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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

    2006-10-01

    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. Understanding protein lids: kinetic analysis of active hinge mutants in triosephosphate isomerase.

    PubMed

    Sun, J; Sampson, N S

    1999-08-31

    In previous work we tested what three amino acid sequences could serve as a protein hinge in triosephosphate isomerase [Sun, J., and Sampson, N. S. (1998) Protein Sci. 7, 1495-1505]. We generated a genetic library encoding all 8000 possible 3 amino acid combinations at the C-terminal hinge and selected for those combinations of amino acids that formed active mutants. These mutants were classified into six phylogenetic families. Two families resembled wild-type hinges, and four families represented new types of hinges. In this work, the kinetic characteristics and thermal stabilities of mutants representing each of these families were determined in order to understand what properties make an efficient protein hinge, and why all of the families are not observed in nature. From a steady-state kinetic analysis of our mutants, it is clear that the partitioning between protonation of intermediate to form product and intermediate release from the enzyme surface to form methylglyoxal (a decomposition product) is not affected. The two most impaired mutants undergo a change in rate-limiting step from enediol formation to dihydroxyacetone phosphate binding. Thus, it appears that k(cat)/K(m)'s are reduced relative to wild type as a result of slower Michaelis complex formation and dissociation, rather than increased loop opening speed.

  6. Formation of distinct soluble microbial products by activated sludge: kinetic analysis and quantitative determination.

    PubMed

    Ni, Bing-Jie; Fang, Fang; Xie, Wen-Ming; Xu, Juan; Yu, Han-Qing

    2012-02-01

    Soluble microbial products (SMP) released by microorganisms in bioreactors are classified into two distinct groups according to their different chemical and degradation kinetics: utilization-associated products (UAP) and biomass-associated products (BAP). SMP are responsible for effluent chemical oxygen demand or for membrane fouling of membrane bioreactor. Here an effective and convenient approach, other than the complicated chemical methods or complex models, is developed to quantify the formation of UAP and BAP together with their kinetics in activated sludge process. In this approach, an integrated substrate utilization equation is developed and used to determine UAP and their production kinetics. On the basis of total SMP measurements, BAP formation is determined with an integrated BAP formation equation. The fraction of substrate electrons diverted to UAP, and the content of BAP derived from biomass can then be calculated. Dynamic quantification data are obtained for UAP and BAP separately and conveniently. The obtained kinetic parameters are found to be reasonable as they are generally bounded and comparable to the literature values. The validity of this approach is confirmed by independent SMP production tests in six different activated sludge systems, which demonstrates its applicability in a wide range of engineered system regarding SMP production. This work provides a widely applied approach to determine the formation of UAP and BAP conveniently, which may offer engineers with basis to optimize bioreactor operation to avoid a high effluent soluble organics from SMP or SMP-based membrane fouling in membrane bioreactors. PMID:22185635

  7. 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

  8. 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%.

  9. 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. PMID:27155412

  10. 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.

  11. Quantitative analysis of the experimental O-J-I-P chlorophyll fluorescence induction kinetics. Apparent activation energy and origin of each kinetic step.

    PubMed

    Boisvert, Steve; Joly, David; Carpentier, Robert

    2006-10-01

    Fluorescence induction has been studied for a long time, but there are still questions concerning what the O-J-I-P kinetic steps represent. Most studies agree that the O-J rise is related to photosystem II primary acceptor (Q(A)) reduction, but several contradictory theories exist for the J-I and I-P rises. One problem with fluorescence induction analysis is that most work done to date has used only qualitative or semiquantitative data analysis by visually comparing traces to observe the effects of different chemicals or treatments. Although this method is useful to observe major changes, a quantitative method must be used to detect more subtle, yet important, differences in the fluorescence induction trace. To achieve this, we used a relatively simple mathematical approach to extract the amplitudes and half-times of the three major fluorescence induction phases obtained from traces measured in thylakoid membranes kept at various temperatures. Apparent activation energies (E(A)) were also obtained for each kinetic step. Our results show that each phase has a different E(A), with E(A O-J) kinetic phase.

  12. 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.

  13. 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.

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

    PubMed

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

    2015-06-01

    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.

  15. Kinetic analysis of DAF-FM activation by NO: toward calibration of a NO-sensitive fluorescent dye.

    PubMed

    Namin, Shabnam M; Nofallah, Sara; Joshi, Mahesh S; Kavallieratos, Konstantinos; Tsoukias, Nikolaos M

    2013-01-15

    Nitric oxide (NO) research in biomedicine has been hampered by the absence of a method that will allow quantitative measurement of NO in biological tissues with high sensitivity and selectivity, and with adequate spatial and temporal resolution. 4-amino-5-methylamino-2',7'-difluorofluorescein (DAF-FM) is a NO sensitive fluorescence probe that has been used widely for qualitative assessment of cellular NO production. However, calibration of the fluorescent signal and quantification of NO concentration in cells and tissues using fluorescent probes, have provided significant challenge. In this study we utilize a combination of mathematical modeling and experimentation to elucidate the kinetics of NO/DAF-FM reaction in solution. Modeling and experiments suggest that the slope of fluorescent intensity (FI) can be related to NO concentration according to the equation: ddtFI=2αk(1)NO(2)O(2)DAF-FMkNO+DAF-FM where α is a proportionality coefficient that relates FI to unit concentration of activated DAF-FM, k(1) is the NO oxidation rate constant, and k was estimated to be 4.3±0.6. The FI slope exhibits saturation kinetics with DAF-FM concentration. Interestingly, the effective half-maximum constant (EC(50)) increases proportionally to NO concentration. This result is not in agreement with the proposition that N(2)O(3) is the NO oxidation byproduct that activates DAF-FM. Kinetic analysis suggests that the reactive intermediate should exhibit NO-dependent consumption and thus NO(2)() is a more likely candidate. The derived rate law can be used for the calibration of DAF-FM fluorescence and the quantification of NO concentration in biological tissues.

  16. 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. PMID:27295438

  17. 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.

  18. Photoemission from activated gallium arsenide. II. Spin polarization versus kinetic energy analysis

    NASA Astrophysics Data System (ADS)

    Drouhin, H.-J.; Hermann, C.; Lampel, G.

    1985-03-01

    The spin polarization of the electrons emitted by a GaAs photocathode under circularly polarized light excitation is investigated as a function of the electron kinetic energy. The photocathode is activated by cesium and oxygen coadsorption under ultrahigh-vacuum conditions to achieve a negative electron affinity. The spin polarization is measured by Mott scattering. The study is performed with a very-high-energy resolution (20 meV), at 300 and 120 K, under well-focused Kr+-laser light excitation (photon energy ranging from 1.55 to 2.60 eV). The polarization-versus-energy distribution curves show typical features related to those observed in the energy distribution curves, which are analyzed in detail in the preceding paper [H.-J. Drouhin, C. Hermann, and G. Lampel, Phys. Rev. B 31, 3859 (1985)]. A model is developed to account for the largest measured polarization, which arises from electrons excited from the heavy-hole band and emitted without suffering any collision: A (2/3) maximum value is expected, which is reduced by spin precession in the internal D'yakonov and Perel' (DP) field, due to the absence of space-inversion symmetry in GaAs. An estimation of the hot-electron mean free path (~0.1 μm for photon energy above 1.96 eV) is deduced. The photoemission polarizations of the electrons excited from each of the two other valence bands are also calculated using a nonparabolic Kane band model. The L and X subsidiary minima give rise to polarization plateaus originating from energy relaxation in the band-bending region. The main contribution to the photocurrent is due to electrons which were thermalized in the central minimum of the bulk crystal and have relaxed their energy in the band-bending region prior to emission into vacuum. Their polarization is studied in relation with the luminescence polarization, measured on the same samples, in the framework of a one-dimensional diffusion model. An additional depolarization, occurring during the escape process, is

  19. Deterministic Modelling of BAK Activation Kinetics

    NASA Astrophysics Data System (ADS)

    Grills, C.; Chacko, A.; Crawford, N.; Johnston, P. G.; Fennell, D. A.; O'Rourke, S. F. C.

    2009-08-01

    The molecular mechanism underlying mitochondrial BAK activation during apoptosis remains highly controversial. Two seemingly conflicting models have been proposed. In the activation model, BAK requires so-called activating BH3 only proteins (aBH3) to initiate its conformation change. In the other, displacement from inhibitory pro-survival BCL-2 proteins (PBPs) and monomerization of BAK by PBP restricted dissociator BH3-only proteins (dBH3) is sufficient. To better understand the kinetic implications of these models and reconcile these conflicting but highly evidence-based models, we have employed dynamical systems analysis to explore the kinetics underlying BAK activation as a non-linear reaction system. Our findings accommodate both pure agonism and dissociation as mutually exclusive mechanisms capable of initiating BAK activation. In addition we find our work supports a modelling based approach for predicting resistance to therapeutically relevant small molecules BH3 mimetics.

  20. 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).

  1. 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.

  2. Catalysis kinetics and porous analysis of rolling activated carbon-PTFE air-cathode in microbial fuel cells.

    PubMed

    Dong, Heng; Yu, Hongbing; Wang, Xin

    2012-12-01

    The microbial fuel cell (MFC), being an environment-friendly technology for wastewater treatment, is limited by low efficiency and high cost. Power output based on capital cost had been greatly increased in our previous work by introducing a novel activated carbon (AC) air-cathode (ACAC). The catalysis behavior of this ACAC was studied here based on catalysis kinetics and pore analysis of both carbon powders and catalyst layers (CLs). Plain AC (AC1#), ultracapacitor AC (AC2#), and non-AC (XC-72) powders were used as catalysts. The electron transfer number (n) of oxygen reduction reaction (ORR) with CLs increased by 5-23% compared to those n values of corresponding carbon powders before being rolled to CLs with PTFE, while the n value of Pt/C decreased by 38% when it was brushed with Nafion as the CL, indicating that rolling procedure with PTFE binder substantially increased the catalytic activity of carbon catalysts. Two-four times larger in micropore area of AC powders than non-AC powder resulted in 1.3-1.9 times increase in power density of MFCs. In addition, more uniform distribution of microporosity was found in AC1# than in AC2#, which could be the reason for the 25% increase in power density of ACAC1# (1355 ± 26 mW·m(-2)) compared to 1086 ± 8 mW·m(-2) of ACAC2#. PMID:23151092

  3. 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...

  4. Kinetic analysis of nonisothermal crystallization

    SciTech Connect

    Kelton, K.F.

    1996-12-31

    A realistic computer model for polymorphic crystallization under isothermal and nonisothermal conditions, which takes proper account of time-dependent nucleation behavior and cluster-size-dependent growth, is presented. A new correction to the standard Johnson-Mehl-Avrami-Kolmogorov (JMAK) statistical analysis that takes account of finite sample size is incorporated to simulate data taken from fine particles and nano-structured materials. Model predictions compare well with experimental data obtained from calorimetric studies of the polymorphic crystallization of lithium disilicate glass. The computer model is employed to evaluate commonly used methods of analysis for calorimetric data and to suggest new approaches for extracting kinetic parameters.

  5. 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

  6. [Effect of SO2 volume fraction in flue gas on the adsorption behaviors adsorbed by ZL50 activated carbon and kinetic analysis].

    PubMed

    Gao, Ji-xian; Wang, Tie-feng; Wang, Jin-fu

    2010-05-01

    The influence of SO2 dynamic adsorption behaviors using ZL50 activated carbon for flue gas desulphurization and denitrification under different SO2 volume fraction was investigated experimentally, and the kinetic analysis was conducted by kinetic models. With the increase of SO2 volume fraction in flue gas, the SO2 removal ratio and the activity ratio of ZL50 activated carbon decreased, respectively, and SO2 adsorption rate and capacity increased correspondingly. The calculated results indicate that Bangham model has the best prediction effect, the chemisorption processes of SO2 was significantly affected by catalytic oxidative reaction. The adsorption rate constant of Lagergren's pseudo first order model increased with the increase of inlet SO, volume fraction, which indicated that catalytic oxidative reaction of SO2 adsorbed by ZL50 activated carbon may be the rate controlling step in earlier adsorption stage. The Lagergren's and Bangham's initial adsorption rate were deduced and defined, respectively. The Ho's and Elovich's initial adsorption rate were also deduced in this paper. The Bangham's initial adsorption rate values were defined in good agreement with those of experiments. The defined Bangham's adsorptive reaction kinetic model can describe the SO2 dynamic adsorption rate well. The studied results indicated that the SO2 partial order of initial reaction rate was one or adjacent to one, while the O2 and water vapor partial order of initial reaction rate were constants ranging from 0.15-0.20 and 0.45-0.50, respectively.

  7. Resorption kinetics of four hydroxyapatite-based ceramics by particle induced X-ray emission and neutron activation analysis

    NASA Astrophysics Data System (ADS)

    Jallot, E.; Irigaray, J. L.; Oudadesse, H.; Brun, V.; Weber, G.; Frayssinet, P.

    1999-05-01

    From the viewpoint of hard tissue response to implant materials, calcium phosphates are probably the most compatible materials presently known. During the last few years, much attention has been paid to hydroxyapatite and β-tricalcium phosphate as potential biomaterials for bone substitute. A good implantation of biomaterials in the skeleton is to reach full integration of non-living implant with living bone. The aim of this study is to compare the resorption kinetics of four kinds of calcium phosphate ceramics: hydroxyapatite (Ca{10}(PO4)6(OH)2), hydroxyapatite doped with manganese or zinc and a composite material of 75% hydroxyapatite and 25% β-tricalcium phosphate (Ca3(PO4)2). Cylinders (5 6 mm in diameter) of these ceramics were packed into holes made in the femur diaphysis of mature ovine. At 2, 4, 8, 12, 16, 20, 28, 36 and 48 weeks after the operation, bone/implant interface was embedded in polymethylmethacrylate. We used the PIXE method (particle induced X-ray emission) to measure the distribution of mineral elements (Ca, P, Sr, Zn, Mn and Fe) at the bone/implant interface. At 4, 8, 16, 28 and 48 weeks after implantation we studied a biopsy of the ceramics by neutron activation method. Then, we have a global measurement of mineral elements in the biomaterial. The results showed that the resorption kinetics of hydroxyapatite doped with zinc was faster than that of the three other bioceramics.

  8. Kinetic analysis of a unique direct prothrombinase, fgl2, and identification of a serine residue critical for the prothrombinase activity.

    PubMed

    Chan, Camie W Y; Chan, Matthew W C; Liu, Mingfeng; Fung, Laisum; Cole, Edward H; Leibowitz, Julian L; Marsden, Philip A; Clark, David A; Levy, Gary A

    2002-05-15

    fgl2 prothrombinase, by its ability to generate thrombin, has been shown to be pivotal to the pathogenesis of viral-induced hepatitis, cytokine-induced fetal loss syndrome, and xeno- and allograft rejection. In this study, the molecular basis of fgl2 prothrombinase activity was examined in detail. Purified fgl2 protein generated in a baculovirus expression system had no measurable prothrombinase activity, whereas the activity was restored when the purified protein was reconstituted into phosphatidyl-L-serine-containing vesicles. Reconstituted fgl2 catalyzed the cleavage of human prothrombin to thrombin with kinetics consistent with a first order reaction, with an apparent V(max) value of 6 mol/min/mol fgl2 and an apparent K(m) value for prothrombin of 8.3 microM. The catalytic activity was totally dependent on calcium, and factor Va (500 nM) enhanced the catalytic efficiency of fgl2 by increasing the apparent V(max) value to 3670 mol/min/mol fgl2 and decreasing the apparent K(m) value for prothrombin to 7.2 microM. By a combination of site-directed mutagenesis and production of truncated proteins, it was clearly shown that residue Ser(89) was critical for the prothrombinase activity of fgl2. Furthermore, fgl2 prothrombinase activity was not inhibited by antithrombin III, soybean trypsin inhibitor, 4-aminobenzamidine, aprotinin, or phenylmethylsulfonyl fluoride, whereas diisopropylfluorophosphate completely abrogated the activity. In this work we provide direct evidence that fgl2 cleaves prothrombin to thrombin consistent with serine protease activity and requires calcium, phospholipids, and factor Va for its full activity. PMID:11994472

  9. 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.

  10. 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. PMID:18584094

  11. Analysis of the Gas Phase Kinetics Active during GaN Deposition from NH3 and Ga(CH3)3.

    PubMed

    Ravasio, Stefano; Momose, Takeshi; Fujii, Katsushi; Shimogaki, Yukihiro; Sugiyama, Masakazu; Cavallotti, Carlo

    2015-07-16

    The results of a systematic investigation aimed at determining the dominant gas phase chemistry active during GaN MOVPE are reported and discussed in this work. This study was performed developing a thermodynamic database including the most stable GaN gas phase species and a gas phase mechanism that could efficiently describe their interconversion kinetics. The thermodynamic data and the kinetic mechanism were calculated combining density functional theory and ab initio simulations. Structures and vibrational frequencies of reactants and transition states were determined at the M062X/6-311+G(d,p) level, while energies were computed at the ROCBS-QB3 level. Rate constants were calculated using transition state theory using the rigid rotor - harmonic oscillator approximation and considering the possible degeneration of internal motions in torsional rotations. The thermodynamic analysis indicated that the Ga gas phase species formed in the highest concentration at the standard GaN deposition temperature (1300 K) is GaNH2, followed by GaH and Ga. The diatomic GaN gas phase species, often considered to be the main precursor to the film growth, is predicted to be unstable with respect to GaNH2. Among the gas phase species containing two Ga atoms, the most stable are GaNHGaH(NH2)3, GaNHGaH2(NH2)2, and GaNHGa(NH2)4, thus indicating that the substitution of the methyl groups of the precursor with H or amino groups is thermodynamically favored. Several kinetic routes leading to the formation of these species were examined. It was found that the condensation of Ga(R1)x(R2)3-x species, with R1 and R2 being either CH3, NH2, or H, is a fast process, characterized by the formation of a precursor state whose decomposition to products requires overcoming submerged energy barriers. It is suggested that these species play a key role in the formation of the first GaN nuclei, whose successive growth leads to the formation of GaN powders. A kinetic analysis performed using a fluid

  12. 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.

  13. 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.

  14. 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. PMID:22951329

  15. 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

  16. 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. PMID:24508656

  17. 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.

  18. Interpretation of current-voltage relationships for "active" ion transport systems: I. Steady-state reaction-kinetic analysis of class-I mechanisms.

    PubMed

    Hansen, U P; Gradmann, D; Sanders, D; Slayman, C L

    1981-01-01

    This paper develops a simple reaction-kinetic model to describe electrogenic pumping and co- (or counter-) transport of ions. It uses the standard steady-state approach for cyclic enzyme- or carrier-mediated transport, but does not assume rate-limitation by any particular reaction step. Voltage-dependence is introduced, after the suggestion of Läuger and Stark (Biochim. Biophys. Acta 211:458-466, 1970), via a symmetric Eyring barrier, in which the charge-transit reaction constants are written as k12 = ko12 exp(zF delta psi/2RT) and k21 = ko21 exp(-zF delta psi/2RT). For interpretation of current-voltage relationships, all voltage-independent reaction steps are lumped together, so the model in its simplest form can be described as a pseudo-2-state model. It is characterized by the two voltage-dependent reaction constants, two lumped voltage-independent reaction constants (k12, k21), and two reserve factors (ri, ro) which formally take account of carrier states that are indistinguishable in the current-voltage (I-V) analysis. The model generates a wide range of I-V relationships, depending on the relative magnitudes of the four reaction constants, sufficient to describe essentially all I-V datas now available on "active" ion-transport systems. Algebraic and numerical analysis of the reserve factors, by means of expanded pseudo-3-, 4-, and 5-state models, shows them to be bounded and not large for most combinations of reaction constants in the lumped pathway. The most important exception to this rule occurs when carrier decharging immediately follows charge transit of the membrane and is very fast relative to other constituent voltage-independent reactions. Such a circumstance generates kinetic equivalence of chemical and electrical gradients, thus providing a consistent definition of ion-motive forces (e.g., proton-motive force, PMF). With appropriate restrictions, it also yields both linear and log-linear relationships between net transport velocity and either

  19. Kinetic analysis of the activation of transducin by photoexcited rhodopsin. Influence of the lateral diffusion of transducin and competition of guanosine diphosphate and guanosine triphosphate for the nucleotide site.

    PubMed Central

    Bruckert, F; Chabre, M; Vuong, T M

    1992-01-01

    The activation of transducin (T) by photoexcited rhodopsin (R*) is kinetically dissected within the framework of Michaelis-Menten enzymology, taking transducin as substrate of the enzyme R*. The light scattering "release" signal (Vuong, T.M., M. Chabre, and L. Stryer, 1984, Nature (Lond.). 311:659-661) was used to monitor the kinetics of transducin activation at 20 degrees C. In addition, the influence of nonuniform distributions of R* on these activation kinetics is also explored. Sinusoidal patterns of R* were created with interference fringes from two crossed laser beams. Two characteristic times were extracted from the Michaelis-Menten analysis: t(form), the diffusion-related time needed to form the enzyme-substrate R*-transducin is 0.25 +/- 0.1 ms, and T(cat), the time taken by R* to perform the chemistry of catalysis on transducin is 1.2 +/- 0.2 ms, in the absence of added guanosine diphosphate (GDP) and at saturating levels of guanosine triphosphate (GTP). With t(form) being but 20% of the total activation time t(form) + t(cat), transducin activation by R* is not limited by lateral diffusion. This is further borne out by the observation that uniform and sinusoidal patterns of R* elicited release signals of indistinguishable kinetics. When (GDP) = (GTP) = 500 microM, t(cat) is lengthened twofold. As the in vivo GDP and GTP levels are comparable, the exchange of nucleotides may well be the rate-limiting process. PMID:1420903

  20. Integrated safety analysis based on spatial kinetics

    SciTech Connect

    Finnemann, H.; Drescher, G.

    1994-12-31

    The continuing progress in computer technology, characterized by the ever-increasing calculational speed of various computer architectures, enables the direct coupling of up to recently separate code systems. As a consequence different areas of analysis like reactor physics, core thermal hydraulics, and plant dynamics can be integrated to increase the accuracy of simulation over that obtained from imposing conservative boundary conditions at the interfaces. The coupling of thermal-hydraulic subchannel analysis with nodal space-time kinetics calculations is an important step toward an even more extensive integration of complex code systems. In this paper we present some results of a transient departure from nucleate boiling ratio (DNBR) calculation integrated in the nodal kinetics code PANBOX.

  1. Kinetic Analysis of Protein Folding Lattice Models

    NASA Astrophysics Data System (ADS)

    Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee

    Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.

  2. Michaelis-Menten Kinetics and the Activation Energy Relate Soil Peroxidase Kinetics to the Lignin Chemistry

    NASA Astrophysics Data System (ADS)

    Triebwasser-Freese, D.; Tharayil, N.; Preston, C. M.; Gerard, P.

    2013-12-01

    Recently, it has been suggested that lignin exhibit a turnover rate of less than 6 years, suggesting that the enzymatic mechanisms mediating the decay of lignin are less understood. One factor that could be affecting the mean residence time of lignin in the soil is the catalytic efficiency of soil oxidoreductase enzymes. We characterized the spatial and seasonal transitions in the Michaelis-Menten kinetics and activation energy of the soil oxidoreductase enzyme, peroxidase, across three ecosystems of differing litter chemistries- pine, deciduous forest, and a cultivated field- and associate it to the soil lignin chemistries. To interpret the combined effect of Vmax and Km, the two parameters were integrated into one term which we defined as the catalytic efficiency. Generally, the peroxidases in pine soils exhibited the highest Vmax and Km, resulting in the lowest catalytic efficiency, followed by that in the deciduous soils. Meanwhile, the agricultural soils which exhibited the lowest Vmax and Km contained the highest catalytic efficiency of peroxidase. Through linear regression analysis of the kinetic parameters to the soil lignin chemistry, we discerned that the catalytic efficiency term best associated to the lignin monomer ratios (C/V, P/V, and SCV/V). The Activation Energy of peroxidase varied by depth, and seasons across the ecosystems. However, the Activation Energy of peroxidase did not relate to the lignin chemistry or quantity. Collectively, our results show that although the peroxidase Vmax and Km in the phenolic-poor soils are low, the degradation efficiency of peroxidases in this soils can be equivalent or exceed that of phenolic-rich soils. This study, through the characterization of Michaelis-Menten kinetics, provides a new insight into the mechanisms that could moderate the decomposition of lignin in soils.

  3. 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.

  4. The use of kinetic N-order model in description of active substance release from various drug forms. Part 2. Analysis of paracetamol and sodium diclofenac release from methylcellulose.

