zaharah

    2013-10-01

    In this study, the adsorption behavior of azo dye Acid Orange 7 (AO7) from aqueous solution onto macrocomposite (MC) was investigated under various experimental conditions. The adsorbent, MC, which consists of a mixture of zeolite and activated carbon, was found to be effective in removing AO7. The MC were characterized by scanning electron microscopy (SEM), energy dispersive X-ray, point of zero charge, and Brunauer-Emmett-Teller surface area analysis. A series of experiments were performed via batch adsorption technique to examine the effect of the process variables, namely, contact time, initial dye concentration, and solution pH. The dye equilibrium adsorption was investigated, and the equilibrium data were fitted to Langmuir, Freundlich, and Tempkin isotherm models. The Langmuir isotherm model fits the equilibrium data better than the Freundlich isotherm model. For the kinetic study, pseudo-first-order, pseudo-second-order, and intraparticle diffusion model were used to fit the experimental data. The adsorption kinetic was found to be well described by the pseudo-second-order model. Thermodynamic analysis indicated that the adsorption process is a spontaneous and endothermic process. The SEM, Fourier transform infrared spectroscopy, ultraviolet-visible spectral and high performance liquid chromatography analysis were carried out before and after the adsorption process. For the phytotoxicity test, treated AO7 was found to be less toxic. Thus, the study indicated that MC has good potential use as an adsorbent for the removal of azo dye from aqueous solution.

  16. A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation.

    PubMed

    Immormino, Robert M; Silversmith, Ruth E; Bourret, Robert B

    2016-10-04

    Two-component regulatory systems, minimally composed of a sensor kinase and a response regulator protein, are common mediators of signal transduction in microorganisms. All response regulators contain a receiver domain with conserved active site residues that catalyze the signal activating and deactivating phosphorylation and dephosphorylation reactions. We explored the impact of variable active site position T+1 (one residue C-terminal to the conserved Thr/Ser) on reaction kinetics and signaling fidelity, using wild type and mutant Escherichia coli CheY, CheB, and NarL to represent the three major sequence classes observed across response regulators: Ala/Gly, Ser/Thr, and Val/Ile/Met, respectively, at T+1. Biochemical and structural data together suggested that different amino acids at T+1 impacted reaction kinetics by altering access to the active site while not perturbing overall protein structure. A given amino acid at position T+1 had similar effects on autodephosphorylation in each protein background tested, likely by modulating access of the attacking water molecule to the active site. Similarly, rate constants for CheY autophosphorylation with three different small molecule phosphodonors were consistent with the steric constraints on access to the phosphorylation site arising from combination of specific phosphodonors with particular amino acids at T+1. Because other variable active site residues also influence response regulator phosphorylation biochemistry, we began to explore how context (here, the amino acid at T+2) affected the influence of position T+1 on CheY autocatalytic reactions. Finally, position T+1 affected the fidelity and kinetics of phosphotransfer between sensor kinases and response regulators but was not a primary determinant of their interaction.

  17. Nonparametric analysis of nonexponential and multidimensional kinetics. I. Quantifying rate dispersion, rate heterogeneity, and exchange dynamics

    NASA Astrophysics Data System (ADS)

    Berg, Mark A.; Kaur, Harveen

    2017-02-01

    The quantification of nonexponential (dispersed) kinetics has relied on empirical functions, which yield parameters that are neither unique nor easily related to the underlying mechanism. Multidimensional kinetics provide more information on dispersed processes, but a good approach to their analysis is even less clear than for standard, one-dimensional kinetics. This paper is the first in a series that analyzes kinetic data in one or many dimensions with a scheme that is nonparametric: it quantifies nonexponential decays without relying on a specific functional form. The quantities obtained are directly related to properties of the mechanism causing the rate dispersion. Log-moments of decays, which parallel the standard moments of distributions (mean, standard deviation, etc.), are introduced for both one- and multi-dimensional decays. Kinetic spectra are defined to visualize the data. The utility of this approach is demonstrated on a simple, but general, model of dispersed kinetics—a nonexponential homogeneous decay combined with slowly exchanging rate heterogeneity. The first log-moments give a geometric-mean relaxation time. Second log-moments quantify the magnitude of rate dispersion, the fraction of the dispersion due to heterogeneity, and the dynamics of exchange between different rate subensembles. A suitable combination of these moments isolates exchange dynamics from three-dimensional kinetics without contamination by the rate-filtering effects that were identified in a recent paper [M. A. Berg and J. R. Darvin, J. Chem. Phys. 145, 054119 (2016)].

  18. Controlling enzymatic activity and kinetics in swollen mesophases by physical nano-confinement.

    PubMed

    Sun, Wenjie; Vallooran, Jijo J; Zabara, Alexandru; Mezzenga, Raffaele

    2014-06-21

    Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them into a highly confined environment. We show that the enzymatic activity of a model enzyme, horseradish peroxidase (HRP), can be accurately controlled by relaxing its confinement within the cubic phases' water channels, when the aqueous channel diameters are systematically swollen with varying amount of hydration-enhancing sugar ester. The in-meso activity and kinetics of HRP are then systematically investigated by UV-vis spectroscopy, as a function of the size of the aqueous mesophase channels. The enzymatic activity of HRP increases with the swelling of the water channels. In swollen mesophases with water channel diameter larger than the HRP size, the enzymatic activity is more than double that measured in standard mesophases, approaching again the enzymatic activity of free HRP in bulk water. We also show that the physically-entrapped enzymes in the mesophases exhibit a restricted-diffusion-induced initial lag period and report the first observation of in-meso enzymatic kinetics significantly deviating from the normal Michaelis-Menten behaviour observed in free solutions, with deviations vanishing when enzyme confinement is released by swelling the mesophase.

  19. Temporal Kinetics and Quantitative Analysis of Cryptococcus neoformans Nonlytic Exocytosis

    PubMed Central

    Stukes, Sabriya A.; Cohen, Hillel W.

    2014-01-01

    Cryptococcus neoformans is a facultative intracellular pathogen and the causative agent of cryptococcosis, a disease that is often fatal to those with compromised immune systems. C. neoformans has the capacity to escape phagocytic cells through a process known as nonlytic exocytosis whereby the cryptococcal cell is released from the macrophage into the extracellular environment, leaving both the host and pathogen alive. Little is known about the mechanism behind nonlytic exocytosis, but there is evidence that both the fungal and host cells contribute to the process. In this study, we used time-lapse movies of C. neoformans-infected macrophages to delineate the kinetics and quantitative aspects of nonlytic exocytosis. We analyzed approximately 800 macrophages containing intracellular C. neoformans and identified 163 nonlytic exocytosis events that were further characterized into three subcategories: type I (complete emptying of macrophage), type II (partial emptying of macrophage), and type III (cell-to-cell transfer). The majority of type I and II events occurred after several hours of intracellular residence, whereas type III events occurred significantly (P < 0.001) earlier in the course of macrophage infection. Our results show that nonlytic exocytosis is a morphologically and temporally diverse process that occurs relatively rapidly in the course of macrophage infection. PMID:24595144

  20. Hardening kinetics investigation of alkali-activated binder by small amplitude oscillatory rheometry

    NASA Astrophysics Data System (ADS)

    Rieger, D.; Kullová, L.; Čekalová, M.; Kovářík, T.

    2017-01-01

    In this study, the rheological behavior of geopolymeric inorganic binder was determined. This binder was synthesized by alkaline activation of mixture, comprising calcined claystone powder and milled blast furnace slag. As an alkaline activator of hardening process, the potassium silicate solution was used. For the investigation of hardening kinetics, the strain controlled small amplitude oscillatory rheometry was used with strain of 0.01%. The reproducibility and versatility of this method is demonstrated for determination of hardening process evolution. The changes of loss tangent shape were studied in this experiment and applied for determination of gelation time. All experiments were conducted at isothermal conditions in temperature range 27-70°C and parallel plate geometry. The results indicate that reaction kinetics is directly depending on temperature. The hardening kinetics was mathematically described and these calculations were compared with self-contained experiment conducted at 2°C. This experiment is described in details and the results of gelation time measurements confirmed calculated data.

  1. Adsorption kinetics of a basic dye from aqueous solutions onto apricot stone activated carbon.

    PubMed

    Demirbas, E; Kobya, M; Sulak, M T

    2008-09-01

    The preparation of activated carbon from apricot stone with H(2)SO(4) activation and its ability to remove a basic dye, astrazon yellow 7 GL, from aqueous solutions were reported in this study. The adsorbent was characterized by FTIR, BET and SEM, respectively. The effects of various experimental parameters, such as initial dye concentration, pH, adsorbent dosage and temperature were investigated in a batch-adsorption technique. The optimum conditions for removal of the basic dye were found to be pH 10, 6g/l of adsorbent dosage and equilibrium time of 35 min, respectively. A comparison of three kinetic models, the pseudo first-order, second-order and diffusion controlled kinetic models, on the basic dye-adsorbent system showed that the removal rate was heavily dependent on diffusion controlled kinetic models. The adsorption isotherm data were fitted well to Langmuir and Freundlich isotherms. The adsorption capacity was calculated as 221.23 mg/g at 50 degrees C. Thermodynamics parameters were also evaluated. The values of enthalpy and entropy were 49.87 kJ/mol and 31.93 J/mol K, respectively, indicating that this process was spontaneous and endothermic. The experimental studies were indicated that ASC had the potential to act as an alternative adsorbent to remove the basic dye from aqueous solutions.

  2. Kinetic arrest, dynamical transitions, and activated relaxation in dense fluids of attractive nonspherical colloids

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Schweizer, Kenneth S.

    2011-06-01

    The coupled translation-rotation activated dynamics in dense suspensions of attractive homogeneous and Janus uniaxial dicolloids are studied using microscopic statistical mechanical theory. Multiple kinetic arrest transitions and reentrant phenomena are predicted that are associated with fluid, gel, repulsive glass, attractive glass, plastic glass, and novel glass-gel states. The activated relaxation rate is a nonuniversal nonmonotonic function of attraction strength at high volume fractions due to the consequences of a change of the transient localization mechanism from caging to physical bonding.

  3. Kinetic studies of the liquid-phase adsorption of a reactive dye onto activated lignite

    SciTech Connect

    Petrolekas, P.D.; Maggenakis, G.

    2007-02-14

    The kinetics of batch adsorption of a commercial reactive dye onto activated lignite has been investigated at temperatures of 26, 40, and 55{sup o}C, using aqueous solutions with initial dye concentrations in the range of 15-60 mg/L. An empirical single parameter relationship of the adsorbent loading versus the square root of contact time was proposed, which was determined to provide a very good description of the batch adsorption transients up to equilibrium. The data were also examined by means of the Elovich equation. The effect of the temperature and the initial dye concentration on the adsorption kinetics was analyzed, and the results were discussed by considering that intraparticle diffusion is the dominant mechanism.

  4. Kinetics of dodecanoic acid adsorption from caustic solution by activated carbon.

    PubMed

    Pendleton, Phillip; Wu, Sophie Hua

    2003-10-15

    This study examines the influences of adsorbent porosity and surface chemistry and of carbon dosage on dodecanoic acid adsorption kinetics from aqueous and 2 M NaOH solutions as batch adsorption processes. Both adsorbents are steam-activated carbons prepared from either coconut or coal precursors. Prior to use the adsorbents were washed in deionized water or 2 M NaOH. Mass transfer coefficients and effective overall diffusion coefficients indicate a minor contribution from adsorbent porosity. In contrast, high surface oxygen content impedes transport to and into the adsorbent structure. Carbon dosage shows a proportional increase in transport coefficients with increasing mass; these coefficients are constant when normalized per unit mass. Neither water nor NaOH treatment of the adsorbents has a significant influence on dodecanoic acid adsorption kinetics. Molecular and Knudsen diffusion coefficients are defined to demonstrate that the overall effective diffusion coefficient values and the diffusion process are controlled by surface diffusion.

  5. Kinetics and thermodynamics studies of silver ions adsorption onto coconut shell activated carbon.

    PubMed

    Silva-Medeiros, Flávia V; Consolin-Filho, Nelson; Xavier de Lima, Mateus; Bazzo, Fernando Previato; Barros, Maria Angélica S D; Bergamasco, Rosângela; Tavares, Célia R G

    2016-12-01

    The presence of silver in the natural water environment has been of great concern because of its toxicity, especially when it is in the free ion form (Ag(+)). This paper aims to study the adsorption kinetics of silver ions from an aqueous solution onto coconut shell activated carbon using batch methods. Batch kinetic data were fitted to the first-order model and the pseudo-second-order model, and this last equation fits correctly the experimental data. Equilibrium experiments were carried out at 30°C, 40°C, and 50°C. The adsorption isotherms were reasonably fit using Langmuir model, and the adsorption process was slightly influenced by changes in temperature. Thermodynamic parameters (ΔH°, ΔG°, and ΔS°) were determined. The adsorption process seems to be non-favorable, exothermic, and have an increase in the orderness.

  6. Thermodynamic and kinetic behaviors of trinitrotoluene adsorption on powdered activated carbons

    SciTech Connect

    Lee, J.W.; Hwang, K.J.; Shim, W.G.; Moon, I.S.

    2006-07-01

    Regulations on the removal of trinitrotoluene (TNT) from wastewater have become increasingly more stringent, demanding faster, less expensive, and more efficient treatment. This study focuses on the adsorption equilibrium and kinetics of TNT on powered activated carbons (PAC). Three types of PACs (i.e., wood based, coal based, and coconut-shell based) were studied as functions of temperature and pH. Thermodynamic properties including Gibbs free energy, enthalpy, and entropy, were evaluated by applying the Van't Hoff equation. In addition, the adsorption energy distribution functions which describe heterogeneous characteristics of porous solid sorbents were calculated by using the generalized nonlinear regularization method. Adsorption kinetic studies were carried out in batch adsorber under important conditions such as PAC types, temperature, pH, and concentration. We found that fast and efficient removal of TNT dissolved in water can be successfully achieved by PAC adsorption.

  7. Development and sensitivity analysis of a fully kinetic model of sequential reductive dechlorination in groundwater.

    PubMed

    Malaguerra, Flavio; Chambon, Julie C; Bjerg, Poul L; Scheutz, Charlotte; Binning, Philip J

    2011-10-01

    A fully kinetic biogeochemical model of sequential reductive dechlorination (SERD) occurring in conjunction with lactate and propionate fermentation, iron reduction, sulfate reduction, and methanogenesis was developed. Production and consumption of molecular hydrogen (H(2)) by microorganisms have been modeled using modified Michaelis-Menten kinetics and has been implemented in the geochemical code PHREEQC. The model have been calibrated using a Shuffled Complex Evolution Metropolis algorithm to observations of chlorinated solvents, organic acids, and H(2) concentrations in laboratory batch experiments of complete trichloroethene (TCE) degradation in natural sediments. Global sensitivity analysis was performed using the Morris method and Sobol sensitivity indices to identify the most influential model parameters. Results show that the sulfate concentration and fermentation kinetics are the most important factors influencing SERD. The sensitivity analysis also suggests that it is not possible to simplify the model description if all system behaviors are to be well described.

  8. Kinetics of positive ions and electrically neutral active particles in afterglow in neon at low pressure

    SciTech Connect

    Pejović, Milić M. Nešić, Nikola T.; Pejović, Momčilo M.

    2014-04-15

    Kinetics of positive ions and electrically neutral active particles formed during breakdown and successive discharge in neon-filled tube at 6.6 millibars pressure had been analyzed. This analysis was performed on the basis of mean value of electrical breakdown time delay t{sup ¯}{sub d} dependence on afterglow period τ (memory curve). It was shown that positive ions are present in the 1μs < τ < 30 ms interval, which is manifested through t{sup ¯}{sub d} slow increase with the increase of τ. A rapid t{sup ¯}{sub d} increase in the 30 ms < τ < 3 s interval is a consequence of significant decrease of positive ions concentration and dominant role in breakdown initiation have ground state nitrogen atoms, which further release secondary electrons from the cathode by catalytic recombination process. These atoms are formed during discharge by dissociation of ground state nitrogen molecules that are present as impurities in neon. For τ > 3 s, breakdown is initiated by cosmic rays and natural radioactivity. The increase of discharge current leads to decrease of t{sup ¯}{sub d} due to the increase of positive ions concentration in inter electrode gap. The increase of applied voltage also decreases t{sup ¯}{sub d} for τ > 30 ms due to the increase of the probability for initial electron to initiate breakdown. The presence of UV radiation leads to the decrease of t{sup ¯}{sub d} due to the increased electron yield caused by photoelectrons. The influence of photoelectrons on breakdown initiation can be noticed for τ > 0.1 ms, while they dominantly determine t{sup ¯}{sub d} for τ > 30 ms.

  9. Active matter beyond mean-field: ring-kinetic theory for self-propelled particles.

    PubMed

    Chou, Yen-Liang; Ihle, Thomas

    2015-02-01

    Recently, Hanke et al. [Phys. Rev. E 88, 052309 (2013)] showed that mean-field kinetic theory fails to describe collective motion in soft active colloids and that correlations must not be neglected. Correlation effects are also expected to be essential in systems of biofilaments driven by molecular motors and in swarms of midges. To obtain correlations in an active matter system from first principles, we derive a ring-kinetic theory for Vicsek-style models of self-propelled agents from the exact N-particle evolution equation in phase space. The theory goes beyond mean-field and does not rely on Boltzmann's approximation of molecular chaos. It can handle precollisional correlations and cluster formation, which are both important to understand the phase transition to collective motion. We propose a diagrammatic technique to perform a small-density expansion of the collision operator and derive the first two equations of the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy. An algorithm is presented that numerically solves the evolution equation for the two-particle correlations on a lattice. Agent-based simulations are performed and informative quantities such as orientational and density correlation functions are compared with those obtained by ring-kinetic theory. Excellent quantitative agreement between simulations and theory is found at not-too-small noises and mean free paths. This shows that there are parameter ranges in Vicsek-like models where the correlated closure of the BBGKY hierarchy gives correct and nontrivial results. We calculate the dependence of the orientational correlations on distance in the disordered phase and find that it seems to be consistent with a power law with an exponent around -1.8, followed by an exponential decay. General limitations of the kinetic theory and its numerical solution are discussed.

  10. Active matter beyond mean-field: Ring-kinetic theory for self-propelled particles

    NASA Astrophysics Data System (ADS)

    Chou, Yen-Liang; Ihle, Thomas

    2015-02-01

    Recently, Hanke et al. [Phys. Rev. E 88, 052309 (2013), 10.1103/PhysRevE.88.052309] showed that mean-field kinetic theory fails to describe collective motion in soft active colloids and that correlations must not be neglected. Correlation effects are also expected to be essential in systems of biofilaments driven by molecular motors and in swarms of midges. To obtain correlations in an active matter system from first principles, we derive a ring-kinetic theory for Vicsek-style models of self-propelled agents from the exact N -particle evolution equation in phase space. The theory goes beyond mean-field and does not rely on Boltzmann's approximation of molecular chaos. It can handle precollisional correlations and cluster formation, which are both important to understand the phase transition to collective motion. We propose a diagrammatic technique to perform a small-density expansion of the collision operator and derive the first two equations of the Bogoliubov-Born-Green-Kirkwood-Yvon (BBGKY) hierarchy. An algorithm is presented that numerically solves the evolution equation for the two-particle correlations on a lattice. Agent-based simulations are performed and informative quantities such as orientational and density correlation functions are compared with those obtained by ring-kinetic theory. Excellent quantitative agreement between simulations and theory is found at not-too-small noises and mean free paths. This shows that there are parameter ranges in Vicsek-like models where the correlated closure of the BBGKY hierarchy gives correct and nontrivial results. We calculate the dependence of the orientational correlations on distance in the disordered phase and find that it seems to be consistent with a power law with an exponent around -1.8 , followed by an exponential decay. General limitations of the kinetic theory and its numerical solution are discussed.

  11. Heat Transfer Analysis and Assessment of Kinetics Systems for PBX 9501

    SciTech Connect

    Jorenby, Jeffrey W.

    2006-07-01

    The study of thermal decomposition in high explosive (HE) charges has been an ongoing process since the early 1900s. This work is specifically directed towards the analysis of PBX 9501. In the early 1970s, Dwight Jaeger of Los Alamos National Laboratory (LANL) developed a single-step, two-species kinetics system that was used in the development of one of the first finite element codes for thermal analyses known as EXPLO. Jaeger's research focused on unconfined spherical samples of HE charges to determine if varied heating ramps would cause detonation or deflagration. Tarver and McGuire of Lawrence Livermore National Laboratory (LLNL) followed soon after with a three-step, four-species kinetics system that was developed for confined spheres under relatively fast heating conditions. Peter Dickson et al. of LANL then introduced a kinetics system with four steps and five species that included bimolecular products to capture the effects of the endothermic phase change that the HE undergoes. The results of four experiments are examined to study the effectiveness of these kinetics systems. The experiments are: (1) The LLNL scaled thermal explosion (STEX) experiments on confined cylindrical charges with long heating ramps in the range of 90 hours. (2) The LLNL one-dimensional time to explosion (ODTX) experiments on spherical charges that include confined, partially confined, and aged HE experiments. (3) The LANL unconfined one-dimensional experiments for small spheres. (4) The Naval Air Warfare Center Weapons Division at China Lake experiments on small confined cylinders. The three kinetics systems are applied to each of the four experiments with the use of the finite element analysis (FEA) heat conduction solver COYOTE. The numerical results using the kinetics systems are compared to each other and to the experimental data to determine which kinetics systems are best suited for analyzing conditions such as time to ignition, containment, heating time, and location of

  12. Hydrolytic activity of vanadate toward serine-containing peptides studied by kinetic experiments and DFT theory.

    PubMed

    Ho, Phuong Hien; Mihaylov, Tzvetan; Pierloot, Kristine; Parac-Vogt, Tatjana N

    2012-08-20

    Hydrolysis of dipeptides glycylserine (Gly-Ser), leucylserine (Leu-Ser), histidylserine (His-Ser), glycylalanine (Gly-Ala), and serylglycine (Ser-Gly) was examined in vanadate solutions by means of (1)H, (13)C, and (51)V NMR spectroscopy. In the presence of a mixture of oxovanadates, the hydrolysis of the peptide bond in Gly-Ser proceeds under the physiological pH and temperature (37 °C, pD 7.4) with a rate constant of 8.9 × 10(-8) s(-1). NMR and EPR spectra did not show evidence for the formation of paramagnetic species, excluding the possibility of V(V) reduction to V(IV) and indicating that the cleavage of the peptide bond is purely hydrolytic. The pD dependence of k(obs) exhibits a bell-shaped profile, with the fastest hydrolysis observed at pD 7.4. Combined (1)H, (13)C, and (51)V NMR experiments revealed formation of three complexes between Gly-Ser and vanadate, of which only one complex, designated Complex 2, formed via coordination of amide oxygen and amino nitrogen to vanadate, is proposed to be hydrolytically active. Kinetic experiments at pD 7.4 performed by using a fixed amount of Gly-Ser and increasing amounts of Na(3)VO(4) allowed calculation of the formation constant for the Gly-Ser/VO(4)(3-) complex (K(f) = 16.1 M(-1)). The structure of the hydrolytically active Complex 2 is suggested also on the basis of DFT calculations. The energy difference between Complex 2 and the major complex detected in the reaction mixture, Complex 1, is calculated to be 7.1 kcal/mol in favor of the latter. The analysis of the molecular properties of Gly-Ser and their change upon different modes of coordination to the vanadate pointed out that only in Complex 2 the amide carbon is suitable for attack by the hydroxyl group in the Ser side chain, which acts as an effective nucleophile. The origin of the hydrolytic activity of vanadate is most likely a combination of the polarization of amide oxygen in Gly-Ser due to the binding to vanadate, followed by the intramolecular

  13. Controlling enzymatic activity and kinetics in swollen mesophases by physical nano-confinement

    NASA Astrophysics Data System (ADS)

    Sun, Wenjie; Vallooran, Jijo J.; Zabara, Alexandru; Mezzenga, Raffaele

    2014-05-01

    Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them into a highly confined environment. We show that the enzymatic activity of a model enzyme, horseradish peroxidase (HRP), can be accurately controlled by relaxing its confinement within the cubic phases' water channels, when the aqueous channel diameters are systematically swollen with varying amount of hydration-enhancing sugar ester. The in-meso activity and kinetics of HRP are then systematically investigated by UV-vis spectroscopy, as a function of the size of the aqueous mesophase channels. The enzymatic activity of HRP increases with the swelling of the water channels. In swollen mesophases with water channel diameter larger than the HRP size, the enzymatic activity is more than double that measured in standard mesophases, approaching again the enzymatic activity of free HRP in bulk water. We also show that the physically-entrapped enzymes in the mesophases exhibit a restricted-diffusion-induced initial lag period and report the first observation of in-meso enzymatic kinetics significantly deviating from the normal Michaelis-Menten behaviour observed in free solutions, with deviations vanishing when enzyme confinement is released by swelling the mesophase.Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them

  14. Pyrolysis and oxy-fuel combustion characteristics and kinetics of petrochemical wastewater sludge using thermogravimetric analysis.

    PubMed

    Chen, Jianbiao; Mu, Lin; Cai, Jingcheng; Yao, Pikai; Song, Xigeng; Yin, Hongchao; Li, Aimin

    2015-12-01

    The pyrolysis and oxy-fuel combustion characteristics of petrochemical wastewater sludge (PS) were studied in air (O2/N2) and oxy-fuel (O2/CO2) atmospheres using non-isothermal thermogravimetric analysis (TGA). Pyrolysis experiments showed that the weight loss profiles were almost similar up to 1050K in both N2 and CO2 atmospheres, while further weight loss took place in CO2 atmosphere at higher temperatures due to char-CO2 gasification. Compared with 20%O2/80%N2, the drying and devolatilization stage of PS were delayed in 20%O2/80%CO2 due to the differences in properties of the diluting gases. In oxy-fuel combustion experiments, with O2 concentration increasing, characteristic temperatures decreased, while characteristic combustion rates and combustion performance indexes increased. Kinetic analysis of PS decomposition under various atmospheres was performed using Coats-Redfern approach. The results indicated that, with O2 concentration increasing, the activation energies of Step 1 almost kept constant, while the values of subsequent three steps increased.

  15. Crystallization Kinetics of a Solid Oxide Fuel Cell Seal Glass by Differential Thermal Analysis

    NASA Technical Reports Server (NTRS)

    Bansal, Narottam P.; Gamble, Eleanor A.

    2005-01-01

    Crystallization kinetics of a barium calcium aluminosilicate glass (BCAS), a sealant material for planar solid oxide fuel cells, have been investigated by differential thermal analysis (DTA). From variation of DTA peak maximum temperature with heating rate, the activation energy for glass crystallization was calculated to be 259 kJ/mol. Development of crystalline phases on thermal treatments of the glass at various temperatures has been followed by powder x-ray diffraction. Microstructure and chemical composition of the crystalline phases were investigated by scanning electron microscopy and energy dispersive spectroscopic (EDS) analysis. BaSiO3 and hexacelsian (BaAl2Si2O8) were the primary crystalline phases whereas monoclinic celsian (BaAl2Si2O8) and (Ba(x), Ca(y))SiO4 were also detected as minor phases. Needle-shaped BaSiO3 crystals are formed first, followed by the formation of other phases at longer times of heat treatments. The glass does not fully crystallize even after long term heat treatments at 750 to 900 C.

  16. Novel degradation pathway and kinetic analysis for buprofezin removal by newly isolated Bacillus sp.

    PubMed

    Wang, Guangli; Xu, Dayong; Xiong, Minghua; Zhang, Hui; Li, Feng; Liu, Yuan

    2016-09-15

    Given the intensive and widespread application of the pesticide, buprofezin, its environmental residues potentially pose a problem; yet little is known about buprofezin's kinetic and metabolic behaviors. In this study, a novel gram-positive strain, designated BF-5, isolated from aerobic activated sludge, was found to be capable of metabolizing buprofezin as its sole energy, carbon, and nitrogen source. Based on its physiological and biochemical characteristics, other aspects of its phenotype, and a phylogenetic analysis, strain BF-5 was identified as Bacillus sp. This study investigated the effect of culture conditions on bacterial growth and substrate degradation, such as pH, temperature, initial concentration, different nitrogen source, and additional nitrogen sources as co-substrates. The degradation rate parameters, qmax, Ks, Ki and Sm were determined to be 0.6918 h(-1), 105.4 mg L(-1), 210.5 mg L(-1), and 148.95 mg L(-1) respectively. The capture of unpublished potential metabolites by gas chromatography-mass spectrometry (GC-MS) analysis has led to the proposal of a novel degradation pathway. Taken together, our results clarify buprofezin's biodegradation pathway(s) and highlight the promising potential of strain BF-5 in bioremediation of buprofezin-contaminated environments.

  17. Tyrosinase kinetics in epidermal melanocytes: analysis of DAG-PKC-dependent signaling pathway

    NASA Astrophysics Data System (ADS)

    Stolnitz, Mikhail M.; Peshkova, Anna Y.

    2001-05-01

    Tyrosinase is the key enzyme of melanogenesis with unusual enzyme kinetics. Protein kinase C plays an important role in regulating of tyrosinase activity. In the paper the mathematical model of PKC-DAG-dependent signal transduction pathway for UV-radiation is presented.

  18. Myosin heavy chain isoform composition and stretch activation kinetics in single fibres of Xenopus laevis iliofibularis muscle

    PubMed Central

    Andruchova, Olena; Stephenson, Gabriela M M; Andruchov, Oleg; Stephenson, D George; Galler, Stefan

    2006-01-01

    Skeletal muscle is composed of specialized fibre types that enable it to fulfil complex and variable functional needs. Muscle fibres of Xenopus laevis, a frog formerly classified as a toad, were the first to be typed based on a combination of physiological, morphological, histochemical and biochemical characteristics. Currently the most widely accepted criterion for muscle fibre typing is the myosin heavy chain (MHC) isoform composition because it is assumed that variations of this protein are the most important contributors to functional diversity. Yet this criterion has not been used for classification of Xenopus fibres due to the lack of an effective protocol for MHC isoform analysis. In the present study we aimed to resolve and visualize electrophoretically the MHC isoforms expressed in the iliofibularis muscle of Xenopus laevis, to define their functional identity and to classify the fibres based on their MHC isoform composition. Using a SDS-PAGE protocol that proved successful with mammalian muscle MHC isoforms, we were able to detect five MHC isoforms in Xenopus iliofibularis muscle. The kinetics of stretch-induced force transients (stretch activation) produced by a fibre was strongly correlated with its MHC isoform content indicating that the five MHC isoforms confer different kinetics characteristics. Hybrid fibre types containing two MHC isoforms exhibited stretch activation kinetics parameters that were intermediate between those of the corresponding pure fibre types. These results clearly show that the MHC isoforms expressed in Xenopus muscle are functionally different thereby validating the idea that MHC isoform composition is the most reliable criterion for vertebrate skeletal muscle fibre type classification. Thus, our results lay the foundation for the unequivocal classification of the muscle fibres in the Xenopus iliofibularis muscle and for gaining further insights into skeletal muscle fibre diversity. PMID:16644798

  19. Myosin heavy chain isoform composition and stretch activation kinetics in single fibres of Xenopus laevis iliofibularis muscle.

    PubMed

    Andruchova, Olena; Stephenson, Gabriela M M; Andruchov, Oleg; Stephenson, D George; Galler, Stefan

    2006-07-01

    Skeletal muscle is composed of specialized fibre types that enable it to fulfil complex and variable functional needs. Muscle fibres of Xenopus laevis, a frog formerly classified as a toad, were the first to be typed based on a combination of physiological, morphological, histochemical and biochemical characteristics. Currently the most widely accepted criterion for muscle fibre typing is the myosin heavy chain (MHC) isoform composition because it is assumed that variations of this protein are the most important contributors to functional diversity. Yet this criterion has not been used for classification of Xenopus fibres due to the lack of an effective protocol for MHC isoform analysis. In the present study we aimed to resolve and visualize electrophoretically the MHC isoforms expressed in the iliofibularis muscle of Xenopus laevis, to define their functional identity and to classify the fibres based on their MHC isoform composition. Using a SDS-PAGE protocol that proved successful with mammalian muscle MHC isoforms, we were able to detect five MHC isoforms in Xenopus iliofibularis muscle. The kinetics of stretch-induced force transients (stretch activation) produced by a fibre was strongly correlated with its MHC isoform content indicating that the five MHC isoforms confer different kinetics characteristics. Hybrid fibre types containing two MHC isoforms exhibited stretch activation kinetics parameters that were intermediate between those of the corresponding pure fibre types. These results clearly show that the MHC isoforms expressed in Xenopus muscle are functionally different thereby validating the idea that MHC isoform composition is the most reliable criterion for vertebrate skeletal muscle fibre type classification. Thus, our results lay the foundation for the unequivocal classification of the muscle fibres in the Xenopus iliofibularis muscle and for gaining further insights into skeletal muscle fibre diversity.

  20. Data Capture and Analysis Using the BBC Microcomputer--an Interfacing Project Applied to Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Jones, Lawrence; Graham, Ian

    1986-01-01

    Reviews the main principles of interfacing and discusses the software developed to perform kinetic data capture and analysis with a BBC microcomputer linked to a recording spectrophotometer. Focuses on the steps in software development. Includes results of a lactate dehydrogenase assay. (ML)

  1. Quantum dot based enzyme activity sensors present deviations from Michaelis-Menten kinetic model

    NASA Astrophysics Data System (ADS)

    Díaz, Sebastián. A.; Brown, Carl W.; Malanoski, Anthony P.; Oh, Eunkeu; Susumu, Kimihiro; Medintz, Igor L.