    PubMed

    Marciniak, Dominik M; Dryś, Andrzej; Pluta, Janusz; Kubis, Aleksander A

    2008-01-01

    The first part of the monograph presented the premises and equations which are the basis for the proposed mathematical n-order model. This non-linear physical model obeying the laws of chemical kinetics was used to describe the processes of active substance release from drug form. The possibilities of its application in the mathematical description and detailed analysis of the kinetics of paracetamol and sodium diclofenac release from various viscosity gels based on methylcellulose were investigated. Moreover, the effect of temperature on the release profiles of the above-mentioned active substances from investigated formulations was analyzed. On the basis of a series of performed experiments and detailed comparative statistical analysis of the estimators of two parameters characterizing n-order model: release rate constant K and order coefficient of the release process N, it was demonstrated that the active substance release rate from formulations with uncontrolled release is correlated with actual order of the process. Also, the proposed n-order model was compared with models obeying the laws of chemical kinetics: 0-order model, 1-order model and with diffusion Higuchi "square root of time" model, and the comparison demonstrated superiority of the n-order model over standard models. A non-linear statistical analysis was performed by means of computer software Statistica Pl. v. 7.1 manufactured by StatSoft Polska and Mathematica v. 5.0 manufactured by Wolfram Research.

  5. Activation analysis

    SciTech Connect

    Alfassi, Z.B. . Dept. of Nuclear Engineering)

    1990-01-01

    This volume contains 16 chapters on the application of activation analysis in the fields of life sciences, biological materials, coal and its effluents, environmental samples, archaeology, material science, and forensics. Each chapter is processed separately for the data base.

  6. Photocatalytic degradation of carbofuran by TiO2-coated activated carbon: Model for kinetic, electrical energy per order and economic analysis.

    PubMed

    Vishnuganth, M A; Remya, Neelancherry; Kumar, Mathava; Selvaraju, N

    2016-10-01

    The photocatalytic removal of carbofuran (CBF) from aqueous solution in the presence of granular activated carbon supported TiO2 (GAC-TiO2) catalyst was investigated under batch-mode experiments. The presence of GAC enhanced the photocatalytic efficiency of the TiO2 catalyst. Experiments were conducted at different concentrations of CBF to clarify the dependence of apparent rate constant (kapp) in the pseudo first-order kinetics on CBF photodegradation. The general relationship between the adsorption equilibrium constant (K) and reaction rate constant (kr) were explained by using the modified Langmuir-Hinshelwood (L-H) model. From the observed kinetics, it was observed that the surface reaction was the rate limiting step in the GAC-TiO2 catalyzed photodegradation of CBF. The values of K and kr for this pseudo first-order reaction were found to be 0.1942 L  mg(-1) and 1.51 mg L(-1) min(-1), respectively. In addition, the dependence of kapp on the half-life time was determined by calculating the electrical energy per order experimentally (EEO experimental) and also by modeling (EEO model). The batch-mode experimental outcomes revealed the possibility of 100% CBF removal (under optimized conditions and at an initial concentration of 50 mg L(-1) and 100 mg L(-1)) at a contact time of 90 min and 120 min, respectively. Both L-H kinetic model and EEO model fitted well with the batch-mode experimental data and also elucidated successfully the phenomena of photocatalytic degradation in the presence of GAC-TiO2 catalyst.

  7. Vampire bat salivary plasminogen activator exhibits a strict and fastidious requirement for polymeric fibrin as its cofactor, unlike human tissue-type plasminogen activator. A kinetic analysis.

    PubMed

    Bergum, P W; Gardell, S J

    1992-09-01

    The vampire bat salivary plasminogen activator (BatPA) is virtually inactive toward Glu-plasminogen in the absence of a fibrin-like cofactor, unlike human tissue-type plasminogen activator (tPA) (the kcat/Km values were 4 and 470 M-1 s-1, respectively). In the presence of fibrin II, tPA and BatPA activated Glu-plasminogen with comparable catalytic efficiencies (158,000 and 174,000 M-1 s-1, respectively). BatPA's cofactor requirement was partially satisfied by polymeric fibrin I (54,000 M-1 s-1), but monomeric fibrin I was virtually ineffective (970 M-1 s-1). By comparison, a variety of monomeric and polymeric fibrin-like species markedly enhanced tPA-mediated activation of Glu-plasminogen. Fragment X polymer was 2-fold better but 9-fold worse as cofactor for tPA and BatPA, respectively, relative to fibrin II. Fibrinogen, devoid of plasminogen, was a 10-fold better cofactor for tPA than fibrinogen rigorously depleted of plasminogen, Factor XIII, and fibronectin; the enhanced stimulatory effect of the less-purified fibrinogen was apparently due to the presence of Factor XIII. By contrast, the two fibrinogen preparations were equally poor cofactors of BatPA-mediated activation of Glu-plasminogen. BatPA possessed only 23 and 4% of the catalytic efficiencies of tPA and two-chain tPA, respectively, in hydrolyzing the chromogenic substrate Spectrozyme tPA. However in the presence of fibrin II, BatPA and tPA exhibited similar kcat/Km values for the hydrolysis of Spectrozyme tPA. Our data revealed that BatPA, unlike tPA, displayed a strict and fastidious requirement for polymeric fibrin I or II. Consequently, BatPA may preferentially promote plasmin generation during a narrow temporal window of fibrin formation and dissolution. PMID:1387641

  8. 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+). PMID:25250980

  9. 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.

  10. 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

  11. Kinetic analysis of complex reactions using FEMLAB

    SciTech Connect

    Cao, Chunshe; Wang, Yong

    2005-06-07

    A finite element method software FEMALB has been implemented to the kinetic analysis of complex reaction systems. The established protocol provides fast solutions to the coupled differential-algebraic equations. It shows significant advantages over the conventional coding process with the standard implicit Runge-Kutta (IRK) method. The accuracy and high efficiency have been demonstrated in the simulation of the reaction processes such as glucose/fructose hydrogenation and catalytic cracking of gasoil. As model validation, the numerical results showed satisfactory agreement with the exact solutions. With the powerful capability of solving large matrixes of differential equations (both ODE and PDE) with nonlinear algebraic constrains, such an algorithm has greatly reduced the coding labor in reaction mechanistic studies and provided a unique tool in reactor design and optimization.

  12. Kinetics of salicylic acid adsorption on activated carbon.

    PubMed

    Polakovic, Milan; Gorner, Tatiana; Villiéras, Frédéric; de Donato, Philippe; Bersillon, Jean Luc

    2005-03-29

    The adsorption and desorption of salicylic acid from water solutions was investigated in HPLC microcolumns packed with activated carbon. The adsorption isotherm was obtained by the step-up frontal analysis method in a concentration range of 0-400 mg/L and was well fitted with the Langmuir equation. The investigation of rate aspects of salicylic acid adsorption was based on adsorption/desorption column experiments where different inlet concentrations of salicylic acid were applied in the adsorption phase and desorption was conducted with pure water. The concentration profiles of individual adsorption/desorption cycles data were fitted using several single-parameter models of the fixed-bed adsorption to assess the influence of different phenomena on the column behavior. It was found that the effects of axial dispersion and extraparticle mass transfer were negligible. A rate-determining factor of fixed-bed column dynamics was the kinetics of pore surface adsorption. A bimodal kinetic model reflecting the heterogeneous character of adsorbent pores was verified by a simultaneous fit of the column outlet concentration in four adsorption/desorption cycles. The fitted parameters were the fraction of mesopores and the adsorption rate constants in micropores and mesopores, respectively. It was shown that the former rate constant was an intrinsic one whereas the latter one was an apparent value due to the effects of pore blocking and diffusional hindrances in the micropores. PMID:15779975

  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. PMID:23528781

  14. 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.

  15. Kinetic Analysis of Metal Ions: An Undergraduate Laboratory Experiment.

    ERIC Educational Resources Information Center

    Williams, Kathryn R.

    1985-01-01

    Reports on the adaptation of a kinetic method of analysis of metal ions for use in an undergraduate teaching laboratory. Background information, procedures used, and analysis of typical results obtained are provided. (JN)

  16. Musk xylene: analysis, occurrence, kinetics, and toxicology.

    PubMed

    Käfferlein, H U; Göen, T; Angerer, J

    1998-09-01

    1,3-Dimethyl-2,4,6-trinitro-5-tert.-butylbenzene (musk xylene, MX), a synthetic musk, is often used in fragrances and soaps to substitute the natural musk. MX belongs to the common group of nitromusk compounds. The main environmental intake of MX occurs after sewage introduction. The consumption of fish and drinking water as well as the use of body care and perfumed household products could lead to an ingestion of this substance in humans. Although the acute oral and dermal toxicity of MX is low, some hint for the carcinogenic potential of MX was found in one animal experiment. These findings and the high potential of MX as environmental contaminant, it is stable against biological and chemical degradation and it is highly lipophil, raised considerable attention in the field of environmental medicine. Biological monitoring and the toxicology of MX, which previously has been described to occur in human milk, human fat tissue, as well as human blood samples, are of central interest. The aim of this article is to summarize the data on the analysis, occurrence, kinetics, and toxicology of MX. As there is a lack of knowledge on human toxicity and human carcinogenicity of MX, a final evaluation of the toxicological data with regard to public health is still impossible. Nevertheless, in view of the published data about MX, there is no evidence for any substantial human risk at the moment.

  17. Kinetics of microtubule catastrophe assessed by probabilistic analysis.

    PubMed

    Odde, D J; Cassimeris, L; Buettner, H M

    1995-09-01

    Microtubules are cytoskeletal filaments whose self-assembly occurs by abrupt switching between states of roughly constant growth and shrinkage, a process known as dynamic instability. Understanding the mechanism of dynamic instability offers potential for controlling microtubule-dependent cellular processes such as nerve growth and mitosis. The growth to shrinkage transitions (catastrophes) and the reverse transitions (rescues) that characterize microtubule dynamic instability have been assumed to be random events with first-order kinetics. By direct observation of individual microtubules in vitro and probabilistic analysis of their distribution of growth times, we found that while the slower growing and biologically inactive (minus) ends obeyed first-order catastrophe kinetics, the faster growing and biologically active (plus) ends did not. The non-first-order kinetics at plus ends imply that growing microtubule plus ends have an effective frequency of catastrophe that depends on how long the microtubules have been growing. This frequency is low initially but then rises asymptotically to a limiting value. Our results also suggest that an additional parameter, beyond the four parameters typically used to describe dynamic instability, is needed to account for the observed behavior and that changing this parameter can significantly affect the distribution of microtubule lengths at steady state. PMID:8519980

  18. Kinetics of microtubule catastrophe assessed by probabilistic analysis.

    PubMed Central

    Odde, D J; Cassimeris, L; Buettner, H M

    1995-01-01

    Microtubules are cytoskeletal filaments whose self-assembly occurs by abrupt switching between states of roughly constant growth and shrinkage, a process known as dynamic instability. Understanding the mechanism of dynamic instability offers potential for controlling microtubule-dependent cellular processes such as nerve growth and mitosis. The growth to shrinkage transitions (catastrophes) and the reverse transitions (rescues) that characterize microtubule dynamic instability have been assumed to be random events with first-order kinetics. By direct observation of individual microtubules in vitro and probabilistic analysis of their distribution of growth times, we found that while the slower growing and biologically inactive (minus) ends obeyed first-order catastrophe kinetics, the faster growing and biologically active (plus) ends did not. The non-first-order kinetics at plus ends imply that growing microtubule plus ends have an effective frequency of catastrophe that depends on how long the microtubules have been growing. This frequency is low initially but then rises asymptotically to a limiting value. Our results also suggest that an additional parameter, beyond the four parameters typically used to describe dynamic instability, is needed to account for the observed behavior and that changing this parameter can significantly affect the distribution of microtubule lengths at steady state. Images FIGURE 1 PMID:8519980

  19. Kinetic and Structural Analysis for Potent Antifolate Inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and Human Dihydrofolate Reductases and Their Active-Site Variants

    PubMed Central

    Cody, Vivian; Pace, Jim; Adair, Ona O.; Gangjee, Aleem

    2013-01-01

    A major concern of immunocompromised patients, in particular those with AIDS, is susceptibility to infection caused by opportunistic pathogens such as Pneumocystis jirovecii, which is a leading cause of pneumonia in immunocompromised patients. We report the first kinetic and structural data for 2,4-diamino-6-[(2′,5′-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine (OAAG324), a potent inhibitor of dihydrofolate reductase (DHFR) from P. jirovecii (pjDHFR), and also for trimethoprim (TMP) and methotrexate (MTX) with pjDHFR, Pneumocystis carinii DHFR (pcDHFR), and human DHFR (hDHFR). OAAG324 shows a 9.0-fold selectivity for pjDHFR (Ki, 2.7 nM) compared to its selectivity for hDHFR (Ki, 24.4 nM), whereas there is only a 2.3-fold selectivity for pcDHFR (Ki, 6.3 nM). In order to understand the determinants of inhibitory potency, active-site mutations of pj-, pc-, and hDHFR were explored to make these enzymes more like each other. The most unexpected observations were that the variant pcDHFR forms with K37Q and K37Q/F69N mutations, which made the enzyme more like the human form, also made these enzymes more sensitive to the inhibitory activity of OAAG324, with Ki values of 0.26 and 0.71 nM, respectively. A similar gain in sensitivity was also observed for the hDHFR N64F variant, which showed a lower Ki value (0.58 nM) than native hDHFR, pcDHFR, or pjDHFR. Structural data are reported for complexes of OAAG324 with hDHFR and its Q35K and Q35S/N64F variants and for the complex of the K37S/F69N variant of pcDHFR with TMP. These results provide useful insight into the role of these residues in the optimization of highly selective inhibitors of DHFR against the opportunistic pathogen P. jirovecii. PMID:23545530

  20. 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

  1. Kinetic Discrimination in T-Cell Activation

    NASA Astrophysics Data System (ADS)

    Rabinowitz, Joshua D.; Beeson, Craig; Lyons, Daniel S.; Davis, Mark M.; McConnell, Harden M.

    1996-02-01

    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.

  2. CCN, hygroscopicity, and activation kinetics of Los Angeles aerosol

    NASA Astrophysics Data System (ADS)

    Lin, J. J.; Lathem, T. L.; Nenes, A.; Suski, K.; Cahill, J. F.; Prather, K. A.; Craven, J. S.; Metcalf, A. R.; Jonsson, H. H.; Flagan, R. C.; Seinfeld, J. H.

    2010-12-01

    The CalNex field campaign was designed as a comprehensive regional air quality and climate assessment study with an emphasis on the interaction between air quality and climate change. The southern California region is an excellent location for the study of air quality and climate change due to the existence and interaction of biogenic, dust, and urban plumes. Research flights aboard the Center for Interdisciplinary Remotely-Piloted Aircraft Studies (CIRPAS) Twin Otter platform focused on the origin and evolution of the Los Angeles plume as it is advected across the basin and outflows into the Coachella valley and Mojave Desert. This study focuses on cloud condensation nuclei (CCN) measurements taken aboard the Twin Otter. A continuous flow streamwise thermal gradient chamber operating in scanning flow CCN analysis (SFCA) mode provided high resolution, in situ CCN spectra (0.4-0.8% supersaturation) once every 40 seconds. In conjuncture with other aerosol instrumentation aboard the Twin Otter, the data provide a comprehensive picture of the interaction of ambient aerosol with water vapor. The analysis presented then quantifies the relationship between aerosol size, chemical composition, mixing state, hygroscopicity, and activation kinetics of aerosol from the variety of sources sampled.

  3. Theoretical analysis of the glutamate dehydrogenase kinetics under physiological conditions.

    PubMed

    Popova, S V; Reich, J G

    1983-01-01

    A kinetic model of the glutamate dehydrogenase reaction has been formulated for the reversible reaction including all seven reactants (substrates and cofactors NAD(H) and NADP(H)). The model parameters have been evaluated from published initial-rate data. Analysis of the model at cofactor concentration near to that in the intact mitochondrion has shown that the competition for active sites between cofactors and substrates simultaneously present in mitochondria diminishes the steady-state rate of the reaction by a factor of 10 to 100 as compared to the maximal reaction rate. The model predicts near-equilibrium of the reaction substrates with NAD+/NADH cofactor pair and off-equilibrium with NADP+/NADPH. Substrate cycling with futile transfer of hydrogen from NADP+-system to NAD+-system has been found to account under in vivo conditions for no more than 2% of the maximal glutamate dehydrogenase activity in the mitochondria.

  4. A propagation of error analysis of the enzyme activity expression. A model for determining the total system random error of a kinetic enzyme analyzer.

    PubMed

    Tiffany, T O; Thayer, P C; Coelho, C M; Manning, G B

    1976-09-01

    We present a total system error evaluation of random error, based on a propagation of error analysis of the expression for the calculation of enzyme activity. A simple expression is derived that contains terms for photometric error, timing uncertainty, temperature-control error, sample and reagent volume errors, and pathlength error. This error expression was developed in general to provide a simple means of evaluating the magnitude of random error in an analytical system and in particular to provide an error evaluation protocol for the assessment of the error components in a prototype Miniature Centrifugal Analyzer system. Individual system components of error are measured. These measured error components are combined in the error expressiion to predict performance. Enzyme activity measurements are made to correlate with the projected error data. In conclusion, it is demonstrated that this is one method for permitting the clinical chemist and the instrument manufacturer to establish reasonable error limits. PMID:954193

  5. A new robust kinetic assay for DAP epimerase activity.

    PubMed

    Hor, Lilian; Peverelli, Martin G; Perugini, Matthew A; Hutton, Craig A

    2013-10-01

    DAP epimerase is the penultimate enzyme in the lysine biosynthesis pathway. The most versatile assay for DAP epimerase catalytic activity employs a coupled DAP epimerase-DAP dehydrogenase enzyme system with a commercial mixture of DAP isomers as substrate. DAP dehydrogenase converts meso-DAP to THDP with concomitant reduction of NADP(+) to NADPH. We show that at high concentrations, accumulation of NADPH results in inhibition of DAPDH, resulting in spurious kinetic data. A new assay has been developed employing DAP decarboxylase that allows the reliable characterisation of DAP epimerase enzyme kinetics. PMID:23838343

  6. Kinetic analysis of the thermal processing of silica and organosilica.

    PubMed

    Kappert, Emiel J; Bouwmeester, Henny J M; Benes, Nieck E; Nijmeijer, Arian

    2014-05-15

    The incorporation of an organic group into sol-gel-derived silica causes significant changes in the structure and properties of these materials. Therefore, the thermal treatment of organosilica materials may require a different approach. In the present paper, kinetic parameters (activation energy, pre-exponential constant, and reaction models) have been determined from mass loss data for the dehydration, dehydroxylation, and decomposition reactions that take place upon heating silica and organosilica. Parameters were obtained by employing model-free isoconversional methods to data obtained under multiple heating rates as well as by multivariate analysis of the kinetics using a multistep reaction model with distributed activation energy. For silica, it can be concluded that the reaction atmosphere (i.e., inert or thermo-oxidative) has no influence on the reaction rate of the dehydration and dehydroxylation reactions that are responsible for the densification of the material. Under inert atmosphere, full dehydration can be reached without affecting the organic moiety. Achieving complete dehydroxylation of the organosilica is practically impossible as decomposition does manifest itself under commonly employed calcination temperatures. This indicates that prudence is required in designing a heat treatment program for these hybrid materials. To aid in optimizing the thermal treatment, a predictive model was developed, which can be used to forecast the extent of dehydration, dehydroxylation, and decomposition reactions under a multitude of temperature programs. PMID:24754674

  7. Modulation of glucokinase by glucose, small-molecule activator and glucokinase regulatory protein: steady-state kinetic and cell-based analysis.

    PubMed

    Bourbonais, Francis J; Chen, Jing; Huang, Cong; Zhang, Yanwei; Pfefferkorn, Jeffrey A; Landro, James A

    2012-02-01

    GK (glucokinase) is an enzyme central to glucose metabolism that displays positive co-operativity to substrate glucose. Small-molecule GKAs (GK activators) modulate GK catalytic activity and glucose affinity and are currently being pursued as a treatment for Type 2 diabetes. GK progress curves monitoring product formation are linear up to 1 mM glucose, but biphasic at 5 mM, with the transition from the lower initial velocity to the higher steady-state velocity being described by the rate constant kact. In the presence of a liver-specific GKA (compound A), progress curves at 1 mM glucose are similar to those at 5 mM, reflecting activation of GK by compound A. We show that GKRP (GK regulatory protein) is a slow tight-binding inhibitor of GK. Analysis of progress curves indicate that this inhibition is time dependent, with apparent initial and final Ki values being 113 and 12.8 nM respectively. When GK is pre-incubated with glucose and compound A, the inhibition observed by GKRP is time dependent, but independent of GKRP concentration, reflecting the GKA-controlled transition between closed and open GK conformations. These data are supported by cell-based imaging data from primary rat hepatocytes. This work characterizes the modulation of GK by a novel GKA that may enable the design of new and improved GKAs.

  8. 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

    2015-05-01

    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.

  9. 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.

  10. 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

  11. 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).

  12. [Adsorption kinetics of reactive dyes on activated carbon fiber].

    PubMed

    Li, Ying; Yue, Qin-Yan; Gao, Bao-Yu; Yang, Jing; Zheng, Yan

    2007-11-01

    The adsorption capability of activated carbon fiber (ACF) to four reactive dyes (reactive brilliant red K-2BP, reactive turquoise blue KN-G, reactive golden yellow K-3RP, reactive black KN-B) in aqueous solution was studied, and adsorption mechanism was focused on from kinetics point of view. The results show that the equilibrium adsorbing capacity (q(e)) of each dye increases with the addition of initial concentration or temperature. On the same condition, the order of q(e) is: reactive brilliant red > reactive golden yellow > reactive black > reactive turquoise blue. The adsorption processes follow a pseudo second-order kinetic rate equation, and the steric structure, size and polarity of dyes are important influence factors to initial adsorption rate. The adsorption activation energy of each dye is low (16.42, 3.56, 5.21, 26.38 kJ x mol(-1) respectively), which indicates that it belongs to physics adsorption.

  13. 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.

  14. 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.

  15. 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.

  16. Activated sludge acclimatisation kinetics to non-ionic surfactants.

    PubMed

    Carvalho, G; Novais, J M; Pinheiro, H M

    2003-01-01

    The biodegradation of surfactants is a frequent and complex problem in domestic and industrial wastewater treatment processes. In addition to the resulting metabolites being sometimes refractory, the complete biodegradation of many of the most employed non-ionic surfactants requires long hydraulic retention times and the presence of specialised bacterial consortia. Preliminary acclimatisation tests highlighted the importance of the sludge acclimatisation state to a specific surfactant substrate for biotreatment efficiency. This paper reports on studies aimed at quantifying activated sludge acclimatisation and memory retention levels when subjected to changes in the type of surfactant included in the feed. Several transitions were tested, namely from an alkylphenol ethoxylate to a linear alkyl ethoxylate and the reverse, and between alkyl ethoxylates with different hydrophobic and hydrophilic molecular chain lengths. The kinetic results showed that sludge activation and memory loss were more dynamic for primary biodegradation It was found that the sludge was harder to adapt to alkylphenol ethoxylate than to alkyl ethoxylate. The former also apparently introduced an inhibitory effect, resulting in very slow degradation kinetics when imposed to alkyl ethoxylate acclimatised sludge. When replacing an alkyl ethoxylate with another surfactant of the same family, a longer ethoxylate chain reduced the degradation rates. This effect was further enhanced by simultaneously increasing the hydrophobic chain length of the substrate. The acclimatisation kinetic after the replacement of an alkyl ethoxylate by a longer counterpart was slower than the reverse case, and memory was also more easily lost. PMID:12641258

  17. 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.

  18. Role of plasma activation in the kinetics of CNT growth in PECVD process

    NASA Astrophysics Data System (ADS)

    Lebedeva, Irina; Gavrikov, Alexey; Baranov, Alexey; Belov, Maxim; Knizhnik, Andrey; Potapkin, Boris; Sommerer, Timothy

    2009-10-01

    The work presents kinetic modeling of the effect of acceleration for the growth kinetics of carbon nanotubes by hydrocarbon gas mixture modification with plasma discharge. The plasma activation creates active species in hydrocarbon gas mixture, which can easily adsorb and dissociate on the catalyst surface. So plasma treatment of the gas mixture in the CVD process allows to increase the carbon supply rate by a few orders of magnitude compared to that in thermal CVD process. On the other hand, plasma can also provide etching of carbon species from the catalyst surface. To correctly reproduce both of these effects of plasma, the kinetic model of growth of carbon nanotubes is developed based on first-principles analysis of heterogeneous processes on the catalyst surface and detailed kinetics of gas phase chemistry. The model is used to compare the growth rates of carbon nanotubes in thermal and plasma-enhanced CVD processes and to determine critical gas pressures, at which CNT growth kinetics switches from the adsorption limitation to the limitation by reaction and diffusion on the catalyst.

  19. 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.

  20. Kinetic, mutational, and structural analysis of malonate semialdehyde decarboxylase from Coryneform bacterium strain FG41: mechanistic implications for the decarboxylase and hydratase activities.

    PubMed

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

    2013-07-16

    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 and 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. In terms of pairwise sequence, MSAD from Coryneform bacterium strain FG41 (designated FG41 MSAD) is 38% identical 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. 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 the 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 Pp 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.

  1. 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

  2. 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,...

  3. Substrate elasticity affects bovine satellite cell activation kinetics in vitro.

    PubMed

    Lapin, M R; Gonzalez, J M; Johnson, S E

    2013-05-01

    Satellite cells support efficient postnatal skeletal muscle hypertrophy through fusion into the adjacent muscle fiber. Nuclear contribution allows for maintenance of the fiber myonuclear domain and proficient transcription of myogenic genes. Niche growth factors affect satellite cell biology; however, the interplay between fiber elasticity and microenvironment proteins remains largely unknown. The objective of the experiment was to examine the effects of hepatocyte growth factor (HGF) and surface elasticity on bovine satellite cell (BSC) activation kinetics in vitro. Young's elastic modulus was calculated for the semimembranosus (SM) and LM muscles of young bulls (5 d; n = 8) and adult cows (27 mo; n = 4) cattle. Results indicate that LM elasticity decreased (P < 0.05) with age; no difference in Young's modulus for the SM was noted. Bovine satellite cells were seeded atop polyacrylamide bioscaffolds with surface elasticities that mimic young bull and adult cow LM or traditional cultureware. Cells were maintained in low-serum media supplemented with 5 ng/mL HGF or vehicle only for 24 or 48 h. Activation was evaluated by proliferating cell nuclear antigen (PCNA) immunocytochemistry. Results indicate that BSC maintained on rigid surfaces were activated at 24 h and refractive to HGF supplementation. By contrast, fewer (P < 0.05) BSC had exited quiescence after 24 h of culture on surfaces reflective of either young bull (8.1 ± 1.7 kPa) or adult cow (14.6 ± 1.6 kPa) LM. Supplementation with HGF promoted activation of BSC cultured on bioscaffolds as measured by an increase (P < 0.05) in PCNA immunopositive cells. Culture on pliant surfaces affected neither activation kinetics nor numbers of Paired box 7 (Pax7) immunopositive muscle stem cells (P > 0.05). However, with increasing surface elasticity, an increase (P < 0.05) in the numbers of muscle progenitors was observed. These results confirm that biophysical and biochemical signals regulate BSC activation.

  4. Enhanced Enzyme Kinetic Stability by Increasing Rigidity within the Active Site*

    PubMed Central

    Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

    2014-01-01

    Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser105 residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T5015, the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability. PMID:24448805

  5. Temperature response of isoprene emission in vivo reflects a combined effect of substrate limitations and isoprene synthase activity: a kinetic analysis.

    PubMed

    Rasulov, Bahtijor; Hüve, Katja; Bichele, Irina; Laisk, Agu; Niinemets, Ulo

    2010-11-01

    The responses of isoprene emission rate to temperature are characterized by complex time-dependent behaviors that are currently not entirely understood. To gain insight into the temperature dependencies of isoprene emission, we studied steady-state and transient responses of isoprene emission from hybrid aspen (Populus tremula × Populus tremuloides) leaves using a fast-response gas-exchange system coupled to a proton-transfer reaction mass spectrometer. A method based on postillumination isoprene release after rapid temperature transients was developed to determine the rate constant of isoprene synthase (IspS), the pool size of its substrate dimethylallyldiphosphate (DMADP), and to separate the component processes of the temperature dependence of isoprene emission. Temperature transients indicated that over the temperature range 25°C to 45°C, IspS was thermally stable and operated in the linear range of its substrate DMADP concentration. The in vivo rate constant of IspS obeyed the Arrhenius law, with an activation energy of 42.8 kJ mol(-1). In contrast, steady-state isoprene emission had a significantly lower temperature optimum than IspS and higher activation energy. The reversible temperature-dependent decrease in the rate of isoprene emission between 35°C and 44°C was caused by decreases in DMADP concentration, possibly reflecting reduced pools of energetic metabolites generated in photosynthesis, particularly of ATP. Strong control of isoprene temperature responses by the DMADP pool implies that transient temperature responses under fluctuating conditions in the field are driven by initial DMADP pool size as well as temperature-dependent modifications in DMADP pool size during temperature transients. These results have important implications for the development of process-based models of isoprene emission.

  6. 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

  7. 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

  8. 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.

  9. Structure-activity studies of the inhibition of FabI, the enoyl reductase from Escherichia coli, by triclosan: kinetic analysis of mutant FabIs.

    PubMed

    Sivaraman, Sharada; Zwahlen, Jacque; Bell, Alasdair F; Hedstrom, Lizbeth; Tonge, Peter J

    2003-04-22

    Triclosan, a common antibacterial additive used in consumer products, is an inhibitor of FabI, the enoyl reductase enzyme from type II bacterial fatty acid biosynthesis. In agreement with previous studies [Ward, W. H., Holdgate, G. A., Rowsell, S., McLean, E. G., Pauptit, R. A., Clayton, E., Nichols, W. W., Colls, J. G., Minshull, C. A., Jude, D. A., Mistry, A., Timms, D., Camble, R., Hales, N. J., Britton, C. J., and Taylor, I. W. (1999) Biochemistry 38, 12514-12525], we report here that triclosan is a slow, reversible, tight binding inhibitor of the FabI from Escherichia coli. Triclosan binds preferentially to the E.NAD(+) form of the wild-type enzyme with a K(1) value of 23 pM. In agreement with genetic selection experiments [McMurry, L. M., Oethinger, M., and Levy, S. B. (1998) Nature 394, 531-532], the affinity of triclosan for the FabI mutants G93V, M159T, and F203L is substantially reduced, binding preferentially to the E.NAD(+) forms of G93V, M159T, and F203L with K(1) values of 0.2 microM, 4 nM, and 0.9 nM, respectively. Triclosan binding to the E.NADH form of F203L can also be detected and is defined by a K(2) value of 51 nM. We have also characterized the Y156F and A197M mutants to compare and contrast the binding of triclosan to InhA, the homologous enoyl reductase from Mycobacterium tuberculosis. As observed for InhA, Y156F FabI has a decreased affinity for triclosan and the inhibitor binds to both E.NAD(+) and E.NADH forms of the enzyme with K(1) and K(2) values of 3 and 30 nM, respectively. The replacement of A197 with Met has no impact on triclosan affinity, indicating that differences in the sequence of the conserved active site loop cannot explain the 10000-fold difference in affinities of FabI and InhA for triclosan.

  10. Structure-activity studies of the inhibition of FabI, the enoyl reductase from Escherichia coli, by triclosan: kinetic analysis of mutant FabIs.

    PubMed

    Sivaraman, Sharada; Zwahlen, Jacque; Bell, Alasdair F; Hedstrom, Lizbeth; Tonge, Peter J

    2003-04-22

    Triclosan, a common antibacterial additive used in consumer products, is an inhibitor of FabI, the enoyl reductase enzyme from type II bacterial fatty acid biosynthesis. In agreement with previous studies [Ward, W. H., Holdgate, G. A., Rowsell, S., McLean, E. G., Pauptit, R. A., Clayton, E., Nichols, W. W., Colls, J. G., Minshull, C. A., Jude, D. A., Mistry, A., Timms, D., Camble, R., Hales, N. J., Britton, C. J., and Taylor, I. W. (1999) Biochemistry 38, 12514-12525], we report here that triclosan is a slow, reversible, tight binding inhibitor of the FabI from Escherichia coli. Triclosan binds preferentially to the E.NAD(+) form of the wild-type enzyme with a K(1) value of 23 pM. In agreement with genetic selection experiments [McMurry, L. M., Oethinger, M., and Levy, S. B. (1998) Nature 394, 531-532], the affinity of triclosan for the FabI mutants G93V, M159T, and F203L is substantially reduced, binding preferentially to the E.NAD(+) forms of G93V, M159T, and F203L with K(1) values of 0.2 microM, 4 nM, and 0.9 nM, respectively. Triclosan binding to the E.NADH form of F203L can also be detected and is defined by a K(2) value of 51 nM. We have also characterized the Y156F and A197M mutants to compare and contrast the binding of triclosan to InhA, the homologous enoyl reductase from Mycobacterium tuberculosis. As observed for InhA, Y156F FabI has a decreased affinity for triclosan and the inhibitor binds to both E.NAD(+) and E.NADH forms of the enzyme with K(1) and K(2) values of 3 and 30 nM, respectively. The replacement of A197 with Met has no impact on triclosan affinity, indicating that differences in the sequence of the conserved active site loop cannot explain the 10000-fold difference in affinities of FabI and InhA for triclosan. PMID:12693936

  11. Kinetics of force recovery following length changes in active skinned single fibres from rabbit psoas muscle: analysis and modelling of the late recovery phase.

    PubMed

    Burton, Kevin; Simmons, Robert M; Sleep, John; Simmons, Robert M; Burton, Kevin; Smith, David A

    2006-06-01

    Redevelopment of isometric force following shortening of skeletal muscle is thought to result from a redistribution of cross-bridge states. We varied the initial force and cross-bridge distribution by applying various length-change protocols to active skinned single fibres from rabbit psoas muscle, and observed the effect on the slowest phase of recovery ('late recovery') that follows transient changes. In response to step releases that reduced force to near zero ( approximately 8 nm (half sarcomere)(-1)) or prolonged shortening at high velocity, late recovery was well described by two exponentials of approximately equal amplitude and rate constants of approximately 2 s(-1) and approximately 9 s(-1) at 5 degrees C. When a large restretch was applied at the end of rapid shortening, recovery was accelerated by (1) the introduction of a slow falling component that truncated the rise in force, and (2) a relative increase in the contribution of the fast exponential component. The rate of the slow fall was similar to that observed after a small isometric step stretch, with a rate of 0.4-0.8 s(-1), and its effects could be reversed by reducing force to near zero immediately after the stretch. Force at the start of late recovery was varied in a series of shortening steps or ramps in order to probe the effect of cross-bridge strain on force redevelopment. The rate constants of the two components fell by 40-50% as initial force was raised to 75-80% of steady isometric force. As initial force increased, the relative contribution of the fast component decreased, and this was associated with a length constant of about 2 nm. The results are consistent with a two-state strain-dependent cross-bridge model. In the model there is a continuous distribution of recovery rate constants, but two-exponential fits show that the fast component results from cross-bridges initially at moderate positive strain and the slow component from cross-bridges at high positive strain.

  12. Kinetic processes in the plasma sheet observed during auroral activity

    NASA Astrophysics Data System (ADS)

    Fillingim, Matthew Owen

    In this dissertation we analyze plasma sheet magnetic field and plasma data observed during varying levels of auroral activity from very small, isolated events known as pseudobreakups to large, global events known as substorms. The plasma and magnetic field data are taken from instruments onboard the WIND spacecraft while it traverses the near-Earth plasma sheet. Simultaneous global auroral images from POLAR/UVI allow us to determine the auroral activity level. The goal of this dissertation is to provide the most complete set of plasma sheet observations during auroral activity currently available. The kinetic aspects of the plasma dynamics which have largely been ingnored in other works are emphasized here. We have the capability to resolve changes in the three dimensional ion distribution functions with a time resolution comparable to or faster than the local ion gyroperiod. In addition, we consider the typically neglected electron dynamics when relating plasma sheet processes to the aurora. We find that the plasma sheet signatures of both pseudobreakups and substorms appear very similar. During both types of events, increases in auroral precipitation into the ionosphere are associated with large amplitude, high frequency magnetic field fluctuations, large Earthward ion < v>, increases in the fluxes of high energy ions and electrons, and hardening of the electron spectrum. Both ion and electron distributions appear to be composed of multiple components. Electromagnetic waves with power at frequencies up to and above the local proton gyrofrequency area also observed. Additionally, the ion distributions can change significantly in one gyroperiod. Together, these results imply that the microphysical processes occurring in the plasma sheet during pseudobreakups and substorms are the same and that kinetic effects are important. Therefore, magnetohydrodynamics (MHD) cannot adequately describe the physics occurring during large ion < v> events.

  13. Thermal characterization and detailed kinetic analysis of Cassava starch thermo-oxidative degradation.

    PubMed

    Janković, Bojan

    2013-06-20

    Detailed kinetic analysis of Cassava starch thermo-oxidative degradation was performed, using thermogravimetric analysis (TGA) and derivative thermogravimetry (DTG) at four different heating rates. It was found that degradation process is very complex, as identified through continuous change of apparent activation energy with degree of degradation. It was established that process proceeds through three main degradation stages with one additional sub-stage attached to the second degradation stage, which was detected by appearance of "shoulder" on DTG curves. It was found that most important degradation stage can be described by "lumped" model, which implies that free radicals simultaneously attack both linear and branched molecular forms of the starch. This is characterized by an unusually high value of obtained reaction order (n=3.49). Application of nonlinear least squares method was confirmed the reliability of evaluated kinetic parameters and function of reaction mechanism, which were derived on the basis of other kinetic methods.

  14. Thermal characterization and detailed kinetic analysis of Cassava starch thermo-oxidative degradation.

    PubMed

    Janković, Bojan

    2013-06-20

    Detailed kinetic analysis of Cassava starch thermo-oxidative degradation was performed, using thermogravimetric analysis (TGA) and derivative thermogravimetry (DTG) at four different heating rates. It was found that degradation process is very complex, as identified through continuous change of apparent activation energy with degree of degradation. It was established that process proceeds through three main degradation stages with one additional sub-stage attached to the second degradation stage, which was detected by appearance of "shoulder" on DTG curves. It was found that most important degradation stage can be described by "lumped" model, which implies that free radicals simultaneously attack both linear and branched molecular forms of the starch. This is characterized by an unusually high value of obtained reaction order (n=3.49). Application of nonlinear least squares method was confirmed the reliability of evaluated kinetic parameters and function of reaction mechanism, which were derived on the basis of other kinetic methods. PMID:23648021

  15. Kinetic analysis of receptor-controlled tracer efflux from sealed membrane fragments

    PubMed Central

    Bernhardt, Julius; Neumann, Eberhard

    1978-01-01

    A detailed kinetic analysis is presented for activator-receptor-mediated efflux of tracer substances from vesicular membrane systems in general and from sealed fragments of excitable membranes in particular. Rate constants and amplitudes, as the primary measurable quantities of the efflux kinetics, are expressed in terms of fundamental properties of vesicular membrane systems containing receptors of chemical gating systems. The experimental determination and theoretical analysis of single contributions to a complex receptor-controlled efflux has been treated for the acetylcholine receptor system; also the effect of “pharmacological densensitization” on efflux is explicitly formulated. The dependence of the measured efflux parameters on the concentration of activators can be used to derive the kinetic and thermodynamic constants for receptor activation and inactivation processes; a general kinetic scheme and two limiting cases are analyzed. The efflux of 22Na from “excitable microsacs” of Torpedo marmorata is treated as an example, and the power of the rigorous analytical method is demonstrated. In particular, the analysis of efflux amplitudes from only a few data points offers an alternative to the longer lasting measurements for obtaining efflux curves when a safety factor is involved, as in the case of tracer ions like 22Na. PMID:16592553

  16. Envelope-kinetic analysis of the electron kinetic effects on Raman backscatter and Raman backward laser amplification

    NASA Astrophysics Data System (ADS)

    Hur, Min Sup; Yoo, Seung Hoon; Suk, Hyyong

    2007-03-01

    The electron kinetic effects on Raman backscattering and Raman backward laser amplification were analyzed. The analysis is based on the envelope-kinetic equations of a plasma wave, which are composed of the conventional envelope equation of a fluid plasma and the kinetic term. One major goal of this paper is to close the envelope-kinetic model by analyzing the kinetic term, which was not fully covered in the previous work [M. S. Hur et al., Phys. Rev. Lett. 95, 115003 (2005)]. It was found that the closed envelope-kinetic equation in the nontrapping regime takes the same form as the envelope equation of the fluid plasma used in the three-wave model. For the closure in the trapping-dominant regime, the test particle technique is employed to calculate the kinetic term. Results from the full kinetic and test particle simulations agree well with each other, while the latter has a great advantage in computation speed. The frequency shift and resonance breaking by the trapped particles are discussed with the help of a new diagnostic inserted in the full kinetic averaged particle-in-cell code.

  17. Envelope-kinetic analysis of the electron kinetic effects on Raman backscatter and Raman backward laser amplification

    SciTech Connect

    Hur, Min Sup; Yoo, Seung Hoon; Suk, Hyyong

    2007-03-15

    The electron kinetic effects on Raman backscattering and Raman backward laser amplification were analyzed. The analysis is based on the envelope-kinetic equations of a plasma wave, which are composed of the conventional envelope equation of a fluid plasma and the kinetic term. One major goal of this paper is to close the envelope-kinetic model by analyzing the kinetic term, which was not fully covered in the previous work [M. S. Hur et al., Phys. Rev. Lett. 95, 115003 (2005)]. It was found that the closed envelope-kinetic equation in the nontrapping regime takes the same form as the envelope equation of the fluid plasma used in the three-wave model. For the closure in the trapping-dominant regime, the test particle technique is employed to calculate the kinetic term. Results from the full kinetic and test particle simulations agree well with each other, while the latter has a great advantage in computation speed. The frequency shift and resonance breaking by the trapped particles are discussed with the help of a new diagnostic inserted in the full kinetic averaged particle-in-cell code.

  18. Combustion kinetics of hydrochar produced from hydrothermal carbonisation of Karanj (Pongamia pinnata) fruit hulls via thermogravimetric analysis.

    PubMed

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

    2015-10-01

    This study examined the combustion profile and kinetics of hydrochar produced from hydrothermal carbonisation (HTC) of Karanj fruit hulls (KFH). The HTC-KFH hydrochar combustion kinetics was investigated at 5, 10, and 20°C/min by thermogravimetric analysis. The kinetics model, Kissinger-Akahira-Sunose revealed the combustion kinetics parameters for the extent of conversion from 0.1 to 0.8; the activation energy varies from 114 to 67 kJ/mol respectively. The hydrochar combustion followed multi-steps kinetics; the Coats-Redfern models predicted the activation energies and pre-exponential constants for the hydrochar combustion zones. The diffusion models are the effective mechanism in the second and third zone.

  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. Kinetic analysis of drug-protein interactions by affinity chromatography.

    PubMed

    Bi, Cong; Beeram, Sandya; Li, Zhao; Zheng, Xiwei; Hage, David S

    2015-10-01

    Information on the kinetics of drug-protein interactions is of crucial importance in drug discovery and development. Several methods based on affinity chromatography have been developed in recent years to examine the association and dissociation rates of these processes. These techniques include band-broadening measurements, the peak decay method, peak fitting methods, the split-peak method, and free fraction analysis. This review will examine the general principles and applications of these approaches and discuss their use in the characterization, screening and analysis of drug-protein interactions in the body. PMID:26724332

  1. Microfluidic rheology of active particle suspensions: Kinetic theory.

    PubMed

    Alonso-Matilla, Roberto; Ezhilan, Barath; Saintillan, David

    2016-07-01

    We analyze the effective rheology of a dilute suspension of self-propelled slender particles confined between two infinite parallel plates and subject to a pressure-driven flow. We use a continuum kinetic model to describe the configuration of the particles in the system, in which the disturbance flows induced by the swimmers are taken into account, and use it to calculate estimates of the suspension viscosity for a range of channel widths and flow strengths typical of microfluidic experiments. Our results are in agreement with previous bulk models, and in particular, demonstrate that the effect of activity is strongest at low flow rates, where pushers tend to decrease the suspension viscosity whereas pullers enhance it. In stronger flows, dissipative stresses overcome the effects of activity leading to increased viscosities followed by shear-thinning. The effects of confinement and number density are also analyzed, and our results confirm the apparent transition to superfluidity reported in recent experiments on pusher suspensions at intermediate densities. We also derive an approximate analytical expression for the effective viscosity in the limit of weak flows and wide channels, and demonstrate good agreement between theory and numerical calculations.

  2. Insights into O-Linked N-Acetylglucosamine ([0-9]O-GlcNAc) Processing and Dynamics through Kinetic Analysis of O-GlcNAc Transferase and O-GlcNAcase Activity on Protein Substrates*

    PubMed Central

    Shen, David L.; Gloster, Tracey M.; Yuzwa, Scott A.; Vocadlo, David J.

    2012-01-01

    Cellular O-linked N-acetylglucosamine (O-GlcNAc) levels are modulated by two enzymes: uridine diphosphate-N-acetyl-d-glucosamine:polypeptidyltransferase (OGT) and O-GlcNAcase (OGA). To quantitatively address the activity of these enzymes on protein substrates, we generated five structurally diverse proteins in both unmodified and O-GlcNAc-modified states. We found a remarkably invariant upper limit for kcat/Km values for human OGA (hOGA)-catalyzed processing of these modified proteins, which suggests that hOGA processing is driven by the GlcNAc moiety and is independent of the protein. Human OGT (hOGT) activity ranged more widely, by up to 15-fold, suggesting that hOGT is the senior partner in fine tuning protein O-GlcNAc levels. This was supported by the observation that Km,app values for UDP-GlcNAc varied considerably (from 1 μm to over 20 μm), depending on the protein substrate, suggesting that some OGT substrates will be nutrient-responsive, whereas others are constitutively modified. The ratios of kcat/Km values obtained from hOGT and hOGA kinetic studies enable a prediction of the dynamic equilibrium position of O-GlcNAc levels that can be recapitulated in vitro and suggest the relative O-GlcNAc stoichiometries of target proteins in the absence of other factors. We show that changes in the specific activities of hOGT and hOGA measured in vitro on calcium/calmodulin-dependent kinase IV (CaMKIV) and its pseudophosphorylated form can account for previously reported changes in CaMKIV O-GlcNAc levels observed in cells. These studies provide kinetic evidence for the interplay between O-GlcNAc and phosphorylation on proteins and indicate that these effects can be mediated by changes in hOGT and hOGA kinetic activity. PMID:22311971

  3. Kinetic energy budgets during the life cycle of intense convective activity

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.; Scoggins, J. R.

    1978-01-01

    Synoptic-scale data at three- and six-hour intervals are employed to study the relationship between changing kinetic energy variables and the life cycles of two severe squall lines. The kinetic energy budgets indicate a high degree of kinetic energy generation, especially pronounced near the jet-stream level. Energy losses in the storm environment are due to the transfer of kinetic energy from grid to subgrid scales of motion; large-scale upward vertical motion carries aloft the kinetic energy generated by storm activity at lower levels. In general, the time of maximum storm intensity is also the time of maximum energy conversion and transport.

  4. 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. PMID:26301850

  5. Evidence for the kinetic partitioning of polymerase activity on G-quadruplex DNA

    PubMed Central

    Eddy, Sarah; Maddukuri, Leena; Ketkar, Amit; Zafar, Maroof K.; Henninger, Erin E.; Pursell, Zachary F.; Eoff, Robert L.

    2015-01-01

    We have investigated the action of the human DNA polymerase epsilon (hpol ε) and eta (hpol η) catalytic cores on G-quadruplex (G4) DNA substrates derived from the promoter of the c-MYC proto-oncogene. The translesion enzyme hpol η exhibits a 6.2-fold preference for binding to G4 DNA relative to non-G4 DNA, while hpol ε binds both G4 and non-G4 substrates with near equal affinity. Kinetic analysis of single-nucleotide insertion by hpol η reveals that it is able to maintain greater than 25% activity on G4 substrates compared to non-G4 DNA substrates, even when the primer template junction is positioned directly adjacent to G22 (the first tetrad-associated guanine in the c-MYC G4 motif). Surprisingly, hpol η fidelity increases ~15-fold when copying G22. By way of comparison, hpol ε retains ~4% activity and has a 33-fold decrease in fidelity when copying G22. The fidelity of hpol η is ~100-fold more accurate than hpol ε when comparing the mis-insertion frequencies of the two enzymes opposite a tetrad-associated guanine. The kinetic differences observed for the B- and Y-family pols on G4 DNA support a model where a simple kinetic switch between replicative and TLS pols could help govern fork progress during G4 DNA replication. PMID:25903680

  6. 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.

  7. In-depth investigation on the pyrolysis kinetics of raw biomass. Part I: kinetic analysis for the drying and devolatilization stages.