    2016-03-01

    Nanosensors employing quantum dots (QDs) and enzyme substrates with fluorescent moieties offer tremendous promise for disease surveillance/diagnostics and as high-throughput co-factor assays. Advantages of QDs over other nanoscaffolds include their small size and inherent photochemical properties such as size tunable fluorescence, ease in attaching functional moieties, and resistance to photobleaching. These properties make QDs excellent Förster Resonance Energy Transfer (FRET) donors; well-suited for rapid, optical measurement applications. We report enzyme sensors designed with a single FRET donor, the QD donor acting as a scaffold to multiple substrates or acceptors. The QD-sensor follows the concrete activity of the enzyme, as compared to the most common methodologies that quantify the enzyme amount or its mRNA precursor. As the sensor reports on the enzyme activity in real-time we can actively follow the kinetics of the enzyme. Though classic Michaelis-Menten (MM) parameters can be obtained to describe the activity. In the course of these experiments deviations, both decreasing and increasing the kinetics, from the common MM model were observed upon close examinations. From these observations additional experiments were undertaken to understand the varying mechanisms. Different enzymes can present different deviations depending on the chosen target, e.g. trypsin appears to present a positive hopping mechanism while collagenase demonstrates a QD caused reversible inhibition.

  2. Anaerobic waste-activated sludge digestion - A bioconversion mechanism and kinetic model

    SciTech Connect

    Shimizu, Tatsuo; Kudo, Kenzo; Nasu, Yoshikazu )

    1993-05-01

    The anaerobic bioconversion of raw and mechanically lysed waste-activated sludge was kinetically investigated. The hydrolysis of the biopolymers, such as protein, which leaked out from the biological sludge with ultrasonic lysis, was a first-order reaction in anaerobic digestion and the rate constant was much higher than the decay rate constant of the raw waste activated sludge. An anaerobic digestion model that is capable of evaluating the effect of the mechanical sludge lysis on digestive performance was developed. The present model includes four major biological processes - the release of intracellular matter with sludge lysis; hydrolysis of biopolymers to volatile acids; the degradation of various volatile acids to acetate; and the conversion of acetate and hydrogen to methane. Each process was assumed to follow first-order kinetics. The model approximately simulated the overall process performance of the anaerobic digestion of waste-activated sludge. The model suggested that when the lysed waste-activated sludge was fed, the overall digestive performance remarkably increased in the two-phase system consisting of an acid forming process and a methanogenic process, which ensured the symbiotic growth of acetogenic and methanogenic bacteria.

  3. Surface heterogeneity effects of activated carbons on the kinetics of paracetamol removal from aqueous solution

    NASA Astrophysics Data System (ADS)

    Ruiz, B.; Cabrita, I.; Mestre, A. S.; Parra, J. B.; Pires, J.; Carvalho, A. P.; Ania, C. O.

    2010-06-01

    The removal of a compound with therapeutic activity (paracetamol) from aqueous solutions using chemically modified activated carbons has been investigated. The chemical nature of the activated carbon material was modified by wet oxidation, so as to study the effect of the carbon surface chemistry and composition on the removal of paracetamol. The surface heterogeneity of the carbon created upon oxidation was found to be a determinant in the adsorption capability of the modified adsorbents, as well as in the rate of paracetamol removal. The experimental kinetic data were fitted to the pseudo-second order and intraparticle diffusion models. The parameters obtained were linked to the textural and chemical features of the activated carbons. After oxidation the wettability of the carbon is enhanced, which favors the transfer of paracetamol molecules to the carbon pores (smaller boundary layer thickness). At the same time the overall adsorption rate and removal efficiency are reduced in the oxidized carbon due to the competitive effect of water molecules.

  4. Cross-bridge kinetics in rat myocardium: effect of sarcomere length and calcium activation.

    PubMed

    Wannenburg, T; Heijne, G H; Geerdink, J H; Van Den Dool, H W; Janssen, P M; De Tombe, P P

    2000-08-01

    We tested the hypotheses that Ca(2+) concentration ([Ca(2+)]) and sarcomere length (SL) modulate force development via graded effects on cross-bridge kinetics in chemically permeabilized rat cardiac trabeculae. Using sinusoidal length perturbations, we derived the transfer functions of stiffness over a range of [Ca(2+)] at a constant SL of 2.1 micrometer (n = 8) and at SL of 2.0, 2.1, and 2.2 micrometer (n = 4). We found that changes in SL affected only the magnitude of stiffness, whereas [Ca(2+)] affected the magnitude and phase-frequency relations. The data were fit to complex functions of two exponential processes. The characteristic frequencies (b and c) of these processes are indexes of cross-bridge kinetics, with b relating to cross-bridge attachment to and c to detachment from certain non-force-generating states. Both were significantly affected by [Ca(2+)], with an increase in b and c of 140 and 44%, respectively, over the range of [Ca(2+)] studied (P < 0.01). In contrast, SL had no effect on the characteristic frequencies (P > 0.6). We conclude that Ca(2+) activation modulates force development in rat myocardium, at least in part, via a graded effect on cross-bridge kinetics, whereas SL effects are mediated mainly by recruitment of cross bridges.

  5. Understanding long-time vacancy aggregation in iron: A kinetic activation-relaxation technique study

    NASA Astrophysics Data System (ADS)

    Brommer, Peter; Béland, Laurent Karim; Joly, Jean-François; Mousseau, Normand

    2014-10-01

    Vacancy diffusion and clustering processes in body-centered-cubic (bcc) Fe are studied using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities. For monovacancies and divacancies, k-ART recovers previously published results while clustering in a 50-vacancy simulation box agrees with experimental estimates. Applying k-ART to the study of clustering pathways for systems containing from one to six vacancies, we find a rich set of diffusion mechanisms. In particular, we show that the path followed to reach a hexavacancy cluster influences greatly the associated mean-square displacement. Aggregation in a 50-vacancy box also shows a notable dispersion in relaxation time associated with effective barriers varying from 0.84 to 1.1 eV depending on the exact pathway selected. We isolate the effects of long-range elastic interactions between defects by comparing to simulations where those effects are deliberately suppressed. This allows us to demonstrate that in bcc Fe, suppressing long-range interactions mainly influences kinetics in the first 0.3 ms, slowing down quick energy release cascades seen more frequently in full simulations, whereas long-term behavior and final state are not significantly affected.

  6. Stochastic Kinetics of Nascent RNA

    NASA Astrophysics Data System (ADS)

    Xu, Heng; Skinner, Samuel O.; Sokac, Anna Marie; Golding, Ido

    2016-09-01

    The stochastic kinetics of transcription is typically inferred from the distribution of RNA numbers in individual cells. However, cellular RNA reflects additional processes downstream of transcription, hampering this analysis. In contrast, nascent (actively transcribed) RNA closely reflects the kinetics of transcription. We present a theoretical model for the stochastic kinetics of nascent RNA, which we solve to obtain the probability distribution of nascent RNA per gene. The model allows us to evaluate the kinetic parameters of transcription from single-cell measurements of nascent RNA. The model also predicts surprising discontinuities in the distribution of nascent RNA, a feature which we verify experimentally.

  7. Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

    PubMed Central

    Prasanphanich, Adam F.; White, Douglas E.; Gran, Margaret A.

    2016-01-01

    The side population (SP) assay, a technique used in cancer and stem cell research, assesses the activity of ABC transporters on Hoechst staining in the presence and absence of transporter inhibition, identifying SP and non-SP cell (NSP) subpopulations by differential staining intensity. The interpretation of the assay is complicated because the transporter-mediated mechanisms fail to account for cell-to-cell variability within a population or adequately control the direct role of transporter activity on staining intensity. We hypothesized that differences in dye kinetics at the single-cell level, such as ABCG2 transporter-mediated efflux and DNA binding, are responsible for the differential cell staining that demarcates SP/NSP identity. We report changes in A549 phenotype during time in culture and with TGFβ treatment that correlate with SP size. Clonal expansion of individually sorted cells re-established both SP and NSPs, indicating that SP membership is dynamic. To assess the validity of a purely kinetics-based interpretation of SP/NSP identity, we developed a computational approach that simulated cell staining within a heterogeneous cell population; this exercise allowed for the direct inference of the role of transporter activity and inhibition on cell staining. Our simulated SP assay yielded appropriate SP responses for kinetic scenarios in which high transporter activity existed in a portion of the cells and little differential staining occurred in the majority of the population. With our approach for single-cell analysis, we observed SP and NSP cells at both ends of a transporter activity continuum, demonstrating that features of transporter activity as well as DNA content are determinants of SP/NSP identity. PMID:27851764

  8. A kinetic analysis of strand breaks on large DNA induced by cigarette smoke extract

    NASA Astrophysics Data System (ADS)

    Kurita, Hirofumi; Takata, Tatsuya; Yasuda, Hachiro; Takashima, Kazunori; Mizuno, Akira

    2010-06-01

    We report a kinetic analysis of strand breakages on large DNA molecules induced by cigarette smoke extract (CSE), an extract of soluble cigarette smoke components. Previously, this DNA damage was analyzed by agarose gel electrophoresis, whereas we used fluorescence to kinetically analyze damage to individual DNA molecules. CSE caused a marked change in length of DNA molecules. The rate of CSE-induced double-strand breakage on large random-coiled DNA molecules was determined using a simple theoretical model, allowing the facile estimation of the rate of double-strand breaks on large DNA molecules.

  9. Adsorption of methylene blue dye onto activated carbons based on agricultural by-products: equilibrium and kinetic studies.

    PubMed

    Ioannou, Z; Simitzis, J

    2013-01-01

    Mixtures of novolac resin and olive stone biomass (20/80 and 40/60 w/w) were cured, pyrolyzed up to 1,000 °C and activated with CO2 under a continuous flow operation (named N20B-cCa and N40B-cCa respectively). Commercial activated charcoal was similarly re-activated with CO2 and used for comparison reasons (AC-a). The characterization of these materials was performed by Fourier transform Infrared (FTIR) analysis and their specific surface area was determined according to DIN 66132. The materials were tested for their adsorption abilities at different temperatures (298, 333 K) and initial dye concentrations (0.01-0.35 g/L) using 1 L of methylene blue (MB) solution in 10 g of activated carbon. MB adsorption kinetic was also studied. The FTIR spectra of all activated carbons show absorption peaks which correspond to -OH, -CH, -C-O-C- groups and to aromatic ring. The presence of the absorption peak at about 1,400 cm(-1) for N20B-cCa, N40B-cCa indicates more acidic groups on them compared to the commercial AC-a. The specific surface area of N20B-cCa, N40B-cCa and AC-a has values equal to 352, 342 and 760 m(2)/g respectively. From the applied kinetic models, pseudo-second-order equation could best describe MB adsorption. Consequently, such adsorbents can be used as filters to adsorb dyes from wastewaters.

  10. Activity-dependent modulation of inhibitory synaptic kinetics in the cochlear nucleus

    PubMed Central

    Nerlich, Jana; Keine, Christian; Rübsamen, Rudolf; Burger, R. Michael; Milenkovic, Ivan

    2014-01-01

    Spherical bushy cells (SBCs) in the anteroventral cochlear nucleus respond to acoustic stimulation with discharges that precisely encode the phase of low-frequency sound. The accuracy of spiking is crucial for sound localization and speech perception. Compared to the auditory nerve input, temporal precision of SBC spiking is improved through the engagement of acoustically evoked inhibition. Recently, the inhibition was shown to be less precise than previously understood. It shifts from predominantly glycinergic to synergistic GABA/glycine transmission in an activity-dependent manner. Concurrently, the inhibition attains a tonic character through temporal summation. The present study provides a comprehensive understanding of the mechanisms underlying this slow inhibitory input. We performed whole-cell voltage clamp recordings on SBCs from juvenile Mongolian gerbils and recorded evoked inhibitory postsynaptic currents (IPSCs) at physiological rates. The data reveal activity-dependent IPSC kinetics, i.e., the decay is slowed with increased input rates or recruitment. Lowering the release probability yielded faster decay kinetics of the single- and short train-IPSCs at 100 Hz, suggesting that transmitter quantity plays an important role in controlling the decay. Slow transmitter clearance from the synaptic cleft caused prolonged receptor binding and, in the case of glycine, spillover to nearby synapses. The GABAergic component prolonged the decay by contributing to the asynchronous vesicle release depending on the input rate. Hence, the different factors controlling the amount of transmitters in the synapse jointly slow the inhibition during physiologically relevant activity. Taken together, the slow time course is predominantly determined by the receptor kinetics and transmitter clearance during short stimuli, whereas long duration or high frequency stimulation additionally engage asynchronous release to prolong IPSCs. PMID:25565972

  11. Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function

    SciTech Connect

    Raswan, T. R. Haryanto, F.

    2014-09-30

    Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.

  12. Dynamic nuclear renography kinetic analysis: Four-compartment model for assessing kidney function

    NASA Astrophysics Data System (ADS)

    Raswan, T. R.; Haryanto, F.

    2014-09-01

    Dynamic nuclear renography method produces TACs of kidneys and bladder. Multiple TACs data can be further analyzed to obtain the overview of urinary system's condition. Tracer kinetic analysis was performed using four-compartment models. The system's model consist of four irreversible compartment with four transport constants (k1, k2, k3 and k4). The mathematical expressions of tracer's distributions is fitted to experimental data (TACs) resulting in model constants. This transport constants represent the urinary system behavior, and later can be used for analyzing system's condition. Different intervals of kinetics parameter are clearly shown by abnormal system with respect to the normal one. Furthermore, the system with delayed uptake has 82% lower uptake parameters (k1 and k2) than normal one. Meanwhile, the system with prolonged clearance time has its kinetics parameters k3 or k4 lower than the others. This model is promising for quantitatively describe urinary system's function especially if supplied with more data.

  13. An explicit expression for determining cometabolism kinetics using progress curve analysis.

    PubMed

    Goudar, Chetan T

    2012-05-31

    We present an explicit expression for describing the kinetics of cometabolic biotransformation of environmental pollutants. This expression is based on the Lambert W function and explicitly relates the substrate concentration, S, to time, t, the two experimentally measured variables. This explicit relationship simplifies kinetic parameter estimation as differential equation solution and iterative estimation of the substrate concentration are eliminated. The applicability of this new expression for nonlinear kinetic parameter estimation was first demonstrated using noise containing synthetic data where final estimates of the kinetic parameters were very close to their actual values. Subsequently 1.1.1-trichloroethane degradation data at initial concentrations of 750 and 375 μM were described using the explicit expression resulting in r and K(s) estimates of 0.26 μM/mg d and 28.08 μM and 0.30 μM/mg d and 28.70 μM, respectively, very similar to 0.276 μM/mg d and 31.2 μM, respectively, that were reported in the original study. The new explicit expression presented in this study simplifies estimation of cometabolic kinetic parameters and can be easily used across all computational platforms thereby providing an attractive alternative for progress curve analysis.

  14. NMR analysis, protonation equilibria and decomposition kinetics of tolperisone.

    PubMed

    Orgován, Gábor; Tihanyi, Károly; Noszál, Béla

    2009-12-05

    The rate constants of spontaneous and hydroxide-catalyzed decomposition and the tautomer-specific protonation constants of tolperisone, a classical muscle relaxant were determined. A solution NMR method without any separation techniques was elaborated to quantitate the progress of decomposition. All the rate and equilibrium constants were determined at four different temperatures and the activation parameters were calculated. The molecular mechanism of decomposition is proposed.

  15. 4-Hydroxy cinnamic acid as mushroom preservation: Anti-tyrosinase activity kinetics and application.

    PubMed

    Hu, Yong-Hua; Chen, Qing-Xi; Cui, Yi; Gao, Huan-Juan; Xu, Lian; Yu, Xin-Yuan; Wang, Ying; Yan, Chong-Ling; Wang, Qin

    2016-05-01

    Tyrosinase is a key enzyme in post-harvest browning of fruit and vegetable. To control and inhibit its activity is the most effective method for delaying the browning and extend the shelf life. In this paper, the inhibitory kinetics of 4-hydroxy cinnamic acid on mushroom tyrosinase was investigated using the kinetics method of substrate reaction. The results showed that the inhibition of tyrosinase by 4-hydroxy cinnamic acid was a slow, reversible reaction with fractional remaining activity. The microscopic rate constants were determined for the reaction on 4-hydroxy cinnamic acid with tyrosinase. Furthermore, the molecular docking was used to simulate 4-hydroxy cinnamic acid dock with tyrosinase. The results showed that 4-hydroxy cinnamic acid interacted with the enzyme active site mainly through the hydroxy competed with the substrate hydroxy group. The cytotoxicity study of 4-hydroxy cinnamic acid indicated that it had no effects on the proliferation of normal liver cells. Moreover, the results of effects of 4-hydroxy cinnamic acid on the preservation of mushroom showed that it could delay the mushroom browning. These results provide a comprehensive underlying the inhibitory mechanisms of 4-hydroxy cinnamic acid and its delaying post-harvest browning, that is beneficial for the application of this compound.

  16. Kinetic Modeling of the Arabidopsis Cryptochrome Photocycle: FADHo Accumulation Correlates with Biological Activity

    PubMed Central

    Procopio, Maria; Link, Justin; Engle, Dorothy; Witczak, Jacques; Ritz, Thorsten; Ahmad, Margaret

    2016-01-01

    Cryptochromes are flavoprotein photoreceptors with multiple signaling roles during plant de-etiolation and development. Arabidopsis cryptochromes (cry1 and cry2) absorb light through an oxidized flavin (FADox) cofactor which undergoes reduction to both FADH° and FADH− redox states. Since the FADH° redox state has been linked to biological activity, it is important to estimate its concentration formed upon illumination in vivo. Here we model the photocycle of isolated cry1 and cry2 proteins with a three-state kinetic model. Our model fits the experimental data for flavin photoconversion in vitro for both cry1 and cry2, providing calculated quantum yields which are significantly lower in cry1 than for cry2. The model was applied to the cryptochrome photocycle in vivo using biological activity in plants as a readout for FADH° concentration. The fit to the in vivo data provided quantum yields for cry1 and cry2 flavin reduction similar to those obtained in vitro, with decreased cry1 quantum yield as compared to cry2. These results validate our assumption that FADH° concentration correlates with biological activity. This is the first reported attempt at kinetic modeling of the cryptochrome photocycle in relation to macroscopic signaling events in vivo, and thereby provides a theoretical framework to the components of the photocycle that are necessary for cryptochrome response to environmental signals. PMID:27446119

  17. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.

    PubMed Central

    Rohwer, J M; Botha, F C

    2001-01-01

    Sucrose accumulation in developing sugar cane (Saccharum officinarum) is accompanied by a continuous synthesis and cleavage of sucrose in the storage tissues. Despite numerous studies, the factors affecting sucrose accumulation are still poorly understood, and no consistent pattern has emerged which pinpoints certain enzyme activities as important controlling steps. Here, we develop an approach based on pathway analysis and kinetic modelling to assess the biochemical control of sucrose accumulation and futile cycling in sugar cane. By using the concept of elementary flux modes, all possible routes of futile cycling of sucrose were enumerated in the metabolic system. The available kinetic data for the pathway enzymes were then collected and assembled in a kinetic model of sucrose accumulation in sugar cane culm tissue. Although no data were fitted, the model agreed well with independent experimental results: in no case was the difference between calculated and measured fluxes and concentrations greater than 2-fold. The model thus validated was then used to assess different enhancement strategies for increasing sucrose accumulation. First, the control coefficient of each enzyme in the system on futile cycling of sucrose was calculated. Secondly, the activities of those enzymes with the numerically largest control coefficients were varied over a 5-fold range to determine the effect on the degree of futile cycling, the conversion efficiency from hexoses into sucrose, and the net sucrose accumulation rate. In view of the modelling results, overexpression of the fructose or glucose transporter or the vacuolar sucrose import protein, as well as reduction of cytosolic neutral invertase levels, appear to be the most promising targets for genetic manipulation. This offers a more directed improvement strategy than cumbersome gene-by-gene manipulation. The kinetic model can be viewed and interrogated on the World Wide Web at http://jjj.biochem.sun.ac.za. PMID:11513743

  18. In situ reaction kinetic analysis of dental restorative materials

    NASA Astrophysics Data System (ADS)

    Younas, Basma; Samad Khan, Abdul; Muzaffar, Danish; Hussain, Ijaz; Chaudhry, Aqif Anwar; Rehman, Ihtesham Ur

    2013-12-01

    The objective of this study was to evaluate in situ structural and thermal changes of dental restorative materials at periodical time intervals. The commercial materials included zinc oxide eugenol (ZOE), zinc phosphate type I (ZnPO4), glass ionomer cement type II (GIC) and resin-based nano-omposite (Filtek Z350 XT). These materials were processed according to manufacturer's instructions. For the structural analysis Fourier transform infrared spectroscopy (FTIR) was used at high resolution. TGA was used to evaluate thermal weight-loss. The FTIR spectra were collected at periodic time intervals. FTIR spectra showed that with time passing all materials exhibited an increase in peak intensities and a new appearance of shoulders and shifting of peaks for example, ZnPO4 (P-O), ZOE (C═O, C═N, C-O-C), GIC (COO-, C-H, Si-OH), composites (C═O, C═C, C═N, C-N-H). The peaks were replaced by bands and these bands became broader with time interval. Composites showed a degree of conversion and new peaks corresponded to the cross-linking of polymer composites. TGA analysis showed that significant changes in weight loss of set materials were observed after 24 h, where ZOE showed continuous changes in thermal degradation. The spectral changes and thermal degradation with time interval elucidated in situ setting behaviour and understanding of their bonding compatibility with tooth structure and change in relation to time.

  19. Engineering GCaMP affinity and kinetics for improved tracking of neuronal activity

    NASA Astrophysics Data System (ADS)

    Sun, Xiaonan Richard

    Fluorescent calcium indicator proteins (FCIPs) are powerful tools for monitoring neural activity. However, they still have significant performance limitations compared with synthetic indicators based on the small-molecule chelator BAPTA. Because of high cooperativity originating from a calmodulin-based recombinant calcium sensor, a given GECI is only sensitive to a small part of a neuron's likely calcium concentration range, which can span a range of 0.1-10 microM. GECIs also have up to 100-fold slower reponse kinetics than BAPTA-based indicators. Overcoming limitations in range and kinetics is a key step toward monitoring spike times and firing rates in cell-type-specific brain circuits. We are engaged in structure-based design to vary the affinity and accelerate the response kinetics of a widely used GECI, GCaMP3. We have designed more than 50 novel variants by targeted mutation of GCaMP3's calmodulin (CaM) domain and its intraprobe peptide partner, RS20. In our cuvet characterizations of purified protein, we have attained a nearly 40-fold (0.16-6 microM) range of KD without impairing per-molecule brightness. In stopped-flow biochemical measurements, off-responses to sharp decreases in calcium are more than 10 times faster than any other published GECI. Most of the gap in off-response speed between G-CaMP3 and BAPTA-based indicators could be closed without perturbing KD. In Drosophila antennal nerve axons, sensory stimulation-evoked fluorescence responses were significantly enhanced in speed and amplitude in two novel GECIs. With our biophysical measurements, we discovered that the N-lobe of the bilobular CaM domain is required for the high-fluorescence state and the C-lobe contributes to high affinity Ca2+ binding. To account for our observations, we propose a molecular dynamics model of GCaMP3 with two kinetic pathways leading to a high-fluorescence state. First, small amounts of Ca 2+ activate a slow "C-like" pathway through sequential binding to the C

  20. Kinetic modeling of the adsorption of basic dyes onto steam-activated bituminous coal

    SciTech Connect

    El Qada, E.N.; Allen, S.J.; Walker, G.M.

    2007-07-15

    The principal aim of this work is to investigate the mechanism of basic dye (methylene blue (MB) and basic red (BR)) adsorption onto activated carbons produced from steam-activated bituminous coal. The rate of adsorption onto various activated carbons, produced in small laboratory-scale and pilot-industrial-scale processes, was investigated under a variety of conditions. The kinetic data from these investigations were correlated to a number of adsorption models in an attempt to elucidate the mechanism of the adsorption processes. The adsorption mechanism was found to follow pseudo-second-order and intraparticle-diffusion models, with external mass transfer predominating in the first 5 min of the experiment. Filtrasorb 400 (Chemviron Carbon) exhibited the highest adsorption rate for the removal of basic dyes followed by activated carbons produced by our research group: PAC1 (activated carbon produced from Venezuelan bituminous coal in small laboratory scale using physical activation technique) and PAC2 (activated carbon produced by the steam activation of New Zealand bituminous coal on a pilot-industrial scale).

  1. Application of model-free methods for analysis of combustion kinetics of coals with different ranks

    SciTech Connect

    Sis, H

    2009-07-01

    Model-free kinetic approaches were employed to investigate the combustion kinetics of coals with different ranks, namely, lignite, bituminous coal, and anthracite. The experimental data were provided under non-isothermal conditions at different heating rates in the range of 2-25C min{sup -1}. The activation energy values were estimated by two model-free methods, that is, Ozawa-Flynn-Wall and Kissinger-Akahira-Sunose methods. Slightly higher activation energy values were obtained by Ozawa-Flynn-Wall method at a wide range of conversion extent. Variation of activation energy was found to be comparably more significant for lower rank lignite (between 44.82 and 287.56 kJ mol{sup -1}) while less significant for higher rank bituminous coal (between 101.97 and 155.64 kJ mol{sup -1}) and anthracite (between 106.04 and 160.31 kJ mol{sup -1}).

  2. Kinetic analysis of structural influences on the susceptibility of peroxiredoxins 2 and 3 to hyperoxidation

    PubMed Central

    Poynton, Rebecca A.; Peskin, Alexander V.; Haynes, Alexina C.; Lowther, W. Todd; Hampton, Mark B.; Winterbourn, Christine C.

    2016-01-01

    Mammalian 2-cysteine peroxiredoxins (Prxs) are susceptible to hyperoxidation by excess H2O2. The cytoplasmic family member Prx2 hyperoxidizes more readily than mitochondrial Prx3 due to slower dimerization of the sulfenic acid (SpOH) intermediate. Four variant amino acids near the C-terminus have been shown to contribute to this difference. We have performed kinetic analysis of the relationship between hyperoxidation and disulfide formation, using whole-protein MS and comparing wild-type (WT) Prx2 and Prx3 with tail-swap mutants in which the four amino acids were reversed. These changes make Prx3 more sensitive and Prx2 less sensitive to hyperoxidation and accounted for ~70% of the difference between the two proteins. The tail swap mutant of Prx3 was also more susceptible when expressed in the mitochondria of HeLa cells. The hyperoxidized product at lower excesses of H2O2 was a semi-hyperoxidized dimer with one active site disulfide and the other a sulfinic acid. For Prx2, increasing the H2O2 concentration resulted in complete hyperoxidation. In contrast, only approximately half the Prx3 active sites underwent hyperoxidation and, even with high H2O2, the predominant product was the hyperoxidized dimer. Size exclusion chromatography (SEC) showed that the oligomeric forms of all redox states of Prx3 dissociated more readily into dimeric units than their Prx2 counterparts. Notably the species with one disulfide and one hyperoxidized active site was decameric for Prx2 and dimeric for Prx3. Reduction and re-oxidation of the hyperoxidized dimer of Prx3 produced hyperoxidized monomers, implying dissociation and rearrangement of the subunits of the functional homodimer. PMID:26614766

  3. Vacuum pyrolysis characteristics and kinetic analysis of liquid crystal from scrap liquid crystal display panels.

    PubMed

    Chen, Ya; Zhang, Lingen; Xu, Zhenming

    2017-04-05

    Recycling of waste liquid crystal display (LCD) panels is an urgent task with the rapid expanding LCD market. However, as important composition of LCD panels, the treatment of liquid crystal is seldom concerned for its low concentration. In present study, a stripping product enriched liquid crystal and indium is gained by mechanical stripping process, in which liquid crystal is enriched from 0.3wt.% to 53wt.% and indium is enriched from 0.02wt.% to 7.95wt.%. For the stripping product, liquid crystal should be removed before indium recovery because (a) liquid crystal will hinder indium recycling; (b) liquid crystal is hazardous waste. Hence, an effective and green approach by vacuum pyrolysis is proposed to treat liquid crystal in the stripping product. The results are summarized as: (i) From the perspective of apparent activation energy, the advantages of vacuum pyrolysis is expounded according to kinetic analysis. (ii) 89.10wt.% of liquid crystal is converted and the content of indium in residue reaches 14.18wt.% under 773K, 15min and system pressure of 20Pa. This study provides reliable information for further industrial application and an essential pretreatment for the next step of indium recycling.

  4. Age-Related Differences in Gait Kinematics, Kinetics, and Muscle Function: A Principal Component Analysis.

    PubMed

    Schloemer, Sarah A; Thompson, Julie A; Silder, Amy; Thelen, Darryl G; Siston, Robert A

    2017-03-01

    Age-related increased hip extensor recruitment during gait is a proposed compensation strategy for reduced ankle power generation and may indicate a distal-to-proximal shift in muscle function with age. Extending beyond joint level analyses, identifying age-related changes at the muscle level could capture more closely the underlying mechanisms responsible for movement. The purpose of this study was to characterize and compare muscle forces and induced accelerations during gait in healthy older adults with those of young adults. Simulations of one gait cycle for ten older (73.9 ± 5.3 years) and six young (21.0 ± 2.1 years) adults walking at their self-selected speed were analyzed. Muscle force and induced acceleration waveforms, along with kinematic, kinetic, and muscle activation waveforms, were compared between age-groups using principal component analysis. Simulations of healthy older adults had greater gluteus maximus force and vertical support contribution, but smaller iliacus force, psoas force, and psoas vertical support contribution. There were no age-group differences in distal muscle force, contribution, or ankle torque magnitudes. Later peak dorsiflexion and peak ankle angular velocity in older adults may have contributed to their greater ankle power absorption during stance. These findings reveal the complex interplay between age-related changes in neuromuscular control, kinematics, and muscle function during gait.

  5. Kinetic Structure of Large-Conductance Ca2+-activated K+ Channels Suggests that the Gating Includes Transitions through Intermediate or Secondary States

    PubMed Central

    Rothberg, Brad S.; Magleby, Karl L.

    1998-01-01

    Mechanisms for the Ca2+-dependent gating of single large-conductance Ca2+-activated K+ channels from cultured rat skeletal muscle were developed using two-dimensional analysis of single-channel currents recorded with the patch clamp technique. To extract and display the essential kinetic information, the kinetic structure, from the single channel currents, adjacent open and closed intervals were binned as pairs and plotted as two-dimensional dwell-time distributions, and the excesses and deficits of the interval pairs over that expected for independent pairing were plotted as dependency plots. The basic features of the kinetic structure were generally the same among single large-conductance Ca2+-activated K+ channels, but channel-specific differences were readily apparent, suggesting heterogeneities in the gating. Simple gating schemes drawn from the Monod- Wyman-Changeux (MWC) model for allosteric proteins could approximate the basic features of the Ca2+ dependence of the kinetic structure. However, consistent differences between the observed and predicted dependency plots suggested that additional brief lifetime closed states not included in MWC-type models were involved in the gating. Adding these additional brief closed states to the MWC-type models, either beyond the activation pathway (secondary closed states) or within the activation pathway (intermediate closed states), improved the description of the Ca2+ dependence of the kinetic structure. Secondary closed states are consistent with the closing of secondary gates or channel block. Intermediate closed states are consistent with mechanisms in which the channel activates by passing through a series of intermediate conformations between the more stable open and closed states. It is the added secondary or intermediate closed states that give rise to the majority of the brief closings (flickers) in the gating. PMID:9607935

  6. Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

    PubMed Central

    Huang, William Y. C.; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K.; Hansen, Scott D.; Christensen, Sune M.; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T.

    2016-01-01

    The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes. PMID:27370798

  7. Degradation kinetics and mechanism of trace nitrobenzene by granular activated carbon enhanced microwave/hydrogen peroxide system.

    PubMed

    Tan, Dina; Zeng, Honghu; Liu, Jie; Yu, Xiaozhang; Liang, Yanpeng; Lu, Lanjing

    2013-07-01

    The kinetics of the degradation of trace nitrobenzene (NB) by a granular activated carbon (GAC) enhanced microwave (MW)/hydrogen peroxide (H202) system was studied. Effects of pH, NB initial concentration and tert-butyl alcohol on the removal efficiency were examined. It was found that the reaction rate fits well to first-order reaction kinetics in the MW/GAC/H202 process. Moreover, GAC greatly enhanced the degradation rate of NB in water. Under a given condition (MW power 300 W, H202 dosage 10 mg/L, pH 6.85 and temperature (60 +/- 5)degrees C), the degradation rate of NB was 0.05214 min-1when 4 g/L GAC was added. In general, alkaline pH was better for NB degradation; however, the optimum pH was 8.0 in the tested pH value range of 4.0-12.0. At H202 dosage of 10 mg/L and GAC dosage of 4 g/L, the removal of NB was decreased with increasing initial concentrations of NB, indicating that a low initial concentration was beneficial for the degradation of NB. These results indicated that the MW/GAC/H202 process was effective for trace NB degradation in water. Gas chromatography-mass spectrometry analysis indicated that a hydroxyl radical addition reaction and dehydrogenation reaction enhanced NB degradation.

  8. Equilibrium and kinetics study on the adsorption of perfluorooctanoic acid from aqueous solution onto powdered activated carbon.

    PubMed

    Qu, Yan; Zhang, Chaojie; Li, Fei; Bo, Xiaowen; Liu, Guangfu; Zhou, Qi

    2009-09-30

    Powdered activated carbon (PAC) was applied to remove perfluorooctanoic acid (PFOA) from the aqueous PFOA solution in this study. Contact time, adsorbent dose and temperature were analyzed as the effect factors in the adsorption reaction. The contact time of maximum PFOA uptake was around 1h while the sorption removal efficiency increased with the PAC concentrations. And the process of adsorption increased from 303 K to 313 K and then decreased from 313 K to 323 K. Among four applied models, the experimental isotherm data were discovered to follow Langmuir isotherm model more closely. Thermodynamically, adsorption was endothermic because enthalpy, entropy and Gibbs constants were 198.5 kJ/mol, 0.709 kJ/mol/K and negative, respectively, which also indicated that the adsorption process was spontaneous and feasible. From kinetic analysis, the adsorption was suggested to be pseudo-second-order model. The adsorption of PFOA on the PAC was mainly controlled by particle diffusion.

  9. Photocatalytic activity enhancement of anatase-graphene nanocomposite for methylene removal: Degradation and kinetics

    NASA Astrophysics Data System (ADS)

    Rezaei, Mostafa; Salem, Shiva

    2016-10-01

    In the present research, the TiO2-graphene nanocomposite was synthesized by an eco-friendly method. The blackberry juice was introduced to graphene oxide (GO) as a reducing agent to produce the graphene nano-sheets. The nanocomposite of anatase-graphene was developed as a photocatalyst for the degradation of methylene blue, owing to the larger specific surface area and synergistic effect of reduced graphene oxide (RGO). The UV spectroscopy measurements showed that the prepared nanocomposite exhibited an excellent photocatalytic activity toward the methylene blue degradation. The rate of electron transfer of redox sheets is much higher than that observed on GO, indicating the applicability of proposed method for the production of anatase-RGO nanocomposite for treatment of water contaminated by cationic dye. The prepared materials were characterized with Fourier transform infrared spectroscopy, X-ray diffraction, Brunauer-Emmett-Teller surface area measurement, scanning electron microscopy and transmission electron microscopy. A facile and rapid route was applied for the uniform deposition of anatase nanoparticles on the sheets. The resulting nanocomposite contained nanoparticles with a mean diameter of 10 nm. A mechanism for the photocatalytic activity of nanocomposite was suggested and the degradation reaction obeyed the second-order kinetics. It was concluded that the degradation kinetics is changed due to the reduction of GO in the presence of blackberry juice.

  10. Photocatalytic activity enhancement of anatase-graphene nanocomposite for methylene removal: Degradation and kinetics.

    PubMed

    Rezaei, Mostafa; Salem, Shiva

    2016-10-05

    In the present research, the TiO2-graphene nanocomposite was synthesized by an eco-friendly method. The blackberry juice was introduced to graphene oxide (GO) as a reducing agent to produce the graphene nano-sheets. The nanocomposite of anatase-graphene was developed as a photocatalyst for the degradation of methylene blue, owing to the larger specific surface area and synergistic effect of reduced graphene oxide (RGO). The UV spectroscopy measurements showed that the prepared nanocomposite exhibited an excellent photocatalytic activity toward the methylene blue degradation. The rate of electron transfer of redox sheets is much higher than that observed on GO, indicating the applicability of proposed method for the production of anatase-RGO nanocomposite for treatment of water contaminated by cationic dye. The prepared materials were characterized with Fourier transform infrared spectroscopy, X-ray diffraction, Brunauer-Emmett-Teller surface area measurement, scanning electron microscopy and transmission electron microscopy. A facile and rapid route was applied for the uniform deposition of anatase nanoparticles on the sheets. The resulting nanocomposite contained nanoparticles with a mean diameter of 10nm. A mechanism for the photocatalytic activity of nanocomposite was suggested and the degradation reaction obeyed the second-order kinetics. It was concluded that the degradation kinetics is changed due to the reduction of GO in the presence of blackberry juice.

  11. Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics

    DOE PAGES

    Callaway, David J. E.; Matsui, Tsutomu; Weiss, Thomas; ...

    2017-03-08

    The phosphorylation of specific residues in a flexible disordered activation loop yields precise control of signal transduction. One paradigm is the phosphorylation of S339/S340 in the intrinsically disordered tail of the multi-domain scaffolding protein NHERF1, which affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt-concentration-dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whip” that is unleashed is near the S339/S340 phosphorylation site and flanks the hydrophobic Ezrin-binding motif. The kinetic association rate constant of the bindingmore » of the S339D/S340D mutant to the FERM domain of Ezrin is sensitive to buffer salt concentration, correlating with the excited nanoscale dynamics. The results suggest that electrostatics modulates the activation of nanoscale dynamics of an intrinsically disordered protein, controlling the binding kinetics of signaling partners. Furthermore NSE can pinpoint the nanoscale dynamics changes in a highly specific manner.« less

  12. Pyrolysis characteristics and kinetics of acid tar waste from crude benzol refining: A thermogravimetry-mass spectrometry analysis.

    PubMed

    Chihobo, Chido H; Chowdhury, Arindrajit; Kuipa, Pardon K; Simbi, David J

    2016-12-01

    Pyrolysis is an attractive thermochemical conversion technology that may be utilised as a safe disposal option for acid tar waste. The kinetics of acid tar pyrolysis were investigated using thermogravimetry coupled with mass spectrometry under a nitrogen atmosphere at different heating rates of 10, 15 and 20 K min(-1) The thermogravimetric analysis shows three major reaction peaks centred around 178 °C, 258 °C, and 336 °C corresponding to the successive degradation of water soluble lower molecular mass sulphonic acids, sulphonated high molecular mass hydrocarbons, and high molecular mass hydrocarbons. The kinetic parameters were evaluated using the iso-conversional Kissinger-Akahira-Sunose method. A variation in the activation energy with conversion revealed that the pyrolysis of the acid tar waste progresses through complex multi-step kinetics. Mass spectrometry results revealed a predominance of gases such as hydrogen, methane and carbon monoxide, implying that the pyrolysis of acid tar waste is potentially an energy source. Thus the pyrolysis of acid tar waste may present a viable option for its environmental treatment. There are however, some limitations imposed by the co-evolution of corrosive gaseous components for which appropriate considerations must be provided in both pyrolysis reactor design and selection of construction materials.

  13. An active learning mammalian skeletal muscle lab demonstrating contractile and kinetic properties of fast- and slow-twitch muscle.

    PubMed

    Head, S I; Arber, M B

    2013-12-01

    The fact that humans possess fast- and slow-twitch muscle in the ratio of ∼50% has profound implications for designing exercise training strategies for power and endurance activities. With the growth of exercise and sport science courses, we have seen the need to develop an undergraduate student laboratory that demonstrates the basic properties of fast- and slow-twitch mammalian skeletal muscle. This laboratory illustrates the major differences in contractile properties and fatigue profiles exhibited by the two muscle types. Students compare and contrast twitch kinetics, fused tetanus characteristics, force-frequency relationships, and fatigue properties of fast- and slow-twitch muscles. Examples of results collected by students during class are used to illustrate the type of data collected and analysis performed. During the laboratory, students are encouraged to connect factual information from their skeletal muscle lectures to their laboratory findings. This enables student learning in an active fashion; in particular, the isolated muscle preparation demonstrates that much of what makes muscle fast or slow is myogenic and not the product of the nervous or circulatory systems. This has far-reaching implications for motor control and exercise behavior and therefore is a crucial element in exercise science, with its focus on power and endurance sport activities. To measure student satisfaction with this active learning technique, a questionnaire was administered after the laboratory; 96% of the comments were positive in their support of active versus passive learning strategies.

  14. Kinetic Analysis of Ex Vivo Human Blood Infection by Leishmania

    PubMed Central

    Moreno, Inmaculada; Domínguez, Mercedes; Cabañes, Darío; Aizpurua, Carmen; Toraño, Alfredo

    2010-01-01

    The leishmanioses, vector-borne diseases caused by the trypanosomatid protozoan Leishmania, are transmitted to susceptible mammals by infected phlebotomine sand flies that inoculate promastigotes into hemorrhagic pools created in host skin. We assumed that promastigotes are delivered to a blood pool, and analyzed early promastigote interactions (0–5 min) with host components, which lead to parasite endocytosis by blood leukocytes, and to host infection. Promastigotes were incubated with NHS or with heparinized blood in near-physiological conditions, and we used cell radioimmunoassay and flow cytometry to measure the on-rate constants (k+1) of promastigote interactions with natural opsonins and erythrocytes. We obtained quantitative data for parasitized cells to determine the time-course of promastigote binding and internalization by blood leukocytes. In these reactions, promastigotes bind natural opsonins, immune adhere to erythrocytes and activate complement cytolysis, which kills ∼95% of promastigotes by 2 min post-infection. C3-promastigote binding is a key step in opsonization; nascent C3-promastigotes are the substrate for two simultaneous reactions, C3-promastigote immune adherence (IA) to erythrocytes and complement-mediated promastigote killing. The k+1 for IA was 75-fold greater than that for promastigote killing, showing that IA facilitates promastigote endocytosis and circumvents lysis. At 5 min post-infection, when reaction velocity is still linear and promastigote concentration is not limiting, 17.4% of granulocytes and 10.7% of monocytes had bound promastigotes, of which ∼50% and ∼25%, respectively, carried surface-bound (live) or internalized (live and dead) leishmanias. Of other leukocyte types, 8.5% of B cells bound but did not internalize promastigotes, and T cells, NK cells and CD209+ dendritic cells did not bind parasites. These data show that, once in contact with blood, promastigote invasion of human leukocytes is an extremely rapid

  15. Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms.

    PubMed

    Villahermosa, Desirée; Corzo, Alfonso; Garcia-Robledo, Emilio; González, Juan M; Papaspyrou, Sokratis

    2016-01-01

    Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm-3 h-1) and oxygen consumption rates (0.01 μmol cm-3 h-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic

  16. Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms

    PubMed Central

    Villahermosa, Desirée; Corzo, Alfonso; Garcia-Robledo, Emilio; González, Juan M.; Papaspyrou, Sokratis

    2016-01-01

    Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm-3 h-1) and oxygen consumption rates (0.01 μmol cm-3 h-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm-3 h-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm-3 h-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic

  17. Effect of the porous structure of activated carbon on the adsorption kinetics of gold(I) cyanide complex

    NASA Astrophysics Data System (ADS)

    Ibragimova, P. I.; Grebennikov, S. F.; Gur'yanov, V. V.; Fedyukevich, V. A.; Vorob'ev-Desyatovskii, N. V.

    2014-06-01

    The effect the porous structure of activated carbons obtained from furfural and coconut shells has on the kinetics of [Au(CN)2]- ion adsorption is studied. Effective diffusion coefficients for [Au(CN)2]- anions in transport and adsorbing pores and mass transfer coefficients in a transport system of the pores and in microporous zones are calculated using the statistical moments of the kinetic curve.

  18. Two pacemaker channels from human heart with profoundly different activation kinetics.

    PubMed Central

    Ludwig, A; Zong, X; Stieber, J; Hullin, R; Hofmann, F; Biel, M

    1999-01-01

    Cardiac pacemaking is produced by the slow diastolic depolarization phase of the action potential. The hyperpolarization-activated cation current (If) forms an important part of the pacemaker depolarization and consists of two kinetic components (fast and slow). Recently, three full-length cDNAs encoding hyperpolarization-activated and cyclic nucleotide-gated cation channels (HCN1-3) have been cloned from mouse brain. To elucidate the molecular identity of cardiac pacemaker channels, we screened a human heart cDNA library using a highly conserved neuronal HCN channel segment and identified two cDNAs encoding HCN channels. The hHCN2 cDNA codes for a protein of 889 amino acids. The HCN2 gene is localized on human chromosome 19p13.3 and contains eight exons spanning approximately 27 kb. The second cDNA, designated hHCN4, codes for a protein of 1203 amino acids. Northern blot and PCR analyses showed that both hHCN2 and hHCN4 are expressed in heart ventricle and atrium. When expressed in HEK 293 cells, either cDNA gives rise to hyperpolarization-activated cation currents with the hallmark features of native If. hHCN2 and hHCN4 currents differ profoundly from each other in their activation kinetics, being fast and slow, respectively. We thus conclude that hHCN2 and hHCN4 may underlie the fast and slow component of cardiac If, respectively. PMID:10228147

  19. Pungency of TRPV1 agonists is directly correlated with kinetics of receptor activation and lipophilicity.

    PubMed

    Ursu, Daniel; Knopp, Kelly; Beattie, Ruth E; Liu, Bin; Sher, Emanuele

    2010-09-01

    TRPV1 (transient receptor potential vanilloid 1) is a ligand-gated ion channel expressed predominantly in nociceptive primary afferents that plays a key role in pain processing. In vivo activation of TRPV1 receptors by natural agonists like capsaicin is associated with a sharp and burning pain, frequently described as pungency. To elucidate the mechanisms underlying pungency we investigated a series of TRPV1 agonists that included both pungent and non-pungent compounds covering a large range of potencies. Pungency of capsaicin, piperine, arvanil, olvanil, RTX (resiniferatoxin) and SDZ-249665 was evaluated in vivo, by determining the increase in the number of eye wipes caused by direct instillation of agonist solutions into the eye. Agonist-induced calcium fluxes were recorded using the FLIPR technique in a recombinant, TRPV1-expressing cell line. Current-clamp recordings were performed in rat DRG (dorsal root ganglia) neurons in order to assess the consequences of TRPV1 activation on neuronal excitability. Using the eye wipe assay the following rank of pungency was obtained: capsaicin>piperine>RTX>arvanil>olvanil>SDZ-249665. We found a strong correlation between kinetics of calcium flux, pungency and lipophilicity of TRPV1 agonists. Current-clamp recordings confirmed that the rate of receptor activation translates in the ability of agonists to generate action potentials in sensory neurons. We have demonstrated that the lipophilicity of the compounds is directly related to the kinetics of TRPV1 activation and that the latter influences their ability to trigger action potentials in sensory neurons and, ultimately, pungency.

  20. Comparison of kinetic variables and muscle activity during a squat vs. a box squat.

    PubMed

    McBride, Jeffrey M; Skinner, Jared W; Schafer, Patrick C; Haines, Tracie L; Kirby, Tyler J

    2010-12-01

    The purpose of this investigation was to determine if there was a difference in kinetic variables and muscle activity when comparing a squat to a box squat. A box squat removes the stretch-shortening cycle component from the squat, and thus, the possible influence of the box squat on concentric phase performance is of interest. Eight resistance trained men (Height: 179.61 ± 13.43 cm; Body Mass: 107.65 ± 29.79 kg; Age: 24.77 ± 3.22 years; 1 repetition maximum [1RM]: 200.11 ± 58.91 kg) performed 1 repetition of squats and box squats using 60, 70, and 80% of their 1RM in a randomized fashion. Subjects completed the movement while standing on a force plate and with 2 linear position transducers attached to the bar. Force and velocity were used to calculate power. Peak force and peak power were determined from the force-time and power-time curves during the concentric phase of the lift. Muscle activity (electromyography) was recorded from the vastus lateralis, vastus medialis, biceps femoris, and longissimus. Results indicate that peak force and peak power are similar between the squat and box squat. However, during the 70% of 1RM trials, the squat resulted in a significantly lower peak force in comparison to the box squat (squat = 3,269 ± 573 N, box squat = 3,364 ± 575 N). In addition, during the 80% of 1RM trials, the squat resulted in significantly lower peak power in comparison to the box squat (squat = 2,050 ± 486 W, box squat = 2,197 ± 544 W). Muscle activity was generally higher during the squat in comparison to the box squat. In conclusion, minimal differences were observed in kinetic variables and muscle activity between the squat and box squat. Removing the stretch-shortening cycle during the squat (using a box) appears to have limited negative consequences on performance.

  1. The evolution of clinical gait analysis part III--kinetics and energy assessment.

    PubMed

    Sutherland, D H

    2005-06-01

    Historically, clinical applications of measurements of force and energy followed electromyography and kinematics in temporal sequence. This sequence is mirrored by the order of topics included in this trilogy on the Evolution of Clinical Gait Analysis, with part I [Sutherland DH. The evolution of clinical gait analysis part I: kinesiological EMG. Gait Posture 2001;14:61-70.] devoted to Kinesiological EMG and part II [Sutherland DH. The evolution of clinical gait analysis part II - kinematics. Gait Posture 2002;16(2):159-179.] to Kinematics. This final review in the series will focus on kinetics as it relates to gait applications. Kinematic measurements give the movements of the body segments, which can be compared with normal controls to identify pathological gait patterns, but they do not deal with the forces controlling the movements. As a major goal of scientifically minded clinicians is to understand the biomechanical forces producing movements, the objective measurement of ground reaction forces is essential. The force plate (platform) is now an indispensable tool in a state-of-the-art motion analysis laboratory. Nonetheless, it is not a stand-alone instrument as both kinematic and EMG measurements are needed for maximum clinical implementation and interpretation of force plate measurements. The subject of energy assessment is also given mention, as there is a compelling interest in whether walking has been made easier with intervention. The goals of this manuscript are to provide a historical background, recognize some of the important contributors, and describe the current multiple uses of the force plate in gait analysis. The widespread use of force plates for postural analyses is an important and more recent application of this technology, but this review will be restricted to measurements of gait rather than balance activities. Finally, this manuscript presents my personal perspective and discusses the developments and contributors that have shaped my

  2. Blueberry polyphenol oxidase: Characterization and the kinetics of thermal and high pressure activation and inactivation.

    PubMed

    Terefe, Netsanet Shiferaw; Delon, Antoine; Buckow, Roman; Versteeg, Cornelis

    2015-12-01

    Partially purified blueberry polyphenol oxidase (PPO) in Mcllvaine buffer (pH=3.6, typical pH of blueberry juice) was subjected to processing at isothermal-isobaric conditions at temperatures from 30 to 80 °C and pressure from 0.1 to 700 MPa. High pressure processing at 30-50 °C at all pressures studied caused irreversible PPO activity increase with a maximum of 6.1 fold increase at 500 MPa and 30 °C. Treatments at mild pressure-mild temperature conditions (0.1-400 MPa, 60 °C) also caused up to 3 fold PPO activity increase. Initial activity increase followed by a decrease occurred at relatively high pressure-mild temperature (400-600 MPa, 60 °C) and mild pressure-high temperature (0.1-400 MPa, 70-80 °C) combinations. At temperatures higher than 76 °C, monotonic decrease in PPO activity occurred at 0.1 MPa and pressures higher than 500 MPa. The activation/inactivation kinetics of the enzyme was successfully modelled assuming consecutive reactions in series with activation followed by inactivation.

  3. Catalytic, kinetic and thermodynamic properties of Bacillus pumilus FH9 keratinase conjugated with activated pectin.

    PubMed

    Abdel-Naby, Mohamed A; Ibrahim, M H A; El-Refai, H A

    2016-04-01

    Bacillus pumilus FH9 keratinase was covalently coupled to several oxidized polysaccharides. The conjugates were evaluated for the retained activity, kinetic and thermodynamic stability. Among all preparations, the conjugated enzyme with oxidized pectin had the highest recovered activity (71.75%) and the highest thermal stability at 60°C (t1/2=333 min). Compared to the native enzyme, the conjugated preparation exhibited higher optimum temperature, lower activation energy (Ea), lower deactivation constant rate (kd), higher t1/2, and higher decimal reduction time values (D) within the temperature range of 50-80°C. The thermodynamic parameters (ΔH*, ΔG*, ΔS*) of irreversible thermal denaturation for the native and conjugated keratinase were also evaluated. The values of enthalpy of activation (ΔH*), free energy of activation (ΔG*), and free energy of transition state binding (ΔG*E-T) for keratin hydrolysis were lower for the conjugated enzyme. Moreover, there was highly significant impact on improving the values of Vmax/Km, kcat, kcat/Km, and ΔG*E-S for the modified enzyme. Both native and conjugated enzymes were slightly activated by CaCl2 and MgCl2. However, the inhibitory effects of EDTA, HgCl2 and ZnSO4 were more pronounced with the native enzyme.

  4. Structural and kinetic analysis of the unnatural fusion protein 4-coumaroyl-CoA ligase::stilbene synthase

    SciTech Connect

    Wang, Yechun; Yi, Hankuil; Wang, Melissa; Yu, Oliver; Jez, Joseph M.

    2012-10-24

    To increase the biochemical efficiency of biosynthetic systems, metabolic engineers have explored different approaches for organizing enzymes, including the generation of unnatural fusion proteins. Previous work aimed at improving the biosynthesis of resveratrol, a stilbene associated a range of health-promoting activities, in yeast used an unnatural engineered fusion protein of Arabidopsis thaliana (thale cress) 4-coumaroyl-CoA ligase (At4CL1) and Vitis vinifera (grape) stilbene synthase (VvSTS) to increase resveratrol levels 15-fold relative to yeast expressing the individual enzymes. Here we present the crystallographic and biochemical analysis of the 4CL::STS fusion protein. Determination of the X-ray crystal structure of 4CL::STS provides the first molecular view of an artificial didomain adenylation/ketosynthase fusion protein. Comparison of the steady-state kinetic properties of At4CL1, VvSTS, and 4CL::STS demonstrates that the fusion protein improves catalytic efficiency of either reaction less than 3-fold. Structural and kinetic analysis suggests that colocalization of the two enzyme active sites within 70 {angstrom} of each other provides the basis for enhanced in vivo synthesis of resveratrol.

  5. Peroxydisulfate activation by [RuII(tpy)(pic)(H2O)]+. Kinetic, mechanistic and anti-microbial activity studies.

    PubMed

    Chatterjee, Debabrata; Banerjee, Priyabrata; Bose, Jagadeesh C K; Mukhopadhyay, Sudit

    2012-03-07

    The oxidation of [Ru(II)(tpy)(pic)H(2)O](+) (tpy = 2,2',6',2''-terpyridine; pic(-) = picolinate) by peroxidisulfate (S(2)O(8)(2-)) as precursor oxidant has been investigated kinetically by UV-VIS, IR and EPR spectroscopy. The overall oxidation of Ru(II)- to Ru(IV)-species takes place in a consecutive manner involving oxidation of [Ru(II)(tpy)(pic)H(2)O](+) to [Ru(III)(tpy)(pic)(OH)](+), and its further oxidation of to the ultimate product [Ru(IV)(tpy)(pic)(O)](+) complex. The time course of the reaction was followed as a function of [S(2)O(8)(2-)], ionic strength (I) and temperature. Kinetic data and activation parameters are interpreted in terms of an outer-sphere electron transfer mechanism. Anti-microbial activity of Ru(II)(tpy)(pic)H(2)O](+) complex by inhibiting the growth of Escherichia coli DH5α in presence of peroxydisulfate has been explored, and the results of the biological studies have been discussed in terms of the [Ru(IV)(tpy)(pic)(O)](+) mediated cleavage of chromosomal DNA of the bacteria.

  6. In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter.

    PubMed

    Mäkelä, Jarno; Kandhavelu, Meenakshisundaram; Oliveira, Samuel M D; Chandraseelan, Jerome G; Lloyd-Price, Jason; Peltonen, Juha; Yli-Harja, Olli; Ribeiro, Andre S

    2013-07-01

    Using a single-RNA detection technique in live Escherichia coli cells, we measure, for each cell, the waiting time for the production of the first RNA under the control of PBAD promoter after induction by arabinose, and subsequent intervals between transcription events. We find that the kinetics of the arabinose intake system affect mean and diversity in RNA numbers, long after induction. We observed the same effect on Plac/ara-1 promoter, which is inducible by arabinose or by IPTG. Importantly, the distribution of waiting times of Plac/ara-1 is indistinguishable from that of PBAD, if and only if induced by arabinose alone. Finally, RNA production under the control of PBAD is found to be a sub-Poissonian process. We conclude that inducer-dependent waiting times affect mean and cell-to-cell diversity in RNA numbers long after induction, suggesting that intake mechanisms have non-negligible effects on the phenotypic diversity of cell populations in natural, fluctuating environments.

  7. Adsorption kinetic and equilibrium study for removal of mercuric chloride by CuCl2-impregnated activated carbon sorbent.

    PubMed

    Li, Xin; Liu, Zhouyang; Lee, Joo-Youp

    2013-05-15

    The intrinsic adsorption kinetics of mercuric chloride (HgCl2) was studied for raw, 4% and 10% CuCl2-impregnated activated carbon (CuCl2-AC) sorbents in a fixed-bed system. An HgCl2 adsorption kinetic model was developed for the AC sorbents by taking into account the adsorption kinetics, equilibrium, and internal and external mass transfer. The adsorption kinetic constants determined from the comparisons between the simulation and experimental results were 0.2, 0.3, and 0.5m(3)/(gs) for DARCO-HG, 4%(wt), and 10%(wt) CuCl2-AC sorbents, respectively, at 140 °C. CuCl2 loading was found to slightly increase the adsorption kinetic constant or at least not to decrease it. The HgCl2 equilibrium adsorption data based on the Langmuir isotherm show that high CuCl2 loading can result in high binding energy of the HgCl2 adsorption onto the carbon surface. The adsorption equilibrium constant was found to increase by ~10 times when CuCl2 loading varied from 0 to 10%(wt), which led to a decrease in the desorption kinetic constant (k2) by ~10 times and subsequently the desorption rate by ~50 times. Intraparticle pore diffusion considered in the model showed good accuracy, allowing for the determination of intrinsic HgCl2 adsorption kinetics.

  8. Sendai virus-erythrocyte membrane interaction: quantitative and kinetic analysis of viral binding, dissociation, and fusion.

    PubMed

    Hoekstra, D; Klappe, K

    1986-04-01

    A kinetic and quantitative analysis of the binding and fusion of Sendai virus with erythrocyte membranes was performed by using a membrane fusion assay based on the relief of fluorescence self-quenching. At 37 degrees C, the process of virus association displayed a half time of 2.5 min; at 4 degrees C, the half time was 3.0 min. The fraction of the viral dose which became cell associated was independent of the incubation temperature and increased with increasing target membrane concentration. On the average, one erythrocyte ghost can accommodate ca. 1,200 Sendai virus particles. The stability of viral attachment was sensitive to a shift in temperature: a fraction of the virions (ca. 30%), attached at 4 degrees C, rapidly (half time, ca. 2.5 min) eluted from the cell surface at 37 degrees C, irrespective of the presence of free virus in the medium. The elution can be attributed to a spontaneous, temperature-induced release, rather than to viral neuraminidase activity. Competition experiments with nonlabeled virus revealed that viruses destined to fuse do not exchange with free particles in the medium but rather bind in a rapid and irreversible manner. The fusion rate of Sendai virus was affected by the density of the virus particles on the cell surface and became restrained when more than 170 virus particles were attached per ghost. In principle, all virus particles added displayed fusion activity. However, at high virus-to-ghost ratios, only a fraction actually fused, indicating that a limited number of fusion sites exist on the erythrocyte membrane. We estimate that ca. 180 virus particles maximally can fuse with one erythrocyte ghost.

  9. Chemorheological analysis and model-free kinetics of acid catalysed furfuryl alcohol polymerization.

    PubMed

    Guigo, Nathanael; Mija, Alice; Vincent, Luc; Sbirrazzuoli, Nicolas

    2007-10-21

    The complete curing of furfuryl alcohol (FA), was studied by chemorheological analysis and model-free kinetics under isothermal and non-isothermal modes. Polymerization of FA under acidic catalysis involves complex reactions, with several steps (such as condensations and Diels-Alder cycloadditions). To account for the polymerization complexity, kinetic analysis of DSC data was performed with a model-free isoconversional method. The obtained E(alpha)-dependencies were closely-correlated with the variation of complex viscosity during curing. Linear condensations are predominant during the early curing stage and are followed by two distinct stages of branching cycloadditions. Gelation and vitrification, identified by rheometric measurements, were associated with a decrease of the overall reaction rate that becomes controlled by diffusion of small oligomers. Before vitrification, the rate of crosslinking is limited by the mobility of longer polymer chains and diffusion encounters a large energy barrier due to the cooperative nature of the motions, leading to higher E(alpha) values.

  10. Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling.

    PubMed

    Bischofberger, Mirko; Iacovache, Ioan; Boss, Daniel; Naef, Felix; van der Goot, F Gisou; Molina, Nacho

    2016-04-12

    Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

  11. Thermochemistry and Kinetic Analysis of the Unimolecular Oxiranyl Radical Dissociation Reaction: A Theoretical Study.

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-07-04

    Oxirane structures are important in organic synthesis, and they are important initial products in the oxidation reactions of alkyl radicals. The thermochemical properties (enthalpy of formation, entropy, and heat capacity) for the reaction steps of the unimolecular oxiranyl radical dissociation reaction are determined and compared with the available literature. The overall ring opening and subsequent steps involve four types of reactions: β-scission ring opening, intramolecular hydrogen transfer, β-scission hydrogen elimination, and β-scission methyl radical elimination. The enthalpies of formation of the transition states are determined and evaluated using six popular Density Functional Theory (DFT) calculation methods (B3LYP, B2PLYP, M06, M06-2X, ωB97X, ωB97XD), each combined with three different basis sets. The DFT enthalpy values are compared with five composite calculation methods (G3, G4, CBS-QB3, CBS-APNO, W1U), and by CCSD(T)/aug-cc-pVTZ. Kinetic parameters are determined versus pressure and temperature for the unimolecular dissociation pathways of an oxiranyl radical, which include the chemical activation reactions of the ring-opened oxiranyl radical relative to the ring-opening barrier. Multifrequency quantum Rice Ramsperger Kassel (QRRK) analysis is used to determine k(E) with master equation analysis for falloff. The major overall reaction pathway at lower combustion temperatures is oxiranyl radical dissociation to a methyl radical and carbon monoxide. Oxiranyl radical dissociation to a ketene and hydrogen atom is the key reaction path above 700 K.

  12. The derivative assay--an analysis of two fast components of DNA rejoining kinetics

    SciTech Connect

    Sandstroem, B.E. )

    1989-11-01

    The DNA rejoining kinetics of human U-118 MG cells were studied after gamma-irradiation with 4 Gy. The analysis of the sealing rate of the induced DNA strand breaks was made with a modification of the DNA unwinding technique. The modification meant that rather than just monitoring the number of existing breaks at each time of analysis, the velocity, at which the rejoining process proceeded, was determined. Two apparent first-order components of single-strand break repair could be identified during the 25 min of analysis. The half-times for the two components were 1.9 and 16 min, respectively.

  13. On-Line Analysis and Kinetic Behavior of Arsenic Release during Coal Combustion and Pyrolysis.

    PubMed

    Shen, Fenghua; Liu, Jing; Zhang, Zhen; Dai, Jinxin

    2015-11-17

    The kinetic behavior of arsenic (As) release during coal combustion and pyrolysis in a fluidized bed was investigated by applying an on-line analysis system of trace elements in flue gas. This system, based on inductively coupled plasma optical emission spectroscopy (ICP-OES), was developed to measure trace elements concentrations in flue gas quantitatively and continuously. Obvious variations of arsenic concentration in flue gas were observed during coal combustion and pyrolysis, indicating strong influences of atmosphere and temperature on arsenic release behavior. Kinetic laws governing the arsenic release during coal combustion and pyrolysis were determined based on the results of instantaneous arsenic concentration in flue gas. A second-order kinetic law was determined for arsenic release during coal combustion, and the arsenic release during coal pyrolysis followed a fourth-order kinetic law. The results showed that the arsenic release rate during coal pyrolysis was faster than that during coal combustion. Thermodynamic calculations were carried out to identify the forms of arsenic in vapor and solid phases during coal combustion and pyrolysis, respectively. Ca3(AsO4)2 and Ca(AsO2)2 are the possible species resulting from As-Ca interaction during coal combustion. Ca(AsO2)2 is the most probable species during coal pyrolysis.

  14. Kinetic study of ZnFe{sub 2}O{sub 4} formation from mechanochemically activated Zn-Fe{sub 2}O{sub 3} mixtures

    SciTech Connect

    Botta, P.M.; Aglietti, E.F.; Porto Lopez, J.M.

    2006-04-13

    The kinetics of ZnFe{sub 2}O{sub 4} formation starting from mechanochemically activated Zn-Fe{sub 2}O{sub 3} powders are studied. Mixtures of metallic Zn and hematite were activated under air atmosphere in a high energy mill and thermally treated at temperatures between 500 and 650 deg. C during several holding times. During the activation, morphological and compositional changes were observed, but ZnFe{sub 2}O{sub 4} formation was not detected. The ZnFe{sub 2}O{sub 4} content in heated samples was determined using quantitative X-ray diffraction analysis. The resulting conversion-time curves were fitted using different kinetic models of solid-state reaction, calculating the kinetic parameters of the studied reaction. The comparison with the conventional synthesis method revealed that the mechanochemical treatment provoked a change of the rate-controlling step and a significant decrease of the activation energy, which was more evident for the more activated mixtures.

  15. Simplified half-life methods for the analysis of kinetic data

    NASA Technical Reports Server (NTRS)

    Eberhart, J. G.; Levin, E.

    1988-01-01

    The analysis of reaction rate data has as its goal the determination of the order rate constant which characterize the data. Chemical reactions with one reactant and present simplified methods for accomplishing this goal are considered. The approaches presented involve the use of half lives or other fractional lives. These methods are particularly useful for the more elementary discussions of kinetics found in general and physical chemistry courses.

  16. Isotherm and kinetics study for acrylic acid removal using powdered activated carbon.

    PubMed

    Kumar, Arvind; Prasad, B; Mishra, I M

    2010-04-15

    The potential of powdered activated carbon (PAC) for the adsorption of acrylic acid (AA) from aqueous solution was studied at the initial concentration (C(0)) in the range of 50-500 mg/l over the temperature range of 303-348 K. The equilibrium adsorption studies were carried out to evaluate the effect of adsorbent dosage and contact time, change in pH by adding adsorbents and the initial concentration. Langmuir, Freundlich and Redlich-Peterson (R-P) equilibrium isotherm models were tested to represent the data. Error functions were used to test their validity to fit of the adsorption data with the isotherm and kinetic models. The Freundlich isotherm equation is found to best represent the equilibrium separation data in the temperature range of 303-348 K. The maximum adsorption capacity of AA onto PAC was obtained as q(m)=36.23 mg/g with an optimum PAC dosage w=20 g/l at 303 K for C(0)=100 mg/l. The pseudo-second-order kinetics is found to represent the experimental AA-PAC data. The negative value of DeltaG(ad)(o) (-16.60 to -18.18 kJ/mol K) indicate the feasibility and spontaneity of the adsorption process.