    PubMed

    Chen, Dengyu; Zheng, Yan; Zhu, Xifeng

    2013-03-01

    An in-depth investigation was conducted on the kinetic analysis of raw biomass using thermogravimetric analysis (TGA), from which the activation energy distribution of the whole pyrolysis process was obtained. Two different stages, namely, drying stage (Stage I) and devolatilization stage (Stage II), were shown in the pyrolysis process in which the activation energy values changed with conversion. The activation energy at low conversions (below 0.15) in the drying stage ranged from 10 to 30 kJ/mol. Such energy was calculated using the nonisothermal Page model, known as the best model to describe the drying kinetics. Kinetic analysis was performed using the distributed activation energy model in a wide range of conversions (0.15-0.95) in the devolatilization stage. The activation energy first ranged from 178.23 to 245.58 kJ/mol and from 159.66 to 210.76 kJ/mol for corn straw and wheat straw, respectively, then increasing remarkably with an irregular trend.

  8. Expression, Purification, and Kinetic Analysis of PTP Domains.

    PubMed

    Mentel, Mihaela; Badea, Rodica A; Necula-Petrareanu, Georgiana; Mallikarjuna, Sujay T; Ionescu, Aura E; Szedlacsek, Stefan E

    2016-01-01

    Protein tyrosine phosphatases (PTP) are a large group of enzymes which work together with protein tyrosine kinases to control the tyrosine phosphorylation of proteins, thus playing a major role in cellular signaling. Here, we provide detailed protocols for expression and purification of the catalytic domain of RPTPμ and full length Eya3 as well as the extracellular region of PTPBR7. Methods are described for evaluation of the purity of the recombinant proteins thus obtained. For the purified Eya3 phosphatase we provide protocols for enzyme activity assay using either chromogenic, fluorescent, or peptide substrates. Determination of kinetic parameters by different graphical and computer-based procedures is also described. PMID:27514799

  9. A uranium (VI) complex: Synthesis, structural and thermal kinetic analysis

    NASA Astrophysics Data System (ADS)

    Goel, Nidhi

    2016-08-01

    A new complex [UO2(2,6-DNP)2phen] (1) (2,6-DNP = 2,6-dinitrophenol, phen = 1,10-phenanthroline) was synthesized, and identified by elemental analysis, IR, Powder XRD and single crystal X-ray crystallography. Crystal structure provides the abundant information's about the bonding and geometry around the U(VI) metal center. The thermal decomposition was studied by TG-DSC, and the kinetics of thermolysis was investigated by applying model fitting as well as isoconversional methods. Explosion delay measurement (De) was also evaluated to determine the response of this complex under the condition of rapid heating.

  10. 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.

  11. Activity and kinetic properties of phosphotransacetylase from intestinal sulfate-reducing bacteria.

    PubMed

    Kushkevych, Ivan V

    2015-01-01

    Phosphotransacetylase activity and the kinetic properties of the enzyme from intestinal sulfate-reducing bacteria Desulfovibrio piger and Desulfomicrobium sp. has never been well-characterized and has not been studied yet. In this paper, the specific activity of phosphotransacetylase and the kinetic properties of the enzyme in cell-free extracts of both D. piger Vib-7 and Desulfomicrobium sp. Rod-9 intestinal bacterial strains were presented at the first time. The microbiological, biochemical, biophysical and statistical methods in this work were used. The optimal temperature and pH for enzyme reaction was determined. Analysis of the kinetic properties of the studied enzyme was carried out. Initial (instantaneous) reaction velocity (V0), maximum amount of the product of reaction (Pmax), the reaction time (half saturation period, τ) and maximum velocity of the phosphotransacetylase reaction (Vmax) were defined. Michaelis constants (Km) of the enzyme reaction (3.36 ± 0.35 mM for D. piger Vib-7, 5.97 ± 0.62 mM for Desulfomicrobium sp. Rod-9) were calculated. The studies of the phosphotransacetylase in the process of dissimilatory sulfate reduction and kinetic properties of this enzyme in intestinal sulfate-reducing bacteria, their production of acetate in detail can be perspective for clarification of their etiological role in the development of the humans and animals bowel diseases. These studies might help in predicting the development of diseases of the gastrointestinal tract, by providing further details on the etiology of bowel diseases which are very important for the clinical diagnosis of these disease types.

  12. 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.

  13. Evaluation of kinetic parameters for water soluble crystals by thermo gravimetric analysis

    NASA Astrophysics Data System (ADS)

    Rama, S.; Surendra Dilip, C.; Perumal, Rajesh Narayana

    2015-01-01

    This work elevates the relevance of kinetic parameters of nucleation and thermal decomposition for water soluble crystals. The positive soluble Potassium Dihydrogen Phosphate (KDP) and negative soluble Lithium Sulfate Monohydrate (LSMH) materials were chosen for the kinetic evaluation. The results obtained from the classical nucleation theory are verified with the kinetic parameters which are evaluated from thermo gravimetric analysis. Nucleation parameters of a crystallization process such as interfacial energy (σ), volume free energy (ΔGv), critical energy barrier for nucleation (ΔG*), radius of the critical nucleus (r*) and nucleation rate (J) of the positive (KDP) and negative solubility (LSMH) crystals are determined from the classical nucleation theory of solubility-enthalpy relation. The kinetic parameters viz. the order of reaction, enthalpy, Gibbs free energy of activation, frequency factor, and entropy of activation are obtained from the TG based models viz. Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova. The effect of varying temperature with relative variation on Gibbs free energy for both positive and negative solubility crystals is also discussed. The developed model holds good for both positive and negative solubility crystals.

  14. 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.

  15. Kinetic analysis and fragment screening with Fujifilm AP-3000.

    PubMed

    Rich, Rebecca L; Myszka, David G

    2010-07-15

    We evaluated the performance of Fujifilm's new AP-3000 surface plasmon resonance biosensor for kinetic analysis and fragment screening. Using carbonic anhydrase II as a model system, we characterized a set of 10 sulfonamide-based inhibitors that range in molecular mass from 98 to 341Da and approximately 10,000-fold in affinity (0.4mM to 20nM). Although the data collected from the AP-3000 were generally similar to those collected using a Biacore T100, the AP-3000's stop-flow analyte delivery system complicated the shapes of the association- and dissociation-phase binding responses. We illustrate how reasonable estimates of the kinetic rate constants can be extracted from AP-3000 data by limiting data analysis to only the regions of the responses collected during flow conditions. We also provide an example of the results obtained for a fragment-screening study with the AP-3000, which is the ideal application of this technology.

  16. 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.

  17. Kinetic modeling and sensitivity analysis of xylose metabolism in Lactococcus lactis IO-1.

    PubMed

    Oshiro, Mugihito; Shinto, Hideaki; Tashiro, Yukihiro; Miwa, Noriko; Sekiguchi, Tatsuya; Okamoto, Masahiro; Ishizaki, Ayaaki; Sonomoto, Kenji

    2009-11-01

    We proposed a kinetic simulation model of xylose metabolism in Lactococcus lactis IO-1 that describes the dynamic behavior of metabolites using the simulator WinBEST-KIT. This model was developed by comparing the experimental time-course data of metabolites in batch cultures grown in media with initial xylose concentrations of 20.3-57.8 g/l with corresponding calculated data. By introducing the terms of substrate activation, substrate inhibition, and product inhibition, the revised model showed a squared correlation coefficient (r2) of 0.929 between the experimental time-course of metabolites and the calculated data. Thus, the revised model is assumed to be one of the best candidates for kinetic simulation describing the dynamic behavior of metabolites. Sensitivity analysis revealed that pyruvate flux distribution is important for higher lactate production. To confirm the validity of our kinetic model, the results of the sensitivity analysis were compared with enzyme activities observed during increasing lactate production by adding natural rubber serum powder to the xylose medium. The experimental results on pyruvate flux distribution were consistent with the prediction by sensitivity analysis.

  18. 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).

  19. 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

  20. Kinetics of acrylamide formation/elimination reactions as affected by water activity.

    PubMed

    De Vleeschouwer, Kristel; Van der Plancken, Iesel; Van Loey, Ann; Hendrickx, Marc E

    2007-01-01

    The influence of water activity on the kinetics of acrylamide formation and elimination reaction was investigated using low-moisture equimolar asparagine-glucose model systems, which were heated at temperatures between 120 and 200 degrees C for variable heating times. To determine the water content corresponding to the water activities tested, a sorption moisture isotherm was constructed experimentally. The acrylamide concentrations measured at different water activities could be modeled on the basis of a reaction scheme including not only acrylamide formation and elimination reactions but also an alternative Maillard reaction between both reactants. The corresponding rate constants and activation energies were estimated using nonlinear regression analysis. Whereas the rate constant for acrylamide formation varied only slightly with the initial water activity of the model system, the elimination rate constant showed a clear minimum around a water activity of 0.82. The opposite trend, namely, a maximum at a water activity of 0.82, was found for the Maillard reaction rate constant as a function of water activity, which confirms data from literature. The activation energies for the different reactions changed in a comparable way as the corresponding rate constant with water activity. PMID:17503764

  1. 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

  2. [Kinetic radiography and functional analysis of the temporomandibular joint (TMJ)].

    PubMed

    Bandai, Natsuko; Sanada, Shigeru; Ueki, Koichiro; Funabasama, Shintaro; Matsui, Takeshi; Tsuduki, Shinji

    2003-03-01

    To develop a method of kinetic radiography and a computer-aided diagnosis (CAD) system for quantitative evaluation of the temporomandibular joint (TMJ), dynamic images of the TMJ from one healthy volunteer were obtained by fluoroscopy in the lateral view on the right and left sides. The accumulated image subtraction technique extracted the condyle in each image. A sequential similarity detection algorithm (SSDA) was employed to trace the movement path and the velocity of the condyle. The shape of the path of the right condyle was smoother than that of the left condyle. The size of the maximum vertical and horizontal movements of the condyle were 4.6+/-0.1 mm and 15.0+/-0.2 mm, respectively. The velocity of the movement of the condyle was higher in the area close to the articular eminence than in any other area during the opening and closing of the mouth. This CAD system will contribute to the kinetic analysis of the TMJ for screening, follow-up study, and informed consent, providing speed, quantitation, and cost-effectiveness.

  3. Computational Study and Kinetic Analysis of the Aminolysis of Thiolactones.

    PubMed

    Desmet, Gilles B; D'hooge, Dagmar R; Sabbe, Maarten K; Marin, Guy B; Du Prez, Filip E; Espeel, Pieter; Reyniers, Marie-Françoise

    2015-09-01

    The aminolysis of three differently α-substituted γ-thiolactones (C4H5OSX, X = H, NH2, and NH(CO)CH3) is modeled based on CBS-QB3 calculated free energies corrected for solvation using COSMO-RS. For the first time, quantitative kinetic and thermodynamic data are provided for the concerted path and the stepwise path over a neutral tetrahedral intermediate. These paths can take place via an unassisted, an amine-assisted, or a thiol-assisted mechanism. Amine assistance lowers the free energy barriers along both paths, while thiol assistance only lowers the formation of the neutral tetrahedral intermediate. Based on the ab initio calculated rate coefficients, a kinetic model is constructed that is able to reliably describe experimental observations for the aminolysis of N-acetyl-dl-homocysteine thiolactone with n-butylamine in THF and CHCl3. Reaction path analysis shows that for all conditions relevant for applications in polymer synthesis and postpolymer modification, an assisted stepwise mechanism is operative in which the formation of the neutral tetrahedral intermediate is rate-determining and which is mainly amine-assisted at low conversions and thiol-assisted at high conversions.

  4. Linking wheelchair kinetics to glenohumeral joint demand during everyday accessibility activities.

    PubMed

    Holloway, Catherine S; Symonds, Andrew; Suzuki, Tatsuto; Gall, Angela; Smitham, Peter; Taylor, Stephen

    2015-01-01

    The aim of the study was to investigate if push-rim kinetics could be used as markers of glenohumeral joint demand during manual wheelchair accessibility activities; demonstrating a method of biomechanical analysis that could be used away from the laboratory. Propulsion forces, trunk and upper limb kinematics and surface electromyography were recorded during four propulsion tasks (level, 2.5% cross slope, 6.5% incline and 12% incline). Kinetic and kinematic data were applied to an OpenSim musculoskeletal model of the trunk and upper limb, to enable calculation of glenohumeral joint contact force. Results demonstrated a positive correlation between propulsion forces and glenohumeral joint contact forces. Both propulsion forces and joint contact forces increased as the task became more challenging. Participants demonstrated increases in trunk flexion angle as the requirement for force application increased, significantly so in the 12% incline. There were significant increases in both resultant glenohumeral joint contact forces and peak and mean normalized muscle activity levels during the incline tasks. This study demonstrated the high demand placed on the glenohumeral joint during accessibility tasks, especially as the gradient of incline increases. A lightweight instrumented wheelchair wheel has potential to guide the user to minimize upper limb demand during daily activity.

  5. Kinetic Gait Analysis Using a Low-Cost Insole.

    PubMed

    Howell, Adam M; Kobayashi, Toshiki; Hayes, Heather A; Foreman, K Bo; Bamberg, Stacy J Morris

    2013-12-01

    Abnormal gait caused by stroke or other pathological reasons can greatly impact the life of an individual. Being able to measure and analyze that gait is often critical for rehabilitation. Motion analysis labs and many current methods of gait analysis are expensive and inaccessible to most individuals. The low-cost, wearable, and wireless insole-based gait analysis system in this study provides kinetic measurements of gait by using low-cost force sensitive resistors. This paper describes the design and fabrication of the insole and its evaluation in six control subjects and four hemiplegic stroke subjects. Subject-specific linear regression models were used to determine ground reaction force plus moments corresponding to ankle dorsiflexion/plantarflexion, knee flexion/extension, and knee abduction/adduction. Comparison with data simultaneously collected from a clinical motion analysis laboratory demonstrated that the insole results for ground reaction force and ankle moment were highly correlated (all >0.95) for all subjects, while the two knee moments were less strongly correlated (generally >0.80). This provides a means of cost-effective and efficient healthcare delivery of mobile gait analysis that can be used anywhere from large clinics to an individual's home.

  6. Thermogravimetric analysis and kinetic study on pyrolysis of representative medical waste composition.

    PubMed

    Deng, Na; Zhang, Yu-feng; Wang, Yan

    2008-01-01

    To obtain detailed information on the pyrolysis characteristics, a thermogravimetric study on the pyrolysis of 14 typical medical waste compositions was carried out in thermogravimetric analysis (TGA) equipment using dynamic techniques in a stream of N2. An index representing pyrolysis reactivity of waste was presented. Kinetic parameters were obtained by Coats-Redfern method and used to model the TG curve. The results showed that: (a) Plastic, protein, cellulosic material, synthetic fibre, and rubber entered pyrolysis process in succession. (b) There was one decomposition stage in the pyrolysis of one-off medical glove, operating glove, cellulosic waste, absorbable catgut suture and adhesive plaster, while other components had two obvious weight loss stages. (c) The obtained apparent activation energy for second stage pyrolysis was comparably higher than that for first stage. (d) Each stage was controlled by only one kinetic mechanism, in which kinetic parameters were constant. (e) The degradation kinetics of medical waste may be affected by special physical and chemical treatment in the product manufacturing process. (f) Among 13 waste samples, the pyrolysis index of cellulosic matter was the highest, which indicated cellulosic matter had strong pyrolysis reactivity. (g) With increasing heating rate, TG curve and DTG peak shifted to high temperatures and main reaction interval of the sample became longer. PMID:17911006

  7. Continuous cultivation of fission yeast: analysis of single-cell protein synthesis kinetics

    SciTech Connect

    Agar, D.W.; Bailey, J.E.

    1981-01-01

    A fundamental problem in microbial reactor analysis is identification of the relation between environment and individual cell metabolic activity. Population balance equations provide a link between experimental measurements of composition frequency functions in microbial populations on the one hand and macromolecule synthesis kinetics and cell division control parameters for single cells on the other. Flow microfluorometry measurements of frequency functions for single-cell protein content in Schizosaccharomyces pombe in balanced exponential growth were analyzed by 2 different methods. One approach utilizes the integrated form of the population balance equation known as the Collins-Richmond equation, and the other method involves optimization of parameters in assumed kinetic and cell division functional forms to fit measured frequency functions with corresponding model solutions. Both data interpretation techniques indicate that rates of protein synthesis increase most in low-protein-content cells as the population specific growth rate increases, leading to parabolic single-cell protein synthesis kinetics at large specific growth rates. Utilization of frequency function data for an asynchronous population is in this case a far more sensitive method for determination of single-cell kinetics than is monitoring the metabolic dynamics of a single cell or, equivalently, synchronous culture analyses.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Analysis of Network Topologies Underlying Ethylene Growth Response Kinetics.

    PubMed

    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

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

    PubMed

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

    2016-01-20

    The hydrogen production electrocatalyst Ni(P(Ph)2N(Ph)2)2(2+) (1) is capable of traversing multiple electrocatalytic pathways. When using dimethylformamidium, DMF(H)(+), the mechanism of H2 formation by 1 changes from an ECEC to an EECC mechanism as the potential approaches the Ni(I/0) couple. Two electrochemical methods, current-potential analysis and foot-of-the-wave analysis (FOWA), were performed on 1 to measure detailed kinetics of the competing ECEC and EECC pathways. A sensitivity analysis was performed on the methods using digital simulations to understand their strengths and limitations. Chemical rate constants were significantly underestimated when not accounting for electron-transfer kinetics, even when electron transfer was fast enough to afford a reversible noncatalytic wave. The EECC pathway of 1 was faster than the ECEC pathway under all conditions studied. Buffered DMF:DMF(H)(+) mixtures afforded an increase in the catalytic rate constant (k(obs)) of the EECC pathway, but k(obs) for the ECEC pathway did not change when using buffered acid. Further kinetic analysis of the ECEC path revealed that base increases the rate of isomerization from exo-protonated Ni(0) isomers to the catalytically active endo-isomers, but decreases the rate of protonation of Ni(I). FOWA did not provide accurate rate constants, but FOWA was used to estimate the reduction potential of the previously undetected exo-protonated Ni(I) intermediate. Comparison of catalytic Tafel plots for 1 under different conditions reveals substantial inaccuracies in the turnover frequency at zero overpotential when the kinetic and thermodynamic effects of the conjugate base are not accounted for properly.

  16. 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. PMID:21172719

  17. 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.

  18. Kinetic energy budget during strong jet stream activity over the eastern United States

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.; Scoggins, J. R.

    1980-01-01

    Kinetic energy budgets are computed during a cold air outbreak in association with strong jet stream activity over the eastern United States. The period is characterized by large generation of kinetic energy due to cross-contour flow. Horizontal export and dissipation of energy to subgrid scales of motion constitute the important energy sinks. Rawinsonde data at 3 and 6 h intervals during a 36 h period are used in the analysis and reveal that energy fluctuations on a time scale of less than 12 h are generally small even though the overall energy balance does change considerably during the period in conjunction with an upper level trough which moves through the region. An error analysis of the energy budget terms suggests that this major change in the budget is not due to random errors in the input data but is caused by the changing synoptic situation. The study illustrates the need to consider the time and space scales of associated weather phenomena in interpreting energy budgets obtained through use of higher frequency data.

  19. Scene kinetics mitigation using factor analysis with derivative factors.

    SciTech Connect

    Larson, Kurt W.; Melgaard, David Kennett; Scholand, Andrew Joseph

    2010-07-01

    Line of sight jitter in staring sensor data combined with scene information can obscure critical information for change analysis or target detection. Consequently before the data analysis, the jitter effects must be significantly reduced. Conventional principal component analysis (PCA) has been used to obtain basis vectors for background estimation; however PCA requires image frames that contain the jitter variation that is to be modeled. Since jitter is usually chaotic and asymmetric, a data set containing all the variation without the changes to be detected is typically not available. An alternative approach, Scene Kinetics Mitigation, first obtains an image of the scene. Then it computes derivatives of that image in the horizontal and vertical directions. The basis set for estimation of the background and the jitter consists of the image and its derivative factors. This approach has several advantages including: (1) only a small number of images are required to develop the model, (2) the model can estimate backgrounds with jitter different from the input training images, (3) the method is particularly effective for sub-pixel jitter, and (4) the model can be developed from images before the change detection process. In addition the scores from projecting the factors on the background provide estimates of the jitter magnitude and direction for registration of the images. In this paper we will present a discussion of the theoretical basis for this technique, provide examples of its application, and discuss its limitations.

  20. 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

  1. 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.

  2. 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.; 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 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

  3. Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks.

    PubMed

    Deng, De-Ming; Chang, Cheng-Hung

    2015-05-14

    Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems. PMID:25978879

  4. Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks

    NASA Astrophysics Data System (ADS)

    Deng, De-Ming; Chang, Cheng-Hung

    2015-05-01

    Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems.

  5. Stochastic lumping analysis for linear kinetics and its application to the fluctuation relations between hierarchical kinetic networks

    SciTech Connect

    Deng, De-Ming; Chang, Cheng-Hung

    2015-05-14

    Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal the same experimentally measured fluctuating behaviors and unique fluctuation related physical properties. To clarify these questions, we introduce stochasticity into the traditional lumping analysis, generalize it from rate equations to chemical master equations and stochastic differential equations, and extract the fluctuation relations between kinetically and thermodynamically equivalent networks under intrinsic and extrinsic noises. The results provide a theoretical basis for the legitimate use of low-dimensional models in the studies of macromolecular fluctuations and, more generally, for exploring stochastic features in different levels of contracted networks in chemical and biological kinetic systems.

  6. Microbial kinetic analysis of three different types of EBNR process.

    PubMed

    Pai, T Y; Tsai, Y P; Chou, Y J; Chang, H Y; Leu, H G; Ouyang, C F

    2004-04-01

    The disadvantages of developed biological nutrient removal (BNR) processes (additional energy for liquid circulation and addition of external carbon substrate for denitrification in anoxic zones) were improved by reconfiguring the process into (1) an anaerobic zone followed by multiple stages of aerobic-anoxic zones (TNCU3 process) or (2) anaerobic, oxic, anoxic, oxic zones in sequence (TNCU2 process). These two pilot plants were operated at a recycling sludge ratio of 0.5 without internal recycle of nitrified supernatant. The sludge retention time was maintained at 10 d. The main objective of this study is to analyze the kinetics of different microorganisms in these two processes and A2O process by using the Activated Sludge Model No. 2d. The effective removal efficiency of carbon, total phosphorus and total nitrogen at 87-98%, 92-100% and 63-80%, respectively, were achieved in the testing runs. According to model simulations, the microbial kinetics in the TNCU3 and TNCU2 processes would be affected by different operations. When the step feeding strategy was adopted, the HRT was longer due to the less influent flowrate in the front stages and the microbes would grow in quantities by about 6% in the aerobic reactors. In the followed anoxic reactors, the microbes would decrease in quantities by about 12% due to the dilution effect. The dilution effects in TNCU3 and TNCU2 processes did not take place in A2O process because the recycling mixed liquid from the aerobic reactor to the anoxic reactor still contained particulate components. The XH, XPAO, and XAUT concentrations in the effluent of the last tank were lower when the step-feeding mode was adopted. The TNCU3 and TNCU2 processes could be operated efficiently without nitrified liquid circulation and addition of external carbon substrate for denitrification.

  7. On the estimation of cooperativity in ion channel kinetics: activation free energy and kinetic mechanism of Shaker K+ channel.

    PubMed

    Banerjee, Kinshuk; Das, Biswajit; Gangopadhyay, Gautam

    2013-04-28

    In this paper, we have explored generic criteria of cooperative behavior in ion channel kinetics treating it on the same footing with multistate receptor-ligand binding in a compact theoretical framework. We have shown that the characterization of cooperativity of ion channels in terms of the Hill coefficient violates the standard Hill criteria defined for allosteric cooperativity of ligand binding. To resolve the issue, an alternative measure of cooperativity is proposed here in terms of the cooperativity index that sets a unified criteria for both the systems. More importantly, for ion channel this index can be very useful to describe the cooperative kinetics as it can be readily determined from the experimentally measured ionic current combined with theoretical modelling. We have analyzed the correlation between the voltage value and slope of the voltage-activation curve at the half-activation point and consequently determined the standard free energy of activation of the ion channel using two well-established mechanisms of cooperativity, namely, Koshland-Nemethy-Filmer (KNF) and Monod-Wyman-Changeux (MWC) models. Comparison of the theoretical results for both the models with appropriate experimental data of mutational perturbation of Shaker K(+) channel supports the experimental fact that the KNF model is more suitable to describe the cooperative behavior of this class of ion channels, whereas the performance of the MWC model is unsatisfactory. We have also estimated the mechanistic performance through standard free energy of channel activation for both the models and proposed a possible functional disadvantage in the MWC scheme.