  17. Desorption kinetics of benzene in a sandy soil in the presence of powdered activated carbon.

    PubMed

    Choi, J-W; Kim, S-B; Kim, D-J

    2007-02-01

    Desorption kinetics of benzene was investigated with a modified biphasic desorption model in a sandy soil with five different powdered activated carbon (PAC) contents (0, 1, 2, 5, 10% w/w) as sorbents. Sorption experiments followed by series dilution desorption were conducted for each sorbent. Desorption of benzene was successively performed at two stages using deionized water and hexane. Modeling was performed on both desorption isotherm and desorption rate for water-induced desorption to elucidate the presence of sorption-desorption hysteresis and biphasic desorption and if present to quantify the desorption-resistant fraction (q (irr)) and labile fraction (F) of desorption site responsible for rapid process. Desorption isotherms revealed that sorption-desorption exhibited a severe hysteresis with a significant fraction of benzene being irreversibly adsorbed onto both pure sand and PAC, and that desorption-resistant fraction (q (irr)) increased with PAC content. Desorption kinetic modeling showed that desorption of benzene was biphasic with much higher (4-40 times) rate constant for rapid process (k (1)) than that for slow process (k (2)), and that the difference in the rate constant increased with PAC content. The labile fraction (F) of desorption site showed a decreasing tendency with PAC. The experimental results would provide valuable information on remediation methods for soils and groundwater contaminated with BTEX.

  18. Antibacterial Activity and Kinetics of Litsea cubeba Oil on Escherichia coli

    PubMed Central

    Li, Wen-Ru; Shi, Qing-Shan; Liang, Qing; Xie, Xiao-Bao; Huang, Xiao-Mo; Chen, Yi-Ben

    2014-01-01

    Litsea cubeba oil is extracted from the fresh fruits of Litsea cubeba by distillation. In this study, its chemical constituents, antibacterial activity, kinetics and effects against Escherichia coli were studied. Its minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were both 0.125% (v/v) by toxic food method. Moreover, the antibacterial kinetic curves indicated 0.0625% (v/v) of litsea cubeba oil was able to prolong the growth lag phase of E. coli cells to approximate 12 hours while 0.125% (v/v) of litsea cubeba oil was able to kill the cells completely. Furthermore, transmission electron microscope (TEM) observation showed most E. coli cells treated with 0.125% (v/v) of litsea cubeba oil were killed or destroyed severely within 2 hours. The litsea cubeba oil might penetrate and destroy the outer and inner membrane of E. coli cells. Thus many holes and gaps were observed on the damaged cells, which led to their death eventually. The antibacterial effects of litsea cubeba oil mainly attributed to the presence of aldehydes, which accounted for approximately 70% in its whole components analyzed by GC/MS. Based on the antimicrobial properties, litsea cubeba oil would have a broad application in the antimicrobial industry. PMID:25372706

  19. Degradation of oxcarbazepine by UV-activated persulfate oxidation: kinetics, mechanisms, and pathways.

    PubMed

    Bu, Lingjun; Zhou, Shiqing; Shi, Zhou; Deng, Lin; Li, Guangchao; Yi, Qihang; Gao, Naiyun

    2016-02-01

    The degradation kinetics and mechanism of the antiepileptic drug oxcarbazepine (OXC) by UV-activated persulfate oxidation were investigated in this study. Results showed that UV/persulfate (UV/PS) process appeared to be more effective in degrading OXC than UV or PS alone. The OXC degradation exhibited a pseudo-first order kinetics pattern and the degradation rate constants (k obs) were affected by initial OXC concentration, PS dosage, initial pH, and humic acid concentration to different degrees. It was found that low initial OXC concentration, high persulfate dosage, and initial pH enhanced the OXC degradation. Additionally, the presence of humic acid in the solution could greatly inhibit the degradation of OXC. Moreover, hydroxyl radical (OH•) and sulfate radical (SO4 (-)••) were identified to be responsible for OXC degradation and SO4 (-)• made the predominant contribution in this study. Finally, major intermediate products were identified and a preliminary degradation pathway was proposed. Results demonstrated that UV/PS system is a potential technology to control the water pollution caused by emerging contaminants such as OXC.

  20. Kinetic analysis using low-molecular mass xyloglucan oligosaccharides defines the catalytic mechanism of a Populus xyloglucan endotransglycosylase

    PubMed Central

    Saura-Valls, Marc; Fauré, Régis; Ragàs, Sergi; Piens, Kathleen; Brumer, Harry; Teeri, Tuula T.; Cottaz, Sylvain; Driguez, Hugues; Planas, Antoni

    2005-01-01

    Plant XETs [XG (xyloglucan) endotransglycosylases] catalyse the transglycosylation from a XG donor to a XG or low-molecular-mass XG fragment as the acceptor, and are thought to be important enzymes in the formation and remodelling of the cellulose-XG three-dimensional network in the primary plant cell wall. Current methods to assay XET activity use the XG polysaccharide as the donor substrate, and present limitations for kinetic and mechanistic studies of XET action due to the polymeric and polydisperse nature of the substrate. A novel activity assay based on HPCE (high performance capillary electrophoresis), in conjunction with a defined low-molecular-mass XGO {XG oligosaccharide; (XXXGXXXG, where G=Glcβ1,4- and X=[Xylα1,6]Glcβ1,4-)} as the glycosyl donor and a heptasaccharide derivatized with ANTS [8-aminonaphthalene-1,3,6-trisulphonic acid; (XXXG-ANTS)] as the acceptor substrate was developed and validated. The recombinant enzyme PttXET16A from Populus tremula x tremuloides (hybrid aspen) was characterized using the donor/acceptor pair indicated above, for which preparative scale syntheses have been optimized. The low-molecular-mass donor underwent a single transglycosylation reaction to the acceptor substrate under initial-rate conditions, with a pH optimum at 5.0 and maximal activity between 30 and 40 °C. Kinetic data are best explained by a ping-pong bi-bi mechanism with substrate inhibition by both donor and acceptor. This is the first assay for XETs using a donor substrate other than polymeric XG, enabling quantitative kinetic analysis of different XGO donors for specificity, and subsite mapping studies of XET enzymes. PMID:16356166

  1. Kinetics of Hydrogen Atom Abstraction from Substrate by an Active Site Thiyl Radical in Ribonucleotide Reductase

    PubMed Central

    2015-01-01

    Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms. Active E. coli class Ia RNR is an α2β2 complex that undergoes reversible, long-range proton-coupled electron transfer (PCET) over a pathway of redox active amino acids (β-Y122 → [β-W48] → β-Y356 → α-Y731 → α-Y730 → α-C439) that spans ∼35 Å. To unmask PCET kinetics from rate-limiting conformational changes, we prepared a photochemical RNR containing a [ReI] photooxidant site-specifically incorporated at position 355 ([Re]-β2), adjacent to PCET pathway residue Y356 in β. [Re]-β2 was further modified by replacing Y356 with 2,3,5-trifluorotyrosine to enable photochemical generation and spectroscopic observation of chemically competent tyrosyl radical(s). Using transient absorption spectroscopy, we compare the kinetics of Y· decay in the presence of substrate and wt-α2, Y731F-α2 ,or C439S-α2, as well as with 3′-[2H]-substrate and wt-α2. We find that only in the presence of wt-α2 and the unlabeled substrate do we observe an enhanced rate of radical decay indicative of forward radical propagation. This observation reveals that cleavage of the 3′-C–H bond of substrate by the transiently formed C439· thiyl radical is rate-limiting in forward PCET through α and has allowed calculation of a lower bound for the rate constant associated with this step of (1.4 ± 0.4) × 104 s–1. Prompting radical propagation with light has enabled observation of PCET events heretofore inaccessible, revealing active site chemistry at the heart of RNR catalysis. PMID:25353063

  2. A kinetic assessment of the C. elegans amyloid disaggregation activity enables uncoupling of disassembly and proteolysis.

    PubMed

    Bieschke, Jan; Cohen, Ehud; Murray, Amber; Dillin, Andrew; Kelly, Jeffery W

    2009-11-01

    Protein aggregation is a common feature of late onset neurodegenerative disorders, including Alzheimer's disease. In Alzheimer's disease, misassembly of the Abeta peptide is genetically linked to proteotoxicity associated with disease etiology. A reduction in Abeta proteotoxicity is accomplished, in part, by the previously reported Abeta disaggregation and proteolysis activities-under partial control of heat shock factor 1, a transcription factor regulating proteostasis in the cytosol and negatively regulated by insulin growth factor signaling. Herein, we report an improved in vitro assay to quantify recombinant fibrillar Abeta disaggregation kinetics accomplished by the exogenous application of C.elegans extracts. With this assay we demonstrate that the Abeta disaggregation and proteolysis activities of C.elegans are separable. The disaggregation activity found in C.elegans preparations is more heat resistant than the proteolytic activity. Abeta disaggregation in the absence of proteolysis was found to be a reversible process. Future discovery of the molecular basis of the disaggregation and proteolysis activities offers the promise of delaying the age-onset proteotoxicity that leads to neurodegeneration in a spectrum of maladies.

  3. Catalytic oxidation ofS(IV) on activated carbon in aqueous suspension: kinetics and mechanism

    SciTech Connect

    Brodzinsky, R.

    1981-02-01

    Activated carbon and combustion produced soot particles have been studied for their catalytic effect on the oxidation of aqueous sulfur(IV) species. Detailed kinetic studies of the reaction were performed on three different activated carbons and on a soot collected in a highway tunnel. Combustion produced soots were tested for their catalytic behavior and found to be similar to the activated carbons. The reaction rate was found to be linearly dependent on the concentration of carbon particles in the solution. The rate was found to follow a Langmuir adsorption isotherm for its dependence on oxygen and the product of two adsorption isotherms for S(IV). The reaction is independent of the pH of the solution when the pH is below 7.6. The reaction does not occur when the pH is above 7.6. The three aqueous S(IV) species are catalyzed in their oxidation by the carbon particles in a similar manner. Activation energies for the reactions on the different carbons are all about 8.5 kcal/mole. A possible four-step reaction mechanism is proposed. It consists of the adsorption of a dissolved oxygen molecule onto the carbon surface, followed by the adsorption of two S(IV) molecules or ions. These are oxidized on the surface to sulfate, which desorbs from the surface, regenerating the catalytically active site.

  4. Heterogeneous and homogeneous catalytic ozonation of benzothiazole promoted by activated carbon: kinetic approach.

    PubMed

    Valdés, Héctor; Zaror, Claudio A

    2006-11-01

    Ozone oxidation combined with activated carbon adsorption (O(3)/AC) has recently started to be developed as a single process for water and wastewater treatment. While a number of aspects of aqueous ozone decomposition are well understood, the importance and relationship between aqueous ozone decomposition and organic contaminant degradation in the presence of activated carbon is still not clear. This study focuses on determining the contribution of homogeneous and heterogeneous reactions to organic contaminants removal in O(3)/AC system. Benzothiazole (BT) was selected as a target organic pollutant due to its environmental concern. A reactor system based on a differential circular flow reactor composed by a 19 cm(3) activated carbon fixed bed column and 1 dm(3) storage tank was used. Ozone was produced from pure and dry oxygen using an Ozocav ozone generator rated at 5 g O(3)h(-1). Experimental results show that BT removal rate was proportional to activated carbon dosage. Activated carbon surface contribution to BT oxidation reactions with ozone, increased with pH in absence of radical scavengers. The radical reaction contribution within the pH range 2-11 accounted for 67-83% for BT removal in O(3)/AC simultaneous treatment. Results suggest that at pH higher than the pH of the point of zero charge of the activated carbon dissociated acid groups such as carboxylic acid anhydrides and carboxylic acids present on activated carbon surface could be responsible for the observed increase in the ozone decomposition reaction rate. A simplified mechanism and a kinetic scheme representing the contribution of homogeneous and heterogeneous reactions on BT ozonation in the presence of activated carbon is proposed.

  5. Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis

    PubMed Central

    Goyal, Puja; Yang, Shuo; Cui, Qiang

    2014-01-01

    Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. For the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. Here we carry out extensive QM/MM free energy simulations to probe the kinetics of relevant proton transfer steps and analyze the effects of local structure and hydration level. We show that protonation of the proton loading site (PLS, taken to be a propionate of heme a3) requires a concerted process in which a key glutamic acid (Glu286H) delivers the proton to the PLS while being reprotonated by an excess proton coming from the D-channel. The concerted nature of the mechanism is a crucial feature that enables the loading of the PLS before the cavity containing Glu286 is better hydrated to lower its pKa to experimentally measured range; the charged rather than dipolar nature of the process also ensures a tight coupling with heme a reduction, as emphasized by Siegbahn and Blomberg. In addition, we find that rotational flexibility of the PLS allows its protonation before that of the binuclear center (the site where oxygen gets reduced to water). Together with our recent study (P. Goyal, et al., Proc. Natl. Acad. Sci. USA, 110:18886-18891, 2013) that focused on the modulation of Glu286 pKa, the current work suggests a mechanism that builds in a natural sequence for the protonation of the PLS prior to that of the binuclear center. This provides microscopic support to the kinetic constraints revealed by kinetic network analysis as essential elements that ensure an efficient vectorial proton transport in cytochrome c oxidase. PMID:25678950

  6. Kinetic Analysis of the Digestion of Bovine Type I Collagen Telopeptides with Porcine Pepsin.

    PubMed

    Qian, Jun; Okada, Yukari; Ogura, Takayuki; Tanaka, Keisuke; Hattori, Shunji; Ito, Shinji; Satoh, Junko; Takita, Teisuke; Yasukawa, Kiyoshi

    2016-01-01

    Collagen is frequently digested using pepsin in industries to produce a triple helical collagen without the N- and C-terminal telopeptides. However, kinetic analysis of this reaction is difficult because several Lys residues in the N- and in the C-terminal telopeptides form covalent bonds, leading to multiple substrates species, and pepsin cleaves collagen at various sites in the N-terminal and in the C-terminal telopeptides, yielding different products. Here we performed kinetic analysis of the digestion of bovine type I collagen with porcine pepsin. The reaction could be monitored by SDS-PAGE by measuring the intensity of the protein bands corresponding to the variant β11 chain. We obtained kinetic parameters relative to the decrease in the variant β11 chain upon digestion. At pH 4.0, the Km and kcat values increased with increasing temperature (30 to 65 °C), although the kcat /Km values were stable. Additional cleavage at the helical region was detected at 45 to 65 °C. At 37 °C, the Km and kcat values increased with decreasing pH, and the kcat /Km values at pH 2.1 to 4.5 were stable and higher than those at pH 5.0 and 5.5. No additional cleavage was detected at the examined pH. Thus, the optimal pH and temperatures for selective digestion of collagen telopeptides with pepsin are 2.1 to 4.5 and 30 to 40 °C, respectively. These results suggest that the method might be useful for the kinetic analysis of the digestion of collagen telopeptides with pepsin.

  7. Gating Kinetics of the Cyclic-GMP-Activated Channel of Retinal Rods: Flash Photolysis and Voltage-Jump Studies

    NASA Astrophysics Data System (ADS)

    Karpen, Jeffrey W.; Zimmerman, Anita L.; Stryer, Lubert; Baylor, Denis A.

    1988-02-01

    The gating kinetics of the cGMP-activated cation channel of salamander retinal rods have been studied in excised membrane patches. Relaxations in patch current were observed after two kinds of perturbation: (i) fast jumps of cGMP concentration, generated by laser flash photolysis of a cGMP ester (``caged'' cGMP), and (ii) membrane voltage jumps, which perturb activation of the channel by cGMP. In both methods the speed of activation increased with the final cGMP concentration. The results are explained by a simple kinetic model in which activation involves three sequential cGMP binding steps with bimolecular rate constants close to the diffusion-controlled limit; fully liganded channels undergo rapid open-closed transitions. Voltage perturbs activation by changing the rate constant for channel closing, which increases with hyperpolarization. Intramolecular transitions of the fully liganded channel limit the kinetics of activation at high cGMP concentrations (>50 μ M), whereas at physiological cGMP concentrations (<5 μ M), the kinetics of activation are limited by the third cGMP binding step. The channel appears to be optimized for rapid responses to changes in cytoplasmic cGMP concentration.

  8. Amyloid-β probes: Review of structure–activity and brain-kinetics relationships

    PubMed Central

    Eckroat, Todd J; Mayhoub, Abdelrahman S

    2013-01-01

    Summary The number of people suffering from Alzheimer’s disease (AD) is expected to increase dramatically in the coming years, placing a huge burden on society. Current treatments for AD leave much to be desired, and numerous research efforts around the globe are focused on developing improved therapeutics. In addition, current diagnostic tools for AD rely largely on subjective cognitive assessment rather than on identification of pathophysiological changes associated with disease onset and progression. These facts have led to numerous efforts to develop chemical probes to detect pathophysiological hallmarks of AD, such as amyloid-β plaques, for diagnosis and monitoring of therapeutic efficacy. This review provides a survey of chemical probes developed to date for AD with emphasis on synthetic methodologies and structure–activity relationships with regards to affinity for target and brain kinetics. Several probes discussed herein show particularly promising results and will be of immense value moving forward in the fight against AD. PMID:23766818

  9. Activated desorption at heterogeneous interfaces and long-time kinetics of hydrocarbon recovery from nanoporous media

    PubMed Central

    Lee, Thomas; Bocquet, Lydéric; Coasne, Benoit

    2016-01-01

    Hydrocarbon recovery from unconventional reservoirs (shale gas) is debated due to its environmental impact and uncertainties on its predictability. But a lack of scientific knowledge impedes the proposal of reliable alternatives. The requirement of hydrofracking, fast recovery decay and ultra-low permeability—inherent to their nanoporosity—are specificities of these reservoirs, which challenge existing frameworks. Here we use molecular simulation and statistical models to show that recovery is hampered by interfacial effects at the wet kerogen surface. Recovery is shown to be thermally activated with an energy barrier modelled from the interface wetting properties. We build a statistical model of the recovery kinetics with a two-regime decline that is consistent with published data: a short time decay, consistent with Darcy description, followed by a fast algebraic decay resulting from increasingly unreachable energy barriers. Replacing water by CO2 or propane eliminates the barriers, therefore raising hopes for clean/efficient recovery. PMID:27327254

  10. Activated desorption at heterogeneous interfaces and long-time kinetics of hydrocarbon recovery from nanoporous media

    NASA Astrophysics Data System (ADS)

    Lee, Thomas; Bocquet, Lydéric; Coasne, Benoit

    2016-06-01

    Hydrocarbon recovery from unconventional reservoirs (shale gas) is debated due to its environmental impact and uncertainties on its predictability. But a lack of scientific knowledge impedes the proposal of reliable alternatives. The requirement of hydrofracking, fast recovery decay and ultra-low permeability--inherent to their nanoporosity--are specificities of these reservoirs, which challenge existing frameworks. Here we use molecular simulation and statistical models to show that recovery is hampered by interfacial effects at the wet kerogen surface. Recovery is shown to be thermally activated with an energy barrier modelled from the interface wetting properties. We build a statistical model of the recovery kinetics with a two-regime decline that is consistent with published data: a short time decay, consistent with Darcy description, followed by a fast algebraic decay resulting from increasingly unreachable energy barriers. Replacing water by CO2 or propane eliminates the barriers, therefore raising hopes for clean/efficient recovery.

  11. Kinetic studies on the adsorption of methylene blue onto vegetal fiber activated carbons

    NASA Astrophysics Data System (ADS)

    Cherifi, Hakima; Fatiha, Bentahar; Salah, Hanini

    2013-10-01

    The vegetable sponge of cylindrical loofa (CL), a natural product which grows in the north of Algeria, was used to prepare activated carbons. Two activated carbons, AC1 and AC2, by two physiochemical activation methods to be used for methylene blue removal from wastewater. The surface structure of AC1, AC2 and CL were analyzed by scanning electron microscopy. Adsorption isotherm of methylene blue onto the prepared activated carbons was determined by batch tests. The effects of various parameters such as contact time, initial concentration, pH, temperature, adsorbent dose and granulometry were investigated, at agitation rate 150 rpm. The results showed that the equilibrium uptake increased with increasing initial MB concentration. The maximum % removal of MB obtained was 99% at 50 °C for AC1 and 82% at 30 °C for AC2. The increase in initial pH in the ranges of 2-10 increases the yields removal of MB on AC2. The pseudo-first-order and pseudo-second-order kinetic models were applied to test the experimental data. The latter provided the best correlation of the experimental data compared to the pseudo-first-order model.

  12. Equilibrium and kinetic modeling of contaminant immobilization by activated carbon amended to sediments in the field.

    PubMed

    Rakowska, Magdalena I; Kupryianchyk, Darya; Koelmans, Albert A; Grotenhuis, Tim; Rijnaarts, Huub H M

    2014-12-15

    Addition of activated carbons (AC) to polluted sediments and soils is an attractive remediation technique aiming at reducing pore water concentrations of hydrophobic organic contaminants (HOCs). In this study, we present (pseudo-)equilibrium as well as kinetic parameters for sorption of a series of PAHs and PCBs to powdered and granular activated carbons (AC) after three different sediment treatments: sediment mixed with powdered AC (PAC), sediment mixed with granular AC (GAC), and addition of GAC followed by 2 d mixing and subsequent removal ('sediment stripping'). Remediation efficiency was assessed by quantifying fluxes of PAHs towards SPME passive samplers inserted in the sediment top layer, which showed that the efficiency decreased in the order of PAC > GAC stripping > GAC addition. Sorption was very strong to PAC, with Log KAC (L/kg) values up to 10.5. Log KAC values for GAC ranged from 6.3-7.1 and 4.8-6.2 for PAHs and PCBs, respectively. Log KAC values for GAC in the stripped sediment were 7.4-8.6 and 5.8-7.7 for PAH and PCB. Apparent first order adsorption rate constants for GAC (kGAC) in the stripping scenario were calculated with a first-order kinetic model and ranged from 1.6 × 10(-2) (PHE) to 1.7 × 10(-5) d(-1) (InP). Sorption affinity parameters did not change within 9 months post treatment, confirming the longer term effectiveness of AC in field applications for PAC and GAC.

  13. A comprehensive analysis of the influence of drug binding kinetics on drug action at molecular and systems levels.

    PubMed

    Yin, Ning; Pei, Jianfeng; Lai, Luhua

    2013-06-01

    Binding kinetics is closely related to the efficacy of drugs. Several aspects of binding kinetics, such as long residence or frequent dissociation, have been proposed to affect drug properties such as efficacy, selectivity, and multi-target potency. However, a comprehensive and balanced study of binding kinetics in various scenarios is still needed. We performed a comprehensive computational analysis of the role of drug binding kinetics in various situations such as enzyme inhibition, receptor binding, multi-target drug targeting, signal transduction pathways, and metabolic networks. Molecular studies of enzyme inhibition, receptor binding, and multi-target drugs have shown that at constant binding affinity, fast associating drugs show better enzyme inhibitory effects, earlier and higher receptor occupancy peaks, and better multi-target performances, while slow dissociating drugs show prolonged receptor occupancy, as suggested by others. Different situations exemplify slightly different kinetic-efficacy relationships, and each must be considered separately. At the systems level, binding kinetics can not only change the overall effect of drugs, but can also affect signaling dynamics. For example, in the tumor necrosis factor α-induced nuclear factor-κB pathway, inhibitor addition can delay the onset of oscillations and decrease their frequencies, with these changes varying with the binding kinetics of the inhibitor. The effects of drug binding kinetics also depend on network topology and where the target is located in the network. For successful drug discovery, both molecular binding kinetics and systems level requirements need to be considered.

  14. Reductive activation of mitomycin C by thiols: kinetics, mechanism, and biological implications.

    PubMed

    Paz, Manuel M

    2009-10-01

    The clinically used antitumor antibiotic mitomycin C requires a reductive activation to be converted to a bis-electrophile that forms several covalent adducts with DNA, including an interstrand cross-link which is considered to be the lesion responsible for the cytotoxic effects of the drug. Enzymes such as cytochrome P450 reductase and DT-diaphorase have traditionally been implicated in the bioreduction of mitomycin C, but recent reports indicate that enzymes containing a dithiol active site are also involved in the metabolism of mitomycin C. The reductive activation can also be effected in vitro with chemical reductants, but until now, mitomycin C was considered to be inert to thiols. We report here that mitomycin C can, in fact, be reductively activated by thiols. We show that the reaction is autocatalytic and that the end product is a relatively stable aziridinomitosene that can be trapped by adding several nucleophiles after the activation reaction. Kinetic studies show that the reaction is highly sensitive to pH and does not proceed or proceeds very slowly at neutral pH, an observation that explains the unsuccessful results on previous attempts to activate mitomycin C with thiols. The optimum pH for the reactions is around the pK(a) values of the thiols used in the activation. A mechanism for the reaction is hypothesized, involving the initial formation of a thiolate-mitomycin adduct, that then evolves to give the hydroquinone of mitomycin C and disulfide. The results presented here provide a chemical mechanism to explain how some biological dithiols containing an unusually acidic thiol group (deprotonated at physiological pH) participate in the modulation of mitomycin C cytotoxicity.

  15. Ligand-receptor binding kinetics in surface plasmon resonance cells: a Monte Carlo analysis

    NASA Astrophysics Data System (ADS)

    Carroll, Jacob; Raum, Matthew; Forsten-Williams, Kimberly; Täuber, Uwe C.

    2016-12-01

    Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation description is appropriate. This approximation however ignores the spatial fluctuations as well as temporal correlations induced by multiple local rebinding events, which become prominent for slow diffusion rates and high binding affinities. We report detailed Monte Carlo simulations of ligand binding kinetics in an SPR cell subject to laminar flow. We extract the binding and dissociation rates by means of the techniques frequently employed in experimental analysis that are motivated by the mean-field approximation. We find major discrepancies in a wide parameter regime between the thus extracted rates and the known input simulation values. These results underscore the crucial quantitative importance of spatio-temporal correlations in binary reaction kinetics in SPR cell geometries, and demonstrate the failure of a mean-field analysis of SPR cells in the regime of high Damköhler number {{Da}}\\gt 0.1, where the spatio-temporal correlations due to diffusive transport and ligand-receptor rebinding events dominate the dynamics of SPR systems.

  16. Thermodynamic Analysis of Chemically Reacting Mixtures and Their Kinetics: Example of a Mixture of Three Isomers.

    PubMed

    Pekař, Miloslav

    2016-10-18

    Thermodynamics provides consequences of and restrictions on chemically reacting mixtures, particularly their kinetics, which have not been fully explored. Herein, a comprehensive thermodynamic analysis is illustrated for a reacting mixture of three isomers. The rate equation is first derived on the basis of the results of nonequilibrium continuum thermodynamics of linear fluids, and is then subjected to the requirement of consistency with entropic inequality (the second law). This consistency test involves the correct representation of the reaction rate as a function of affinities. It is shown that entropic inequality restricts the signs or values of coefficients in the constitutive equations for reaction rates/rate constants. The use of reverse rate constants and the identification of thermodynamic and kinetic equilibrium constants are not necessary in this approach. Although the presented thermodynamic analysis works only for independent reactions, the rates of dependent reactions are not excluded from having effects on kinetics. It is shown that the rates of dependent reactions are combined from the rates of independent reactions differently than dependent reactions are combined from independent reactions. The results are compared to the classical mass-action rate equations, and new restrictions on the values of the classical rate constants are derived.

  17. Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

    PubMed

    Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

    2009-09-01

    The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

  18. Quantitative kinetic analysis of hydrogen transfer reactions from dietary polyphenols to the DPPH radical.

    PubMed

    Goupy, Pascale; Dufour, Claire; Loonis, Michele; Dangles, Olivier

    2003-01-29

    Diphenylpicrylhydrazyl (DPPH) is widely used for quickly assessing the ability of polyphenols to transfer labile H atoms to radicals, a likely mechanism of antioxidant protection. This popular test generally pays no attention to the kinetics of H atom transfer, which however could be even more important than the total H-atom-donating capacities (stoichiometry, EC50) typically evaluated. In the present work, a series of dietary polyphenols belonging to the most representative families (flavonols from onion, flavanol monomers and oligomers from barley, and caffeic acid and caffeoyl esters from artichoke and endive) are characterized not only by their total stoichiometries (n(tot)) but also by their rate constants of first H atom abstraction by DPPH (k(1)), deduced from the kinetic analysis of the decay of the DPPH visible band following addition of the antioxidant. The mildly reactive DPPH radical allows a good discrimation between polyphenols, as demonstrated by the relatively large ranges of k(1) (ca. 400-5000 M(-)(1) s(-)(1)) and n(tot) (ca. 1-5) values typically measured with antioxidants having a single polyphenolic nucleus. With antioxidants displaying more than one polyphenolic nucleus (procyanidin oligomers, dicaffeoyl esters), the kinetic analysis makes it possible to demonstrate significant differences in reactivity between the subunits (two distinct k(1) values whose ratio lies in the range 3-10) and nonadditive stoichiometries.

  19. Analysis of proton exchange kinetics with time-dependent exchange rate.

    PubMed

    Rutkowska-Wlodarczyk, Izabela; Kierdaszuk, Borys; Wlodarczyk, Jakub

    2010-04-01

    Mass spectrometry is used to probe the kinetics of hydrogen-deuterium exchange in lysozyme in pH 5, 6 and 7.4. An analysis based on a Verhulst growth model is proposed and effectively applied to the kinetics of the hydrogen exchange. The data are described by a power-like function which is based on a time-dependence of the exchange rate. Experimental data ranging over many time scales is considered and accurate fits of a power-like function are obtained. Results of fittings show correlation between faster hydrogen-deuterium exchange and increase of pH. Furthermore a model is presented that discriminates between easily exchangeable hydrogens (located in close proximity to the protein surface) and those protected from the exchange (located in the protein interior). A possible interpretation of the model and its biological significance are discussed.

  20. Kinetic analysis of artificial peptide self-replication. Part I: the homochiral case.

    PubMed

    Islas, Jesús Rivera; Pimienta, Véronique; Micheau, Jean-Claude; Buhse, Thomas

    2003-03-25

    Computational kinetic analysis of a lately discovered homochiral peptide self-replicator is presented. A 6-step kinetic model was designed that addresses the main reactions and hydrophobic interactions involved in this template-directed, autocatalytic system and that gave rise to excellent fitting of 4 previously published independent experimental series. The model sheds light on the mechanistic principle of the reaction system and illustrates directly a number of dynamic properties such as the observed autocatalytic efficiency. It was found that the dynamics are basically governed by two reversible hydrophobic interactions: between the template and a peptide fragment and between two template species. The later association was determined to be considerably more favored, which leads to the predominant presence of the catalytically inactive template dimer in the reaction system. Our results show that the involvement of a template trimer is not necessary to obtain the observed fittings.

  1. Kinetic analysis of high-concentration isopropanol biodegradation by a solvent-tolerant mixed microbial culture.

    PubMed

    Bustard, Mark T; Meeyoo, Vissanu; Wright, Phillip C

    2002-06-20

    The ability of a previously enriched microbial population to utilize isopropanol (IPA) as the sole carbon source within a minimal salts medium is studied. The advantage of prior enrichment procedures for the improvement of IPA biodegradation performance is demonstrated for an IPA concentration of up to 24 g L(-1). Results showing the interrelationship between temperature and substrate utilization and inhibition levels at temperatures of between 2 degrees C and 45 degrees C are examined. Models of inhibition based on enzyme kinetics are assessed via nonlinear analysis, in order to accurately represent the growth kinetics of this solvent-tolerant mixed culture. The model that best describes the data is the Levenspiel substrate inhibition model, which can predict the maximum substrate level above which growth is completely limited. This is the first report of IPA treatment of up to 24 g L(-1) by an aerobic solvent-tolerant population.

  2. LSENS, a general chemical kinetics and sensitivity analysis code for gas-phase reactions: User's guide

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Bittker, David A.

    1993-01-01

    A general chemical kinetics and sensitivity analysis code for complex, homogeneous, gas-phase reactions is described. The main features of the code, LSENS, are its flexibility, efficiency and convenience in treating many different chemical reaction models. The models include static system, steady, one-dimensional, inviscid flow, shock initiated reaction, and a perfectly stirred reactor. In addition, equilibrium computations can be performed for several assigned states. An implicit numerical integration method, which works efficiently for the extremes of very fast and very slow reaction, is used for solving the 'stiff' differential equation systems that arise in chemical kinetics. For static reactions, sensitivity coefficients of all dependent variables and their temporal derivatives with respect to the initial values of dependent variables and/or the rate coefficient parameters can be computed. This paper presents descriptions of the code and its usage, and includes several illustrative example problems.

  3. Kinetic analysis and molecular modeling of the inhibition mechanism of roneparstat (SST0001) on human heparanase.

    PubMed

    Pala, Daniele; Rivara, Silvia; Mor, Marco; Milazzo, Ferdinando Maria; Roscilli, Giuseppe; Pavoni, Emiliano; Giannini, Giuseppe

    2016-06-01

    Heparanase is a β-d-glucuronidase which cleaves heparan sulfate chains in the extracellular matrix and on cellular membranes. A dysregulated heparanase activity is intimately associated with cell invasion, tumor metastasis and angiogenesis, making heparanase an attractive target for the development of anticancer therapies. SST0001 (roneparstat; Sigma-Tau Research Switzerland S.A.) is a non-anticoagulant 100% N-acetylated and glycol-split heparin acting as a potent heparanase inhibitor, currently in phase I in advanced multiple myeloma. Herein, the kinetics of heparanase inhibition by roneparstat is reported. The analysis of dose-inhibition curves confirmed the high potency of roneparstat (IC50 ≈ 3 nM) and showed, at higher concentrations, a Hill coefficient consistent with the engagement of two molecules of inhibitor. A homology model of human heparanase GS3 construct was built and used for docking experiments with inhibitor fragments. The model has high structural similarity with the recently reported crystal structure of human heparanase. Different interaction schemes are proposed, which support the hypothesis of a complex binding mechanism involving the recruitment of one or multiple roneparstat chains, depending on its concentration. In particular, docking solutions were obtained in which (i) a single roneparstat molecule interacts with both heparin-binding domains (HBDs) of heparanase or (ii) two fragments of roneparstat interact with either HBD-1 or HBD-2, consistent with the possibility of different inhibitor:enzyme binding stoichiometries. This study provides unique insights into the mode of action of roneparstat as well as clues of its interaction with heparanase at a molecular level, which could be exploited to design novel potential inhibitor molecules.