  8. Kinetic analysis of biomolecular interactions by surface plasmon enhanced ellipsometry

    NASA Astrophysics Data System (ADS)

    Cho, Hyun Mo; Chegal, Won; Cho, Yong Jai; Won, Jong Myoung; Lee, Hak Min; Jo, Jae Heung

    2011-10-01

    We present the application of ellipsometry to the phase measurement of surface plasmon resonance (SPR) in biomolecular detection. In this work, the experimental setup for the SPR sensor was based on a custom-built rotating analyzer ellipsometer, which was equipped with a SPR cell and a microfluidic system. We investigate the sensitivity of SPR sensor which is dependent on the thickness and roughness of metal film, alignment of optical system, and stability of microfluidics. In the drug discovery process, to directly monitor the interaction of small molecule-protein, it is necessary to design a high-sensitivity SPR sensor with a sensitivity of greater than 1 pg/mm2. Our sensor demonstrates a much better sensitivity in comparison to other SPR sensors based on reflectometry or phase measurements. The results of calibration indicate that the phase change, δ▵, had an almost linear response to the concentration of ethanol in the double-distilled water solutions. A quantitative analysis of refractive index variation was possible using the results of the ellipsometric model fits for the multilayered thin film on the gold film. Thus, this method is applicable not only to sensor applications, such as affinity biosensors, but also to highly sensitive kinetics for drug discovery. In this paper, we demonstrate how a custom-built rotating analyzer ellipsometer in the SPR condition can be used to directly obtain the interactions and binding kinetics of analytes (biotins, peptides) with immobilized ligand (streptavidin, antibody). We achieved a detection limit of lower than 1.0 x10-7 RIU, which is the equivalent of 0.1 pg/mm2.

  9. Cryoprotectant kinetic analysis of a human articular cartilage vitrification protocol.

    PubMed

    Shardt, Nadia; Al-Abbasi, Khaled K; Yu, Hana; Jomha, Nadr M; McGann, Locksley E; Elliott, Janet A W

    2016-08-01

    We recently published a protocol to vitrify human articular cartilage and a method of cryoprotectant removal in preparation for transplantation. The current study's goal was to perform a cryoprotectant kinetic analysis and theoretically shorten the procedure used to vitrify human articular cartilage. First, the loading of the cryoprotectants was modeled using Fick's law of diffusion, and this information was used to predict the kinetics of cryoprotectant efflux after the cartilage sample had been warmed. We hypothesized that diffusion coefficients obtained from the permeation of individual cryoprotectants into porcine articular cartilage could be used to provide a reasonable prediction of the cryoprotectant loading and of the combined cryoprotectant efflux from vitrified human articular cartilage. We tested this hypothesis with experimental efflux measurements. Osteochondral dowels from three patients were vitrified, and after warming, the articular cartilage was immersed in 3 mL X-VIVO at 4 °C in two consecutive solutions, each for 24 h, with the solution osmolality recorded at various times. Measured equilibrium values agreed with theoretical values within a maximum of 15% for all three samples. The results showed that diffusion coefficients for individual cryoprotectants determined from experiments with 2-mm thick porcine cartilage can be used to approximate the rate of efflux of the combined cryoprotectants from vitrified human articular cartilage of similar thickness. Finally, Fick's law of diffusion was used in a computational optimization to shorten the protocol with the constraint of maintaining the theoretical minimum cryoprotectant concentration needed to achieve vitrification. The learning provided by this study will enable future improvements in tissue vitrification.

  10. [Degradation kinetics of naphthalene by anaerobic sludge and analysis of the bacterial biodiversity].

    PubMed

    Cao, Xin-Kai; Yang, Qi; Hao, Chun-Bo

    2012-10-01

    For efficient biological treatment of naphthalene in the industrial wastewater, activated anaerobic sludge was collected from a wastewater treatment plant of petroleum industry, and domesticated with naphthalene, naphthalene and lactate as electron donors, respectively. When the removal efficiency of naphthalene reached more than 90% in a domestication cycle, degradation kinetics were investigated in batch reactions with naphthalene, naphthalene and lactate as electron donors, respectively. Meanwhile, the microbial DNA was extracted from the sludge with high naphthalene removal efficiency, the 16S rDNA clone library was built up, and the bacterial community was analyzed. The results indicated that the degradation rate of naphthalene in reaction with naphthalene as the sole electron donor was much lower than that with naphthalene and lactate as electron donors. In both domestication modes, the naphthalene concentration and the time followed the first order reaction kinetics model and the kinetic constant K were 3.5 x 10(-3) h(-1) and 16 x 10(-3) h(-1), respectively. In addition, phylogenetic analysis indicated that the bacterial communities in naphthalene and lactate co-metabolism sludge were mainly composed of Deltaproteobacteria, Thermotogae, Bacteroidetes, Chloroflexi and Unclassified bacteria. Deltaproteobacteria was the main phylum in the sludge. In mature anaerobic activated sludge, Desulfobulbus sp. and Kosmotoga accounted for 24.2% and 21.0%, respectively. Smithella, Syntrophobacter and Levilinea were also found in the bioreactor. The study of the bacteria diversity in the anaerobic sludge is conducive to the optimization of reaction conditions for efficient removal of naphthalene.

  11. Studies on the kinetics of plasminogen activation by tissue plasminogen activator.

    PubMed

    Rånby, M

    1982-06-24

    The steady-state rate of plasminogen activation by tissue plasminogen activator has been determined at various plasminogen concentrations. A plasmin substrate method similar to that presented by Christensen and Müllertz (Biochim. Biophys. Acta 480 (1977) 257-281) was used. The reaction was studied using one-chain type and two-chain type tissue plasminogen activator, N-terminal glutamic acid and N-terminal lysine plasminogen in the presence and in the absence of fibrin (eight studies). The kinetic data were fitted to a general Wong-Hanes equation and the simplest equation with significant parameters was found. In the absence of fibrin N-terminal glutamic acid plasminogen activation obeyed the Michaelis-Menten rate equation (Km 4.9 and 7.6 micro M and kcat 0.0013 and 0.0078 s-1 for one-chain type and two-chain type tissue plasminogen activator, respectively. In the absence of fibrin the activation of N-terminal lysine plasminogen activation failed to obey the Michaelis-Menten rate equation. Fibrin was found to stimulate greatly (up to 1000-fold) the steady-state activation rate. A theory for the fibrin stimulating mechanism is presented.

  12. Adsorption and desorption kinetics of n-octane and n-nonane vapors on activated carbon

    SciTech Connect

    Fletcher, A.J.; Thomas, K.M.

    1999-09-28

    This investigation has involved the study of the adsorption and desorption kinetics of two n-alkanes on a wood-based active carbon (BAX950). The adsorption and desorption characteristics of n-octane vapor on the activated carbon were investigated over the relative pressure (p/p{sup o}) range 0--0.97 for temperatures in the range 288--313 K in a static vapor system. The adsorption characteristics of n-nonane were studied over the relative pressure range 0--0.977 and temperature range 303--323 K. The adsorption and desorption kinetics were studied with different amounts of preadsorbed n-octane for set changes in relative vapor pressure (p/p{sup o}). The desorption kinetics were much slower than the corresponding adsorption kinetics for the same pressure step. The rate constants for adsorption increased with increasing relative pressure and surface coverage. The kinetic data for adsorption were used to calculate the activation energies for each increase in relative pressure. The activation energy was highest at low p/p{sup o} and decreased with increasing p/p{sup o} until a maximum was reached at p/p{sup o}{approximately}0.075. n-Nonane adsorption showed similar trends in adsorption kinetics and activation energies to the n-octane adsorption isotherm and mechanism.

  13. 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…

  14. 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

  15. Kinetic analysis of MHD ballooning modes in tokamaks

    SciTech Connect

    Tang, W.M.; Rewoldt, G.; Cheng, C.Z.; Chance, M.S.

    1984-10-01

    A comprehensive analysis of the stability properties of the appropriate kinetically generalized form of MHD ballooning modes together with the usual trapped-particle drift modes is presented. The calculations are fully electromagnetic and include the complete dynamics associated with compressional ion acoustic waves. Trapped-particle effects along with all forms of collisionless dissipation are taken into account without approximations. The influence of collisions is estimated with a model Krook operator. Results from the application of this analysis to realistic tokamak operating conditions indicate that unstable short-wavelength modes with significant growth rates can extend from ..beta.. = 0 to value above the upper ideal-MHD-critical-beta associated with the so-called second stability regime. Since the strength of the relevant modes appears to vary gradually with ..beta.., these results support a soft beta limit picture involving a continuous (rather than abrupt or hard) modification of anomalous transport already present in low-..beta..-tokamaks. However, at higher beta the increasing dominance of the electromagnetic component of the perturbations indicated by these calculations could also imply significantly different transport scaling properties.

  16. Kinetic analysis of an autocatalytic process coupled to a reversible inhibition: the inhibition of the system trypsinogen-trypsin by p-aminobenzamidine.

    PubMed

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

    1995-09-01

    A kinetic analysis of the mechanism of autocatalytic activation in the presence of a reversible inhibitor is presented. The kinetic equations of both the transient phase and the steady state are derived for this mechanism. We have extended the kinetic equations derived to a particular case in rapid equilibrium conditions. This analysis is illustrated by the experimental study of the inhibition by p-aminobenzamidine of trypsin activity in its action on trypsinogen. In such system, the amount of active enzyme increases exponentially, as expected from an autocatalytic process. The results obtained show that the apparent activation rate constant decreases non-linearly with the initial concentration of inhibitor, according to the equations obtained in the kinetic analysis. PMID:8561917

  17. A coupled observation - modeling approach for studying activation kinetics from measurements of CCN activity

    NASA Astrophysics Data System (ADS)

    Raatikainen, T.; Moore, R. H.; Lathem, T. L.; Nenes, A.

    2012-01-01

    This paper presents an approach to study droplet activation kinetics from measurements of CCN activity by the Continuous Flow Streamwise Thermal Gradient CCN Chamber (CFSTGC) and a comprehensive model of the instrument and droplet growth. The model is evaluated against a series of experiments with ammonium sulfate calibration aerosol. Observed and model predicted droplet sizes are in excellent agreement for a water vapor uptake coefficient ~0.2, which is consistent with theoretical expectations. The model calculations can be considerably accelerated without significant loss of accuracy by assuming simplified instrument geometry and constant parabolic flow velocity profiles. With these assumptions, the model can be applied to large experimental data sets (to infer kinetic growth parameters) while fully accounting for water vapor depletion effects and changes in instrument operation parameters such as the column temperature, flow rates, sheath and sample flow relative humidities, and pressure. When the effects of instrument operation parameters, water vapor depletion and equilibrium dry particle properties on droplet size are accounted for, the remaining variations in droplet size are most likely due to non-equilibrium processes such as those caused by organic surface films, slow solute dissociation and glassy or highly viscous particle states. As an example of model application, data collected during a research flight in the ARCTAS 2008 campaign are analyzed. The model shows that water vapor depletion effects can explain changes in the observed average droplet size.

  18. Analysis by kinetic modeling of the temperature dependence of thermal electron attachment to CF3Br.

    PubMed

    Troe, Jürgen; Miller, Thomas M; Shuman, Nicholas S; Viggiano, Albert A

    2012-07-14

    Experimental data from the literature for cross sections and rate constants for dissociative electron attachment to CF(3)Br, with separately varied electron and gas temperatures, are analyzed by a kinetic modeling approach. The analysis suggests that electronic and nuclear contributions to the rate constants can be roughly separated, the former leading to a negative temperature coefficient, the latter to a positive temperature coefficient. The nuclear factor in the rate constant is found to be of Arrhenius form with an activation energy which is close to the energy of crossing of the CF(3)Br and CF(3)Br(-) potential curves along the CBr bond. PMID:22803532

  19. Kinetic analysis of gill (Na⁺,K⁺)-ATPase activity in selected ontogenetic stages of the Amazon River shrimp, Macrobrachium amazonicum (Decapoda, Palaemonidae): interactions at ATP- and cation-binding sites.

    PubMed

    Leone, Francisco Assis; Masui, Douglas Chodi; de Souza Bezerra, Thais Milena; Garçon, Daniela Pereira; Valenti, Wagner Cotroni; Augusto, Alessandra Silva; McNamara, John Campbell

    2012-04-01

    We investigated modulation by ATP, Mg²⁺, Na⁺, K⁺ and NH₄⁺ and inhibition by ouabain of (Na⁺,K⁺)-ATPase activity in microsomal homogenates of whole zoeae I and decapodid III (formerly zoea IX) and whole-body and gill homogenates of juvenile and adult Amazon River shrimps, Macrobrachium amazonicum. (Na⁺,K⁺)-ATPase-specific activity was increased twofold in decapodid III compared to zoea I, juveniles and adults, suggesting an important role in this ontogenetic stage. The apparent affinity for ATP (K(M) = 0.09 ± 0.01 mmol L⁻¹) of the decapodid III (Na⁺,K⁺)-ATPase, about twofold greater than the other stages, further highlights this relevance. Modulation of (Na⁺,K⁺-ATPase activity by K⁺ also revealed a threefold greater affinity for K⁺ (K₀.₅ = 0.91 ± 0.04 mmol L⁻¹) in decapodid III than in other stages; NH₄⁺ had no modulatory effect. The affinity for Na⁺ (K₀.₅ = 13.2 ± 0.6 mmol L⁻¹) of zoea I (Na⁺,K⁺)-ATPase was fourfold less than other stages. Modulation by Na⁺, Mg²⁺ and NH₄⁺ obeyed cooperative kinetics, while K⁺ modulation exhibited Michaelis-Menten behavior. Rates of maximal Mg²⁺ stimulation of ouabain-insensitive ATPase activity differed in each ontogenetic stage, suggesting that Mg²⁺-stimulated ATPases other than (Na⁺,K⁺)-ATPase are present. Ouabain inhibition suggests that, among the various ATPase activities present in the different stages, Na⁺-ATPase may be involved in the ontogeny of osmoregulation in larval M. amazonicum. The NH₄⁺-stimulated, ouabain-insensitive ATPase activity seen in zoea I and decapodid III may reflect a stage-specific means of ammonia excretion since functional gills are absent in the early larval stages.

  20. Nicotine evokes kinetic tremor by activating the inferior olive via α7 nicotinic acetylcholine receptors.

    PubMed

    Kunisawa, Naofumi; Iha, Higor A; Shimizu, Saki; Tokudome, Kentaro; Mukai, Takahiro; Kinboshi, Masato; Serikawa, Tadao; Ohno, Yukihiro

    2016-11-01

    Nicotinic acetylcholine (nACh) receptors are implicated in the pathogenesis of movement disorders (e.g., tremor) and epilepsy. Here, we performed behavioral and immunohistochemical studies using mice and rats to elucidate the mechanisms underlying nicotine-induced tremor. Treatments of animals with nicotine (0.5-2mg/kg, i.p.) elicited kinetic tremor, which was completely suppressed by the nACh receptor antagonist mecamylamine (MEC). The specific α7 nACh receptor antagonist methyllycaconitine (MLA) also inhibited nicotine-induced tremor, whereas the α4β2 nACh antagonist dihydro-β-erythroidine (DHβE) or the peripheral α3β4 nACh antagonist hexamethonium showed no effects. Mapping analysis of Fos protein expression, a biological marker of neural excitation, revealed that a tremorgenic dose (1mg/kg) of nicotine region-specifically elevated Fos expression in the piriform cortex (PirC), medial habenula, solitary nucleus and inferior olive (IO) among 44 brain regions examined. In addition, similarly to the tremor responses, nicotine-induced Fos expression in the PirC and IO was selectively antagonized by MLA, but not by DHβE. Furthermore, an electrical lesioning of the IO, but not the PirC, significantly suppressed the induction of nicotine tremor. The present results suggest that nicotine elicits kinetic tremor in rodents by activating the IO neurons via α7 nACh receptors.

  1. Nicotine evokes kinetic tremor by activating the inferior olive via α7 nicotinic acetylcholine receptors.

    PubMed

    Kunisawa, Naofumi; Iha, Higor A; Shimizu, Saki; Tokudome, Kentaro; Mukai, Takahiro; Kinboshi, Masato; Serikawa, Tadao; Ohno, Yukihiro

    2016-11-01

    Nicotinic acetylcholine (nACh) receptors are implicated in the pathogenesis of movement disorders (e.g., tremor) and epilepsy. Here, we performed behavioral and immunohistochemical studies using mice and rats to elucidate the mechanisms underlying nicotine-induced tremor. Treatments of animals with nicotine (0.5-2mg/kg, i.p.) elicited kinetic tremor, which was completely suppressed by the nACh receptor antagonist mecamylamine (MEC). The specific α7 nACh receptor antagonist methyllycaconitine (MLA) also inhibited nicotine-induced tremor, whereas the α4β2 nACh antagonist dihydro-β-erythroidine (DHβE) or the peripheral α3β4 nACh antagonist hexamethonium showed no effects. Mapping analysis of Fos protein expression, a biological marker of neural excitation, revealed that a tremorgenic dose (1mg/kg) of nicotine region-specifically elevated Fos expression in the piriform cortex (PirC), medial habenula, solitary nucleus and inferior olive (IO) among 44 brain regions examined. In addition, similarly to the tremor responses, nicotine-induced Fos expression in the PirC and IO was selectively antagonized by MLA, but not by DHβE. Furthermore, an electrical lesioning of the IO, but not the PirC, significantly suppressed the induction of nicotine tremor. The present results suggest that nicotine elicits kinetic tremor in rodents by activating the IO neurons via α7 nACh receptors. PMID:27506652

  2. Adsorption kinetics and isotherms of pesticides onto activated carbon-cloth.

    PubMed

    Ayranci, Erol; Hoda, Numan

    2005-09-01

    Adsorption of pesticides ametryn, aldicarb, dinoseb and diuron from aqueous solution onto high specific area activated carbon-cloth was studied. Kinetics of adsorption was followed by in situ UV-spectroscopy and the data were treated according to various rate models. The extent of adsorption was determined at the end of 125 min adsorption period. Rate constants and the extent of adsorption for the four pesticides were found to follow the order: dinoseb > ametryn > diuron > aldicarb. Adsorption isotherms were derived at 25 degrees C on the basis of batch analysis. Isotherm data were treated according to Langmuir and Freundlich models. The fits of experimental data to these equations were examined. The types of interactions between the surface and pesticide molecules were discussed. PMID:16083766

  3. 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.

  4. 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.

  5. 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. PMID:23450172

  6. Simplification and analysis of models of calcium dynamics based on IP3-sensitive calcium channel kinetics.

    PubMed

    Tang, Y; Stephenson, J L; Othmer, H G

    1996-01-01

    We study the models for calcium (Ca) dynamics developed in earlier studies, in each of which the key component is the kinetics of intracellular inositol-1,4,5-trisphosphate-sensitive Ca channels. After rapidly equilibrating steps are eliminated, the channel kinetics in these models are represented by a single differential equation that is linear in the state of the channel. In the reduced kinetic model, the graph of the steady-state fraction of conducting channels as a function of log10(Ca) is a bell-shaped curve. Dynamically, a step increase in inositol-1,4,5-trisphosphate induces an incremental increase in the fraction of conducting channels, whereas a step increase in Ca can either potentiate or inhibit channel activation, depending on the Ca level before and after the increase. The relationships among these models are discussed, and experimental tests to distinguish between them are given. Under certain conditions the models for intracellular calcium dynamics are reduced to the singular perturbed form epsilon dx/d tau = f(x, y, p), dy/d tau = g(x, y, p). Phase-plane analysis is applied to a generic form of these simplified models to show how different types of Ca response, such as excitability, oscillations, and a sustained elevation of Ca, can arise. The generic model can also be used to study frequency encoding of hormonal stimuli, to determine the conditions for stable traveling Ca waves, and to understand the effect of channel properties on the wave speed.

  7. Kinetic analysis of pre-ribosome structure in vivo.

    PubMed

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

    2012-12-01

    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.

  8. 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.

  9. Fast and slow activation kinetics of voltage-gated sodium channels in molluscan neurons.

    PubMed

    Gilly, W F; Gillette, R; McFarlane, M

    1997-05-01

    Whole cell patch-clamp recordings of Na current (I(Na)) were made under identical experimental conditions from isolated neurons from cephalopod (Loligo, Octopus) and gastropod (Aplysia, Pleurobranchaea, Doriopsilla) species to compare properties of activation gating. Voltage dependence of peak Na conductance (gNa) is very similar in all cases, but activation kinetics in the gastropod neurons studied are markedly slower. Kinetic differences are very pronounced only over the voltage range spanned by the gNa-voltage relation. At positive and negative extremes of voltage, activation and deactivation kinetics of I(Na) are practically indistinguishable in all species studied. Voltage-dependent rate constants underlying activation of the slow type of Na channel found in gastropods thus appear to be much more voltage dependent than are the equivalent rates in the universally fast type of channel that predominates in cephalopods. Voltage dependence of inactivation kinetics shows a similar pattern and is representative of activation kinetics for the two types of Na channels. Neurons with fast Na channels can thus make much more rapid adjustments in the number of open Na channels at physiologically relevant voltages than would be possible with only slow Na channels. This capability appears to be an adaptation that is highly evolved in cephalopods, which are well known for their high-speed swimming behaviors. Similarities in slow and fast Na channel subtypes in molluscan and mammalian neurons are discussed. PMID:9163364

  10. 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.

  11. 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.

  12. 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

  13. A coupled observation - modeling approach for studying activation kinetics from measurements of CCN activity

    NASA Astrophysics Data System (ADS)

    Raatikainen, T.; Moore, R. H.; Lathem, T. L.; Nenes, A.

    2012-05-01

    This paper presents an approach to study droplet activation kinetics from measurements of CCN activity by the Continuous Flow Streamwise Thermal Gradient CCN Chamber (CFSTGC) and a comprehensive model of the instrument and droplet growth. The model, which can be downloaded from http://nenes.eas.gatech.edu/Experiments/CFSTGC.html , is evaluated against a series of experiments with ammonium sulfate calibration aerosol. Observed and modeled droplet sizes are in excellent agreement for a water vapor uptake coefficient ~0.2, which is consistent with theoretical expectations. The model calculations can be considerably accelerated without significant loss of accuracy by assuming simplified instrument geometry and constant parabolic flow velocity profiles. With these assumptions, the model can be applied to large experimental data sets to infer kinetic growth parameters while fully accounting for water vapor depletion effects and changes in instrument operation parameters such as the column temperature, flow rates, sheath and sample flow relative humidities, and pressure. When the effects of instrument operation parameters, water vapor depletion and equilibrium dry particle properties on droplet size are accounted for, the remaining variations in droplet size are most likely due to non-equilibrium processes such as those caused by organic surface films, slow solute dissociation and glassy or highly viscous particle states. As an example of model application, data collected during a research flight in the ARCTAS 2008 campaign are analyzed. The model shows that water vapor depletion effects can explain changes in the observed average droplet size.

  14. Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

    PubMed

    Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

    2008-12-25

    Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

  15. 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.

  16. Full Time Course Kinetics of the Streptokinase-Plasminogen Activation Pathway*

    PubMed Central

    Nolan, Miranda; Bouldin, Samantha D.; Bock, Paul E.

    2013-01-01

    Our previously hypothesized mechanism for the pathway of plasminogen (Pg) activation by streptokinase (SK) was tested by the use of full time course kinetics. Three discontinuous chromogenic substrate initial rate assays were developed with different quenching conditions that enabled quantitation of the time courses of Pg depletion, plasmin (Pm) formation, transient formation of the conformationally activated SK·Pg* catalytic complex intermediate, formation of the SK·Pm catalytic complex, and the free concentrations of Pg, Pm, and SK. Analysis of full time courses of Pg activation by five concentrations of SK along with activity-based titrations of SK·Pg* and SK·Pm formation yielded rate and dissociation constants within 2-fold of those determined previously by continuous measurement of parabolic chromogenic substrate hydrolysis and fluorescence-based equilibrium binding. The results obtained with orthogonal assays provide independent support for a mechanism in which the conformationally activated SK·Pg* complex catalyzes an initial cycle of Pg proteolytic conversion to Pm that acts as a trigger. Higher affinity binding of the formed Pm to SK outcompetes Pg binding, terminating the trigger cycle and initiating the bullet catalytic cycle by the SK·Pm complex that converts the residual Pg into Pm. The new assays can be adapted to quantitate SK-Pg activation in the context of SK- or Pg-directed inhibitors, effectors, and SK allelic variants. To support this, we show for the first time with an assay specific for SK·Pg* that fibrinogen forms a ternary SK·Pg*·fibrinogen complex, which assembles with 200-fold enhanced SK·Pg* affinity, signaled by a perturbation of the SK·Pg* active site. PMID:23970549

  17. 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.