  4. Quantitative analysis of irbesartan in commercial dosage forms by kinetic spectrophotometry.

    PubMed

    Rahman, Nafisur; Siddiqui, Masoom Raza; Azmi, Syed Najmul Hejaz

    2006-05-01

    The objective of this work is to develop a new kinetic spectrophotometric method for the determination of irbesartan in pharmaceutical formulations. The method is based on the reaction of carboxylic acid group of the oxidized irbesartan with a mixture of potassium iodate (KIO(3)) and iodide (KI) to form yellow colored triiodide ions in aqueous medium at 30+/-1 degrees C. The reaction is followed spectrophotometrically by measuring the rate of change of absorbance at 352 nm. The initial-rate and fixed-time (DeltaA) methods are adopted for constructing the calibration curves, which were found to be linear over the concentration ranges of 10.0-60.0 and 7.5-60.0 microg ml(-1) respectively. The regression analysis of calibration data yielded the linear equations: rate=-2.138 x 10(-6)+1.058 x 10(-4)C and DeltaA=-3.75 x 10(-3)+3.25 x 10(-3)C for initial rate and fixed time (DeltaA) methods, respectively. The limit of detection for initial rate and fixed time methods are 0.21 and 2.40 mug ml(-1), respectively. The various activation parameters such as E(a), DeltaH++, DeltaS++ and DeltaG++ are also calculated for the reaction and found to be 70.95+/-0.43 kJ mol(-1), 68.48+/-0.21 kJ mol(-1), 16.54+/-0.24 J K(-1) mol(-1) and -4.94+/-0.07 kJ mol(-1), respectively. The proposed methods are optimized and validated as per the guidelines of International Conference on Harmonisation (U.S.A.). The point and interval hypothesis tests have been performed which indicate that there is no significant difference between the proposed methods and the reference method. The methods have been successfully applied to the determination of irbesartan in commercial dosage forms.

  5. Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function

    SciTech Connect

    He, Lian; Wu, Stephen G.; Wan, Ni; Reding, Adrienne C.; Tang, Yinjie J.

    2015-12-24

    In this study, genome-scale models (GSMs) are widely used to predict cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs mainly focus on fluxome that result in maximal yields. Cyanobacterial metabolism is controlled by both intracellular enzymes and photobioreactor conditions. To connect both intracellular and extracellular information and achieve a better understanding of PBRs productivities, this study integrates a genome-scale metabolic model of Synechocystis 6803 with growth kinetics, cell movements, and a light distribution function. The hybrid platform not only maps flux dynamics in cells of sub-populations but also predicts overall production titer and rate in PBRs. Analysis of the integrated GSM demonstrates several results. First, cyanobacteria are capable of reaching high biomass concentration (>20 g/L in 21 days) in PBRs without light and CO2 mass transfer limitations. Second, fluxome in a single cyanobacterium may show stochastic changes due to random cell movements in PBRs. Third, insufficient light due to cell self-shading can activate the oxidative pentose phosphate pathway in subpopulation cells. Fourth, the model indicates that the removal of glycogen synthesis pathway may not improve cyanobacterial bio-production in large-size PBRs, because glycogen can support cell growth in the dark zones. Based on experimental data, the integrated GSM estimates that Synechocystis 6803 in shake flask conditions has a photosynthesis efficiency of ~2.7 %. Conclusions: The multiple-scale integrated GSM, which examines both intracellular and extracellular domains, can be used to predict production yield/rate/titer in large-size PBRs. More importantly, genetic engineering strategies predicted by a traditional GSM may work well only in optimal growth conditions. In contrast, the integrated GSM may reveal mutant physiologies in diverse bioreactor conditions, leading to the design of robust strains with high

  6. Kinetic analysis and molecular modeling of the inhibition mechanism of roneparstat (SST0001) on human heparanase

    PubMed Central

    Pala, Daniele; Rivara, Silvia; Mor, Marco; Milazzo, Ferdinando Maria; Roscilli, Giuseppe; Pavoni, Emiliano; Giannini, Giuseppe

    2016-01-01

    Heparanase is a β-d-glucuronidase which cleaves heparan sulfate chains in the extracellular matrix and on cellular membranes. A dysregulated heparanase activity is intimately associated with cell invasion, tumor metastasis and angiogenesis, making heparanase an attractive target for the development of anticancer therapies. SST0001 (roneparstat; Sigma-Tau Research Switzerland S.A.) is a non-anticoagulant 100% N-acetylated and glycol-split heparin acting as a potent heparanase inhibitor, currently in phase I in advanced multiple myeloma. Herein, the kinetics of heparanase inhibition by roneparstat is reported. The analysis of dose-inhibition curves confirmed the high potency of roneparstat (IC50 ≈ 3 nM) and showed, at higher concentrations, a Hill coefficient consistent with the engagement of two molecules of inhibitor. A homology model of human heparanase GS3 construct was built and used for docking experiments with inhibitor fragments. The model has high structural similarity with the recently reported crystal structure of human heparanase. Different interaction schemes are proposed, which support the hypothesis of a complex binding mechanism involving the recruitment of one or multiple roneparstat chains, depending on its concentration. In particular, docking solutions were obtained in which (i) a single roneparstat molecule interacts with both heparin-binding domains (HBDs) of heparanase or (ii) two fragments of roneparstat interact with either HBD-1 or HBD-2, consistent with the possibility of different inhibitor:enzyme binding stoichiometries. This study provides unique insights into the mode of action of roneparstat as well as clues of its interaction with heparanase at a molecular level, which could be exploited to design novel potential inhibitor molecules. PMID:26762172

  7. Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function

    DOE PAGES

    He, Lian; Wu, Stephen G.; Wan, Ni; ...

    2015-12-24

    In this study, genome-scale models (GSMs) are widely used to predict cyanobacterial phenotypes in photobioreactors (PBRs). However, stoichiometric GSMs mainly focus on fluxome that result in maximal yields. Cyanobacterial metabolism is controlled by both intracellular enzymes and photobioreactor conditions. To connect both intracellular and extracellular information and achieve a better understanding of PBRs productivities, this study integrates a genome-scale metabolic model of Synechocystis 6803 with growth kinetics, cell movements, and a light distribution function. The hybrid platform not only maps flux dynamics in cells of sub-populations but also predicts overall production titer and rate in PBRs. Analysis of the integratedmore » GSM demonstrates several results. First, cyanobacteria are capable of reaching high biomass concentration (>20 g/L in 21 days) in PBRs without light and CO2 mass transfer limitations. Second, fluxome in a single cyanobacterium may show stochastic changes due to random cell movements in PBRs. Third, insufficient light due to cell self-shading can activate the oxidative pentose phosphate pathway in subpopulation cells. Fourth, the model indicates that the removal of glycogen synthesis pathway may not improve cyanobacterial bio-production in large-size PBRs, because glycogen can support cell growth in the dark zones. Based on experimental data, the integrated GSM estimates that Synechocystis 6803 in shake flask conditions has a photosynthesis efficiency of ~2.7 %. Conclusions: The multiple-scale integrated GSM, which examines both intracellular and extracellular domains, can be used to predict production yield/rate/titer in large-size PBRs. More importantly, genetic engineering strategies predicted by a traditional GSM may work well only in optimal growth conditions. In contrast, the integrated GSM may reveal mutant physiologies in diverse bioreactor conditions, leading to the design of robust strains with high chances of success in

  8. Model-based analysis for kinetic complexation study of Pizda and Cu(II)

    NASA Astrophysics Data System (ADS)

    Vosough, M.; Maeder, M.; Jalali-Heravi, M.; Norman, S. E.

    2008-08-01

    In the present work, the multivariate kinetic complexation of a new synthesized ligand, 1-(2″-hydroxyl cyclohexyl)-3'-[aminopropyl]-4-[3'-aminopropyl]piperazine (Pizda) and Cu 2+ in 50% ethanol-water solution is investigated using the UV-vis stopped-flow technique and state-of-the-art multi-wavelength numerical analysis. Model-based least squares fitting analysis or hard modeling is a specific part of chemometrics which is based on mathematical relationships for describing the measurements. Some recent developments include the incorporation of the effects of non-ideal experimental conditions into the fitting algorithm so it can substantially simplify experimental procedures. In this study no buffers are required because pH changes are taken into computations. Some 21 multi-wavelength kinetic measurements, taken at various initial concentrations of [H +] were analyzed globally, i.e. simultaneously applying an all inclusive reaction mechanism and a common set of species spectra. Using numerical analysis, the pH of the experimental solutions was allowed to vary as a consequence of the proceeding reactions. This enabled the complete kinetic analysis of the formation and dissociation of Cu(Pizda) n+ . Here protonation equilibria have been directly incorporated into the rate law, so thus variable pH values have been allowed during each measurement. Using the independently estimated stability constants (from spectrophotometric and potentiometric measurements) for the Cu(Pizda) n+ complexes, a total of six rate constants and one protonation constant could be elucidated. The results of the analysis include the concentration distribution and spectra of all chemical species involved in the reaction. A low standard deviation and residual profiles obtained validate the results.

  9. Model-based analysis for kinetic complexation study of Pizda and Cu(II).

    PubMed

    Vosough, M; Maeder, M; Jalali-Heravi, M; Norman, S E

    2008-08-01

    In the present work, the multivariate kinetic complexation of a new synthesized ligand, 1-(2''-hydroxyl cyclohexyl)-3'-[aminopropyl]-4-[3'-aminopropyl]piperazine (Pizda) and Cu(2+) in 50% ethanol-water solution is investigated using the UV-vis stopped-flow technique and state-of-the-art multi-wavelength numerical analysis. Model-based least squares fitting analysis or hard modeling is a specific part of chemometrics which is based on mathematical relationships for describing the measurements. Some recent developments include the incorporation of the effects of non-ideal experimental conditions into the fitting algorithm so it can substantially simplify experimental procedures. In this study no buffers are required because pH changes are taken into computations. Some 21 multi-wavelength kinetic measurements, taken at various initial concentrations of [H(+)] were analyzed globally, i.e. simultaneously applying an all inclusive reaction mechanism and a common set of species spectra. Using numerical analysis, the pH of the experimental solutions was allowed to vary as a consequence of the proceeding reactions. This enabled the complete kinetic analysis of the formation and dissociation of Cu(Pizda)(n+). Here protonation equilibria have been directly incorporated into the rate law, so thus variable pH values have been allowed during each measurement. Using the independently estimated stability constants (from spectrophotometric and potentiometric measurements) for the Cu(Pizda)(n+) complexes, a total of six rate constants and one protonation constant could be elucidated. The results of the analysis include the concentration distribution and spectra of all chemical species involved in the reaction. A low standard deviation and residual profiles obtained validate the results.

  10. Kinetic and thermodynamic investigation on ascorbate oxidase activity and stability of a Cucurbita maxima extract.

    PubMed

    Porto, Tatiana S; Porto, Camila S; Cavalcanti, Maria T H; Filho, José L Lima; Perego, Patrizia; Porto, Ana L F; Converti, Attilio; Pessoa, Adalberto

    2006-01-01

    The kinetic and thermodynamic properties of ascorbate oxidase (AO) activity and stability of a Cucurbita maxima extract were investigated. Activity tests performed at 25 degrees C using initial ascorbic acid concentration in the range 50-750 M allowed estimating the Michaelis constant for this substrate (Km = 126 microM) and the maximum initial rate of ascorbic acid oxidation (A0,max = 1.57 mM min-1). The main thermodynamic parameters of the enzyme reaction (DeltaH* = 10.3 kJ mol-1; DeltaG* = 87.2 kJ mol-1; DeltaS* = -258 J mol-1 K-1) were estimated through activity tests performed at 25-48 C. Within such a temperature range, no decrease in the initial reaction rate was detected. The long-term thermostability of the raw extract was then investigated by means of residual activity tests carried out at 10-70 degrees C, which allowed estimating the thermodynamic parameters of the irreversible enzyme inactivation as well (DeltaH*D = 51.7 kJ mol-1; DeltaG*D = 103 kJ mol-1; S*D = -160 J mol-1 K-1). Taking into account the specific rate of AO inactivation determined at different temperatures, we also estimated the enzyme half-life (1047 min at 10 degrees C and 21.2 min at 70 degrees C) and predicted the integral activity of a continuous system using this enzyme preparation. This work should be considered as a preliminary attempt to characterize the AO activity of a C. maxima extract before its concentration by liquid-liquid extraction techniques.

  11. Kinetics and Mechanism of Ultrasonic Activation of Persulfate: An in Situ EPR Spin Trapping Study.

    PubMed

    Wei, Zongsu; Villamena, Frederick A; Weavers, Linda K

    2017-03-21

    Ultrasound (US) was shown to activate persulfate (PS) providing an alternative activation method to base or heat as an in situ chemical oxidation (ISCO) method. The kinetics and mechanism of ultrasonic activation of PS were examined in aqueous solution using an in situ electron paramagnetic resonance (EPR) spin trapping technique and radical trapping with probe compounds. Using the spin trap, 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), hydroxyl radical ((•)OH) and sulfate radical anion (SO4(•-)) were measured from ultrasonic activation of persulfate (US-PS). The yield of (•)OH was up to 1 order of magnitude greater than that of SO4(•-). The comparatively high (•)OH yield was attributed to the hydrolysis of SO4(•-) in the warm interfacial region of cavitation bubbles formed from US. Using steady-state approximations, the dissociation rate of PS in cavitating bubble systems was determined to be 3 orders of magnitude greater than control experiments without sonication at ambient temperature. From calculations of the interfacial volume surrounding cavitation bubbles and using the Arrhenius equation, an effective mean temperature of 340 K at the bubble-water interface was estimated. Comparative studies using the probe compounds tert-butyl alcohol and nitrobenzene verified the bubble-water interface as the location for PS activation by high temperature with (•)OH contributing a minor role in activating PS to SO4(•-). The mechanisms unveiled in this study provide a basis for optimizing US-PS as an ISCO technology.

  12. Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics.

    PubMed

    Khanin, R; Vinciotti, V; Mersinias, V; Smith, C P; Wit, E

    2007-09-01

    The basic building block of a gene regulatory network consists of a gene encoding a transcription factor (TF) and the gene(s) it regulates. Considerable efforts have been directed recently at devising experiments and algorithms to determine TFs and their corresponding target genes using gene expression and other types of data. The underlying problem is that the expression of a gene coding for the TF provides only limited information about the activity of the TF, which can also be controlled posttranscriptionally. In the absence of a reliable technology to routinely measure the activity of regulators, it is of great importance to understand whether this activity can be inferred from gene expression data. We here develop a statistical framework to reconstruct the activity of a TF from gene expression data of the target genes in its regulatory module. The novelty of our approach is that we embed the deterministic Michaelis-Menten model of gene regulation in this statistical framework. The kinetic parameters of the gene regulation model are inferred together with the profile of the TF regulator. We also obtain a goodness-of-fit test to verify the fit of the model. The model is applied to a time series involving the Streptomyces coelicolor bacterium. We focus on the transcriptional activator cdaR, which is partly responsible for the production of a particular type of antibiotic. The aim is to reconstruct the activity profile of this regulator. Our approach can be extended to include more complex regulatory relationships, such as multiple regulatory factors, competition, and cooperativity.

  13. Revealing the activation pathway for TMEM16A chloride channels from macroscopic currents and kinetic models.

    PubMed

    Contreras-Vite, Juan A; Cruz-Rangel, Silvia; De Jesús-Pérez, José J; Figueroa, Iván A Aréchiga; Rodríguez-Menchaca, Aldo A; Pérez-Cornejo, Patricia; Hartzell, H Criss; Arreola, Jorge

    2016-07-01

    TMEM16A (ANO1), the pore-forming subunit of calcium-activated chloride channels, regulates several physiological and pathophysiological processes such as smooth muscle contraction, cardiac and neuronal excitability, salivary secretion, tumour growth and cancer progression. Gating of TMEM16A is complex because it involves the interplay between increases in intracellular calcium concentration ([Ca(2+)]i), membrane depolarization, extracellular Cl(-) or permeant anions and intracellular protons. Our goal here was to understand how these variables regulate TMEM16A gating and to explain four observations. (a) TMEM16A is activated by voltage in the absence of intracellular Ca(2+). (b) The Cl(-) conductance is decreased after reducing extracellular Cl(-) concentration ([Cl(-)]o). (c) ICl is regulated by physiological concentrations of [Cl(-)]o. (d) In cells dialyzed with 0.2 μM [Ca(2+)]i, Cl(-) has a bimodal effect: at [Cl(-)]o <30 mM TMEM16A current activates with a monoexponential time course, but above 30 mM, [Cl(-)]o ICl activation displays fast and slow kinetics. To explain the contribution of Vm, Ca(2+) and Cl(-) to gating, we developed a 12-state Markov chain model. This model explains TMEM16A activation as a sequential, direct, and Vm-dependent binding of two Ca(2+) ions coupled to a Vm-dependent binding of an external Cl(-) ion, with Vm-dependent transitions between states. Our model predicts that extracellular Cl(-) does not alter the apparent Ca(2+) affinity of TMEM16A, which we corroborated experimentally. Rather, extracellular Cl(-) acts by stabilizing the open configuration induced by Ca(2+) and by contributing to the Vm dependence of activation.

  14. Chemkin-II: A Fortran chemical kinetics package for the analysis of gas-phase chemical kinetics

    SciTech Connect

    Kee, R.J.; Rupley, F.M.; Miller, J.A.

    1989-09-01

    This document is the user's manual for the second-generation Chemkin package. Chemkin is a software package for whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides an especially flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutine Library. This library is a collection of about 100 highly modular Fortran subroutines that may be called to return information on equation of state, thermodynamic properties, and chemical production rates.

  15. Structure-activity relationship studies of resveratrol and its analogues by the reaction kinetics of low density lipoprotein peroxidation.

    PubMed

    Cheng, Jin-Chun; Fang, Jian-Guo; Chen, Wei-Feng; Zhou, Bo; Yang, Li; Liu, Zhong-Li

    2006-06-01

    Resveratrol (3,5,4'-trans-trihydroxystibene) is a natural phytoalexin present in grapes and red wine, which possesses a variety of biological activities including antioxidative activity. To find more active antioxidants, with resveratrol as the lead compound, we synthesized resveratrol analogues, i.e., 3,4,3',4'-tetrahydroxy-trans-stilbene (3,4,3',4'-THS), 3,4,4'-trihydroxy-trans-stilbene (3,4,4'-THS), 2,4,4'-trihydroxy-trans-stilbene (2,4,4'-THS), 3,3'-dimethoxy-4,4'-dihydroxy-trans-stilbene (3,3'-DM-4,4'-DHS), 3,4-dihydroxy-trans-stilbene (3,4-DHS), 4,4'-dihydroxy-trans-stilbene (4,4'-DHS), 3,5-dihydroxy-trans-stilbene (3,5-DHS) and 2,4-dihydroxy-trans-stilbene (2,4-DHS). Antioxidative effects of resveratrol and its analogues against free-radical-induced peroxidation of human low density lipoprotein (LDL) were studied. The peroxidation was initiated either by a water-soluble initiator 2,2'-azobis(2-amidinopropane hydrochloride) (AAPH), or by cupric ion (Cu(2+)). The reaction kinetics were monitored either by the uptake of oxygen and the depletion of alpha-tocopherol (TOH) presented in the native LDL, or by the formation of thiobarbituric acid reactive substances (TBARS). Kinetic analysis of the antioxidation process demonstrates that these trans-stilbene derivatives are effective antioxidants against both AAPH- and Cu(2+)-induced LDL peroxidation with the activity sequence of 3,4,3',4'-THS approximately 3,3'-DM-4,4'-DHS>3,4-DHS approximately 3,4,4'-THS>2,4,4'-THS>resveratrol approximately 3,5-DHS>4,4'-DHS approximately 2,4-HS, and 3,4,3',4'-THS approximately 3,4-DHS approximately 3,4,4'-THS>3,3'-DM-4,4'-DHS>4,4'-DHS>resveratrol approximately 2,4-HS>2,4,4'-THS approximately 3,5-DHS, respectively. Molecules bearing ortho-dihydroxyl or 4-hydroxy-3-methoxyl groups possess significantly higher antioxidant activity than those bearing no such functionalities.

  16. Wanderlust kinetics and variable Ca(2+)-sensitivity of Drosophila, a large conductance Ca(2+)-activated K+ channel, expressed in oocytes.

    PubMed Central

    Silberberg, S D; Lagrutta, A; Adelman, J P; Magleby, K L

    1996-01-01

    Cloned large conductance Ca(2+)-activated K+ channels (BK or maxi-K+ channels) from Drosophila (dSlo) were expressed in Xenopus oocytes and studied in excised membrane patches with the patch-clamp technique. Both a natural variant and a mutant that eliminated a putative cyclic AMP-dependent protein kinase phosphorylation site exhibited large, slow fluctuations in open probability with time. These fluctuations, termed "wanderlust kinetics," occurred with a time course of tens of seconds to minutes and had kinetic properties inconsistent with simple gating models. Wanderlust kinetics was still observed in the presence of 5 mM caffeine or 50 nM thapsigargin, or when the Ca2+ buffering capacity of the solution was increased by the addition of 5 mM HEDTA, suggesting that the wanderlust kinetics did not arise from Ca2+ release from caffeine and thapsigargin sensitive internal stores in the excised patch. The slow changes in kinetics associated with wanderlust kinetics could be generated with a discrete-state Markov model with transitions among three or more kinetic modes with different levels of open probability. To average out the wanderlust kinetics, large amounts of data were analyzed and demonstrated up to a threefold difference in the [Ca2+]i required for an open probability of 0.5 among channels expressed from the same injected mRNA. These findings indicate that cloned dSlo channels in excised patches from Xenopus oocytes can exhibit large variability in gating properties, both within a single channel and among channels. PMID:8744301

  17. Unique nucleation activity of inorganic fullerene-like WS2 nanoparticles in polyphenylene sulfide nanocomposites: isokinetic and isoconversional study of dynamic crystallization kinetics.

    PubMed

    Naffakh, Mohammed; Marco, Carlos; Gómez, Marián A; Jiménez, Ignacio

    2009-05-21

    The dynamic crystallization kinetics of polyphenylene sulfide (PPS) nanocomposites with inorganic fullerene WS2 nanopartices (IF-WS2) content varying from 0.05 to 8 wt % has been studied using differential scanning calorimetry (DSC). The analysis of the crystallization at different cooling rates demonstrates that the completely isokinetic description of the crystallization process is not possible. However, the isoconversional methods in combination with the JMAEK equation provide a better understanding of the kinetics of the dynamic crystallization process. The addition of IF-WS2 influences the crystallization kinetics of PPS but in ways unexpected for polymer nanocomposites. A drastic change from retardation to promotion of crystallization is observed with increasing nanoparticle content. In the same way, the results of the nucleation activity and the effective energy barrier confirmed the unique dependence of the crystallization behavior of PPS on composition. In addition, the morphological data obtained from the polarized optical microscopy (POM) and time-resolved synchrotron X-ray diffraction is consistent with results of the crystallization kinetics of PPS/IF-WS2 nanocomposites.

  18. Purification and kinetic analysis of cytosolic and mitochondrial thioredoxin glutathione reductase extracted from Taenia solium cysticerci.

    PubMed

    Plancarte, Agustin; Nava, Gabriela

    2015-02-01

    Thioredoxin glutathione reductases (TGRs) (EC 1.8.1.9) were purified to homogeneity from the cytosolic (cTsTGR) and mitochondrial (mTsTGR) fractions of Taenia solium, the agent responsible for neurocysticercosis, one of the major central nervous system parasitic diseases in humans. TsTGRs had a relative molecular weight of 132,000, while the corresponding value per subunit obtained under denaturing conditions, was of 62,000. Specific activities for thioredoxin reductase and glutathione reductase substrates for both TGRs explored were in the range or lower than values obtained for other platyhelminths and mammalian TGRs. cTsTGR and mTsTGR also showed hydroperoxide reductase activity using hydroperoxide as substrate. Km(DTNB) and Kcat(DTNB) values for cTsTGR and mTsTGR (88 µM and 1.9 s(-1); 45 µM and 12.6 s(-1), respectively) and Km(GSSG) and Kcat(GSSG) values for cTsTGR and mTsTGR (6.3 µM and 0.96 s(-1); 4 µM and 1.62 s(-1), respectively) were similar to or lower than those reported for mammalian TGRs. Mass spectrometry analysis showed that 12 peptides from cTsTGR and seven from mTsTGR were a match for gi|29825896 thioredoxin glutathione reductase [Echinococcus granulosus], confirming that both enzymes are TGRs. Both T. solium TGRs were inhibited by the gold compound auranofin, a selective inhibitor of thiol-dependent flavoreductases (I₅₀ = 3.25, 2.29 nM for DTNB and GSSG substrates, respectively for cTsTGR; I₅₀ = 5.6, 25.4 nM for mTsTGR toward the same substrates in the described order). Glutathione reductase activity of cTsTGR and mTsTGR exhibited hysteretic behavior with moderate to high concentrations of GSSG; this result was not observed either with thioredoxin, DTNB or NADPH. However, the observed hysteretic kinetics was suppressed with increasing amounts of both parasitic TGRs. These data suggest the existence of an effective substitute which may account for the lack of the detoxification enzymes glutathione reductase

  19. Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

    PubMed

    Martí-Rujas, Javier; Kawano, Masaki

    2013-02-19

    Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific

  20. Ground-state kinetics of bistable redox-active donor-acceptor mechanically interlocked molecules.

    PubMed

    Fahrenbach, Albert C; Bruns, Carson J; Li, Hao; Trabolsi, Ali; Coskun, Ali; Stoddart, J Fraser

    2014-02-18

    The ability to design and confer control over the kinetics of theprocesses involved in the mechanisms of artificial molecular machines is at the heart of the challenge to create ones that can carry out useful work on their environment, just as Nature is wont to do. As one of the more promising forerunners of prototypical artificial molecular machines, chemists have developed bistable redox-active donor-acceptor mechanically interlocked molecules (MIMs) over the past couple of decades. These bistable MIMs generally come in the form of [2]rotaxanes, molecular compounds that constitute a ring mechanically interlocked around a dumbbell-shaped component, or [2]catenanes, which are composed of two mechanically interlocked rings. As a result of their interlocked nature, bistable MIMs possess the inherent propensity to express controllable intramolecular, large-amplitude, and reversible motions in response to redox stimuli. In this Account, we rationalize the kinetic behavior in the ground state for a large assortment of these types of bistable MIMs, including both rotaxanes and catenanes. These structures have proven useful in a variety of applications ranging from drug delivery to molecular electronic devices. These bistable donor-acceptor MIMs can switch between two different isomeric states. The favored isomer, known as the ground-state co-conformation (GSCC) is in equilibrium with the less favored metastable state co-conformation (MSCC). The forward (kf) and backward (kb) rate constants associated with this ground-state equilibrium are intimately connected to each other through the ground-state distribution constant, KGS. Knowing the rate constants that govern the kinetics and bring about the equilibration between the MSCC and GSCC, allows researchers to understand the operation of these bistable MIMs in a device setting and apply them toward the construction of artificial molecular machines. The three biggest influences on the ground-state rate constants arise from

  1. Nucleosome positioning and kinetics near transcription-start-site barriers are controlled by interplay between active remodeling and DNA sequence.

    PubMed

    Parmar, Jyotsana J; Marko, John F; Padinhateeri, Ranjith

    2014-01-01

    We investigate how DNA sequence, ATP-dependent chromatin remodeling and nucleosome-depleted 'barriers' co-operate to determine the kinetics of nucleosome organization, in a stochastic model of nucleosome positioning and dynamics. We find that 'statistical' positioning of nucleosomes against 'barriers', hypothesized to control chromatin structure near transcription start sites, requires active remodeling and therefore cannot be described using equilibrium statistical mechanics. We show that, unlike steady-state occupancy, DNA site exposure kinetics near a barrier is dominated by DNA sequence rather than by proximity to the barrier itself. The timescale for formation of positioning patterns near barriers is proportional to the timescale for active nucleosome eviction. We also show that there are strong gene-to-gene variations in nucleosome positioning near barriers, which are eliminated by averaging over many genes. Our results suggest that measurement of nucleosome kinetics can reveal information about sequence-dependent regulation that is not apparent in steady-state nucleosome occupancy.

  2. Glass Stability and Kinetic Analysis of Iron-Metalloid Bulk Metallic Glass

    NASA Astrophysics Data System (ADS)

    Santhaweesuk, Charuayporn

    Multicomponent Fe-based bulk metallic glasses (BMGs) with a combination of excellent properties such as good soft magnetic properties, high strength, high hardness, and high corrosion resistance have attracted increasing attention both from a basic science research standpoint and due to their industrial application potential. However, many of the elemental additions which lead to the easiest glass formation are expensive. The identification of alloys composed of abundant and inexpensive elements that still retain excellent properties would promote applications for engineering and industry. In short, the development of the Fe-based BMG without any glass-forming metal elements and with high glass forming ability is desired. This study shows that the thermal stability of the Fe-based alloys can be improved beyond a simple rule of mixtures prediction by utilizing a well-balance multi-metalloid approach. The kinetics aspect of glass-forming ability is studied experimentally for Fe-B-Si-P alloys. The systematic variation in alloy composition gives access to differences in phase selection and the final dimensions of glass formation. Two alloys, representing the best glass-forming composition and the poorest glass-forming composition, were studied in terms of their stability to crystallization, solidification microstructure evolution and thermal history. The utility of the wedge-casting technique is developed to examine bulk glass-forming alloys by combining multiple temperature profiles of the quenching melt with a measurement-based kinetic analysis of the phase selection competition and critical cooling rate conditions. Based upon direct thermal measurement, microstructural analysis and kinetic modeling, it was found that both representative alloys show a board spectrum of solidification microstructures which include a critical cooling rate range. The kinetic competition in the formation of certain phases can enhance or detract from the final dimension of bulk glass

  3. Equilibrium isotherm and kinetic studies for the simultaneous removal of phenol and cyanide by use of S. odorifera (MTCC 5700) immobilized on coconut shell activated carbon

    NASA Astrophysics Data System (ADS)

    Singh, Neetu; Balomajumder, Chandrajit

    2016-09-01

    In this study, simultaneous removal of phenol and cyanide by a microorganism S. odorifera (MTCC 5700) immobilized onto coconut shell activated carbon surface (CSAC) was studied in batch reactor from mono and binary component aqueous solution. Activated carbon was derived from coconut shell by chemical activation method. Ferric chloride (Fecl3), used as surface modification agents was applied to biomass. Optimum biosorption conditions were obtained as a function of biosorbent dosage, pH, temperature, contact time and initial phenol and cyanide concentration. To define the equilibrium isotherms, experimental data were analyzed by five mono component isotherm and six binary component isotherm models. The higher uptake capacity of phenol and cyanide onto CSAC biosorbent surface was 450.02 and 2.58 mg/g, respectively. Nonlinear regression analysis was used for determining the best fit model on the basis of error functions and also for calculating the parameters involved in kinetic and isotherm models. The kinetic study results revealed that Fractal-like mixed first second order model and Brouser-Weron-Sototlongo models for phenol and cyanide were capable to offer accurate explanation of biosorption kinetic. According to the experimental data results, CSAC with immobilization of bacterium S. odorifera (MTCC 5700) seems to be an alternative and effective biosorbent for the elimination of phenol and cyanide from binary component aqueous solution.

  4. Myoelectric activation and kinetics of different plyometric push-up exercises.

    PubMed

    García-Massó, Xavier; Colado, Juan C; González, Luis M; Salvá, Pau; Alves, Joao; Tella, Víctor; Triplett, N Travis

    2011-07-01

    The kinetic and myoelectric differences between 3 types of plyometric push-ups were investigated. Twenty-seven healthy, physically active men served as subjects and completed both familiarization and testing sessions. During these sessions, subjects performed 2 series of 3 plyometric push-up variations in a counterbalanced order according to the following techniques: Countermovement push-ups (CPUs) were push-ups performed with the maximum speed of movement; jump push-ups (JPUs) were similar to clapping push-ups; and fall push-ups (FPUs) required kneeling subjects to drop and then attempt to return to their initial position. Vertical ground reaction forces were determined by using a force plate. Myoelectric activity was recorded by means of electromyography. Impact force and impact rate of force development were significantly (p < 0.05) higher for FPUs than for JPUs. The maximum rate of force development was higher for CPUs (p < 0.05) than for JPUs, and the maximum force was higher for the CPUs than for the FPUs (p < 0.05). There were differences among exercises for the mean muscle activation of the pectoralis major (PM; p < 0.001), triceps brachii (p < 0.001), external oblique (p < 0.005) and anterior deltoid (p < 0.001), and in the maximum muscle activation of the PM (p < 0.001). Plyometric push-ups with countermovement achieved a higher maximum force and rate of force and did not cause impact forces. Thus, this type of push-up exercise may be regarded as the best for improving explosive force. The FPU exercise achieved higher levels of muscular activation in the agonist and synergist muscle groups, and greater impact forces and impact force development rates.

  5. Enzyme immobilization in porous silicon: quantitative analysis of the kinetic parameters for glutathione-S-transferases.

    PubMed

    Delouise, Lisa A; Miller, Benjamin L

    2005-04-01

    Porous silicon matrixes are attractive materials for the construction of biosensors and may also have utility for the production of immobilized enzyme bioreactors. In an effort to gain a quantitative understanding of the effects of immobilization on enzyme activity, we compared the activity of glutathione-S-transferase immobilized in electrochemically etched porous silicon films (approximately 6.5 microm thick) with the enzyme in solution. Kinetic measurements were made by varying the glutathione concentration while maintaining a fixed saturating concentration of 1-chloro-2,4-dinitrobenzene. The reaction kinetics follow steady-state equilibrium behavior. The specific activity of the free enzyme in solution is approximately 4x higher than the immobilized enzyme, for which we measured an apparent K'(m)(GSH) value of 1.0 +/- 0.3. The maximum velocity, V'(max), is linearly proportional to immobilized enzyme concentration, but the magnitude is approximately 20 times lower than that in solution. Results suggest approximately 25% of the enzyme is bound with the catalytic site in an inactive conformation or in a hindered orientation. Finally, the effects of hydration and exposure to denaturants on the immobilized enzyme activity are presented.