  18. 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

  19. 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. PMID:25931393

  20. 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.

  1. 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.

  2. k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.

    PubMed

    Famili, Iman; Mahadevan, Radhakrishnan; Palsson, Bernhard O

    2005-03-01

    The absence of comprehensive measured kinetic values and the observed inconsistency in the available in vitro kinetic data has hindered the formulation of network-scale kinetic models of biochemical reaction networks. To meet this challenge we present an approach to construct a convex space, termed the k-cone, which contains all the allowable numerical values of the kinetic constants in large-scale biochemical networks. The definition of the k-cone relies on the incorporation of in vivo concentration data and a simplified approach to represent enzyme kinetics within an established constraint-based modeling approach. The k-cone approach was implemented to define the allowable combination of numerical values for a full kinetic model of human red blood cell metabolism and to study its correlated kinetic parameters. The k-cone approach can be used to determine consistency between in vitro measured kinetic values and in vivo concentration and flux measurements when used in a network-scale kinetic model. k-Cone analysis was successful in determining whether in vitro measured kinetic values used in the reconstruction of a kinetic-based model of Saccharomyces cerevisiae central metabolism could reproduce in vivo measurements. Further, the k-cone can be used to determine which numerical values of in vitro measured parameters are required to be changed in a kinetic model if in vivo measured values are not reproduced. k-Cone analysis could identify what minimum number of in vitro determined kinetic parameters needed to be adjusted in the S. cerevisiae model to be consistent with the in vivo data. Applying the k-cone analysis a priori to kinetic model development may reduce the time and effort involved in model building and parameter adjustment. With the recent developments in high-throughput profiling of metabolite concentrations at a whole-cell scale and advances in metabolomics technologies, the k-cone approach presented here may hold the promise for kinetic

  3. k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network Scale

    PubMed Central

    Famili, Iman; Mahadevan, Radhakrishnan; Palsson, Bernhard O.

    2005-01-01

    The absence of comprehensive measured kinetic values and the observed inconsistency in the available in vitro kinetic data has hindered the formulation of network-scale kinetic models of biochemical reaction networks. To meet this challenge we present an approach to construct a convex space, termed the k-cone, which contains all the allowable numerical values of the kinetic constants in large-scale biochemical networks. The definition of the k-cone relies on the incorporation of in vivo concentration data and a simplified approach to represent enzyme kinetics within an established constraint-based modeling approach. The k-cone approach was implemented to define the allowable combination of numerical values for a full kinetic model of human red blood cell metabolism and to study its correlated kinetic parameters. The k-cone approach can be used to determine consistency between in vitro measured kinetic values and in vivo concentration and flux measurements when used in a network-scale kinetic model. k-Cone analysis was successful in determining whether in vitro measured kinetic values used in the reconstruction of a kinetic-based model of Saccharomyces cerevisiae central metabolism could reproduce in vivo measurements. Further, the k-cone can be used to determine which numerical values of in vitro measured parameters are required to be changed in a kinetic model if in vivo measured values are not reproduced. k-Cone analysis could identify what minimum number of in vitro determined kinetic parameters needed to be adjusted in the S. cerevisiae model to be consistent with the in vivo data. Applying the k-cone analysis a priori to kinetic model development may reduce the time and effort involved in model building and parameter adjustment. With the recent developments in high-throughput profiling of metabolite concentrations at a whole-cell scale and advances in metabolomics technologies, the k-cone approach presented here may hold the promise for kinetic

  4. A Numerical Approach for Kinetic Analysis of the Nonexponential Thermoinactivation Process of Uricase.

    PubMed

    Wu, Jing; Yang, Xiaolan; Wang, Deqiang; Hu, Xiaolei; Liao, Juan; Rao, JingJing; Pu, Jun; Zhan, Chang-Guo; Liao, Fei

    2016-08-01

    Prior to the exponential decrease of activity of a uricase from Candida sp. during storage at 37 °C, there was a plateau period of about 4 days at pH 7.4, 12 days at pH 9.2, and about 22 days in the presence of 30 μM oxonate at pH 7.4 or 9.2, but no degradation of polypeptides and no activity of resolved homodimers. To reveal determinants of the plateau period, a dissociation model involving a serial of conformation intermediates of homotetramer were proposed for kinetic analysis of the thermoinactivation process. In the dissociation model, the roles of interior noncovalent interactions essential for homotetramer integrity were reflected by an equivalent number of the artificial weakest noncovalent interaction; to avoid covariance among parameters, the rate constant for disrupting the artificial weakest noncovalent interaction was fixed at the minimum for physical significance of other parameters; among thermoinactivation curves simulated by numerical integration with different sets of parameters, the one for least-squares fitting to an experimental one gave the solution. Results found that the equivalent number of the artificial weakest noncovalent interaction primarily determined the plateau period; kinetics rather than thermodynamics for homotetramer dissociation determined the thermoinactivation process. These findings facilitated designing thermostable uricase mutants. PMID:27480193

  5. Characteristics and kinetic study on pyrolysis of five lignocellulosic biomass via thermogravimetric analysis.

    PubMed

    Chen, Zhihua; Hu, Mian; Zhu, Xiaolei; Guo, Dabin; Liu, Shiming; Hu, Zhiquan; Xiao, Bo; Wang, Jingbo; Laghari, Mahmood

    2015-09-01

    Pyrolysis characteristics and kinetic of five lignocellulosic biomass pine wood sawdust, fern (Dicranopteris linearis) stem, wheat stalk, sugarcane bagasse and jute (Corchorus capsularis) stick were investigated using thermogravimetric analysis. The pyrolysis of five lignocellulosic biomass could be divided into three stages, which correspond to the pyrolysis of hemicellulose, cellulose and lignin, respectively. Single Gaussian activation energy distributions of each stage are 148.50-201.13 kJ/mol with standard deviations of 2.60-13.37 kJ/mol. The kinetic parameters of different stages were used as initial guess values for three-parallel-DAEM model calculation with good fitting quality and fast convergence rate. The mean activation energy ranges of hemicellulose, cellulose and lignin were 148.12-164.56 kJ/mol, 171.04-179.54 kJ/mol and 175.71-201.60 kJ/mol, with standard deviations of 3.91-9.89, 0.29-1.34 and 23.22-27.24 kJ/mol, respectively. The mass fractions of hemicellulose, cellulose and lignin in lignocellulosic biomass were respectively estimated as 0.12-0.22, 0.54-0.65 and 0.17-0.29.

  6. Transient-State Kinetic Analysis of the RNA Polymerase I Nucleotide Incorporation Mechanism.

    PubMed

    Appling, Francis D; Lucius, Aaron L; Schneider, David A

    2015-12-01

    Eukaryotes express three or more multisubunit nuclear RNA polymerases (Pols) referred to as Pols I, II, and III, each of which synthesizes a specific subset of RNAs. Consistent with the diversity of their target genes, eukaryotic cells have evolved divergent cohorts of transcription factors and enzymatic properties for each RNA polymerase system. Over the years, many trans-acting factors that orchestrate transcription by the individual Pols have been described; however, little effort has been devoted to characterizing the molecular mechanisms of Pol I activity. To begin to address this gap in our understanding of eukaryotic gene expression, here we establish transient-state kinetic approaches to characterize the nucleotide incorporation mechanism of Pol I. We collected time courses for single turnover nucleotide incorporation reactions over a range of substrate ATP concentrations that provide information on both Pol I's nucleotide addition and nuclease activities. The data were analyzed by model-independent and model-dependent approaches, resulting in, to our knowledge, the first minimal model for the nucleotide addition pathway for Pol I. Using a grid searching approach we provide rigorous bounds on estimated values of the individual elementary rate constants within the proposed model. This work reports the most detailed analysis of Pol I mechanism to date. Furthermore, in addition to their use in transient state kinetic analyses, the computational approaches applied here are broadly applicable to global optimization problems. PMID:26636949

  7. 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

  8. Characteristics and kinetic study on pyrolysis of five lignocellulosic biomass via thermogravimetric analysis.

    PubMed

    Chen, Zhihua; Hu, Mian; Zhu, Xiaolei; Guo, Dabin; Liu, Shiming; Hu, Zhiquan; Xiao, Bo; Wang, Jingbo; Laghari, Mahmood

    2015-09-01

    Pyrolysis characteristics and kinetic of five lignocellulosic biomass pine wood sawdust, fern (Dicranopteris linearis) stem, wheat stalk, sugarcane bagasse and jute (Corchorus capsularis) stick were investigated using thermogravimetric analysis. The pyrolysis of five lignocellulosic biomass could be divided into three stages, which correspond to the pyrolysis of hemicellulose, cellulose and lignin, respectively. Single Gaussian activation energy distributions of each stage are 148.50-201.13 kJ/mol with standard deviations of 2.60-13.37 kJ/mol. The kinetic parameters of different stages were used as initial guess values for three-parallel-DAEM model calculation with good fitting quality and fast convergence rate. The mean activation energy ranges of hemicellulose, cellulose and lignin were 148.12-164.56 kJ/mol, 171.04-179.54 kJ/mol and 175.71-201.60 kJ/mol, with standard deviations of 3.91-9.89, 0.29-1.34 and 23.22-27.24 kJ/mol, respectively. The mass fractions of hemicellulose, cellulose and lignin in lignocellulosic biomass were respectively estimated as 0.12-0.22, 0.54-0.65 and 0.17-0.29. PMID:26080101

  9. 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

    2016-01-01

    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. PMID:26824388

  10. 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…

  11. 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

  12. 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

  13. 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. PMID:26050736

  14. Adsorption of methylene blue onto hazelnut shell: Kinetics, mechanism and activation parameters.

    PubMed

    Doğan, Mehmet; Abak, Harun; Alkan, Mahir

    2009-05-15

    The adsorption kinetics of methylene blue (MB) on the hazelnut shell with respect to the initial dye concentration, pH, ionic strength, particle size and temperature were investigated. The rate and the transport/kinetic processes of MB adsorption were described by applying the first-order Lagergren, the pseudo-second-order, mass transfer coefficient and the intraparticle diffusion models. Kinetic studies showed that the kinetic data were well described by the pseudo-second-order kinetic model. Significant increases in initial adsorption rate were observed with the increase in temperature followed by pH and initial MB concentration. The intraparticle diffusion was found to be the rate-limiting step in the adsorption process. Adsorption activation energy was calculated to be 45.6kJmol(-1). The values of activation parameters such as free energy (DeltaG(*)), enthalpy (DeltaH(*)) and entropy (DeltaS(*)) were also determined as 83.4kJmol(-1), 42.9kJmol(-1) and -133.5Jmol(-1)K(-1), respectively.

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

    PubMed

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

    2011-06-01

    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.

  16. Aerosol hygroscopicity and CCN activation kinetics in a boreal forest environment during the 2007 EUCAARI campaign

    NASA Astrophysics Data System (ADS)

    Cerully, K. M.; Raatikainen, T.; Lance, S.; Tkacik, D.; Tiitta, P.; Petäjä, T.; Ehn, M.; Kulmala, M.; Worsnop, D. R.; Laaksonen, A.; Smith, J. N.; Nenes, A.

    2011-12-01

    Measurements of size-resolved cloud condensation nuclei (CCN) concentrations, subsaturated hygroscopic growth, size distribution, and chemical composition were collected from March through May, 2007, in the remote Boreal forests of Hyytiälä, Finland, as part of the European Integrated project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaign. Hygroscopicity parameter, κ, distributions were derived independently from Continuous Flow-Streamwise Thermal Gradient CCN Chamber (CFSTGC) and Hygroscopicity Tandem Differential Mobility Analyzer (HTDMA) measurements. CFSTGC-derived κ values for 40, 60, and 80 nm particles range mostly between 0.10 and 0.40 with an average characteristic of highly oxidized organics of 0.20 ± 0.10, indicating that organics play a dominant role for this environment. HTDMA-derived κ were generally 30% lower. Diurnal trends of κ show a minimum at sunrise and a maximum in the late afternoon; this trend covaries with inorganic mass fraction and the m/z 44 organic mass fraction given by a quadrupole aerosol mass spectrometer, further illustrating the importance of organics in aerosol hygroscopicity. The chemical dispersion inferred from the observed κ distributions indicates that while 60 and 80 nm dispersion increases around midday, 40 nm dispersion remains constant. Additionally, 80 nm particles show a markedly higher level of chemical dispersion than both 40 and 60 nm particles. An analysis of droplet activation kinetics for the sizes considered indicates that most of the CCN activate as rapidly as (NH4)2SO4 calibration aerosol.

  17. Aerosol hygroscopicity and CCN activation kinetics in a boreal forest environment during the 2007 EUCAARI campaign

    NASA Astrophysics Data System (ADS)

    Cerully, K. M.; Raatikainen, T.; Lance, S.; Tkacik, D.; Tiitta, P.; Petäjä, T.; Ehn, M.; Kulmala, M.; Worsnop, D. R.; Laaksonen, A.; Smith, J. N.; Nenes, A.

    2011-05-01

    Measurements of size-resolved cloud condensation nuclei (CCN), subsaturated hygroscopic growth, size distribution, and chemical composition were collected from March through May, 2007, in the remote Boreal forests of Hyytiälä, Finland, as part of the European Integrated project on Aerosol Cloud Climate and Air Quality Interactions (EUCAARI) campaign. Hygroscopicity parameter, κ, distributions were derived independently from Continuous Flow-Streamwise Thermal Gradient CCN Chamber (CFSTGC) and Hygroscopicity Tandem Differential Mobility Analyzer (HTDMA) measurements. CFSTGC-derived κ values for 40, 60, and 80 nm particles range mostly between 0.10 and 0.40 with an average of 0.20 ± 0.10; this is characteristic of highly oxidized organics and reflect their dominant influence in this environment. HTDMA-derived κ were generally 30 % lower. Diurnal trends of κ show a minimum at sunrise and a maximum in the late afternoon; this trend covaries with inorganic mass fraction and the m/z 44 organic mass fraction given by a quadrupole aerosol mass spectrometer, further illustrating the importance of ageing on aerosol hygroscopicity. The chemical dispersion inferred from the observed κ distributions indicates that while 60 and 80 nm dispersion increases around midday, 40 nm dispersion remains constant. Additionally, 80 nm particles show a markedly higher level of chemical dispersion than both 40 and 60 nm particles. An analysis of droplet activation kinetics for the sizes considered indicates that the CCN activate as rapidly as (NH4)2SO4 calibration aerosol.

  18. 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

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

    PubMed

    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

  20. 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…

  1. 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.

  2. 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.

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

    DOE PAGES

    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 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

  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. Progress Toward the Analysis of the Kinetic Stabilizer Concept

    SciTech Connect

    Post, R F; Byers, J A; Cohen, R H; Fowler, T K; Ryutov, D D; Tung, L S

    2005-02-08

    The Kinetic Stabilizer (K-S) concept [1] represents a means for stabilizing axisymmetric mirror and tandem-mirror (T-M) magnetic fusion systems against MHD interchange instability modes. Magnetic fusion research has given us examples of axisymmetric mirror confinement devices in which radial transport rates approach the classical ''Spitzer'' level, i.e. situations in which turbulence if present at all, is at too low a level to adversely affect the radial transport [2,3,4]. If such a low-turbulence condition could be achieved in a T-M system it could lead to a fusion power system that would be simpler, smaller, and easier to develop than one based on closed-field confinement, e.g., the tokamak, where the transport is known to be dominated by turbulence. However, since conventional axisymmetric mirror systems suffer from the MHD interchange instability, the key to exploiting this new opportunity is to find a practical way to stabilize this mode. The K-S represents one avenue to achieving this goal. The starting point for the K-S concept is a theoretical analysis by Ryutov [5]. He showed that a MHD-unstable plasma contained in an axisymmetric mirror cell can be MHD-stabilized by the presence of a low-density plasma on the expanding field lines outside the mirrors. If this plasma communicates well electrically with the plasma in the then this exterior plasma can stabilize the interior, confined, plasma. This stabilization technique was conclusively demonstrated in the Gas Dynamic Trap (GDT) experiment [6] at Novosibirsk, Russia, at mirror-cell plasma beta values of 40 percent. The GDT operates in a high collisionality regime. Thus the effluent plasma leaking through the mirrors, though much lower in density than that of the confined plasma, is still high enough to satisfy the stabilization criterion. This would not, however, be the case in a fusion T-M with axisymmetric plug and central cell fields. In such a case the effluent plasma would be far too low in density to

  6. 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.

  7. 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.

  8. Pyrolytic and Kinetic Analysis of Two Coastal Plant Species: Artemisia annua and Chenopodium glaucum

    PubMed Central

    Wang, Xiaoning; Sun, Jinsheng; Zhang, Yichen; Qin, Song

    2013-01-01

    The large amount of coastal plant species available makes them ideal candidates for energy production. In this study, thermogravimetric analysis was used to evaluate the fuel properties of two coastal plant species, and the distributed activation energy model (DAEM) was employed in kinetic analysis. The major mass loss due to devolatilization started at 154 and 162°C at the heating rate of 10°C min−1 for Artemisia annua and Chenopodium glaucum, respectively. The results showed that the average activation energies of Artemisia annua and Chenopodium glaucum were 169.69 and 170.48 kJ mol−1, respectively. Furthermore, the activation energy changed while the conversion rate increased, and the frequency factor k0 decreased greatly while the activation energy decreased. The results also indicated that the devolatilization of the two coastal plant species underwent a set of first-order reactions and could be expressed by the DAEM. Additionally, a simplified mathematical model was proposed to facilitate the prediction of devolatilization curves. PMID:24350245

  9. Pyrolytic and kinetic analysis of two coastal plant species: Artemisia annua and Chenopodium glaucum.

    PubMed

    Li, Lili; Wang, Xiaoning; Sun, Jinsheng; Zhang, Yichen; Qin, Song

    2013-01-01

    The large amount of coastal plant species available makes them ideal candidates for energy production. In this study, thermogravimetric analysis was used to evaluate the fuel properties of two coastal plant species, and the distributed activation energy model (DAEM) was employed in kinetic analysis. The major mass loss due to devolatilization started at 154 and 162°C at the heating rate of 10°C min(-1) for Artemisia annua and Chenopodium glaucum, respectively. The results showed that the average activation energies of Artemisia annua and Chenopodium glaucum were 169.69 and 170.48 kJ mol(-1), respectively. Furthermore, the activation energy changed while the conversion rate increased, and the frequency factor k 0 decreased greatly while the activation energy decreased. The results also indicated that the devolatilization of the two coastal plant species underwent a set of first-order reactions and could be expressed by the DAEM. Additionally, a simplified mathematical model was proposed to facilitate the prediction of devolatilization curves. PMID:24350245

  10. 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.

  11. 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)

  12. Adsorption kinetics of herbicide paraquat from aqueous solution onto activated bleaching earth.

    PubMed

    Tsai, W T; Lai, C W; Hsien, K J

    2004-05-01

    In the present study, the activated bleaching earth was used as adsorbent for the herbicide paraquat adsorption in a batch adsorber. The rate of adsorption has been investigated under the controlled process parameters like agitation speed, initial paraquat concentration, adsorbent dosage and temperature. A batch kinetic model, based on the assumption of a pseudo-second order mechanism, has been tested to predict the rate constant of adsorption, equilibrium adsorption capacity, time of half-adsorption, and equilibrium concentration by the fittings of the experimental data. The results of the kinetic studies show that the adsorption process can be well described with the pseudo-second order equation. Based on the isotherm data obtained from the fittings of the adsorption kinetics, Freundlich model appears to fit the adsorption better than Langmuir model. In addition, the effective diffusion coefficient has also been estimated based on the restrictive diffusion model.

  13. Inhibition of acetylcholinesterase by two genistein derivatives: kinetic analysis, molecular docking and molecular dynamics simulation.

    PubMed

    Fang, Jiansong; Wu, Ping; Yang, Ranyao; Gao, Li; Li, Chao; Wang, Dongmei; Wu, Song; Liu, Ai-Lin; Du, Guan-Hua

    2014-12-01

    In this study two genistein derivatives (G1 and G2) are reported as inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE), and differences in the inhibition of AChE are described. Although they differ in structure by a single methyl group, the inhibitory effect of G1 (IC50=264 nmol/L) on AChE was 80 times stronger than that of G2 (IC50=21,210 nmol/L). Enzyme-kinetic analysis, molecular docking and molecular dynamics (MD) simulations were conducted to better understand the molecular basis for this difference. The results obtained by kinetic analysis demonstrated that G1 can interact with both the catalytic active site and peripheral anionic site of AChE. The predicted binding free energies of two complexes calculated by the molecular mechanics/generalized born surface area (MM/GBSA) method were consistent with the experimental data. The analysis of the individual energy terms suggested that a difference between the net electrostatic contributions (ΔE ele+ΔG GB) was responsible for the binding affinities of these two inhibitors. Additionally, analysis of the molecular mechanics and MM/GBSA free energy decomposition revealed that the difference between G1 and G2 originated from interactions with Tyr124, Glu292, Val294 and Phe338 of AChE. In conclusion, the results reveal significant differences at the molecular level in the mechanism of inhibition of AChE by these structurally related compounds. PMID:26579414

  14. 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.

  15. Analysis of kinematic, kinetic and electromyographic patterns during root canal preparation with rotary and manual instruments

    PubMed Central

    PASTERNAK-JÚNIOR, Braulio; de SOUSA NETO, Manoel Damião; DIONÍSIO, Valdeci Carlos; PÉCORA, Jesus Djalma; SILVA, Ricardo Gariba

    2012-01-01

    Objective This study assessed the muscular activity during root canal preparation through kinematics, kinetics, and electromyography (EMG). Material and Methods The operators prepared one canal with RaCe rotary instruments and another with Flexo-files. The kinematics of the major joints was reconstructed using an optoelectronic system and electromyographic responses of the flexor carpi radialis, extensor carpi radialis, brachioradialis, biceps brachii, triceps brachii, middle deltoid, and upper trapezius were recorded. The joint torques of the shoulder, elbow and wrist were calculated using inverse dynamics. In the kinematic analysis, angular movements of the wrist and elbow were classified as low risk factors for work-related musculoskeletal disorders. With respect to the shoulder, the classification was medium-risk. Results There was no significant difference revealed by the kinetic reports. The EMG results showed that for the middle deltoid and upper trapezius the rotary instrumentation elicited higher values. The flexor carpi radialis and extensor carpi radialis, as well as the brachioradialis showed a higher value with the manual method. Conclusion The muscular recruitment for accomplishment of articular movements for root canal preparation with either the rotary or manual techniques is distinct. Nevertheless, the rotary instrument presented less difficulty in the generation of the joint torque in each articulation, thus, presenting a greater uniformity of joint torques. PMID:22437679

  16. 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.

  17. 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.

  18. 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. PMID:25545092

  19. Determination of Phosphate-activated Glutaminase Activity and Its Kinetics in Mouse Tissues using Metabolic Mapping (Quantitative Enzyme Histochemistry)

    PubMed Central

    Botman, Dennis; Tigchelaar, Wikky

    2014-01-01

    Phosphate-activated glutaminase (PAG) converts glutamine to glutamate as part of the glutaminolysis pathway in mitochondria. Two genes, GLS1 and GLS2, which encode for kidney-type PAG and liver-type PAG, respectively, differ in their tissue-specific activities and kinetics. Tissue-specific PAG activity and its kinetics were determined by metabolic mapping using a tetrazolium salt and glutamate dehydrogenase as an auxiliary enzyme in the presence of various glutamine concentrations. In kidney and brain, PAG showed Michaelis-Menten kinetics with a Km of 0.6 mM glutamine and a Vmax of 1.1 µmol/mL/min when using 5 mM glutamine. PAG activity was high in the kidney cortex and inner medulla but low in the outer medulla, papillary tip, glomeruli and the lis of Henle. In brain tissue sections, PAG was active in the grey matter and inactive in myelin-rich regions. Liver PAG showed allosteric regulation with a Km of 11.6 mM glutamine and a Vmax of 0.5 µmol/mL/min when using 20 mM glutamine. The specificity of the method was shown after incubation of brain tissue sections with the PAG inhibitor 6-diazo-5-oxo-L-norleucine. PAG activity was decreased to 22% in the presence of 2 mM 6-diazo-5-oxo-L-norleucine. At low glutamine concentrations, PAG activity was higher in periportal regions, indicating a lower Km for periportal PAG. When compared with liver, kidney and brain, other tissues showed 3-fold to 6-fold less PAG activity. In conclusion, PAG is mainly active in mouse kidney, brain and liver, and shows different kinetics depending on which type of PAG is expressed. PMID:25163927

  20. 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

  1. Activation kinetics of calcium currents in bull-frog sympathetic neurones.

    PubMed Central

    Sala, F

    1991-01-01

    1. Calcium currents were recorded in dissociated bull-frog sympathetic neurones (BSNs) through patch pipettes using discontinuous voltage clamp. Activation kinetics were examined by analysing turn-on and turn-off currents. 2. After short depolarizing pulses turn-off tail currents were fitted with the sum of two exponentials. The fast component (time constant, tau approximately 240 microseconds at -40 mV) was undoubtedly due to the closure of calcium channels. The significance of a small and slower component is discussed. 3. Neither activation nor deactivation time courses changed as channels inactivated during progressively longer pulses or when the holding potential was less negative. No specific component was selectively suppressed by these manipulations. 4. Steady-state activation of the Ca2+ current was described by the Boltzmann distribution raised to the second power. Currents had an apparent threshold at -30 mV and were half-activated at +5 mV. 5. Calcium current turned on following m2 kinetics throughout the range of activation. The slowest time constant was around 1.2 ms between 0 and +10 mV. Turn-on was faster at negative or more positive potentials. 6. The time course of decay of tail currents became progressively faster at more negative potentials. 7. The instantaneous current-voltages (I-V) curve was obtained from tail current measurements and fitted by a modified constant-field equation. 8. The measured peak I-V curve could be reconstructed from the activation curve and the instantaneous I-V curve. 9. The activation kinetics of the calcium current in BSNs were consistent with the existence of a single kinetic class of channels and can be described with a simple m2 Hodgkin-Huxley model. PMID:1653852

  2. Systems biology of coagulation initiation: kinetics of thrombin generation in resting and activated human blood.

    PubMed

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

    2010-09-30

    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 (T(i)) of 1 to 2 hours (depending on donor), while activation of platelets with the GPVI-activator convulxin reduces T(i) 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 T(i) 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

  3. Pre-Steady-State Kinetic Analysis of Single-Nucleotide Incorporation by DNA Polymerases.

    PubMed

    Su, Yan; Peter Guengerich, F

    2016-06-01

    Pre-steady-state kinetic analysis is a powerful and widely used method to obtain multiple kinetic parameters. This protocol provides a step-by-step procedure for pre-steady-state kinetic analysis of single-nucleotide incorporation by a DNA polymerase. It describes the experimental details of DNA substrate annealing, reaction mixture preparation, handling of the RQF-3 rapid quench-flow instrument, denaturing polyacrylamide DNA gel preparation, electrophoresis, quantitation, and data analysis. The core and unique part of this protocol is the rationale for preparation of the reaction mixture (the ratio of the polymerase to the DNA substrate) and methods for conducting pre-steady-state assays on an RQF-3 rapid quench-flow instrument, as well as data interpretation after analysis. In addition, the methods for the DNA substrate annealing and DNA polyacrylamide gel preparation, electrophoresis, quantitation and analysis are suitable for use in other studies. © 2016 by John Wiley & Sons, Inc.

  4. Kinetic and Mechanical Analysis of Live Tube Morphogenesis

    PubMed Central

    Cheshire, Alan M.; Kerman, Bilal E.; Zipfel, Warren R.; Spector, Alexander A.; Andrew, Deborah J.

    2008-01-01

    Ribbon is a nuclear BTB-domain protein required for morphogenesis of the salivary gland and trachea. We recently showed that ribbon mutants exhibit decreased Crumbs and Rab11-coincident apical vesicles and increased apical Moesin activity and microvillar structure during tube elongation. To learn how these molecular and morphological changes affect the dynamics of tubulogenesis, we optimized an advanced two-photon microscope to enable high-resolution live imaging of the salivary gland and trachea. Live imaging revealed that ribbon mutant tissues exhibit slowed and incomplete lumenal morphogenesis, consistent with previously described apical defects. Since Moesin activity correlates with cortical stiffness, we hypothesize that ribbon mutants suffer from increased apical stiffness during morphogenesis. We develop this hypothesis through mechanical analysis, using the advantages of live imaging to construct computational elastic and analytical viscoelastic models of tube elongation, which suggest that ribbon mutant tubes exhibit three- to five-fold increased apical stiffness and two-fold increased effective apical viscosity. PMID:18816822

  5. Units of analysis and kinetic structure of behavioral repertoires.

    PubMed

    Thompson, T; Lubinski, D

    1986-09-01

    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.

  6. 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

  7. 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.

  8. Process kinetics of an activated-sludge reactor system treating poultry slaughterhouse wastewater.

    PubMed

    Hsiao, Ting-Hsun; Huang, Ju-Sheng; Huang, Yu-I

    2012-01-01

    The principal objective was to generate the essential kinetic parameters for model simulation and operation management of an activated-sludge reactor (ASR) system treating poultry slaughterhouse wastewater. By varying four different mean cell residence times (theta(c) = 4.6-24.3 d), the ASR system (26 degrees C) removed effectively 93.5%-97.2% of chemical oxygen demand (COD) from wastewater. Ifa high COD removal efficiency and a low effluent volatile suspended solids (VSS) concentration are of great concern, a theta(c) of 15-24 d or a food to microorganism (F/M) ratio of 0.3-0.7 kg COD/kg VSS-d is suggested; if resource sustainability and enhanced operation of the ASR system are of great concern, a theta(c) of 9 d or an F/M ratio of 0.9 kg COD/kg VSS-d is suggested. The COD residual concentrations and COD removal efficiencies calculated by using the Monod model agreed well with the experimental results. When the parameters k and Ks (deltaP/P) were respectively varied from -100% to +100%, the parametric sensitivity analysis showed that the COD residual concentration change (deltaS/S) was highly sensitive to k in the deltaP/P range between 0% and -40%, causing a marked increase in COD residual concentration.

  9. 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).

  10. Dual diffusion and finite mass exchange model for adsorption kinetics in activated carbon

    SciTech Connect

    Do, D.D.; Wang, K.

    1998-01-01

    A model allowing for the finite mass exchange between the two phases is proposed for the description of adsorption kinetics in activated carbon. This model based on Do`s earlier structural model for activated carbon involves three mass-transfer processes: pore diffusion, adsorbed phase diffusion, and finite mass interchange between the fluid and adsorbed phases. The solid phase is heterogeneous, which is characterized by the micropore size distribution. The interaction between the adsorbate molecule and the micropore is calculated from the Lennard-Jones potential theory. The model developed for nonpolar adsorbates is tested with the experimental data of seven adsorbates (paraffin gases, aromatics, carbon dioxide, and sulfur dioxide) on pellets of different shapes and sizes and at various operating conditions. The finite kinetics play an important role in the overall kinetics. Failure to account for this finite kinetics makes the model unable to describe correctly the desorption behavior, since under such conditions, the ability of the particle to release adsorbed molecules is dictated mostly by the resistance at the pore mouth of the micropore.

  11. 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.

  12. From kinetic-structure analysis to engineering crystalline fiber networks in soft materials.

    PubMed

    Wang, Rong-Yao; Wang, Peng; Li, Jing-Liang; Yuan, Bing; Liu, Yu; Li, Li; Liu, Xiang-Yang

    2013-03-01

    Understanding the role of kinetics in fiber network microstructure formation is of considerable importance in engineering gel materials to achieve their optimized performances/functionalities. In this work, we present a new approach for kinetic-structure analysis for fibrous gel materials. In this method, kinetic data is acquired using a rheology technique and is analyzed in terms of an extended Dickinson model in which the scaling behaviors of dynamic rheological properties in the gelation process are taken into account. It enables us to extract the structural parameter, i.e. the fractal dimension, of a fibrous gel from the dynamic rheological measurement of the gelation process, and to establish the kinetic-structure relationship suitable for both dilute and concentrated gelling systems. In comparison to the fractal analysis method reported in a previous study, our method is advantageous due to its general validity for a wide range of fractal structures of fibrous gels, from a highly compact network of the spherulitic domains to an open fibrous network structure. With such a kinetic-structure analysis, we can gain a quantitative understanding of the role of kinetic control in engineering the microstructure of the fiber network in gel materials.

  13. Interaction of Nitric Oxide with Catalase: Structural and Kinetic Analysis

    PubMed Central

    2011-01-01

    We present the structures of bovine catalase in its native form and complexed with ammonia and nitric oxide, obtained by X-ray crystallography. Using the NO generator 1-(N,N-diethylamino)diazen-1-ium-1,2-diolate, we were able to generate sufficiently high NO concentrations within the catalase crystals that substantial occupation was observed despite a high dissociation rate. Nitric oxide seems to be slightly bent from the heme normal that may indicate some iron(II) character in the formally ferric catalase. Microspectrophotometric investigations inline with the synchrotron X-ray beam reveal photoreduction of the central heme iron. In the cases of the native and ammonia-complexed catalase, reduction is accompanied by a relaxation phase. This is likely not the case for the catalase NO complex. The kinetics of binding of NO to catalase were investigated using NO photolyzed from N,N′-bis(carboxymethyl)-N,N′-dinitroso-p-phenylenediamine using an assay that combines catalase with myoglobin binding kinetics. The off rate is 1.5 s–1. Implications for catalase function are discussed. PMID:21524057

  14. 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.

  15. Reaction progress kinetic analysis of a copper-catalyzed aerobic oxidative coupling reaction with N-phenyl tetrahydroisoquinoline.

    PubMed

    Scott, Martin; Sud, Abhishek; Boess, Esther; Klussmann, Martin

    2014-12-19

    The results from a kinetic investigation of a Cu-catalyzed oxidative coupling reaction between N-phenyl tetrahydroisoquinoline and a silyl enol ether using elemental oxygen as oxidant are presented. By using reaction progress kinetic analysis as an evaluation method for the obtained data, we discovered information regarding the reaction order of the substrates and catalysts. Based on this information and some additional experiments, a refined model for the initial oxidative activation of the amine substrate and the activation of the nucleophile by the catalyst was developed. The mechanistic information also helped to understand why silyl nucleophiles have previously failed in a related Cu-catalyzed reaction using tert-butyl hydroperoxide as oxidant and how to overcome this limitation. PMID:25203932

  16. Study of the kinetic parameters for synthesis and hydrolysis of pharmacologically active salicin isomer catalyzed by baker's yeast maltase

    NASA Astrophysics Data System (ADS)

    Veličković, D. V.; Dimitrijević, A. S.; Bihelović, F. J.; Jankov, R. M.; Milosavić, N.

    2011-12-01

    One of the key elements for understanding enzyme reactions is determination of its kinetic parameters. Since transglucosylation is kinetically controlled reaction, besides the reaction of synthesis, very important is the reaction of enzymatic hydrolysis of created product. Therefore, in this study, kinetic parameters for synthesis and secondary hydrolysis of pharmacologically active α isosalicin by baker's yeast maltase were calculated, and it was shown that specifity of maltase for hydrolysis is approximately 150 times higher then for synthesis.

  17. 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.

  18. Two dimensional kinetic analysis of electrostatic harmonic plasma waves

    NASA Astrophysics Data System (ADS)

    Fonseca-Pongutá, E. C.; Ziebell, L. F.; Gaelzer, R.; Yoon, P. H.

    2016-06-01

    Electrostatic harmonic Langmuir waves are virtual modes excited in weakly turbulent plasmas, first observed in early laboratory beam-plasma experiments as well as in rocket-borne active experiments in space. However, their unequivocal presence was confirmed through computer simulated experiments and subsequently theoretically explained. The peculiarity of harmonic Langmuir waves is that while their existence requires nonlinear response, their excitation mechanism and subsequent early time evolution are governed by essentially linear process. One of the unresolved theoretical issues regards the role of nonlinear wave-particle interaction process over longer evolution time period. Another outstanding issue is that existing theories for these modes are limited to one-dimensional space. The present paper carries out two dimensional theoretical analysis of fundamental and (first) harmonic Langmuir waves for the first time. The result shows that harmonic Langmuir wave is essentially governed by (quasi)linear process and that nonlinear wave-particle interaction plays no significant role in the time evolution of the wave spectrum. The numerical solutions of the two-dimensional wave spectra for fundamental and harmonic Langmuir waves are also found to be consistent with those obtained by direct particle-in-cell simulation method reported in the literature.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. On the determination of activation energy and the order of kinetics in thermoluminescence

    NASA Astrophysics Data System (ADS)

    Karmakar, Mahua; Bhattacharyya, S.; Mazumdar, P. S.; Singh, S. D.

    2015-12-01

    The study of thermoluminescence (TL) glow-peaks forms the background of important and useful methods for estimating the kinetic parameters such as activation energy ? and the order of kinetics ?. These parameters are, in general, determined by using glow curve deconvolution or peak shape methods. In the present paper, we have investigated the suitability of the modified peak shape method and Kirsh method in order to perform simultaneous evaluation of these kinetic parameters ? and ? in TL. For this purpose, we have considered numerically computed TL peaks resulting from (i) General Order Kinetics model, (ii) Non-interactive MultiTrap System model (or Modified One Trap One Recombination centre (M-OTOR) model), and (iii) Interactive MultiTrap System model. We have also considered the application of these methods to experimental TL glow peaks of γ-irradiated colourless calcite that exhibits two intense TL glow peaks at 516 and 613 K, respectively. Theoretical results obtained by using different methods corresponding to different models show good agreement with experiments and, hence, point towards the model independence of methods under consideration, except the cases of strong retrapping.

  6. Roles of divergent and rotational winds in the kinetic energy balance during intense convective activity

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.; Browning, P. A.

    1983-01-01

    Contributions of divergent and rotational wind components to the synoptic-scale kinetic energy balance are described using rawinsonde data at 3 and 6 h intervals from NASA's fourth Atmospheric Variability experiment. Two intense thunderstorm complexes occurred during the period. Energy budgets are described for the entire computational region and for limited volumes that enclosed storm-induced, upper level wind maxima located poleward of convection. Although small in magnitude, the divergent wind component played an important role in the cross-contour generation and horizontal flux divergence of kinetic energy. The importance of V(D) appears directly related to the presence and intensity of convection. Although K(D) usually comprised less than 10 percent of the total kinetic energy content, generation of kinetic energy by V(D) was a major factor in the creation of upper-level wind maxima to the north of the storm complexes. Omission of the divergent wind apparently would lead to serious misrepresentations of the energy balance. A random error analysis is presented to assess confidence limits in the various energy parameters.

  7. 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.

  8. 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

  9. Combustion behavior and kinetics of low-lipid microalgae via thermogravimetric analysis.

    PubMed

    Gai, Chao; Liu, Zhengang; Han, Guanghua; Peng, Nana; Fan, Aonan

    2015-04-01

    Thermogravimetric analysis and differential thermal analysis were employed to investigate combustion characteristics of two low-lipid microalgae, Chlorella pyrenoidosa (CP) and Spirulina platensis (SP) and iso-conversional Starink approach was used to calculate the kinetic parameters in the present study. The results showed that three stages of mass loss, including dehydration, devolatilization and char oxidation, were observed during combustion of both of two low-lipid microalgae. The whole weight loss of combustion of two microalgae was both shifted to higher temperature zones with increased heating rates from 10 to 40 K/min. In the 0.1-0.9 conversion range, the apparent activation energy of CP increased first from 51.96 to 79.53 kJ/mol, then decreased to 55.59 kJ/mol. Finally, it slightly increased to 67.27 kJ/mol. In the case of SP, the apparent activation energy gradually increased from 68.51 to 91.06 kJ/mol.

  10. Combustion behavior and kinetics of low-lipid microalgae via thermogravimetric analysis.

    PubMed

    Gai, Chao; Liu, Zhengang; Han, Guanghua; Peng, Nana; Fan, Aonan

    2015-04-01

    Thermogravimetric analysis and differential thermal analysis were employed to investigate combustion characteristics of two low-lipid microalgae, Chlorella pyrenoidosa (CP) and Spirulina platensis (SP) and iso-conversional Starink approach was used to calculate the kinetic parameters in the present study. The results showed that three stages of mass loss, including dehydration, devolatilization and char oxidation, were observed during combustion of both of two low-lipid microalgae. The whole weight loss of combustion of two microalgae was both shifted to higher temperature zones with increased heating rates from 10 to 40 K/min. In the 0.1-0.9 conversion range, the apparent activation energy of CP increased first from 51.96 to 79.53 kJ/mol, then decreased to 55.59 kJ/mol. Finally, it slightly increased to 67.27 kJ/mol. In the case of SP, the apparent activation energy gradually increased from 68.51 to 91.06 kJ/mol. PMID:25647025

  11. 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.

  12. 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

  13. Kinetic evidence for surface residues influencing the active site of Coprinus cinereus peroxidase: analysis of the pH dependence of G154E, P90H and P90H-G154E substrate entrance mutants.

    PubMed

    Di Cerbo, P; Welinder, K G; Schiødt, C B

    2001-01-12

    Three mutants of Coprinus cinereus peroxidase (CIP) were made to mimic the substrate entrance histidine 82-glutamic acid 146 pair of the substrate channel in lignin peroxidase (LIP). Compound I formation of LIP has a low pH optimum around pH 3, while optimal formation of CIP compound I is obtained at pH 6-11. The mutants were glycine 154-->glutamic acid (G154E), proline 90-->histidine (P90H) and the double mutant P90H-G154E. All three showed kinetics of compound I formation similar to that of wt CIP between pH 3 and 9. However, the stability of compound I was strongly affected by these mutations. In wt CIP compound I is stable for approximately 30 min, while compound I of the mutants were stable for 5 s or less. The P90H and P90H-G154E mutants showed pK(a) values for the alkaline transition at least one pH unit lower than for wt CIP and the G154E mutant. We suggest that the changed electrostatic field results in destabilisation of the oxidised heme in compound I and II and that the P90H residue increases the electrostatic potential in the distal cavity thereby decreasing the pK(a) for the alkaline transition.

  14. Determination of Pulmozyme (dornase alpha) stability using a kinetic colorimetric DNase I activity assay.

    PubMed

    Lichtinghagen, Ralf

    2006-07-01

    An enzymatic activity assay was developed for the determination of dornase alpha human recombinant desoxyribonuclease (DNase I) stability. The method was adapted from a colorimetric endpoint enzyme activity assay for DNase I based on the degradation of a DNA/methyl green complex. With the described modifications the kinetic measurement of enzyme activity is feasible on an automated analyzer system within a rather short time. The development of this assay was based on the need for reliable detection of a possible loss of enzyme activity after transferring the commercial therapeutic agent into sealed glass vials required for a placebo-controlled study. The measuring range of this stability test was from 0 to 3000 U/L corresponding to 0-120% of the original enzyme activity; CV values of control solutions inside the measuring range were between 3% and 5%. The enzyme activity decreased less than 15% during the observation period of 180 days. In conclusion the current kinetic assay is a reliable method for a simple time-saving determination of DNase I activity to test Pulmozyme stability as required for quality control. As dornase alpha is used for inhalation, this method also proved its reliability in testing DNase stability during aerosolization with new inhalation devices (e-flow). PMID:16682175

  15. k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

    PubMed Central

    Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.

    2014-01-01

    Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and substrate-level enzyme regulation while identifying metabolic interventions. In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of interest. It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric information). Application of k-OptForce to the overproduction of L-serine in E. coli and triacetic acid lactone (TAL) in S. cerevisiae revealed that the identified interventions tend to cause less dramatic rearrangements of the flux distribution so as not to violate concentration bounds. In some cases the incorporation of kinetic information leads to the need for additional interventions as kinetic expressions render stoichiometry-only derived interventions infeasible by violating concentration bounds, whereas in other cases the kinetic expressions impart flux changes that favor the overproduction of the target product thereby requiring fewer direct interventions. A sensitivity analysis on metabolite concentrations shows that the required number of interventions can be significantly affected by changing the imposed bounds on metabolite concentrations. Furthermore, k-OptForce was capable of finding non-intuitive interventions aiming at alleviating the substrate-level inhibition of key enzymes in order to enhance the flux towards the product of interest, which cannot be captured by stoichiometry-alone analysis. This study paves

  16. Kinetic Analysis of an Efficient DNA-Dependent TNA Polymerase

    PubMed Central

    Horhota, Allen; Zou, Keyong; Ichida, Justin K.; Yu, Biao; McLaughlin, Larry W.; Szostak, Jack W.

    2005-01-01

    α-l-Threofuranosyl nucleoside triphosphates (tNTPs) are tetrafuranose nucleoside derivatives and potential progenitors of present-day β-d-2‘-deoxyribofuranosyl nucleoside triphosphates (dNTPs). Therminator DNA polymerase, a variant of the 9°N DNA polymerase, is an efficient DNA-directed threosyl nucleic acid (TNA) polymerase. Here we report a detailed kinetic comparison of Therminator-catalyzed TNA and DNA syntheses. We examined the rate of single-nucleotide incorporation for all four tNTPs and dNTPs from a DNA primer−template complex and carried out parallel experiments with a chimeric DNA−TNA primer−DNA template containing five TNA residues at the primer 3‘-terminus. Remarkably, no drop in the rate of TNA incorporation was observed in comparing the DNA−TNA primer to the all-DNA primer, suggesting that few primer-enzyme contacts are lost with a TNA primer. Moreover, comparison of the catalytic efficiency of TNA synthesis relative to DNA synthesis at the downstream positions reveals a difference of no greater than 5-fold in favor of the natural DNA substrate. This disparity becomes negligible when the TNA synthesis reaction mixture is supplemented with 1.25 mM MnCl2. These results indicate that Therminator DNA polymerase can recognize both a TNA primer and tNTP substrates and is an effective catalyst of TNA polymerization despite changes in the geometry of the reactants. PMID:15898792

  17. 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

  18. Kinetic analysis of biliary lipid excretion in man and dog.

    PubMed Central

    Wagner, C I; Trotman, B W; Soloway, R D

    1976-01-01

    To understand better the mechanisms involved in biliary lipid excretion and to evaluate their role in cholesterol gallstone formation, the rates of biliary excretion of bile salts, cholesterol, and phospholipids were measured in two species, man and dog. Seven cholecystectomized patients with balloon-occludable reinfusion T-tubes were studied during intact and interrupted enterohepatic circulation and four cholecystectomized dogs were studied during interrupted enterohepatic circulation. In man and dog both cholesterol and phospholipid outputs were hyperbolically related to bile salt output by the equation y = x/(a + bx). The output curves intersected the origin and showed an initial rapid rise, followed by a slower increase to a maximum, suggesting a rate-limited mechanism. The shape of the curves permitted calculation of the theoretical maximal outputs and the rates of rise to those outputs. Comparison of these values showed that in both man and dog phospholipid output was greater than cholesterol output and that cholesterol and phospholipid were excreted at different rates. These studies (a) indicate that cholesterol, phospholipids, and bile salts are not excreted in a fixed relationship and (b) demonstrate the usefulness of the derived theoretical maximal lipid output, and the rate of rise of lipid excretion to a maximum, in evaluating the kinetics of biliary lipid excretion. PMID:943421

  19. Active mechanics in living oocytes reveal molecular-scale force kinetics

    NASA Astrophysics Data System (ADS)

    Ahmed, Wylie; Fodor, Etienne; Almonacid, Maria; Bussonnier, Matthias; Verlhac, Marie-Helene; Gov, Nir; Visco, Paolo; van Wijland, Frederic; Betz, Timo

    Unlike traditional materials, living cells actively generate forces at the molecular scale that change their structure and mechanical properties. This nonequilibrium activity is essential for cellular function, and drives processes such as cell division. Single molecule studies have uncovered the detailed force kinetics of isolated motor proteins in-vitro, however their behavior in-vivo has been elusive due to the complex environment inside the cell. Here, we quantify active forces and intracellular mechanics in living oocytes using in-vivo optical trapping and laser interferometry of endogenous vesicles. We integrate an experimental and theoretical framework to connect mesoscopic measurements of nonequilibrium properties to the underlying molecular- scale force kinetics. Our results show that force generation by myosin-V drives the cytoplasmic-skeleton out-of-equilibrium (at frequencies below 300 Hz) and actively softens the environment. In vivo myosin-V activity generates a force of F ~ 0 . 4 pN, with a power-stroke of length Δx ~ 20 nm and duration τ ~ 300 μs, that drives vesicle motion at vv ~ 320 nm/s. This framework is widely applicable to characterize living cells and other soft active materials.