  6. Submaximal oxygen uptake kinetics, functional mobility, and physical activity in older adults with heart failure and reduced ejection fraction

    PubMed Central

    Hummel, Scott L; Herald, John; Alpert, Craig; Gretebeck, Kimberlee A; Champoux, Wendy S; Dengel, Donald R; Vaitkevicius, Peter V; Alexander, Neil B

    2016-01-01

    Background Submaximal oxygen uptake measures are more feasible and may better predict clinical cardiac outcomes than maximal tests in older adults with heart failure (HF). We examined relationships between maximal oxygen uptake, submaximal oxygen kinetics, functional mobility, and physical activity in older adults with HF and reduced ejection fraction. Methods Older adults with HF and reduced ejection fraction (n = 25, age 75 ± 7 years) were compared to 25 healthy age- and gender-matched controls. Assessments included a maximal treadmill test for peak oxygen uptake (VO2peak), oxygen uptake kinetics at onset of and on recovery from a submaximal treadmill test, functional mobility testing [Get Up and Go (GUG), Comfortable Gait Speed (CGS), Unipedal Stance (US)], and self-reported physical activity (PA). Results Compared to controls, HF had worse performance on GUG, CGS, and US, greater delays in submaximal oxygen uptake kinetics, and lower PA. In controls, VO2peak was more strongly associated with functional mobility and PA than submaximal oxygen uptake kinetics. In HF patients, submaximal oxygen uptake kinetics were similarly associated with GUG and CGS as VO2peak, but weakly associated with PA. Conclusions Based on their mobility performance, older HF patients with reduced ejection fraction are at risk for adverse functional outcomes. In this population, submaximal oxygen uptake measures may be equivalent to VO2 peak in predicting functional mobility, and in addition to being more feasible, may provide better insight into how aerobic function relates to mobility in older adults with HF. PMID:27594875

  7. Theoretical analysis of the kinetic performance of laboratory- and full-scale composting systems.

    PubMed

    Baptista, Marco; Silveira, Ana; Antunes, Fernando

    2012-07-01

    Composting research at laboratory-scale is critical for the development of optimized full-scale plants. Discrepancies between processes at laboratory-scale and full-scale systems have been investigated in terms of heat balances, but a kinetic analysis of this issue is still missing. In this study, the composting rate at laboratory-scale was, on average, between 1.9 and 5.7 times faster than in full-scale systems for a set of published studies using municipal solid waste, food waste or similar materials. Laboratory-scale performance and full-scale systems were limited to 71 and 46%, respectively, of their maximum potential due to poor management of environmental process conditions far from their optimum. The main limiting environmental factor was found to be moisture content, followed by temperature. Besides environmental factors, waste composition and particle size were identified as factors accounting for kinetic differences between laboratory- and full-scale systems. Overall, this study identifies those factors that affect the kinetics of the composting process most and revealed a significant margin for reducing process time in full-scale composting.

  8. Direct determination of enzyme kinetic parameters from single reactions using a new progress curve analysis tool.

    PubMed

    Bäuerle, Felix; Zotter, Agnes; Schreiber, Gideon

    2016-10-15

    With computer-based data-fitting methods becoming a standard tool in biochemistry, progress curve analysis of enzyme kinetics is a feasible, yet seldom used tool. Here we present a versatile Matlab-based tool (PCAT) to analyze catalysis progress curves with three complementary model approaches. The first two models are based on the known closed-form solution for this problem: the first describes the required Lambert W function with an analytical approximation and the second provides a numerical solution of the Lambert W function. The third model is a direct simulation of the enzyme kinetics. Depending on the chosen model, the tools excel in speed, accuracy or initial value requirements. Using simulated and experimental data, we show the strengths and pitfalls of the different fitting models. Direct simulation proves to have the highest level of accuracy, but it also requires reasonable initial values to converge. Finally, we propose a standard procedure to obtain optimized enzyme kinetic parameters from single progress curves.

  9. Solvent-induced lysozyme gels: rheology, fractal analysis, and sol-gel kinetics.

    PubMed

    da Silva, Marcelo A; Arêas, Elizabeth P G

    2005-09-15

    In this work, the gelation kinetics and fractal character of lysozyme gel matrices developed in tetramethylurea (TMU)-water media were investigated. Gelation times were determined from the temporal crossover point between the storage, G', and loss, G'', moduli, as a function of the binary solvent composition and of protein concentration. The inverse dependence of the upper limit of the linear viscoelastic region (gamma0) on protein concentration indicate that the lysozyme gels belong to the "strong link" kind, a gel category where interparticle links are stronger than intraparticle ones. Lysozyme gel fractal dimensions (Df) were determined from the analysis of rheological data according to a scaling theory by Shih et al. [Phys. Rev. A 42 (1990) 4772-4779] and were found to be compatible with a diffusion-limited cluster-aggregation kinetics (DLCA) for lysozyme gels formed at the TMU mass fraction in the binary organic-aqueous solvent, wTMU=0.9, and with a reaction-limited cluster aggregation kinetics (RLCA) for wTMU in the 0.6< or =wTMU< or =0.8 range.

  10. Quantification of exocytosis kinetics by DIC image analysis of cortical lawns.

    PubMed

    Mooney, James; Thakur, Saumitra; Kahng, Peter; Trapani, Josef G; Poccia, Dominic

    2014-04-01

    Cortical lawns prepared from sea urchin eggs have offered a robust in vitro system for study of regulated exocytosis and membrane fusion events since their introduction by Vacquier almost 40 years ago (Vacquier in Dev Biol 43:62-74, 1975). Lawns have been imaged by phase contrast, darkfield, differential interference contrast, and electron microscopy. Quantification of exocytosis kinetics has been achieved primarily by light scattering assays. We present simple differential interference contrast image analysis procedures for quantifying the kinetics and extent of exocytosis in cortical lawns using an open vessel that allows rapid solvent equilibration and modification. These preparations maintain the architecture of the original cortices, allow for cytological and immunocytochemical analyses, and permit quantification of variation within and between lawns. When combined, these methods can shed light on factors controlling the rate of secretion in a spatially relevant cellular context. We additionally provide a subroutine for IGOR Pro® that converts raw data from line scans of cortical lawns into kinetic profiles of exocytosis. Rapid image acquisition reveals spatial variations in time of initiation of individual granule fusion events with the plasma membrane not previously reported.

  11. Curing kinetics of visible light curing dental resin composites investigated by dielectric analysis (DEA).

    PubMed

    Steinhaus, Johannes; Hausnerova, Berenika; Haenel, Thomas; Großgarten, Mandy; Möginger, Bernhard

    2014-03-01

    During the curing process of light curing dental composites the mobility of molecules and molecule segments is reduced leading to a significant increase of the viscosity as well as the ion viscosity. Thus, the kinetics of the curing behavior of 6 different composites was derived from dielectric analysis (DEA) using especially redesigned flat sensors with interdigit comb electrodes allowing for irradiation at the top side and measuring the ion viscosity at the bottom side. As the ion viscosities of dental composites change 1-3 orders of magnitude during the curing process, DEA provides a sensitive approach to evaluate their curing behavior, especially in the phase of undisturbed chain growth. In order to determine quantitative kinetic parameters a kinetic model is presented and examined for the evaluation of the ion viscosity curves. From the obtained results it is seen that DEA might be employed in the investigation of the primary curing process, the quality assurance of ingredients as well as the control of processing stability of the light curing dental composites.

  12. Fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics.

    PubMed

    Pujol-Vila, F; Vigués, N; Díaz-González, M; Muñoz-Berbel, X; Mas, J

    2015-05-15

    Global urban and industrial growth, with the associated environmental contamination, is promoting the development of rapid and inexpensive general toxicity methods. Current microbial methodologies for general toxicity determination rely on either bioluminescent bacteria and specific medium solution (i.e. Microtox(®)) or low sensitivity and diffusion limited protocols (i.e. amperometric microbial respirometry). In this work, fast and sensitive optical toxicity bioassay based on dual wavelength analysis of bacterial ferricyanide reduction kinetics is presented, using Escherichia coli as a bacterial model. Ferricyanide reduction kinetic analysis (variation of ferricyanide absorption with time), much more sensitive than single absorbance measurements, allowed for direct and fast toxicity determination without pre-incubation steps (assay time=10 min) and minimizing biomass interference. Dual wavelength analysis at 405 (ferricyanide and biomass) and 550 nm (biomass), allowed for ferricyanide monitoring without interference of biomass scattering. On the other hand, refractive index (RI) matching with saccharose reduced bacterial light scattering around 50%, expanding the analytical linear range in the determination of absorbent molecules. With this method, different toxicants such as metals and organic compounds were analyzed with good sensitivities. Half maximal effective concentrations (EC50) obtained after 10 min bioassay, 2.9, 1.0, 0.7 and 18.3 mg L(-1) for copper, zinc, acetic acid and 2-phenylethanol respectively, were in agreement with previously reported values for longer bioassays (around 60 min). This method represents a promising alternative for fast and sensitive water toxicity monitoring, opening the possibility of quick in situ analysis.

  13. Chromatographic preparation and kinetic analysis of interactions between tabun enantiomers and acetylcholinesterase.

    PubMed

    Tenberken, O; Thiermann, H; Worek, F; Reiter, G

    2010-06-02

    The easy accessibility to highly toxic OP (organophosphorus)-type chemical warfare agents (nerve agents) underlines the necessity for an effective medical treatment. Acute OP toxicity is primarily caused by inhibition of acetylcholinesterase (AChE, EC 3.1.1.7). Reactivators (oximes) of inhibited AChE are a mainstay of treatment. However, the commercially available compounds, obidoxime and pralidoxime, are considered rather ineffective against various nerve agents, including tabun. OP-type chemical warfare agents include an asymmetrical P-atom and consist of at least two stereoisomers. Previous studies with the nerve agents sarin and soman showed marked differences between (-)- and (+)-P isomers regarding AChE inhibition and stability in biological matrices. Hence, stereoselectivity is a key parameter for the development of optimized treatment. In the present study, the tabun enantiomers were isolated by semi-preparative liquid-chromatography (LC) with offline analysis by GC-PCI-MS and final characterization of optical purity (99.98% (-)-tabun and 99.83% (+)-tabun) and specific optical rotation. The inhibition and reactivation kinetics of the tabun enantiomers were determined with human and swine AChE and the aging kinetics with human AChE. The results show a large difference in the inhibitory potency between (-)- and (+)-tabun. The determination of reactivation and aging kinetics indicates that both reactions are at least in part determined by the residual (-)-tabun contamination (0.17%) of the (+)-tabun preparation. These data provide further insight into the kinetic interactions between tabun enantiomers and AChE and may contribute to the development of more effective treatment options.

  14. CCN spectra, hygroscopicity, and droplet activation kinetics of secondary organic aerosol resulting from the 2010 Deepwater Horizon oil spill.

    PubMed

    Moore, Richard H; Raatikainen, Tomi; Langridge, Justin M; Bahreini, Roya; Brock, Charles A; Holloway, John S; Lack, Daniel A; Middlebrook, Ann M; Perring, Anne E; Schwarz, Joshua P; Spackman, J Ryan; Nenes, Athanasios

    2012-03-20

    Secondary organic aerosol (SOA) resulting from the oxidation of organic species emitted by the Deepwater Horizon oil spill were sampled during two survey flights conducted by a National Oceanic and Atmospheric Administration WP-3D aircraft in June 2010. A new technique for fast measurements of cloud condensation nuclei (CCN) supersaturation spectra called Scanning Flow CCN Analysis was deployed for the first time on an airborne platform. Retrieved CCN spectra show that most particles act as CCN above (0.3 ± 0.05)% supersaturation, which increased to (0.4 ± 0.1)% supersaturation for the most organic-rich aerosol sampled. The aerosol hygroscopicity parameter, κ, was inferred from both measurements of CCN activity and from humidified-particle light extinction, and varied from 0.05 to 0.10 within the emissions plumes. However, κ values were lower than expected from chemical composition measurements, indicating a degree of external mixing or size-dependent chemistry, which was reconciled assuming bimodal, size-dependent composition. The CCN droplet effective water uptake coefficient, γ(cond), was inferred from the data using a comprehensive instrument model, and no significant delay in droplet activation kinetics from the presence of organics was observed, despite a large fraction of hydrocarbon-like SOA present in the aerosol.

  15. Kinetics of photo-activated charge carriers in Sn:CdS

    NASA Astrophysics Data System (ADS)

    Patidar, Manju Mishra; Panda, Richa; Gorli, V. R.; Gangrade, Mohan; Nath, R.; Ganesan, V.

    2016-05-01

    Kinetics of the photo-activated charge carriers has been investigated in Tin substituted Cadmium Sulphide, Cd1-xSnxS (x=0, 0.05, 0.10 and 0.15), thin films prepared by spray pyrolysis. X-Ray Diffraction shows an increase in strain that resulted in the decreased crystallite size upon Sn substitution. At the first sight, the photo current characteristics show a quenching effect on Sn substitution. However, survival of persistent photocurrents is seen even up to 15% of Sn substitution. Transient photo current decay could be explained with a 2τ relaxation model. CdS normally has an n-type character and the Sn doping expected to inject hole carriers. The two fold increase in τ1, increase in activation energy and the decrease in photocurrents upon Sn substitution point towards a band gap cleaning scenario that include compensation and associated carrier injection dynamics. In addition Atomic Force Microscopy shows a drastic change in microstructure that modulates the carrier dynamics as a whole.

  16. Effect of acoustically assisted treatments on vitamins, antioxidant activity, organic acids and drying kinetics of pineapple.

    PubMed

    Rodríguez, Óscar; Gomes, Wesley; Rodrigues, Sueli; Fernandes, Fabiano A N

    2017-03-01

    The effects of the application of an acoustically assisted treatment on the vitamins (C, B1, B2, B3, and B5), the antioxidant activity (DPPH, FRAP), the polyphenol and flavonoid contents, the organic acid contents (citric and malic) and drying kinetics of pineapple (Ananas comosus var. Perola) have been studied. Treatments were carried out using two different soaking media: distilled water and pineapple juice at 30°C during 10, 20 and 30min without and with acoustic assistance (23.2W/L). After treatment, samples were dried at 60°C and 0.5m/s during 8h. The quality parameters were determined in untreated, treated, and treated-dried samples. The acoustic assistance promoted an increment of vitamins B1, B2, B3 and B5, total flavonoid and malic acid contents, and a reduction of vitamin C, total polyphenol content, antioxidant activity and citric acid content in treated samples. However, in all treated-dried samples the final content of those quality parameters was higher than the observed in the untreated dried sample.

  17. Active food packaging based on molecularly imprinted polymers: study of the release kinetics of ferulic acid.

    PubMed

    Otero-Pazos, Pablo; Rodríguez-Bernaldo de Quirós, Ana; Sendón, Raquel; Benito-Peña, Elena; González-Vallejo, Victoria; Moreno-Bondi, M Cruz; Angulo, Immaculada; Paseiro-Losada, Perfecto

    2014-11-19

    A novel active packaging based on molecularly imprinted polymer (MIP) was developed for the controlled release of ferulic acid. The release kinetics of ferulic acid from the active system to food simulants (10, 20, and 50% ethanol (v/v), 3% acetic acid (w/v), and vegetable oil), substitutes (95% ethanol (v/v) and isooctane), and real food samples at different temperatures were studied. The key parameters of the diffusion process were calculated by using a mathematical modeling based on Fick's second law. The ferulic acid release was affected by the temperature as well as the percentage of ethanol of the simulant. The fastest release occurred in 95% ethanol (v/v) at 20 °C. The diffusion coefficients (D) obtained ranged between 1.8 × 10(-11) and 4.2 × 10(-9) cm(2)/s. A very good correlation between experimental and estimated data was obtained, and consequently the model could be used to predict the release of ferulic acid into food simulants and real food samples.

  18. Molecular and Kinetic Characterization of Planktonic Nitrospira spp. Selectively Enriched from Activated Sludge.

    PubMed

    Park, Mee-Rye; Park, Hongkeun; Chandran, Kartik

    2017-03-07

    Nitrospira spp. are chemolithoautotrophic nitrite-oxidizing bacteria (NOB), which are ubiquitous in natural and engineered environments. However, there exist few independent biokinetic studies on Nitrospira spp., likely because their isolation and selective enrichment from environmental consortia such as activated sludge can be challenging. Herein, planktonic Nitrospira spp. cultures closely related to Candidatus Nitrospira defluvii (Nitrospira lineage I) were successfully enriched from activated sludge in a sequencing batch reactor by maintaining sustained limiting extant nitrite and dissolved oxygen concentrations. Morphologically, the enrichment consisted largely of planktonic cells with an average characteristic diameter of 1.3 ± 0.6 μm. On the basis of respirometric assays, estimated maximum specific growth rate (μmax), nitrite half saturation coefficient (KS), oxygen half saturation coefficient (KO), and biomass yield coefficient (Y) of the enriched cultures were 0.69 ± 0.10 d(-1), 0.52 ± 0.14 mg-N/L, 0.33 ± 0.14 mg-O2/L, and 0.14 ± 0.02 mg-COD/mg-N, respectively. These parameters collectively reflect not just higher affinities of this enrichment for nitrite and oxygen, respectively, but also a higher biomass yield and energy transfer efficiency relative to Nitrobacter spp. Used in combination, these kinetic and thermodynamic parameters can help toward the development and application of energy-efficient biological nutrient removal processes through effective Nitrospira out-selection.

  19. A two-dimensional adsorption kinetic model for thermal hysteresis activity in antifreeze proteins

    NASA Astrophysics Data System (ADS)

    Li, Q. Z.; Yeh, Y.; Liu, J. J.; Feeney, R. E.; Krishnan, V. V.

    2006-05-01

    Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs), collectively abbreviated as AF(G)Ps, are synthesized by various organisms to enable their cells to survive in subzero environments. Although the AF(G)Ps are markedly diverse in structure, they all function by adsorbing to the surface of embryonic ice crystals to inhibit their growth. This adsorption results in a freezing temperature depression without an appreciable change in the melting temperature. The difference between the melting and freezing temperatures, termed thermal hysteresis (TH), is used to detect and quantify the antifreeze activity. Insights from crystallographic structures of a number of AFPs have led to a good understanding of the ice-protein interaction features. Computational studies have focused either on verifying a specific model of AFP-ice interaction or on understanding the protein-induced changes in the ice crystal morphology. In order to explain the origin of TH, we propose a novel two-dimensional adsorption kinetic model between AFPs and ice crystal surfaces. The validity of the model has been demonstrated by reproducing the TH curve on two different β-helical AFPs upon increasing the protein concentration. In particular, this model is able to accommodate the change in the TH behavior observed experimentally when the size of the AFPs is increased systematically. Our results suggest that in addition to the specificity of the AFPs for the ice, the coverage of the AFPs on the ice surface is an equally necessary condition for their TH activity.

  20. Elution kinetics, antimicrobial activity, and mechanical properties of 11 different antibiotic loaded acrylic bone cement.

    PubMed

    Gálvez-López, Ruben; Peña-Monje, Alejandro; Antelo-Lorenzo, Ramón; Guardia-Olmedo, Juan; Moliz, Juan; Hernández-Quero, José; Parra-Ruiz, Jorge

    2014-01-01

    Antibiotic-loaded acrylic bone cements (ALABC) spacers are routinely used in the treatment of prosthetic joint infections. The objectives of our study were to evaluate different ALABC for elution kinetics, thermal stability, and mechanical properties. A 10 or 20% mixture (w/w) beads of medium viscosity bone cement (DePuy, Inc) and vancomycin (VAN), gentamycin (GM), daptomycin (DAP), moxifloxacin (MOX), rifampicin (RIF), cefotaxime (CTX), cefepime (FEP), amoxicillin clavulanate (AmC), ampicillin (AMP), meropenem (MER), and ertapenem (ERT) were formed and placed into wells filled with phosphate-buffered saline. Antibiotic concentrations were determined using high-performance liquid chromatography. Antimicrobial activity was tested against Micrococcus luteus ATCC 9341 or Escherichia coli ATCC 25922. AmC, AMP, and FEP concentration rapidly decreased after day 2, being almost undetectable at day 4. Sustained and high elution rates were observed with VAN, GM, MOX, and RIF for the 30-day duration of the experiment. DAP, MER, ERT, and CTX elution rates constantly decreased from day 4. All antibiotics tested retained antimicrobial activity proving thermal stability. Mechanical properties of ALABC were maintained except when RIF was used.

  1. Pattern, growth, and aging in aggregation kinetics of a Vicsek-like active matter model

    NASA Astrophysics Data System (ADS)

    Das, Subir K.

    2017-01-01

    Via molecular dynamics simulations, we study kinetics in a Vicsek-like phase-separating active matter model. Quantitative results, for isotropic bicontinuous pattern, are presented on the structure, growth, and aging. These are obtained via the two-point equal-time density-density correlation function, the average domain length, and the two-time density autocorrelation function. Both the correlation functions exhibit basic scaling properties, implying self-similarity in the pattern dynamics, for which the average domain size exhibits a power-law growth in time. The equal-time correlation has a short distance behavior that provides reasonable agreement between the corresponding structure factor tail and the Porod law. The autocorrelation decay is a power-law in the average domain size. Apart from these basic similarities, the overall quantitative behavior of the above-mentioned observables is found to be vastly different from those of the corresponding passive limit of the model which also undergoes phase separation. The functional forms of these have been quantified. An exceptionally rapid growth in the active system occurs due to fast coherent motion of the particles, mean-squared-displacements of which exhibit multiple scaling regimes, including a long time ballistic one.

  2. Kinetic study on the tyrosinase and melanin formation inhibitory activities of carthamus yellow isolated from Carthamus tinctorius L.

    PubMed

    Chen, Yi-Shyan; Lee, Shu-Mei; Lin, Chih-Chien; Liu, Chia-Yi; Wu, Meng-Chen; Shi, Wun-Ling

    2013-03-01

    Carthamus yellow (CY) is the major component of the yellow pigments of Carthamus tinctorius L. CY has been extensively used as a natural color additive for food and cosmetics. Here, our results demonstrate that carthamus yellow reduced the activity of mushroom tyrosinase in a dose-dependent manner with a half maximal inhibitory concentration (IC(50)) value of approximately 1.01 ± 0.03 mg/mL. A kinetic study of carthamus yellow on tyrosinase exhibited a mode of competitive inhibition with a Ki of 0.607 mg/mL. Moreover, cell viability analysis indicated that carthamus yellow used at concentrations of 1.0-4.0 mg/mL had no cytotoxicity in B16F10 melanoma cells. Melanin content analysis showed that melanin production in B16F10 melanoma cells treated with 4 mg/mL carthamus yellow can decrease to 82.3 ± 0.4% of the levels of melanin production of untreated cells. Thus, carthamus yellow has the potential to become a useful skin-whitening agent in the future.

  3. Kinetic Features of L,D-Transpeptidase Inactivation Critical for β-Lactam Antibacterial Activity

    PubMed Central

    Lecoq, Lauriane; Bougault, Catherine; Mainardi, Jean-Luc; Rice, Louis B.; Ethève-Quelquejeu, Mélanie; Gutmann, Laurent; Marie, Arul; Dubost, Lionel; Hugonnet, Jean-Emmanuel; Simorre, Jean-Pierre; Arthur, Michel

    2013-01-01

    Active-site serine D,D-transpeptidases belonging to the penicillin-binding protein family (PBPs) have been considered for a long time as essential for peptidoglycan cross-linking in all bacteria. However, bypass of the PBPs by an L,D-transpeptidase (Ldtfm) conveys high-level resistance to β-lactams of the penam class in Enterococcus faecium with a minimal inhibitory concentration (MIC) of ampicillin >2,000 µg/ml. Unexpectedly, Ldtfm does not confer resistance to β-lactams of the carbapenem class (imipenem MIC = 0.5 µg/ml) whereas cephems display residual activity (ceftriaxone MIC = 128 µg/ml). Mass spectrometry, fluorescence kinetics, and NMR chemical shift perturbation experiments were performed to explore the basis for this specificity and identify β-lactam features that are critical for efficient L,D-transpeptidase inactivation. We show that imipenem, ceftriaxone, and ampicillin acylate Ldtfm by formation of a thioester bond between the active-site cysteine and the β-lactam-ring carbonyl. However, slow acylation and slow acylenzyme hydrolysis resulted in partial Ldtfm inactivation by ampicillin and ceftriaxone. For ampicillin, Ldtfm acylation was followed by rupture of the C5–C6 bond of the β-lactam ring and formation of a secondary acylenzyme prone to hydrolysis. The saturable step of the catalytic cycle was the reversible formation of a tetrahedral intermediate (oxyanion) without significant accumulation of a non-covalent complex. In agreement, a derivative of Ldtfm blocked in acylation bound ertapenem (a carbapenem), ceftriaxone, and ampicillin with similar low affinities. Thus, oxyanion and acylenzyme stabilization are both critical for rapid L,D-transpeptidase inactivation and antibacterial activity. These results pave the way for optimization of the β-lactam scaffold for L,D-transpeptidase-inactivation. PMID:23861815

  4. Kinetic analysis of Enterococcus faecium L,D-transpeptidase inactivation by carbapenems.

    PubMed

    Dubée, Vincent; Arthur, Michel; Fief, Hélène; Triboulet, Sébastien; Mainardi, Jean-Luc; Gutmann, Laurent; Sollogoub, Matthieu; Rice, Louis B; Ethève-Quelquejeu, Mélanie; Hugonnet, Jean-Emmanuel

    2012-06-01

    Bypass of classical penicillin-binding proteins by the L,D-transpeptidase of Enterococcus faecium (Ldt(fm)) leads to high-level ampicillin resistance in E. faecium mutants, whereas carbapenems remain the lone highly active β-lactams. Kinetics of Ldt(fm) inactivation was determined for four commercial carbapenems and a derivative obtained by introducing a minimal ethyl group at position 2. We show that the bulky side chains of commercial carbapenems have both positive and negative effects in preventing hydrolysis of the acyl enzyme and impairing drug binding.

  5. Determination of kinetic parameters of Phlomis bovei de Noé using thermogravimetric analysis.

    PubMed

    Yahiaoui, Meriem; Hadoun, Hocine; Toumert, Idir; Hassani, Aicha

    2015-11-01

    This paper reports the pyrolysis study of Phlomis bovei biomass by thermogravimetric experiments in order to determine the thermal degradation behavior and kinetic parameters. The weight losses were found to occur in three stages. In the DTG thermograms, an increase of the heating rate tended to delay thermal degradation processes towards higher temperatures. The average values of activation energy and pre-exponential factor calculated from Ozawa-Flynn-Wall, Kissinger-Akahira-Sunose and Kissinger methods are 134.83, 134.06, 223.31kJ/mol and 4.1610(13), 1.1810(10), 2.8110(11)/s, respectively. The three-pseudo-component method shows that the activation energy increases with increasing the heating rate for hemicellulose and cellulose while the activation energy of the lignin decreased with an increase of the heating rate. Predicted results and experimental data exhibit similar tendencies and the three pseudo-components model with n different from unity 1 is recommended as the most suitable for prediction of kinetic behavior of Phlomis bovei de Noé.

  6. Transient Kinetic Analysis of Hydrogen Sulfide Oxidation Catalyzed by Human Sulfide Quinone Oxidoreductase.

    PubMed

    Mishanina, Tatiana V; Yadav, Pramod K; Ballou, David P; Banerjee, Ruma

    2015-10-09

    The first step in the mitochondrial sulfide oxidation pathway is catalyzed by sulfide quinone oxidoreductase (SQR), which belongs to the family of flavoprotein disulfide oxidoreductases. During the catalytic cycle, the flavin cofactor is intermittently reduced by sulfide and oxidized by ubiquinone, linking H2S oxidation to the electron transfer chain and to energy metabolism. Human SQR can use multiple thiophilic acceptors, including sulfide, sulfite, and glutathione, to form as products, hydrodisulfide, thiosulfate, and glutathione persulfide, respectively. In this study, we have used transient kinetics to examine the mechanism of the flavin reductive half-reaction and have determined the redox potential of the bound flavin to be -123 ± 7 mV. We observe formation of an unusually intense charge-transfer (CT) complex when the enzyme is exposed to sulfide and unexpectedly, when it is exposed to sulfite. In the canonical reaction, sulfide serves as the sulfur donor and sulfite serves as the acceptor, forming thiosulfate. We show that thiosulfate is also formed when sulfide is added to the sulfite-induced CT intermediate, representing a new mechanism for thiosulfate formation. The CT complex is formed at a kinetically competent rate by reaction with sulfide but not with sulfite. Our study indicates that sulfide addition to the active site disulfide is preferred under normal turnover conditions. However, under pathological conditions when sulfite concentrations are high, sulfite could compete with sulfide for addition to the active site disulfide, leading to attenuation of SQR activity and to an alternate route for thiosulfate formation.

  7. Blood, urine, and hair kinetic analysis following an acute lead intoxication.

    PubMed

    Ho, G; Keutgens, A; Schoofs, R; Kotolenko, S; Denooz, R; Charlier, C

    2011-01-01

    A case of lead exposure resulting from the accidental ingestion of a lead-containing solution is reported. Because of clinical management rapidly performed through chelation therapy by 2,3-dimercaptopropane sulfonate sodium and meso-2,3-dimercaptosuccinic acid, blood lead levels of this 51-year-old patient were moderate (412.9 μg/L) and no clinical symptoms were observed. Numerous blood and urine samples were collected for kinetic analysis of lead elimination. However, we report the first case in which hair samples were analyzed to determine the excretion level of lead after acute intoxication.

  8. A kinetic and equilibrium analysis of silicon carbide chemical vapor deposition on monofilaments

    NASA Technical Reports Server (NTRS)

    Gokoglu, S. A.; Kuczmarski, M. A.

    1993-01-01

    Chemical kinetics of atmospheric pressure silicon carbide (SiC) chemical vapor deposition (CVD) from dilute silane and propane source gases in hydrogen is numerically analyzed in a cylindrical upflow reactor designed for CVD on monofilaments. The chemical composition of the SiC deposit is assessed both from the calculated total fluxes of carbon and silicon and from chemical equilibrium considerations for the prevailing temperatures and species concentrations at and along the filament surface. The effects of gas and surface chemistry on the evolution of major gas phase species are considered in the analysis.

  9. Exploring Secondary Students' Understanding of Chemical Kinetics through Inquiry-Based Learning Activities

    ERIC Educational Resources Information Center

    Chairam, Sanoe; Klahan, Nutsuda; Coll, Richard K.

    2015-01-01

    This research is trying to evaluate the feedback of Thai secondary school students to inquiry-based teaching and learning methods, exemplified by the study of chemical kinetics. This work used the multiple-choice questions, scientifically practical diagram and questionnaire to assess students' understanding of chemical kinetics. The findings…

  10. DURIP: Electrokinetic Injection and Separation System for Analysis of Protein and Peptide Transport, Adsorption and Kinetics Instrumentation Proposal

    DTIC Science & Technology

    2015-03-18

    SECURITY CLASSIFICATION OF: We requested equipment necessary to build an electrokinetic injection and separation system for the analysis of protein...Jul-2014 Approved for Public Release; Distribution Unlimited Final Report: DURIP: Electrokinetic Injection and Separation System for Analysis of...Injection and Separation System for Analysis of Protein and Peptide Transport, Adsorption and Kinetics Instrumentation Proposal Report Title We requested

  11. Developmental kinetics of pig embryos by parthenogenetic activation or by handmade cloning.

    PubMed

    Li, J; Li, R; Liu, Y; Villemoes, K; Purup, S; Callesen, H

    2013-10-01

    The developmental kinetics of pig embryos produced by parthenogenetic activation without (PAZF) or with (PAZI) zona pellucida or by handmade cloning (HMC) was compared by time-lapse videography. After cumulus cell removal, the matured oocytes were either left zona intact (PAZI) or were made zona free by pronase digestion (PAZF) before they were activated (PA). Other matured oocytes were used for HMC based on foetal fibroblast cells. On Day 0 (day of PA or reconstruction), the embryos were cultured for 7 days in vitro in our time-lapse system. Pictures were taken every 30 min, and afterwards, each cell cycle was identified for each embryo to be analysed. Results showed that the PA embryos (both PAZF and PAZI) had shorter first cell cycle compared with HMC (17.4. 17.8 vs 23.6 h), but had a longer time length from four cell to morula stages (57.9, 53.8 vs 44.9 h). However, at the second cell cycle, PAZF embryos needed shorter time, while PAZI embryos had similar time length as HMC embryos, and both were longer than PAZF (23.4, 24.8 vs 14.6 h). Both PAZF and PAZI embryos used similar time to reach the blastocyst stage, and this was later than HMC embryos. In addition, when all of these embryos were grouped into viable (developed to blastocysts) and non-viable (not developed to blastocysts), the only difference in the time length was observed on the first cell cycle (18.6 vs 24.5 h), but not on the later cell cycles. In conclusion, our results not only give detailed information regarding the time schedule of in vitro-handled pig embryos, but also indicate that the first cell cycle could be used as a selecting marker for embryo viability. However, to evaluate the effect of the produced techniques, the whole time schedule of the pre-implantation developmental kinetics should be observed.

  12. Silica coating and photocatalytic activities of ZnO nanoparticles: effect of operational parameters and kinetic study.

    PubMed

    Ismail, L F M; Emara, M M; El-Moselhy, M M; Maziad, N A; Hussein, O K

    2014-10-15

    Silica-coating ZnO nanoparticles were prepared using the hydrothermal method. The prepared nanoparticles were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy dispersive X-ray Spectroscopy (EDX). It was found that ultrafine core/shell structured silica-coating ZnO nanoparticles were successfully obtained. TEM analysis revealed a continuous and uniform silica coating layer of about 8nm in thickness on the surface of ZnO nanoparticles. The photocatalytic performance of silica-coating ZnO core/shell nanoparticles in methylene blue aqueous solution was investigated. The effects of some operational parameters such as pH value, nanocatalyst loading and initial MB concentration on the degradation efficiency were discussed. Kinetic parameters were experimentally determined and a pseudo-first-order kinetic was observed. Thus, the main advantage of the coating is the stability of the photocatalysts and the better performance in acidic or alkaline solutions. Compared to ZnO the maximum apparent rate constant is obtained at pH 8.5 (pH 11.5 in case of bare ZnO). Moreover, the Langmuir adsorption model was applied to describe the equilibrium isotherm at different MB concentration. The applicability of the Langmuir isotherm suggests monolayer coverage of the MB onto surface of silica-coating ZnO nanoparticles. The kinetics of the adsorption with respect to the initial dye concentration, were also investigated. The pseudo-first-order and second-order kinetic models were used and the rate constants were evaluated. The kinetic studies revealed that the pseudo-second-order kinetic model better represented the adsorption kinetics, suggesting that the adsorption process may be chemisorption.

  13. Application of the distributed activation energy model to the kinetic study of pyrolysis of the fresh water algae Chlorococcum humicola.

    PubMed

    Kirtania, Kawnish; Bhattacharya, Sankar

    2012-03-01

    Apart from capturing carbon dioxide, fresh water algae can be used to produce biofuel. To assess the energy potential of Chlorococcum humicola, the alga's pyrolytic behavior was studied at heating rates of 5-20K/min in a thermobalance. To model the weight loss characteristics, an algorithm was developed based on the distributed activation energy model and applied to experimental data to extract the kinetics of the decomposition process. When the kinetic parameters estimated by this method were applied to another set of experimental data which were not used to estimate the parameters, the model was capable of predicting the pyrolysis behavior, in the new set of data with a R(2) value of 0.999479. The slow weight loss, that took place at the end of the pyrolysis process, was also accounted for by the proposed algorithm which is capable of predicting the pyrolysis kinetics of C. humicola at different heating rates.

  14. Kinetic and structural requirements for carbapenemase activity in GES-type β-lactamases

    DOE PAGES

    Stewart, Nichole K.; Smith, Clyde A.; Frase, Hilary; ...

    2014-12-08

    Carbapenems are the last resort antibiotics for treatment of life-threatening infections. The GES β-lactamases are important contributors to carbapenem resistance in clinical bacterial pathogens. A single amino acid difference at position 170 of the GES-1, GES-2, and GES-5 enzymes is responsible for the expansion of their substrate profile to include carbapenem antibiotics. This highlights the increasing need to understand the mechanisms by which the GES β-lactamases function to aid in development of novel therapeutics. We demonstrate that the catalytic efficiency of the enzymes with carbapenems meropenem, ertapenem, and doripenem progressively increases (100-fold) from GES-1 to -5, mainly due to anmore » increase in the rate of acylation. The data reveal that while acylation is rate limiting for GES-1 and GES-2 for all three carbapenems, acylation and deacylation are indistinguishable for GES-5. The ertapenem–GES-2 crystal structure shows that only the core structure of the antibiotic interacts with the active site of the GES-2 β-lactamase. The identical core structures of ertapenem, doripenem, and meropenem are likely responsible for the observed similarities in the kinetics with these carbapenems. The lack of a methyl group in the core structure of imipenem may provide a structural rationale for the increase in turnover of this carbapenem by the GES β-lactamases. As a result, our data also show that in GES-2 an extensive hydrogen-bonding network between the acyl-enzyme complex and the active site water attenuates activation of this water molecule, which results in poor deacylation by this enzyme.« less

  15. Kinetic and structural requirements for carbapenemase activity in GES-type β-lactamases

    SciTech Connect

    Stewart, Nichole K.; Smith, Clyde A.; Frase, Hilary; Black, D. J.; Vakulenko, Sergei B.

    2014-12-08

    Carbapenems are the last resort antibiotics for treatment of life-threatening infections. The GES β-lactamases are important contributors to carbapenem resistance in clinical bacterial pathogens. A single amino acid difference at position 170 of the GES-1, GES-2, and GES-5 enzymes is responsible for the expansion of their substrate profile to include carbapenem antibiotics. This highlights the increasing need to understand the mechanisms by which the GES β-lactamases function to aid in development of novel therapeutics. We demonstrate that the catalytic efficiency of the enzymes with carbapenems meropenem, ertapenem, and doripenem progressively increases (100-fold) from GES-1 to -5, mainly due to an increase in the rate of acylation. The data reveal that while acylation is rate limiting for GES-1 and GES-2 for all three carbapenems, acylation and deacylation are indistinguishable for GES-5. The ertapenem–GES-2 crystal structure shows that only the core structure of the antibiotic interacts with the active site of the GES-2 β-lactamase. The identical core structures of ertapenem, doripenem, and meropenem are likely responsible for the observed similarities in the kinetics with these carbapenems. The lack of a methyl group in the core structure of imipenem may provide a structural rationale for the increase in turnover of this carbapenem by the GES β-lactamases. As a result, our data also show that in GES-2 an extensive hydrogen-bonding network between the acyl-enzyme complex and the active site water attenuates activation of this water molecule, which results in poor deacylation by this enzyme.

  16. Importance of surface diffusivities in pesticide adsorption kinetics onto granular versus powdered activated carbon: experimental determination and modeling.

    PubMed

    Baup, S; Wolbert, D; Laplanche, A

    2002-10-01

    Three pesticides (atrazine, bromoxynil and diuron) and two granular activated carbons are involved in equilibrium and kinetic adsorption experiments. Equilibrium is represented by Freundlich isotherm law and kinetic is described by the Homogeneous Surface Diffusion Model, based on external mass transfer and intraparticle surface diffusion. Equilibrium and long-term experiments are conducted to compare Powdered Activated Carbon and Granular Activated Carbon. These first investigations show that crushing GAC into PAC improves the accessibility of the adsorption sites without increasing the number of these sites. In a second part, kinetics experiments are carried out using a Differential Column Batch Reactor. Thanks to this experimental device, the external mass transfer coefficient k(f) is calculated from empirical correlation and the effect of external mass transfer on adsorption is likely to be minimized. In order to obtain the intraparticle surface diffusion coefficient D. for these pesticides, comparisons between experimental kinetic data and simulations are conducted and the best agreement leads to the Ds coefficient. This procedure appears to be an efficient way to acquire surface diffusion coefficients for the adsorption of pesticides onto GAC. Finally it points out the role of surface diffusivity in the adsorption rate. As a matter of fact, even if the amount of the target-compound that could be potentially adsorbed is really important, its surface diffusion coefficient may be small, so that its adsorption may not have enough contact time to be totally achieved.

  17. Adsorption of Pb(II) ions from aqueous solution by native and activated bentonite: kinetic, equilibrium and thermodynamic study.

    PubMed

    Kul, Ali Riza; Koyuncu, Hülya

    2010-07-15

    In this study, the adsorption kinetics, equilibrium and thermodynamics of Pb(II) ions on native (NB) and acid activated (AAB) bentonites were examined. The specific surface areas, pore size and pore-size distributions of the samples were fully characterized. The adsorption efficiency of Pb(II) onto the NB and AAB was increased with increasing temperature. The kinetics of adsorption of Pb(II) ions was discussed using three kinetic models, the pseudo-first-order, the pseudo-second-order and the intra-particle diffusion model. The experimental data fitted very well the pseudo-second-order kinetic model. The initial sorption rate and the activation energy were also calculated. The activation energy of the sorption was calculated as 16.51 and 13.66 kJ mol(-1) for NB and AAB, respectively. Experimental results were also analysed by the Langmuir, Freundlich and Dubinin-Redushkevich (D-R) isotherm equations at different temperatures. R(L) separation factor for Langmuir and the n value for Freundlich isotherm show that Pb(II) ions are favorably adsorbed by NB and AAB. Thermodynamic quantities such as Gibbs free energy (DeltaG), the enthalpy (DeltaH) and the entropy change of sorption (DeltaS) were determined as about -5.06, 10.29 and 0.017 kJ mol(-1) K(-1), respectively for AAB. It was shown that the sorption processes were an endothermic reactions, controlled by physical mechanisms and spontaneously.

  18. Functional analysis, overexpression, and kinetic characterization of pyruvate kinase from methicillin-resistant Staphylococcus aureus.

    PubMed

    Zoraghi, Roya; See, Raymond H; Gong, Huansheng; Lian, Tian; Swayze, Rick; Finlay, B Brett; Brunham, Robert C; McMaster, William R; Reiner, Neil E

    2010-09-07

    Novel antimicrobial targets are urgently needed to overcome rising antibiotic resistance of important human pathogens including methicillin-resistant Staphylococcus aureus (MRSA). Here we report the essentiality and kinetic properties of MRSA pyruvate kinase (PK). Targetron-mediated gene disruption demonstrated PK is essential for S. aureus growth and survival, suggesting that this protein may be a potential drug target. The presence of the pfk (6-phosphofructokinase)-pyk operon in MRSA252, and the nonessential nature of PFK shown by targetron, further emphasized the essential role of PK in cell viability. The importance of PK in bacterial growth was confirmed by showing that its enzymatic activity peaked during the logarithmic phase of S. aureus growth. PK from Staphylococcus and several other species of bacteria have an extra C-terminal domain (CT) containing a phosphoenolpyruvate (PEP) binding motif. To elucidate the possible structure and function of this sequence, the quaternary structures and kinetic properties of the full-length MRSA PK and truncated MRSA PK lacking the CT domain were characterized. Our results showed that (1) MRSA PK is an allosteric enzyme with homotetramer architecture activated by AMP or ribose 5-phosphate (R5P), but not by fructose 1,6-bisphosphate (FBP), which suggests a different mode of allosteric regulation when compared with human isozymes, (2) the CT domain is not required for the tetramerization of the enzyme; homotetramerization occurred in a truncated PK lacking the domain, (3) truncated enzyme exhibited high affinity toward both PEP and ADP and exhibited hyperbolic kinetics toward PEP in the presence of activators (AMP and R5P) consistent with kinetic properties of full-length enzyme, indicating that the CT domain is not required for substrate binding or allosteric regulation observed in the holoenzyme, (4) the kinetic efficiency (k(cat)/S(0.5)) of truncated enzyme was decreased by 24- and 16-fold, in ligand-free state, toward

  19. Respirometric measurement of kinetic parameters: effect of activated sludge floc size.

    PubMed

    Chu, K H; van Veldhuizen, H M; van Loosdrecht, M C M

    2003-01-01

    The variation of activated sludge floc size with the mixing intensity of a mechanically stirred respirometer, expressed in terms of the mean energy dissipation rate, was characterized using a photometric dispersion analyzer. The floc size decreased rapidly when the energy dissipation rate was increased from 1.33 x 10(-3) to 2.68 x 10(-3) W/kg. Experiments were performed to investigate the effect of floc size on the oxygen saturation coefficient measured under the condition of acetate oxidation. The respirometric data were interpreted by considering only the kinetics of biochemical reactions. The variation of the oxygen saturation coefficient with mixing intensity was found to correlate with the variation of floc size with mixing intensity. The oxygen saturation coefficient was found to decrease from 0.23 to 0.08 mg/L when the mean energy dissipation rate was increased from 1.33 x 10(-3) to 2.68 x 10(-3) W/kg. The dependence of the oxygen saturation coefficient on floc size or mixing intensity suggests the presence of mass transfer resistances in large flocs.

  20. The Biginelli reaction with an imidazolium-tagged recyclable iron catalyst: kinetics, mechanism, and antitumoral activity.

    PubMed

    Ramos, Luciana M; Guido, Bruna C; Nobrega, Catharine C; Corrêa, José R; Silva, Rafael G; de Oliveira, Heibbe C B; Gomes, Alexandre F; Gozzo, Fábio C; Neto, Brenno A D

    2013-03-25

    The present work describes the synthesis, characterization, and application of a new ion-tagged iron catalyst. The catalyst was employed in the Biginelli reaction with impressive performance. High yields have been achieved when the reaction was carried out in imidazolium-based ionic liquids (BMI⋅PF6, BMI⋅NTf2, and BMI⋅BF4), thus showing that the ionic-liquid effects play a role in the reaction. Moreover, the ion-tagged catalyst could be recovered and reused up to eight times without any noticeable loss in activity. Mechanistic studies performed by using high-resolution electrospray-ionization quadrupole-time-of-flight mass (HR-EI-QTOF) spectrometry and kinetic experiments indicate only one reaction pathway and rule out the other two possibilities under the development conditions. The theoretical calculations are in accordance with the proposed mechanism of action of the iron catalyst. Finally, the 37 dihydropyrimidinone derivatives, products of the Biginelli reaction, had their cytotoxicity evaluated in assays against MCF-7 cancer cell linages with encouraging results of some derivatives, which were virtually non-toxic against healthy cell linages (fibroblasts).

  1. Peroxidase-coupled method for kinetic colorimetry of total creatine kinase activity in serum.

    PubMed

    Wimmer, M C; Artiss, J D; Zak, B

    1985-10-01

    We describe a peroxidase-coupled method involving a colorimetric indicator reaction for determining the total activity of creatine kinase (EC 2.7.3.2) in serum. The kinetically favorable reverse reaction is exploited to generate adenosine 5'-triphosphate, which is used in the glycerol kinase-catalyzed phosphorylation of glycerol. The glycerol 3-phosphate so generated is oxidized in the presence of alpha-glycerophosphate oxidase to produce hydrogen peroxide, which is reduced in the presence of peroxidase with the simultaneous oxidation and coupling of 4-aminoantipyrene and 2-hydroxy-3,5-dichlorobenzenesulfonate to produce an intensely colored red chromogen. Results of the proposed method (y) correlate well with those of the Boehringer-Mannheim "CK-NAC UV" method as applied to the Hitachi 705 chemistry analyzer (y = 1.025 chi - 18.1, r = 0.9985, n = 100, range = 19-4531 U/L). The sensitivity of the method, based on molar absorptivities, is nearly fourfold that of procedures involving the reduction of NADP+.

  2. In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity

    USGS Publications Warehouse

    Harris, S.H.; Smith, R.L.; Suflita, J.M.

    2007-01-01

    There are few methods available for broadly assessing microbial community metabolism directly within a groundwater environment. In this study, hydrogen consumption rates were estimated from in situ injection/withdrawal tests conducted in two geochemically varying, contaminated aquifers as an approach towards developing such a method. The hydrogen consumption first-order rates varied from 0.002 nM h-1 for an uncontaminated, aerobic site to 2.5 nM h-1 for a contaminated site where sulfate reduction was a predominant process. The method could accommodate the over three orders of magnitude range in rates that existed between subsurface sites. In a denitrifying zone, the hydrogen consumption rate (0.02 nM h-1) was immediately abolished in the presence of air or an antibiotic mixture, suggesting that such measurements may also be sensitive to the effects of environmental perturbations on field microbial activities. Comparable laboratory determinations with sediment slurries exhibited hydrogen consumption kinetics that differed substantially from the field estimates. Because anaerobic degradation of organic matter relies on the rapid consumption of hydrogen and subsequent maintenance at low levels, such in situ measures of hydrogen turnover can serve as a key indicator of the functioning of microbial food webs and may be more reliable than laboratory determinations. ?? 2007 Federation of European Microbiological Societies.

  3. Detailed characterization of lithium diffusion mechanisms in crystalline silicon using the kinetic Activation-Relaxation Technique

    NASA Astrophysics Data System (ADS)

    Trochet, Mickaël; Restrepo Gutierrez, Oscar Antonio; Mousseau, Normand

    Silicon displays a potential for high-capacity anode material for lithium-ion batteries as it can absorb large quantities of this metal. Yet, very little is understood about the evolution of diffusion mechanisms and migration barriers as the concentration of lithium increases. Until now, for example, simulations studies were limited by the time scale over which diffusion takes place. Here, we use the kinetic activation relaxation technique (kART), an unbiased off-lattice Monte Carlo method with on-the fly catalog building, coupled with the ReaxFF forcefield to follow diffusion of Li in c - Si over timescale of seconds and more at room temperature, obtaining detailed information about the whole set of possible diffusion mechanisms as the local environment evolves. We first present a detailed characterization of Li diffusion in the presence of 1 to 3 impurities and then show the evolution of systems with a higher concentration of solute as Li aggregate. These results provide a first detailed picture of the onset of Li aggregating into this high-capacity material, as it modifies the structure through local rearrangements and long-range elastic deformations, crucial information for the development of the next generation of high-capacity anode. ∖pard ∖pard.

  4. Degradation of diclofenac by UV-activated persulfate process: Kinetic studies, degradation pathways and toxicity assessments.

    PubMed

    Lu, Xian; Shao, Yisheng; Gao, Naiyun; Chen, Juxiang; Zhang, Yansen; Xiang, Huiming; Guo, Youluo

    2017-03-21

    Diclofenac (DCF) is the frequently detected non-steroidal pharmaceuticals in the aquatic environment. In this study, the degradation of DCF was evaluated by UV-254nm activated persulfate (UV/PS). The degradation of DCF followed the pseudo first-order kinetics pattern. The degradation rate constant (kobs) was accelerated by UV/PS compared to UV alone and PS alone. Increasing the initial PS dosage or solution pH significantly enhanced the degradation efficiency. Presence of various natural water constituents had different effects on DCF degradation, with an enhancement or inhibition in the presence of inorganic anions (HCO3(-) or Cl(-)) and a significant inhibition in the presence of NOM. In addition, preliminary degradation mechanisms and major products were elucidated using LC-MS/MS. Hydroxylation, decarbonylation, ring-opening and cyclation reaction involving the attack of SO4(•)(-) or other substances, were the main degradation mechanism. TOC analyzer and Microtox bioassay were employed to evaluate the mineralization and cytotoxicity of solutions treated by UV/PS at different times, respectively. Limited elimination of TOC (32%) was observed during the mineralization of DCF. More toxic degradation products and their related intermediate species were formed, and the UV/PS process was suitable for removing the toxicity. Of note, longer degradation time may be considered for the final toxicity removal.

  5. Effect of moderate electric field frequency on growth kinetics and metabolic activity of Lactobacillus acidophilus.

    PubMed

    Loghavi, Laleh; Sastry, Sudhir K; Yousef, Ahmed E

    2008-01-01

    Moderate electric fields (MEF) have been previously shown to alter the metabolic activity of microbial cells; thus, the effect of frequency and electric field would be of considerable interest. We investigated herein the effects of MEF frequency on microbial growth kinetics and bacteriocin (Lacidin A) production of Lactobacillus acidophilus OSU 133 during fermentation. The following fermentation treatments were compared: conventional (for 40 h), MEF (1 V cm(-1), for 40 h), combination of MEF (1 V cm(-1), for the first 5 h) and conventional (for 35 h) at various frequency levels (45, 60, and 90 Hz) all at 30 degrees C, and control (conventional) fermentation at 37 degrees C. MEF treatments with purely sinusoidal waveforms at all frequencies at 30 degrees C produced a shorter lag phase than conventional fermentation. However, no lag phase reduction was found for a 60 Hz waveform that contained high-frequency harmonics. There was, however, a significant increase in the bacteriocin production under early MEF treatment at 60 Hz with high-frequency harmonics. On the basis of these observations, the fermentation process is accelerated by applying pure sinusoidal MEF at the early stage of growth while a significant increase in the bacteriocin production occurs when sinusoidal field at 60 Hz with harmonics is applied at the early stage of the growth.

  6. [Adsorption kinetics and mechanism of lead (II) on polyamine-functionalized mesoporous activated carbon].

    PubMed

    Li, Kun-Quan; Wang, Yan-Jin; Yang, Mei-Rong; Zhu, Zhi-Qiang; Zheng, Zheng

    2014-08-01

    Bagasse mesoporous carbon was prepared by microwave assisted H3 PO4 activation. Amido and imido groups were modified with ethanediamine on the channels' surface of mesoporous carbon through nitric oxidation and amide reaction. The influence of Pb(II) concentration, adsorption time on Pb(II) adsorption on the ethanediamine-modified mesoporous carbon (AC-EDA) was investigated. The adsorption kinetics and mechanism were also discussed. The results showed that AC-EDA had a great performance for Pb(II) adsorption, and more than 70% of Pb(II) was adsorbed in 5 minutes. The adsorption amount of Pb(II) on the carbon increased with the increase of solution pH in acidic conditions. It was found that AC-EDA had different binding energies on different adsorption sites for Pb(II) separation. The Pb(II) adsorption process on AC-EDA was controlled by intra-particle diffusion in the first 3 min, and then film diffusion played the important pole on the adsorption. The adsorption amount increased with the increase of temperature, indicating the adsorption was an endothermic reaction. The high adsorption energy (> 11 kJ x mol(-1)) implied that the) adsorption was a chemical adsorption. The XPS of AC-EDA before and after Pb(II) adsorption showed that the polyamine group was involved in the adsorption, and should be a main factor of the high efficient adsorption.

  7. Different antibacterial activity of novel theophylline-based ionic liquids - Growth kinetic and cytotoxicity studies.

    PubMed

    Borkowski, Andrzej; Ławniczak, Łukasz; Cłapa, Tomasz; Narożna, Dorota; Selwet, Marek; Pęziak, Daria; Markiewicz, Bartosz; Chrzanowski, Łukasz

    2016-08-01

    The aim of this study was to investigate novel theophylline-based ionic liquids and their cytotoxic effects towards model Gram-positive and Gram-negative bacteria (Bacillus cereus and Escherichia coli, respectively). Growth kinetics, respiratory rates and dehydrogenase activities were studied in the presence of ionic liquids at concentrations ranging from 10 to 1000mg/L. Additionally, the influence of ionic liquids on bacterial cells associated with specific interactions based on the structure of cell wall was evaluated. This effect was assessed by viability tests and scanning electron microscope observations. The obtained results confirmed that ionic liquids exhibit different levels of toxicity in relation to Gram-positive and Gram-negative bacteria. Those effects are associated with the chemical structure of the cationic species of the ionic liquids and their critical micelle concentration value. It was established that the presence of an alkyl or allyl group increased the toxicity, whereas the presence of an aryl group in the cation decreased the toxic effect of ILs. Results presented in this study also revealed unexpected effects of self-aggregation of E. coli cells. Overall, it was established that the studied ILs exhibited higher toxicity towards Gram-positive bacteria due to different interactions between the ILs and the cell membranes. These findings may be of importance for the design of ILs with targeted antimicrobial properties.

  8. Study on carvacrol and cinnamaldehyde polymeric films: mechanical properties, release kinetics and antibacterial and antibiofilm activities.

    PubMed

    Nostro, A; Scaffaro, R; D'Arrigo, M; Botta, L; Filocamo, A; Marino, A; Bisignano, G

    2012-11-01

    Polyethylene-co-vinylacetate (EVA) films with different concentrations (3.5 wt% and 7 wt%) of essential oil constituents, carvacrol or cinnamaldehyde, were prepared and characterized by mechanical, antibacterial and antibiofilm properties. The incorporation of the compounds into copolymer films affected their elastic modulus, tensile stress and elongation at break. Carvacrol and cinnamaldehyde act as plasticizers which reduce the intermolecular forces of polymer chains, thus improving the flexibility and extensibility of the film. The analysis of the surface characteristics demonstrated that essential oil constituents lowered the contact angle values without causing any remarkable variation of the surface roughness. The films allowed progressive diffusion of the bioactive molecules and the kinetic of release was correlated with the damaging effect on bacterial growth. The kill curves proved that the film with essential oil constituents (7 wt%) had a significant bactericidal effect (reduction of 4 and 2 log CFU) against Staphylococcus aureus and Escherichia coli and a bacteriostatic effect against Staphylococcus epidermidis and Listeria monocytogenes (reduction of about 1 log CFU). With regard to biofilm formation the biomass formed on polymeric films surface was significantly reduced if compared with the pure copolymer control. The results were confirmed by fluorescence microscopy images by Live/dead staining. The reduction in the surface tension coupled to an inherent bactericidal property of carvacrol and cinnamaldehyde could in turn affect the initial attachment phase of bacteria and compromise the normal biofilm development.

  9. A kinetic study of pyrolysis and combustion of microalgae Chlorella vulgaris using thermo-gravimetric analysis.

    PubMed

    Agrawal, Ankit; Chakraborty, Saikat

    2013-01-01

    This work uses thermo-gravimetric, differential thermo-gravimetric and differential thermal analyses to evaluate the kinetics of pyrolysis (in inert/N(2) atmosphere) and (oxidative) combustion of microalgae Chlorella vulgaris by heating from 50 to 800 °C at heating rates of 5-40 °C/min. This study shows that combustion produces higher biomass conversion than pyrolysis, and that three stages of decomposition occur in both cases, of which, the second one--consisting of two temperature zones--is the main stage of devolatization. Proteins and carbohydrates are decomposed in the first of the two zones at activation energies of 51 and 45 kJ/mol for pyrolysis and combustion, respectively, while lipids are decomposed in its second zone at higher activation energies of 64 and 63 kJ/mol, respectively. The kinetic expressions of the reaction rates in the two zones for pyrolysis and combustion have been obtained and it has been shown that increased heating rates result in faster and higher conversion.

  10. A common neighbor analysis of crystallization kinetics and excess entropy of charged spherical colloids

    NASA Astrophysics Data System (ADS)

    Urrutia Bañuelos, Efraín; Contreras Aburto, Claudio; Maldonado Arce, Amir

    2016-03-01

    The topological analysis tool known as the common neighbor analysis (CNA) is used for the first time in this work to analyze crystallization kinetics and excess entropy of charge-stabilized colloidal suspensions. For this purpose, Brownian dynamics computer simulations are implemented to investigate the crystallization kinetics of homogeneously melted colloidal crystals that are composed of hard-core-screened-Coulomb interacting particles. The results are in agreement with recent static structure factor measurements that could indicate the presence of icosahedral units in the metastable melt, and with the fact that weakly screened charged colloids crystallize into body-centered-cubic (bcc) ordering. A two-step crystallization pathway is found, in which the population of bcc-subunit CNA-pairs satisfactorily obeys a Verhulst model. Moreover, the CNA helped to unveil that the excess entropy obeys a quasi-universal functional form, relating the behavior of colloidal, molecular, and metallic liquid systems. The work contributes to the scientific understanding of the crystallization pathway of charged colloids, and to the development of new ways to assess the degree of crystalline order, starting from the excess entropy.

  11. Characterization of the efficiency of microbore liquid chromatography columns by van Deemter and kinetic plot analysis.

    PubMed

    Hetzel, Terence; Loeker, Denise; Teutenberg, Thorsten; Schmidt, Torsten C

    2016-10-01

    The efficiency of miniaturized liquid chromatography columns with inner diameters between 200 and 300 μm has been investigated using a dedicated micro-liquid chromatography system. Fully porous, core-shell and monolithic commercially available stationary phases were compared applying van Deemter and kinetic plot analysis. The sub-2 μm fully porous as well as the 2.7 μm core-shell particle packed columns showed superior efficiency and similar values for the minimum reduced plate heights (2.56-2.69) before correction for extra-column contribution compared to normal-bore columns. Moreover, the influence of extra-column contribution was investigated to demonstrate the difference between apparent and intrinsic efficiency by replacing the column by a zero dead volume union to determine the band spreading caused by the system. It was demonstrated that 72% of the intrinsic efficiency could be reached. The results of the kinetic plot analysis indicate the superior performance of the sub-2 μm fully porous particle packed column for ultra-fast liquid chromatography.

  12. Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides.

    PubMed Central

    Livshits, M A; Mirzabekov, A D

    1996-01-01

    A new method of DNA sequencing by hybridization using a microchip containing a set of immobilized oligonucleotides is being developed. A theoretical analysis is presented of the kinetics of DNA hybridization with deoxynucleotide molecules chemically tethered in a polyacrylamide gel layer. The analysis has shown that long-term evolution of the spatial distribution and of the amount of DNA bound in a hybridization cell is governed by "retarded diffusion," i.e., diffusion of the DNA interrupted by repeated association and dissociation with immobile oligonucleotide molecules. Retarded diffusion determines the characteristic time of establishing a final equilibrium state in a cell, i.e., the state with the maximum quantity and a uniform distribution of bound DNA. In the case of cells with the most stable, perfect duplexes, the characteristic time of retarded diffusion (which is proportional to the equilibrium binding constant and to the concentration of binding sites) can be longer than the duration of the real hybridization procedure. This conclusion is indirectly confirmed by the observation of nonuniform fluorescence of labeled DNA in perfect-match hybridization cells (brighter at the edges). For optimal discrimination of perfect duplexes from duplexes with mismatches the hybridization process should be brought to equilibrium under low-temperature nonsaturation conditions for all cells. The kinetic differences between perfect and nonperfect duplexes in the gel allow further improvement in the discrimination through additional washing at low temperature after hybridization. Images FIGURE 1 PMID:8913616

  13. A common neighbor analysis of crystallization kinetics and excess entropy of charged spherical colloids.

    PubMed

    Urrutia Bañuelos, Efraín; Contreras Aburto, Claudio; Maldonado Arce, Amir

    2016-03-07

    The topological analysis tool known as the common neighbor analysis (CNA) is used for the first time in this work to analyze crystallization kinetics and excess entropy of charge-stabilized colloidal suspensions. For this purpose, Brownian dynamics computer simulations are implemented to investigate the crystallization kinetics of homogeneously melted colloidal crystals that are composed of hard-core-screened-Coulomb interacting particles. The results are in agreement with recent static structure factor measurements that could indicate the presence of icosahedral units in the metastable melt, and with the fact that weakly screened charged colloids crystallize into body-centered-cubic (bcc) ordering. A two-step crystallization pathway is found, in which the population of bcc-subunit CNA-pairs satisfactorily obeys a Verhulst model. Moreover, the CNA helped to unveil that the excess entropy obeys a quasi-universal functional form, relating the behavior of colloidal, molecular, and metallic liquid systems. The work contributes to the scientific understanding of the crystallization pathway of charged colloids, and to the development of new ways to assess the degree of crystalline order, starting from the excess entropy.

  14. CHEMKIN-III: A FORTRAN chemical kinetics package for the analysis of gas-phase chemical and plasma kinetics

    SciTech Connect

    Kee, R.J.; Rupley, F.M.; Meeks, E.; Miller, J.A.

    1996-05-01

    This document is the user`s manual for the third-generation CHEMKIN package. CHEMKIN is a software package whose purpose is to facilitate the formation, solution, and interpretation of problems involving elementary gas-phase chemical kinetics. It provides a flexible and powerful tool for incorporating complex chemical kinetics into simulations of fluid dynamics. The package consists of two major software components: an Interpreter and a Gas-Phase Subroutine Library. The Interpreter is a program that reads a symbolic description of an elementary, user-specified chemical reaction mechanism. One output from the Interpreter is a data file that forms a link to the Gas-Phase Subroutine Library. This library is a collection of about 100 highly modular FORTRAN subroutines that may be called to return information on equations of state, thermodynamic properties, and chemical production rates. CHEMKIN-III includes capabilities for treating multi-fluid plasma systems, that are not in thermal equilibrium. These new capabilities allow researchers to describe chemistry systems that are characterized by more than one temperature, in which reactions may depend on temperatures associated with different species; i.e. reactions may be driven by collisions with electrons, ions, or charge-neutral species. These new features have been implemented in such a way as to require little or no changes to CHEMKIN implementation for systems in thermal equilibrium, where all species share the same gas temperature. CHEMKIN-III now has the capability to handle weakly ionized plasma chemistry, especially for application related to advanced semiconductor processing.

  15. A potential Kazal-type serine protease inhibitor involves in kinetics of protease inhibition and bacteriostatic activity.

    PubMed

    Kumaresan, Venkatesh; Harikrishnan, Ramaswamy; Arockiaraj, Jesu

    2015-02-01

    Kazal-type serine protease inhibitor (KSPI) is a pancreatic secretary trypsin inhibitor which involves in various cellular component regulations including development and defense process. In this study, we have characterized a KSPI cDNA sequence of freshwater striped murrel fish Channa striatus (Cs) at molecular level. Cellular location analysis predicted that the CsKSPI was an extracellular protein. The domain analysis showed that the CsKSPI contains a Kazal domain at 47-103 along with its family signature between 61 and 83. Phylogenetically, CsKSPI is closely related to KSPI from Maylandia zebra and formed a sister group with mammals. The 2D structure of CsKSPI showed three α-helical regions which are connected with random coils, one helix at signal sequence and two at the Kazal domain region. The relative gene expression showed that the CsKSPI was highly expressed in gills and its expression was induced upon fungus (Aphanomyces invadans), bacteria (Aeromonas hydrophila) and poly I:C (a viral analogue) challenge. The CsKSPI recombinant protein was produced to characterize and study the CsKSPI gene specific functions. The recombinant CsKSPI strongly inhibited trypsin compared to other tested proteases. The results of the kinetic activity of CsKSPI against trypsin was V(max)s = 1.62 nmol/min, K(M)s = 0.21 mM and K(i)s = 15.37 nM. Moreover, the recombinant CsKSPI inhibited the growth of Gram-negative bacteria A. hydrophila at 20 μM and Gram-positive bacteria Bacillus subtilis at the MIC50 of 15 μM. Overall, the study indicated that the CsKSPI was a potential trypsin inhibitor which involves in antimicrobial activity.

  16. The calcium-independent transient outward potassium current in isolated ferret right ventricular myocytes. I. Basic characterization and kinetic analysis

    PubMed Central

    1993-01-01

    Enzymatically isolated myocytes from ferret right ventricles (12-16 wk, male) were studied using the whole cell patch clamp technique. The macroscopic properties of a transient outward K+ current I(to) were quantified. I(to) is selective for K+, with a PNa/PK of 0.082. Activation of I(to) is a voltage-dependent process, with both activation and inactivation being independent of Na+ or Ca2+ influx. Steady-state inactivation is well described by a single Boltzmann relationship (V1/2 = -13.5 mV; k = 5.6 mV). Substantial inactivation can occur during a subthreshold depolarization without any measurable macroscopic current. Both development of and recovery from inactivation are well described by single exponential processes. Ensemble averages of single I(to) channel currents recorded in cell-attached patches reproduce macroscopic I(to) and indicate that inactivation is complete at depolarized potentials. The overall inactivation/recovery time constant curve has a bell-shaped potential dependence that peaks between -10 and -20 mV, with time constants (22 degrees C) ranging from 23 ms (-90 mV) to 304 ms (-10 mV). Steady-state activation displays a sigmoidal dependence on membrane potential, with a net aggregate half- activation potential of +22.5 mV. Activation kinetics (0 to +70 mV, 22 degrees C) are rapid, with I(to) peaking in approximately 5-15 ms at +50 mV. Experiments conducted at reduced temperatures (12 degrees C) demonstrate that activation occurs with a time delay. A nonlinear least- squares analysis indicates that three closed kinetic states are necessary and sufficient to model activation. Derived time constants of activation (22 degrees C) ranged from 10 ms (+10 mV) to 2 ms (+70 mV). Within the framework of Hodgkin-Huxley formalism, Ito gating can be described using an a3i formulation. PMID:8505627

  17. Engineering substrate preference in subtilisin: structural and kinetic analysis of a specificity mutant.

    PubMed

    Ruan, Biao; London, Viktoriya; Fisher, Kathryn E; Gallagher, D Travis; Bryan, Philip N

    2008-06-24

    Bacillus subtilisin has been a popular model protein for engineering altered substrate specificity. Although some studies have succeeded in increasing the specificity of subtilisin, they also demonstrate that high specificity is difficult to achieve solely by engineering selective substrate binding. In this paper, we analyze the structure and transient state kinetic behavior of Sbt160, a subtilisin engineered to strongly prefer substrates with phenylalanine or tyrosine at the P4 position. As in previous studies, we measure improvements in substrate affinity and overall specificity. Structural analysis of an inactive version of Sbt160 in complex with its cognate substrate reveals improved interactions at the S4 subsite with a P4 tyrosine. Comparison of transient state kinetic behavior against an optimal sequence (DFKAM) and a similar, but suboptimal, sequence (DVRAF) reveals the kinetic and thermodynamic basis for increased specificity, as well as the limitations of this approach. While highly selective substrate binding is achieved in Sbt160, several factors cause sequence specificity to fall short of that observed with natural processing subtilisins. First, for substrate sequences which are nearly optimal, the acylation reaction becomes faster than substrate dissociation. As a result, the level of discrimination among these substrates diminishes due to the coupling between substrate binding and the first chemical step (acylation). Second, although Sbt160 has 24-fold higher substrate affinity for the optimal substrate DFKAM than for DVRAF, the increased substrate binding energy is not translated into improved transition state stabilization of the acylation reaction. Finally, as interactions at subsites become stronger, the rate-determining step in peptide hydrolysis changes from acylation to product release. Thus, the release of the product becomes sluggish and leads to a low k(cat) for the reaction. This also leads to strong product inhibition of substrate

  18. Synthesis, crystal structure, photodegradation kinetics and photocatalytic activity of novel photocatalyst ZnBiYO4.

    PubMed

    Cui, Yanbing; Luan, Jingfei

    2015-03-01

    ZnBiYO4 was synthesized by a solid-state reaction method for the first time. The structural and photocatalytic properties of ZnBiYO4 were characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy and UV-Vis diffuse reflectance. ZnBiYO4 crystallized with a tetragonal spinel structure with space group I41/A. The lattice parameters for ZnBiYO4 were a=b=11.176479Å and c=10.014323Å. The band gap of ZnBiYO4 was estimated to be 1.58eV. The photocatalytic activity of ZnBiYO4 was assessed by photodegradation of methyl orange under visible light irradiation. The results showed that ZnBiYO4 had higher catalytic activity compared with N-doped TiO2 under the same experimental conditions using visible light irradiation. The photocatalytic degradation of methyl orange with ZnBiYO4 or N-doped TiO2 as catalyst followed first-order reaction kinetics, and the first-order rate constant was 0.01575 and 0.00416 min(-1) for ZnBiYO4 and N-doped TiO2, respectively. After visible light irradiation for 220 min with ZnBiYO4 as catalyst, complete removal and mineralization of methyl orange were observed. The reduction of total organic carbon, formation of inorganic products, SO4(2-) and NO3-, and evolution of CO2 revealed the continuous mineralization of methyl orange during the photocatalytic process. The intermediate products were identified using liquid chromatography-mass spectrometry. The ZnBiYO4/(visible light) photocatalysis system was found to be suitable for textile industry wastewater treatment and could be used to solve other environmental chemical pollution problems.

  19. The Potential of Soft Soil Improvement Through a Coupled Technique Between Electro Kinetic and Alkaline Activation of Soft Soil

    NASA Astrophysics Data System (ADS)

    Ahmed, G. E.; Ismail, H. B.; Huat, B. K.; Afshin, A.; Azhar, A. T. S.

    2016-07-01

    Soil stabilization techniques have been in development for decades with different rates of success. Alkaline activation of soft soil is one of those techniques that has proved to deliver some of the best shear strength values with minor drawbacks in comparison with conventional soil stabilization methods. However, environmental considerations have not been taken into account, as major mineral glassy phase activators are poisoning alkaline solutions, such as sodium-, potassium-hydroxide, and sodium-, potassium-silicate, which poses serious hazards to man and environment. This paper addresses the ways of discarding the involvement of the aforementioned alkaline solutions in soft soil stabilization by investigating the potential of a coupled electro kinetic alkaline activation technique for soft soil strengthening, through which the provision of alkaline pH is governed by electro kinetic potential. Uncertainties in regard to the dissolution of aluminosilicate as well as the dominance of acidic front are challenges that need to be overcome.

  20. Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance.

    PubMed

    Schermerhorn, Kelly M; Gardner, Andrew F

    2015-09-04

    Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a Family D DNA polymerase from Thermococcus sp. 9°N. Pre-steady-state single-turnover nucleotide incorporation assays were performed to obtain the kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporation by exonuclease-deficient polD. Correct nucleotide incorporation kinetics revealed a relatively slow maximal rate of polymerization (kpol ∼ 2.5 s(-1)) and especially tight nucleotide binding (Kd (dNTP) ∼ 1.7 μm), compared with DNA polymerases from Families A, B, C, X, and Y. Furthermore, pre-steady-state nucleotide incorporation assays revealed that polD prevents the incorporation of incorrect nucleotides and ribonucleotides primarily through reduced nucleotide binding affinity. Pre-steady-state single-turnover assays on wild-type 9°N polD were used to examine 3'-5' exonuclease hydrolysis activity in the presence of Mg(2+) and Mn(2+). Interestingly, substituting Mn(2+) for Mg(2+) accelerated hydrolysis rates > 40-fold (kexo ≥ 110 s(-1) versus ≥ 2.5 s(-1)). Preference for Mn(2+) over Mg(2+) in exonuclease hydrolysis activity is a property unique to the polD family. The kinetic assays performed in this work provide critical insight into the mechanisms that polD employs to accurately and efficiently replicate the archaeal genome. Furthermore, despite the unique properties of polD, this work suggests that a conserved polymerase kinetic pathway is present in all known DNA polymerase families.

  1. Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance*

    PubMed Central

    Schermerhorn, Kelly M.; Gardner, Andrew F.

    2015-01-01

    Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a Family D DNA polymerase from Thermococcus sp. 9°N. Pre-steady-state single-turnover nucleotide incorporation assays were performed to obtain the kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporation by exonuclease-deficient polD. Correct nucleotide incorporation kinetics revealed a relatively slow maximal rate of polymerization (kpol ∼2.5 s−1) and especially tight nucleotide binding (Kd(dNTP) ∼1.7 μm), compared with DNA polymerases from Families A, B, C, X, and Y. Furthermore, pre-steady-state nucleotide incorporation assays revealed that polD prevents the incorporation of incorrect nucleotides and ribonucleotides primarily through reduced nucleotide binding affinity. Pre-steady-state single-turnover assays on wild-type 9°N polD were used to examine 3′-5′ exonuclease hydrolysis activity in the presence of Mg2+ and Mn2+. Interestingly, substituting Mn2+ for Mg2+ accelerated hydrolysis rates >40-fold (kexo ≥110 s−1 versus ≥2.5 s−1). Preference for Mn2+ over Mg2+ in exonuclease hydrolysis activity is a property unique to the polD family. The kinetic assays performed in this work provide critical insight into the mechanisms that polD employs to accurately and efficiently replicate the archaeal genome. Furthermore, despite the unique properties of polD, this work suggests that a conserved polymerase kinetic pathway is present in all known DNA polymerase families. PMID:26160179

  2. Kinetic mechanism of the Zn-dependent aryl-phosphatase activity of myo-inositol-1-phosphatase.

    PubMed

    Caselli, Anna; Casolaro, Mario; Ranaldi, Francesco; Manao, Giampaolo; Camici, Guido; Giachetti, Eugenio

    2007-02-01

    Myo-inositol-1-phosphatase (EC 3.1.3.25) is able to hydrolyze myo-inositol-1-phosphate in the presence of Mg(2+) ions at neutral pH, and also p-nitrophenyl phosphate in the presence of Zn(2+)-ions at acidic pH. This enzyme plays a role in phosphatidylinositol cell signalling and is a putative target of lithium therapy in manic depression. We elucidate here the kinetic mechanism of the Zn-dependent activity of myo-inositol-1-phosphatase. As part of this analysis it was necessary to determine the basicity constants of p-nitrophenyl phosphate and the stability constant of its metal-complex in the presence of zinc chloride. We find that the Zn-dependent reaction may be described either by a rapid-equilibrium random mechanism or an ordered steady-state mechanism in which the substrate binds to the free enzyme prior to the metal ion. In both models the Zn-substrate complex acts as a high affinity inhibitor, yielding a dead-end species through its binding to the enzyme-Zn-substrate in rapid-equilibrium or to the enzyme-phosphate complexes in a steady-state model. Phosphate is a competitive inhibitor of the enzyme with respect to the substrate and an uncompetitive inhibitor with respect to zinc ions.

  3. Active Site Formation, Not Bond Kinetics, Limits Adhesion Rate between Human Neutrophils and Immobilized Vascular Cell Adhesion Molecule 1

    PubMed Central

    Waugh, Richard E.; Lomakina, Elena B.

    2009-01-01

    Abstract The formation of receptor ligand bonds at the interface between different cells and between cells and substrates is a widespread phenomenon in biological systems. Physical measurements of bond formation rates between cells and substrates have been exploited to increase our understanding of the biophysical mechanisms that regulate bond formation at interfaces. Heretofore, these measurements have been interpreted in terms of simple bimolecular reaction kinetics. Discrepancies between this simple framework and the behavior of neutrophils adhering to surfaces expressing vascular cell adhesion molecule 1 (VCAM-1) motivated the development of a new kinetic framework in which the explicit formation of active bond formation sites (reaction zones) are a prerequisite for bond formation to occur. Measurements of cells interacting with surfaces having a wide range of VCAM-1 concentrations, and for different durations of contact, enabled the determination of novel kinetic rate constants for the formation of reaction zones and for the intrinsic bond kinetics. Comparison of these rates with rates determined previously for other receptor-ligand pairs points to a predominant role of extrinsic factors such as surface topography and accessibility of active molecules to regions of close contact in determining forward rates of bond formation at cell interfaces. PMID:19134479

  4. Adsorption behavior of activated carbon derived from pyrolusite-modified sewage sludge: equilibrium modeling, kinetic and thermodynamic studies.

    PubMed

    Chen, Yao; Jiang, Wenju; Jiang, Li; Ji, Xiujuan

    2011-01-01

    Activated carbon was developed from sewage sludge using pyrolusite as an additive. It was demonstrated that the removal efficiency of two synthetic dyes (Tracid orange GS and Direct fast turquoise blue GL) by the produced adsorbent was up to 97.6%. The activated carbon with pyrolusite addition had 38.2% higher surface area, 43.8% larger micropore and 54.4% larger mesopore production than ordinary sludge-based activated carbons. Equilibrium adsorption isotherms and kinetics were also investigated based on dyes adsorption tests. The experimental data were analyzed by the Langmuir and Freundlich models of adsorption, and the results fitted well to the Langmuir isotherm. The kinetic data have been analyzed using pseudo-first-order, pseudo-second-order and intraparticle diffusion equation. The experimental data fitted very well with pseudo-second-order kinetic model. Activation energies for the adsorption processes ranged between 8.7 and 19.1 kJ mol 1. Thermodynamic parameters such as standard free energy (deltaG0), standard enthalpy (deltaH0) and standard entropy (deltaS0) were evaluated. The adsorption of these two dyes on the activated carbon was found to be a spontaneous and endothermic process in nature.

  5. Kinetic analysis of enhanced thermal stability of an alkaline protease with engineered twin disulfide bridges and calcium-dependent stability.

    PubMed

    Ikegaya, Kazuo; Sugio, Shigetoshi; Murakami, Kohji; Yamanouchi, Kouichi

    2003-01-20

    The thermal stability of a cysteine-free alkaline protease (Alp) secreted by the eukaryote Aspergillus oryzae was improved both by the introduction of engineered twin disulfide bridges (Cys-69/Cys-101 and Cys-169/Cys-200), newly constructed as part of this study, and by the addition of calcium ions. We performed an extensive kinetic analysis of the increased thermal stability of the mutants as well as the role of calcium dependence. The thermodynamic activation parameters for irreversible thermal inactivation, the activation free energy (deltaG), the activation enthalpy (deltaH), and the activation entropy (deltaS) were determined from absolute reaction rate theory. The values of deltaH and deltaS were significantly and concomitantly increased as a result of introducing the twin disulfide bridges, for which the increase in the value of deltaH outweighed that of deltaS, resulting in significant increases in the value of deltaG. The enhancement of the thermal stability obtained by introducing the twin disulfide bridges is an example of the so-called low-temperature stabilization of enzymes. The stabilizing effect of calcium ions on wild-type Alp is similar to the results we obtained by introducing the engineered twin disulfide bridges.

  6. Kinetic analysis and probability mapping applied to the detection of ovarian cancer by radioimmunoscintigraphy

    SciTech Connect

    Granowska, M.; Nimmon, C.C.; Britton, K.E.; Crowther, M.; Mather, S.J.; Slevin, M.L.; Shepherd, J.H.

    1988-05-01

    Kinetic analysis with probability mapping is an objective method of serial image analysis applicable to radioimmunoscintigraphy. The technique is described and subjected to clinical testing by comparing the prediction of biopsy histology from the probability map in patients coming to operation. In those with ovarian cancer undergoing second-look laparotomy after completing full courses of chemotherapy, the prediction of histology in 108 biopsy sites was 45 true positives and 38 true negatives, sensitivity 80%, specificity 73%, accuracy 77% p less than 0.001. In patients with tumors less than 2 cm diameter, 41 biopsy sites were predicted with a specificity of 78% and an accuracy of 76%, p less than 0.01. The technique is reducing the need for second-look laparotomy in patients with subclinical and subradiological disease. Such disease is suitable for intraperitoneal radioimmunotherapy.

  7. Activation energy distributions predicted by dispersive kinetic models for nucleation and denucleation: anomalous diffusion resulting from quantization.

    PubMed

    Skrdla, Peter J

    2011-06-23

    The activation energy distributions underpinning the two complementary dispersive kinetic models described by the author in a recent work (Skrdla, P. J. J. Phys. Chem. A 2009, 113, 9329) are derived and investigated. In the case of nucleation rate-limited conversions, which exhibit "acceleratory" sigmoidal transients (a kind of S-shaped stretched exponential conversion profile), an activation energy distribution visually similar to the Maxwell-Boltzmann (M-B) distribution is recovered, consistent with the original derivation of that model. In the case of predominantly "deceleratory" conversions, the activation energy distribution is skewed from normal in the opposite direction. While the "M-B-like" activation energy distribution supports the empirical observation of a rate enhancement as a function of the conversion time in nucleation rate-limited processes, the complementary distribution, with its pronounced low-energy tail, reflects a slow-down in the specific rate as the conversion progresses, consistent with experimentally observed denucleation rate-limited conversions. Activation energy distributions were also plotted for real-world data (Qu, H.; Louhi-Kultanen, M.; Kallas, J. Cryst. Growth Des. 2007, 7, 724), depicting the impact of various additives on the nucleation rate-limited kinetics of the solvent-mediated phase transformation of the crystalline drug carbamazepine. Last, by coupling the author's dispersive kinetic description of the time-dependent activation energy for nucleation to the classical description of the critical nucleus energy provided by the Kelvin equation, an accelerated hopping mechanism for the diffusion of monomers to the growing embryo surface was observed. That hopping mechanism was rationalized by modifying the Einstein-Smoluchowski (E-S) equation to allow it to describe the "supra-brownian" molecular motion thought to lie at the heart of nucleation kinetics.

  8. Two-point method for kinetic analysis of a thermoluminescence glow peak

    NASA Astrophysics Data System (ADS)

    Ogundare, F. O.; Chithambo, M. L.

    2006-05-01

    We present a method for the estimation of defect (trap) physical parameters from thermoluminescence (TL) glow peaks. In this method, the order of kinetics b is determined using two values of TL intensity each of which corresponds to the same temperature (T-1) on two separate glow peaks of a phosphor. The two glow peaks are obtained from two aliquots of the phosphor irradiated to same dose but read out at different heating rates. The proposed method requires a minimum of only two data points in contrast to standard peak shape (PS) methods that require three points corresponding to three different temperatures on the same glow peak. Once the order of kinetics b is determined, the activation energy E is calculated by taking a second point (T-2) on any one of the two glow peaks. The values of b and E thus obtained are used to evaluate the frequency factor S'' and the number of trapped electrons before the heating begins n(o). The validity of the method was checked using two numerically generated glow peaks. For the two cases, the method reproduced the input values reasonably well. The method was also used to analyse two experimental glow peaks. The results obtained provide a reasonably good fit to the experimental data. The kinetic parameters calculated using the present technique are comparable to those calculated using PS and initial rise methods. Initial guesses can easily be obtained for E and S'' using the present technique when a glow curve is to be deconvoluted with a model consisting of many unknown parameters with E and S'' inclusive.

  9. ZnS:Cu nanoparticles loaded on activated carbon as novel adsorbent for kinetic, thermodynamic and isotherm studies of Reactive Orange 12 and Direct yellow 12 adsorption.

    PubMed

    Ghaedi, Mehrorang; Ansari, Amin; Sahraei, Reza

    2013-10-01

    The objective of this work is the study of adsorption of Reactive Orange 12 (RO-12) and Direct yellow 12 (DY 12) by zinc sulfide:copper (ZnS-Cu-NP-AC) nanoparticles loaded on activated carbon. This new material with high efficiency in a routine manner was synthesized in our laboratory and its surface properties viz surface area, pore volume and functional groups was characterized with different techniques such FT-IR, SEM, and BET analysis. Generally, in batch adsorption procedure variables including amount of adsorbent, initial dyes concentration, contact time, temperature on dyes removal percentage has great effect on removal percentage that their influence was optimized. The kinetic of proposed adsorption processes efficiently followed, pseudo-second-order, and intra-particle diffusion kinetic models. The equilibrium data the removal strongly follow Langmuir monolayer adsorption with high adsorption capacity in short time. This novel adsorbent by small amount (0.08 g) really is applicable for removal of high amount of both dyes (RO 12 and DY 12) in short time (<20 min). Based on the calculated thermodynamic parameters such as enthalpy (ΔH), entropy (ΔS), activation energy (Ea), sticking probability (S*) and Gibb's free energy changes (ΔG), it is noticeable that the sorption of both dyes onto ZnS:Cu-AC was spontaneous and endothermic process. At optimum values all variables the effect of contact time on adsorption was investigated and the dependency of adsorption data to different kinetic model such as pseudo-first-order, pseudo-second-order, Elovich and intra-particle diffusion was assessed and it was found that the removal processes follow pseudo second order kinetics and interparticle diffusion mechanism.

  10. Microbial respiration and kinetics of extracellular enzymes activities through rhizosphere and detritusphere at agricultural site

    NASA Astrophysics Data System (ADS)

    Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2014-05-01

    Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and

  11. 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.

  12. Multijoint kinetic chain analysis of knee extension during the soccer instep kick.

    PubMed

    Naito, Kozo; Fukui, Yosuke; Maruyama, Takeo

    2010-04-01

    Although previous studies have shown that motion-dependent interactions between adjacent segments play an important role in producing knee extension during the soccer instep kick, detailed knowledge about the mechanisms underlying those interactions is lacking. The present study aimed to develop a 3-D dynamical model for the multijoint kinetic chain of the instep kick in order to quantify the contributions of the causal dynamical factors to the production of maximum angular velocity during knee extension. Nine collegiate soccer players volunteered to participate in the experiment and performed instep kicking movements while 3-D positional data and the ground reaction force were measured. A dynamical model was developed in the form of a linked system containing 8 segments and 18 joint rotations, and the knee extension/flexion motion was decomposed into causal factors related to muscular moment, gyroscopic moment, centrifugal force, Coriolis force, gravity, proximal endpoint linear acceleration, and external force-dependent terms. The rapid knee extension during instep kicking was found to result almost entirely from kicking leg centrifugal force, trunk rotation muscular moment, kicking leg Coriolis force, and trunk rotation gyroscopic-dependent components. Based on the finding that rapid knee extension during instep kicking stems from multiple dynamical factors, it is suggested that the multijoint kinetic chain analysis used in the present study is more useful for achieving a detailed understanding of the cause of rapid kicking leg movement than the previously used 2-D, two-segment kinetic chain model. The present results also indicated that the centrifugal effect due to the kicking hip flexion angular velocity contributed substantially to the generation of a rapid knee extension, suggesting that the adjustment between the kicking hip flexion angular velocity and the leg configuration (knee flexion angle) is more important for effective instep kicking than other

  13. Simultaneous kinetic spectrophotometric analysis of five synthetic food colorants with the aid of chemometrics.

    PubMed

    Ni, Yongnian; Wang, Yong; Kokot, Serge

    2009-04-30

    This paper describes a simple and sensitive kinetic spectrophotometric method for the simultaneous determination of Amaranth, Ponceau 4R, Sunset Yellow, Tartrazine and Brilliant Blue in mixtures with the aid of chemometrics. The method involved two coupled reactions, viz. the reduction of iron(III) by the analytes to iron(II) in sodium acetate/hydrochloric acid solution (pH 1.71) and the chromogenic reaction between iron(II) and hexacyanoferrate(III) ions to yield a Prussian blue peak at 760 nm. The spectral data were recorded over the 500-1000 nm wavelength range every 2s for 600 s. The kinetic data were collected at 760 nm and 600 s, and linear calibration models were satisfactorily constructed for each of the dyes with detection limits in the range of 0.04-0.50 mg L(-1). Multivariate calibration models for kinetic data were established and verified for methods such as the Iterative target transform factor analysis (ITTFA), principal component regression (PCR), partial least squares (PLS), and principal component-radial basis function-artificial neural network (PC-RBF-ANN) with and without wavelet packet transform (WPT) pre-treatment. The PC-RBF-ANN with WPT calibration performed somewhat better than others on the basis of the %RPE(T) (approximately 9) and %Recovery parameters (approximately 108), although the effect of the WPT pre-treatment was marginal (approximately 0.5% RPE(T)). The proposed method was applied for the simultaneous determination of the five colorants in foodstuff samples, and the results were comparable with those from a reference HPLC method.

  14. Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations.

    PubMed

    Arampatzis, Georgios; Katsoulakis, Markos A

    2014-03-28

    In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-"coupled"- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz-Kalos-Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary MATLAB

  15. Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

    SciTech Connect

    Arampatzis, Georgios; Katsoulakis, Markos A.

    2014-03-28

    In this paper we propose a new class of coupling methods for the sensitivity analysis of high dimensional stochastic systems and in particular for lattice Kinetic Monte Carlo (KMC). Sensitivity analysis for stochastic systems is typically based on approximating continuous derivatives with respect to model parameters by the mean value of samples from a finite difference scheme. Instead of using independent samples the proposed algorithm reduces the variance of the estimator by developing a strongly correlated-“coupled”- stochastic process for both the perturbed and unperturbed stochastic processes, defined in a common state space. The novelty of our construction is that the new coupled process depends on the targeted observables, e.g., coverage, Hamiltonian, spatial correlations, surface roughness, etc., hence we refer to the proposed method as goal-oriented sensitivity analysis. In particular, the rates of the coupled Continuous Time Markov Chain are obtained as solutions to a goal-oriented optimization problem, depending on the observable of interest, by considering the minimization functional of the corresponding variance. We show that this functional can be used as a diagnostic tool for the design and evaluation of different classes of couplings. Furthermore, the resulting KMC sensitivity algorithm has an easy implementation that is based on the Bortz–Kalos–Lebowitz algorithm's philosophy, where events are divided in classes depending on level sets of the observable of interest. Finally, we demonstrate in several examples including adsorption, desorption, and diffusion Kinetic Monte Carlo that for the same confidence interval and observable, the proposed goal-oriented algorithm can be two orders of magnitude faster than existing coupling algorithms for spatial KMC such as the Common Random Number approach. We also provide a complete implementation of the proposed sensitivity analysis algorithms, including various spatial KMC examples, in a supplementary

  16. The (kinetic) theory of active particles applied to learning dynamics. Comment on "Collective learning modeling based on the kinetic theory of active particles" by D. Burini et al.

    NASA Astrophysics Data System (ADS)

    Nieto, J.

    2016-03-01

    The learning phenomena, their complexity, concepts, structure, suitable theories and models, have been extensively treated in the mathematical literature in the last century, and [4] contains a very good introduction to the literature describing the many approaches and lines of research developed about them. Two main schools have to be pointed out [5] in order to understand the two -not exclusive- kinds of existing models: the stimulus sampling models and the stochastic learning models. Also [6] should be mentioned as a survey where two methods of learning are pointed out, the cognitive and the social, and where the knowledge looks like a mathematical unknown. Finally, as the authors do, we refer to the works [9,10], where the concept of population thinking was introduced and which motivate the game theory rules as a tool (both included in [4] to develop their theory) and [7], where the ideas of developing a mathematical kinetic theory of perception and learning were proposed.

  17. Desorption kinetics of N,N-dimethylformamide vapor from granular activated carbon and hydrophobic zeolite

    SciTech Connect

    Ching-Yuan Chang; Wen-Tien Tsai; Horng-Chia Lee

    1996-07-01

    Such thermodynamic properties as enthalpy, free energy, and entropy of adsorption have been computed for N,N-dimethylformamide (DMF) vapor on two commercial adsorbents: coconut shell Type PCB of activated carbon and Type DAY of hydrophobic zeolite. The computation is based on the Langmuir adsorption isotherms obtained at 293, 303, and 313 K as reported by Tsai et al. The laden adsorbents were regenerated with hot inert nitrogen gas and studied by thermal gravimetric analysis at three different heating rates. The apparent activation energies (E{sub des}) of thermal desorption were determined by using the Friedman method. The zeolite DAY has an adsorption potential higher than that of activated carbon PCB as indicated by the more negative value of the adsorption enthalpy of DMF vapor. The average value of E{sub des} of zeolite DAY is larger than that of activated carbon PCB.

  18. Approaching a Conceptual Understanding of Enzyme Kinetics and Inhibition: Development of an Active Learning Inquiry Activity for Prehealth and Nonscience Majors

    ERIC Educational Resources Information Center

    House, Chloe; Meades, Glen; Linenberger, Kimberly J.

    2016-01-01

    Presented is a guided inquiry activity designed to be conducted with prenursing students using an analogous system to help develop a conceptual understanding of factors impacting enzyme kinetics and the various types of enzyme inhibition. Pre- and postconceptual understanding evaluations and effectiveness of implementation surveys were given to…

  19. Activated carbon derived from carbon residue from biomass gasification and its application for dye adsorption: Kinetics, isotherms and thermodynamic studies.

    PubMed

    Maneerung, Thawatchai; Liew, Johan; Dai, Yanjun; Kawi, Sibudjing; Chong, Clive; Wang, Chi-Hwa

    2016-01-01

    In this work, activated carbon (AC) as an effective and low-cost adsorbent was successfully prepared from carbon residue (or char, one of the by-products from woody biomass gasification) via physical activation. The surface area of char was significantly increased from 172.24 to 776.46m(2)/g after steam activation at 900°C. The obtained activated carbons were then employed for the adsorption of dye (Rhodamine B) and it was found that activated carbon obtained from steam activation exhibited the highest adsorption capability, which is mainly attributed to the higher surface area and the abundance of hydroxyl (-OH) and carboxyl (-COOH) groups on the activated carbon surface. Moreover, it was also found that the adsorption capability significantly increased under the basic condition, which can be attributed to the increased electrostatic interaction between the deprotonated (negatively charged) activated carbon and dye molecules. Furthermore, the equilibrium data were fitted into different adsorption isotherms and found to fit well with Langmuir model (indicating that dye molecules form monolayer coverage on activated carbon) with a maximum monolayer adsorption capability of 189.83mg/g, whereas the adsorption kinetics followed the pseudo-second-order kinetics.

  20. Identification and analysis of novel R308K mutation in glucokinase of type 2 diabetic patient and its kinetic correlation.

    PubMed

    Yellapu, Nanda Kumar; Valasani, Koteswara Rao; Pasupuleti, Santhosh Kumar; Gopal, Sowjenya; Potukuchi Venkata Gurunadha Krishna, Sarma; Matcha, Bhaskar

    2014-01-01

    Glucokinase (GK) plays a critical role in glucose homeostasis and the mutations in GK gene result in pathogenic complications known as Maturity Onset Diabetes of the Young 2, an autosomal dominant form of diabetic condition. In the present study, GK was purified from human liver tissue and the pure enzyme showed single band in SDS-PAGE with a molecular weight of 50 kDa. The kinetics of pure GK showed enzyme activity of 0.423±0.02 µM glucose-6-phosphate (G6P)/mL/Min and Km value of 6.66±0.02 µM. These values were compared in the liver biopsy of a clinically proven type 2 diabetic patient, where GK kinetics showed decreased enzyme activity of 0.16±0.025 µM G6P/mL/Min and increased Km of 23±0.9 µM, indicating the hyperglycemic condition in the patient. The genetic analysis of 10th exon of GK gene from this patient showed a R308K mutation. To substantiate these results, comparative molecular dynamics and docking studies were carried out where a higher docking score (-10.218 kcal/mol) was observed in the mutated GK than wild-type GK structure (-12.593 kcal/mol) indicating affinity variations for glucose. During the simulation process, glucose was expelled out from the mutant conformation but not from wild-type GK, making glucose unavailable for phosphorylation. Therefore, these results conclusively explain hyperglycemic condition in this patient.

  1. Discussion of the Separation of Chemical and Relaxational Kinetics of Chemically Activated Intermediates in Master Equation Simulations.

    PubMed

    Döntgen, Malte; Leonhard, Kai

    2017-03-02

    Chemical activation of intermediates, such as hydrogen abstraction products, is emerging as a basis for a fully new reaction type: hot β-scission. While for thermally equilibrated intermediates chemical kinetics are typically orders of magnitude slower than relaxational kinetics, chemically activated intermediates raise the issue of inseparable chemical and relaxational kinetics. Here, this separation problem is discussed in the framework of master equation simulations, proposing three cases often encountered in chemistry: insignificant chemical activation, predominant chemical activation, and the transition between these two limits. These three cases are illustrated via three example systems: methoxy (CH3Ȯ), diazenyl (ṄNH), and methyl formate radicals (CH3OĊO). For diazenyl, it is found that hot β-scission fully replaces the sequence of hydrogen abstraction and β-scission of thermally equilibrated diazenyl. Building on the example systems, a rule of thumb is proposed that can be used to intuitively judge the significance of hot β-scission: if the reverse hydrogen abstraction barrier height is comparable to or larger than the β-scission barrier height, hot β-scission should be considered in more detail.

  2. Towards theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

    PubMed Central

    König, P. H.; Ghosh, N.; Hoffmann, M.; Elstner, M.; Tajkhorshid, E.; Frauenheim, Th.; Cui, Q.

    2008-01-01

    Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, a number of technical developments were made in the framework of QM/MM simulations. A set of collective reaction co-ordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly non-linear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework. PMID:16405327

  3. Statistical assessment of change point detectors for single molecule kinetic analysis.

    PubMed

    Parsons, Sean P; Huizinga, Jan D

    2013-05-01

    Change point detectors (CPDs) are used to segment recordings of single molecules for the purpose of kinetic analysis. The assessment of the accuracy of CPD algorithms has usually been based on testing them with simulated data. However, there have not been methods to assess the output of CPDs from real data independent of simulation. Here we present one method to do this based on the assumption that the elementary kinetic unit is a stationary period (SP) with a normal distribution of samples, separated from other SPs by change points (CPs). Statistical metrics of normality can then be used to assess SPs detected by a CPD algorithm (detected SPs, DSPs). Two statistics in particular were found to be useful, the z-transformed skew (S(Z)) and z-transformed kurtosis (K(Z)). K(Z)(S(Z)) plots of DSP from noise, simulated data and single ion channel recordings showed that DSPs with false negative CP could be distinguished. Also they showed that filtering had a significant effect on the normality of data and so filtering should be taken into account when calculating statistics. This method should be useful for analyzing single molecule recordings where there is no simple model for the data.

  4. Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.

    PubMed

    König, P H; Ghosh, N; Hoffmann, M; Elstner, M; Tajkhorshid, E; Frauenheim, Th; Cui, Q

    2006-01-19

    Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.

  5. Photoacoustic Analysis of the Penetration Kinetics of Cordia verbenacea DC in Human Skin

    NASA Astrophysics Data System (ADS)

    Carvalho, S. S.; Barja, P. R.

    2012-11-01

    Phonophoresis consists of the utilization of ultrasound radiation associated to pharmacological agents in order to enhance transdermal penetration of applied drugs. It is a widely employed resource in physiotherapy practice, normally associated with anti-inflammatory drugs, such as Acheflan. This drug was developed in Brazil from the essential oil of Cordia verbenacea DC, a native plant of the Brazilian southern coast. In previous studies, the photoacoustic (PA) technique proved effective in the study of the penetration kinetics of topically applied products and in the evaluation of drug delivery after phonophoresis application. The present work aimed to evaluate the penetration kinetics of Acheflan in human skin, employing in vivo PA measurements after massage application or phonophoresis application. Ten volunteers (aged between 18 and 30 years) took part in the study. Time evolution of the PA signal was fitted to a Boltzmann curve, S-shaped. After statistical analysis, PA measurements have shown drug penetration for both application forms, but drug delivery was more evident after phonophoresis application, with a characteristic penetration time of less than 15 min for the stratum corneum.