  20. 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. PMID:18093829

  1. Colloidal particle adsorption at liquid interfaces: capillary driven dynamics and thermally activated kinetics.

    PubMed

    Rahmani, Amir M; Wang, Anna; Manoharan, Vinothan N; Colosqui, Carlos E

    2016-08-14

    The adsorption of single colloidal microparticles (0.5-1 μm radius) at a water-oil interface has been recently studied experimentally using digital holographic microscopy [Kaz et al., Nat. Mater., 2012, 11, 138-142]. An initially fast adsorption dynamics driven by capillary forces is followed by an unexpectedly slow relaxation to equilibrium that is logarithmic in time and can span hours or days. The slow relaxation kinetics has been attributed to the presence of surface "defects" with nanoscale dimensions (1-5 nm) that induce multiple metastable configurations of the contact line perimeter. A kinetic model considering thermally activated transitions between such metastable configurations has been proposed [Colosqui et al., Phys. Rev. Lett., 2013, 111, 028302] to predict both the relaxation rate and the crossover point to the slow logarithmic regime. However, the adsorption dynamics observed experimentally before the crossover point has remained unstudied. In this work, we propose a Langevin model that is able to describe the entire adsorption process of single colloidal particles by considering metastable states produced by surface defects and thermal motion of the particle and liquid interface. Invoking the fluctuation dissipation theorem, we introduce a drag term that considers significant dissipative forces induced by thermal fluctuations of the liquid interface. Langevin dynamics simulations based on the proposed adsorption model yield close agreement with experimental observations for different microparticles, capturing the crossover from (fast) capillary driven dynamics to (slow) thermally activated kinetics. PMID:27373956

  2. Lipase-catalyzed synthesis of palmitanilide: Kinetic model and antimicrobial activity study.

    PubMed

    Liu, Kuan-Miao; Liu, Kuan-Ju

    2016-01-01

    Enzymatic syntheses of fatty acid anilides are important owing to their wide range of industrial applications in detergents, shampoo, cosmetics, and surfactant formulations. The amidation reaction of Mucor miehei lipase Lipozyme IM20 was investigated for direct amidation of triacylglycerol in organic solvents. The process parameters (reaction temperature, substrate molar ratio, enzyme amount) were optimized to achieve the highest yield of anilide. The maximum yield of palmitanilide (88.9%) was achieved after 24 h of reaction at 40 °C at an enzyme concentration of 1.4% (70 mg). Kinetics of lipase-catalyzed amidation of aniline with tripalmitin has been investigated. The reaction rate could be described in terms of the Michaelis-Menten equation with a Ping-Pong Bi-Bi mechanism and competitive inhibition by both the substrates. The kinetic constants were estimated by using non-linear regression method using enzyme kinetic modules. The enzyme operational stability study showed that Lipozyme IM20 retained 38.1% of the initial activity for the synthesis of palmitanilide (even after repeated use for 48 h). Palmitanilide, a fatty acid amide, exhibited potent antimicrobial activity toward Bacillus cereus. PMID:26672452

  3. Relationship between gluteal muscle activation and upper extremity kinematics and kinetics in softball position players.

    PubMed

    Oliver, Gretchen D

    2014-03-01

    As the biomechanical literature concerning softball pitching is evolving, there are no data to support the mechanics of softball position players. Pitching literature supports the whole kinetic chain approach including the lower extremity in proper throwing mechanics. The purpose of this project was to examine the gluteal muscle group activation patterns and their relationship with shoulder and elbow kinematics and kinetics during the overhead throwing motion of softball position players. Eighteen Division I National Collegiate Athletic Association softball players (19.2 ± 1.0 years; 68.9 ± 8.7 kg; 168.6 ± 6.6 cm) who were listed on the active playing roster volunteered. Electromyographic, kinematic, and kinetic data were collected while players caught a simulated hit or pitched ball and perform their position throw. Pearson correlation revealed a significant negative correlation between non-throwing gluteus maximus during the phase of maximum external rotation to maximum internal rotation (MIR) and elbow moments at ball release (r = -0.52). While at ball release, trunk flexion and rotation both had a positive relationship with shoulder moments at MIR (r = 0.69, r = 0.82, respectively) suggesting that the kinematic actions of the pelvis and trunk are strongly related to the actions of the shoulder during throwing.

  4. Properties and active substance release kinetics from gelatin-alginate matrices.

    PubMed

    Pluta, Janusz; Haznar, Dorota

    2006-01-01

    The aim of the study was to evaluate the effect of composition and technological processing on pharmaceutical availability of active substance as well as on the properties of porous gelatin-alginate matrices. The active substance carrier included glycerol or peanut oil apart from gelatin and sodium alginate, and some matrices were additionally modified with calcium lactate. The obtained matrices were characterized by good sorption properties and high resistance to proteolytic enzymes. The release of the model antibiotic followed the pattern of first order kinetics, while half-release time in vitro (in the experimental conditions) was 1.5 to 3 hrs.

  5. Optimization of the activated sludge anoxic reactor configuration as a means to control nutrient removal kinetically.

    PubMed

    Plósz, Benedek Gy

    2007-04-01

    Factors influencing the determination of optimum reactor configuration for activated sludge denitrification are investigated in this paper. A kinetic optimization method is presented to evaluate optimal pre- and post-denitrification bioreactor stages. Applying the method developed, simulation studies were carried out to investigate the impacts of the ratio of the influent readily biodegradable and slowly biodegradable substrates and the oxygen entering the denitrification zones on the optimal anoxic reactor configuration. In addition, the paper describes the effects of the slowly biodegradable substrate on the denitrification efficiency using external substrate dosing, and it demonstrates kinetic considerations concerning the hydrolysis process. It has been shown that as a function of the biodegradable substrate composition, the stage system design with three optimized reactor compartments can effectively increase reaction rates in the denitrification zones, and can provide flexibility for varying operation conditions. PMID:17321565

  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. Molecular kinetics. Ras activation by SOS: allosteric regulation by altered fluctuation dynamics.

    PubMed

    Iversen, Lars; Tu, Hsiung-Lin; Lin, Wan-Chen; Christensen, Sune M; Abel, Steven M; Iwig, Jeff; Wu, Hung-Jen; Gureasko, Jodi; Rhodes, Christopher; Petit, Rebecca S; Hansen, Scott D; Thill, Peter; Yu, Cheng-Han; Stamou, Dimitrios; Chakraborty, Arup K; Kuriyan, John; Groves, Jay T

    2014-07-01

    Activation of the small guanosine triphosphatase H-Ras by the exchange factor Son of Sevenless (SOS) is an important hub for signal transduction. Multiple layers of regulation, through protein and membrane interactions, govern activity of SOS. We characterized the specific activity of individual SOS molecules catalyzing nucleotide exchange in H-Ras. Single-molecule kinetic traces revealed that SOS samples a broad distribution of turnover rates through stochastic fluctuations between distinct, long-lived (more than 100 seconds), functional states. The expected allosteric activation of SOS by Ras-guanosine triphosphate (GTP) was conspicuously absent in the mean rate. However, fluctuations into highly active states were modulated by Ras-GTP. This reveals a mechanism in which functional output may be determined by the dynamical spectrum of rates sampled by a small number of enzymes, rather than the ensemble average.

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    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¯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 ¯d slow increase with the increase of τ. A rapid t¯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¯d due to the increase of positive ions concentration in inter electrode gap. The increase of applied voltage also decreases t¯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¯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¯d for τ > 30 ms.

  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. 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.

  12. 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

  13. Quantitative FRET (Förster Resonance Energy Transfer) analysis for SENP1 protease kinetics determination.

    PubMed

    Liu, Yan; Liao, Jiayu

    2013-02-21

    Reversible posttranslational modifications of proteins with ubiquitin or ubiquitin-like proteins (Ubls) are widely used to dynamically regulate protein activity and have diverse roles in many biological processes. For example, SUMO covalently modifies a large number or proteins with important roles in many cellular processes, including cell-cycle regulation, cell survival and death, DNA damage response, and stress response 1-5. SENP, as SUMO-specific protease, functions as an endopeptidase in the maturation of SUMO precursors or as an isopeptidase to remove SUMO from its target proteins and refresh the SUMOylation cycle (1,3,6,7). The catalytic efficiency or specificity of an enzyme is best characterized by the ratio of the kinetic constants, kcat/KM. In several studies, the kinetic parameters of SUMO-SENP pairs have been determined by various methods, including polyacrylamide gel-based western-blot, radioactive-labeled substrate, fluorescent compound or protein labeled substrate (8-13). However, the polyacrylamide-gel-based techniques, which used the "native" proteins but are laborious and technically demanding, that do not readily lend themselves to detailed quantitative analysis. The obtained kcat/KM from studies using tetrapeptides or proteins with an ACC (7-amino-4-carbamoylmetylcoumarin) or AMC (7-amino-4-methylcoumarin) fluorophore were either up to two orders of magnitude lower than the natural substrates or cannot clearly differentiate the iso- and endopeptidase activities of SENPs. Recently, FRET-based protease assays were used to study the deubiquitinating enzymes (DUBs) or SENPs with the FRET pair of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) (9,10,14,15). The ratio of acceptor emission to donor emission was used as the quantitative parameter for FRET signal monitor for protease activity determination. However, this method ignored signal cross-contaminations at the acceptor and donor emission wavelengths by acceptor and donor

  14. Sequence analysis and enzyme kinetics of the L2 serine beta-lactamase from Stenotrophomonas maltophilia.

    PubMed Central

    Walsh, T R; MacGowan, A P; Bennett, P M

    1997-01-01

    The L2 serine active-site beta-lactamase from Stenotrophomonas maltophilia has been classified as a clavulanic acid-sensitive cephalosporinase. The gene encoding this enzyme from S. maltophilia 1275 IID has been cloned on a 3.3-kb fragment into pK18 under the control of a Ptac promoter to generate recombinant plasmid pUB5840; when expressed in Escherichia coli, this gene confers resistance to cephalosporins and penicillins. Sequence analysis has revealed an open reading frame (ORF) of 909 bp with a GC content of 71.6%, comparable to that of the L1 metallo-beta-lactamase gene (68.4%) from the same bacterium. The ORF encodes an unmodified protein of 303 amino acids with a predicted molecular mass of 31.5 kDa, accommodating a putative leader peptide of 27 amino acids. Comparison of the amino acid sequence with those of other beta-lactamases showed it to be most closely related (54% identity) to the BLA-A beta-lactamase from Yersinia enterocolitica. Sequence identity is most obvious near the STXK active-site motif and the SDN loop motif common to all serine active-site penicillinases. Sequences outside the conserved regions display low homology with comparable regions of other class A penicillinases. Kinetics of the enzyme from the cloned gene demonstrated an increase in activity with cefotaxime but markedly less activity with imipenem than previously reported. Hence, the S. maltophilia L2 beta-lactamase is an inducible Ambler class A beta-lactamase which would account for the sensitivity to clavulanic acid. PMID:9210666

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. Kinetic analysis of dehydration of a bituminous coal using the TGA technique

    SciTech Connect

    Hai-Hui Wang

    2007-12-15

    The current investigation focuses on the kinetics of water liberation during a drying process of a bituminous coal. Using the technique of thermogravimetric analysis (TGA), the mass change of a sample was recorded over the temperature range from 35 to 115{sup o}C at a heating rate of 0.1, 0.2, 0.4, or 0.8{sup o}C/min. The measurements were then analyzed by applying the Coats-Redfern method. The analysis indicates that the water liberated from the coal samples originates from moisture residing in coal particles, including bulk water, capillary water in coal pores, and multilayer water at pore surfaces. The bulk and capillary moisture is easily removed with no energy barrier, while the removal of the multilayer moisture requires an activation energy of 19.7 kJ/mol on average, which corresponds to the dissociation energy of hydrogen bonds between the water molecules and the hydrophilic sites in the coal structure. The reaction order for desorption of multilayer water is found to be unity. Calculations of the amount of water liberated from the samples during the TGA measurements demonstrate that the multilayer water at the surface of coal pores takes up at least 1.6% of the sample mass, with the overall moisture content of the present coal of 6.9%. 21 refs., 5 figs., 2 tabs.

  20. 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

  1. Monte-Carlo modelling of nano-material photocatalysis: bridging photocatalytic activity and microscopic charge kinetics.

    PubMed

    Liu, Baoshun

    2016-04-28

    In photocatalysis, it is known that light intensity, organic concentration, and temperature affect the photocatalytic activity by changing the microscopic kinetics of holes and electrons. However, how the microscopic kinetics of holes and electrons relates to the photocatalytic activity was not well known. In the present research, we developed a Monte-Carlo random walking model that involved all of the charge kinetics, including the photo-generation, the recombination, the transport, and the interfacial transfer of holes and electrons, to simulate the overall photocatalytic reaction, which we called a "computer experiment" of photocatalysis. By using this model, we simulated the effect of light intensity, temperature, and organic surface coverage on the photocatalytic activity and the density of the free electrons that accumulate in the simulated system. It was seen that the increase of light intensity increases the electron density and its mobility, which increases the probability for a hole/electron to find an electron/hole for recombination, and consequently led to an apparent kinetics that the quantum yield (QY) decreases with the increase of light intensity. It was also seen that the increase of organic surface coverage could increase the rate of hole interfacial transfer and result in the decrease of the probability for an electron to recombine with a hole. Moreover, the increase of organic coverage on the nano-material surface can also increase the accumulation of electrons, which enhances the mobility for electrons to undergo interfacial transfer, and finally leads to the increase of photocatalytic activity. The simulation showed that the temperature had a more complicated effect, as it can simultaneously change the activation of electrons, the interfacial transfer of holes, and the interfacial transfer of electrons. It was shown that the interfacial transfer of holes might play a main role at low temperature, with the temperature-dependence of QY

  2. Monte-Carlo modelling of nano-material photocatalysis: bridging photocatalytic activity and microscopic charge kinetics.

    PubMed

    Liu, Baoshun

    2016-04-28

    In photocatalysis, it is known that light intensity, organic concentration, and temperature affect the photocatalytic activity by changing the microscopic kinetics of holes and electrons. However, how the microscopic kinetics of holes and electrons relates to the photocatalytic activity was not well known. In the present research, we developed a Monte-Carlo random walking model that involved all of the charge kinetics, including the photo-generation, the recombination, the transport, and the interfacial transfer of holes and electrons, to simulate the overall photocatalytic reaction, which we called a "computer experiment" of photocatalysis. By using this model, we simulated the effect of light intensity, temperature, and organic surface coverage on the photocatalytic activity and the density of the free electrons that accumulate in the simulated system. It was seen that the increase of light intensity increases the electron density and its mobility, which increases the probability for a hole/electron to find an electron/hole for recombination, and consequently led to an apparent kinetics that the quantum yield (QY) decreases with the increase of light intensity. It was also seen that the increase of organic surface coverage could increase the rate of hole interfacial transfer and result in the decrease of the probability for an electron to recombine with a hole. Moreover, the increase of organic coverage on the nano-material surface can also increase the accumulation of electrons, which enhances the mobility for electrons to undergo interfacial transfer, and finally leads to the increase of photocatalytic activity. The simulation showed that the temperature had a more complicated effect, as it can simultaneously change the activation of electrons, the interfacial transfer of holes, and the interfacial transfer of electrons. It was shown that the interfacial transfer of holes might play a main role at low temperature, with the temperature-dependence of QY

  3. 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.

  4. 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)

  5. Rational ligand design for the arylation of hindered primary amines guided by reaction progress kinetic analysis.

    PubMed

    Ruiz-Castillo, Paula; Blackmond, Donna G; Buchwald, Stephen L

    2015-03-01

    We report the Pd-catalyzed arylation of very hindered α,α,α-trisubstituted primary amines. Kinetics-based mechanistic analysis and rational design have led to the development of two biarylphosphine ligands that allow the transformation to proceed with excellent efficiency. The process was effective in coupling a wide range of functionalized aryl and heteroaryl halides under mild conditions.

  6. 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.

  7. 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.

  8. Pyrethroid modifications of the activation and inactivation kinetics of the sodium channels in squid giant axons.

    PubMed

    de Weille, J R; Brown, L D; Narahashi, T

    1990-03-26

    The kinetics of sodium channel activation and inactivation were analyzed in the squid giant axons internally treated with various pyrethroids. Pyrethroids increased the steady-state sodium current in squid giant axons by removing the inactivation. The steady-state sodium conductances in control and pyrethroid-treated axons showed the same voltage dependence, indicating that the removal of inactivation by pyrethroids did not lead to an alteration of gating charge transfer. The pyrethroid-modified sodium channels were activated with a biphasic time course involving the movement of at least two gating particles, and both components were voltage-dependent. The slower component was abolished by treatment with either pronase or N-bromoacetamide. The net elementary charges transported in the electric membrane field were reduced in the course of slow activation of the pyrethroid-induced sodium current. It appears that the 'immobilization' of gating charge is related to the slow activation rather than the inactivation of the sodium channel.

  9. Lignin-based activated carbons for adsorption of sodium dodecylbenzene sulfonate: Equilibrium and kinetic studies.

    PubMed

    Cotoruelo, Luis M; Marqués, María D; Rodríguez-Mirasol, José; Rodríguez, Juan J; Cordero, Tomás

    2009-04-01

    The adsorption of sodium dodecylbenzene sulfonate (SDBS) from its aqueous solution at different temperatures has been studied using three activated carbons prepared in our laboratory. Lignin was used as raw material for the preparation of activated carbons (ACs). The results of the adsorption equilibrium were analyzed and fitted to the Langmuir model. Thermodynamic magnitudes were estimated as well, and their values indicated that the adsorption processes were spontaneous and exothermic. The kinetic study showed that the processes are of second apparent order related to the concentration of the vacant active centers on the surface of the activated carbons. The values of the effective internal diffusion coefficients have been calculated applying the equations developed by Crank and Vermeulen.

  10. 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.

  11. 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.

  12. 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.

  13. Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.

    PubMed

    Manzo, Carlo; Finzi, Laura

    2010-01-01

    In this chapter we show the application of a maximum-likelihood-based method to the reconstruction of DNA-looping single-molecule time traces from tethered particle motion experiments. The method does not require time filtering of the data and improves the time resolution by an order of magnitude with respect to the threshold-crossing approach. Moreover, it is not based on presumed kinetic models, overcoming the limitations of other approaches proposed previously, and allowing its applications to mechanisms with complex kinetic schemes. Numerical simulations have been used to test the performances of this analysis over a wide range of time scales. We have then applied this method to determine the looping kinetics of a well-known DNA-looping protein, the lambda-repressor.

  14. Pyrolysis and combustion kinetics of date palm biomass using thermogravimetric analysis.

    PubMed

    Sait, Hani H; Hussain, Ahmad; Salema, Arshad Adam; Ani, Farid Nasir

    2012-08-01

    The present research work is probably the first attempt to focus on the kinetics of pyrolysis and combustion process for date palm biomass wastes like seed, leaf and leaf stem by using Thermogravimetric Analysis (TGA) technique. The physical properties of biomass wastes were also examined. Proximate and ultimate analysis of the date palm biomass was investigated. FT-IR analysis was conducted to determine possible chemical functional groups in the biomass. Results showed that date palm seed and leaf can be characterized as high calorific values and high volatile content biomass materials as compared to the leaf stem. Kinetic analysis of this biomass was also given a particular attention. It is concluded that these biomasses can become useful source of energy, chemicals and bio-char. PMID:22705960

  15. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells.

    PubMed Central

    Arkin, A; Ross, J; McAdams, H H

    1998-01-01

    Fluctuations in rates of gene expression can produce highly erratic time patterns of protein production in individual cells and wide diversity in instantaneous protein concentrations across cell populations. When two independently produced regulatory proteins acting at low cellular concentrations competitively control a switch point in a pathway, stochastic variations in their concentrations can produce probabilistic pathway selection, so that an initially homogeneous cell population partitions into distinct phenotypic subpopulations. Many pathogenic organisms, for example, use this mechanism to randomly switch surface features to evade host responses. This coupling between molecular-level fluctuations and macroscopic phenotype selection is analyzed using the phage lambda lysis-lysogeny decision circuit as a model system. The fraction of infected cells selecting the lysogenic pathway at different phage:cell ratios, predicted using a molecular-level stochastic kinetic model of the genetic regulatory circuit, is consistent with experimental observations. The kinetic model of the decision circuit uses the stochastic formulation of chemical kinetics, stochastic mechanisms of gene expression, and a statistical-thermodynamic model of promoter regulation. Conventional deterministic kinetics cannot be used to predict statistics of regulatory systems that produce probabilistic outcomes. Rather, a stochastic kinetic analysis must be used to predict statistics of regulatory outcomes for such stochastically regulated systems. PMID:9691025

  16. 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.

  17. Kinetic Modeling of the Arabidopsis Cryptochrome Photocycle: FADH(o) Accumulation Correlates with Biological Activity.

    PubMed

    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

  18. 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

  19. Oxidation of chlorinated ethenes by heat-activated persulfate: kinetics and products.

    PubMed

    Waldemer, Rachel H; Tratnyek, Paul G; Johnson, Richard L; Nurmi, James T

    2007-02-01

    In situ chemical oxidation (ISCO) and in situ thermal remediation (ISTR) are applicable to treatment of groundwater contaminated with chlorinated ethenes. ISCO with persulfate (S2O8(2-)) requires activation, and this can be achieved with the heat from ISTR, so there may be advantages to combining these technologies. To explore this possibility, we determined the kinetics and products of chlorinated ethene oxidation with heat-activated persulfate and compared them to the temperature dependence of other degradation pathways. The kinetics of chlorinated ethene disappearance were pseudo-first-order for 1-2 half-lives, and the resulting rate constants-measured from 30 to 70 degrees C--fit the Arrhenius equation, yielding apparent activation energies of 101 +/- 4 kJ mol(-1) for tetrachloroethene (PCE), 108 +/- 3 kJ mol(-1) for trichloroethene (TCE), 144 +/- 5 kJ mol(-1) for cis-1,2-dichloroethene (cis-DCE), and 141 +/- 2 kJ mol(-1) for trans-1,2-dichloroethene (trans-DCE). Chlorinated byproducts were observed, but most of the parent material was completely dechlorinated. Arrhenius parameters for hydrolysis and oxidation by persulfate or permanganate were used to calculate rates of chlorinated ethene degradation by these processes over the range of temperatures relevant to ISTR and the range of oxidant concentrations and pH relevant to ISCO.

  20. Noise analysis of ionization kinetics in a protein ion channel

    NASA Astrophysics Data System (ADS)

    Bezrukov, Sergey M.; Kasianowicz, John J.

    1993-08-01

    We observed excess current noise generated by the reversible ionization of sites in a transmembrane protein ion channel, which is analogous to current fluctuations found recently in solid state microstructure electronic devices. Specifically the current through fully open single channels formed by Staphylococcus aureus α-toxin shows pH dependent fluctuations. We show that noise analysis of the open channel current can be used to evaluate the ionization rate constants, the number of sites participating in the ionization process, and the effect of recharging a single site on the channel conductance.

  1. 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

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

    PubMed

    Rohwer, J M; Botha, F C

    2001-09-01

    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.

  3. Kinetic analysis of guanosine 5'-O-(3-thiotriphosphate) effects on phosphatidylinositol turnover in NRK cell homogenates

    SciTech Connect

    Chahwala, S.B.; Fleischman, L.F.; Cantley, L.

    1987-01-27

    Addition of the guanine nucleotide analogue guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) to (/sup 3/H)inositol-labeled NRK cell homogenates resulted in rapid breakdown of cellular polyphosphoinositides. GTP gamma S stimulated phospholipase C, resulting in a more than 4-fold increase in the hydrolysis rates of phosphatidylinositol 4-phosphate (PIP) and phosphatidylinositol 4,5-bis(phosphate) (PIP2). No significant effect of GTP gamma S on direct phosphatidylinositol (PI) hydrolysis was detected. There was an increase in water-soluble inositols, with inositol tris(phosphate) (IP3) levels increasing at least 10 times over the decrease seen in PIP2, indicating that PIP kinase activity was also accelerated following GTP gamma S addition. Inositol 1,4,5-tris(phosphate) peaked rapidly after GTP gamma S addition (less than 2 min) while inositol 1,3,4-tris-(phosphate) was produced more slowly and leveled off after approximately 10 min. The differential equations describing conversion between intermediates in the PI turnover pathway were solved and fitted to data obtained from both (/sup 3/H)inositol and (/sup 32/P)phosphate fluxes by nonlinear least-squares analysis. GTP gamma S effects on the pseudo-first-order rate constants for the lipase, kinase, and phosphatase steps were determined from the analysis. From these measurements it can be estimated that, in the presence of GTP gamma S and calcium buffered to 130 nM, hydrolysis of PIP2 accounts for at least 10 times as much diacylglycerol as direct PI breakdown despite the 100-fold excess of PI over PIP2. From the kinetic model it is predicted that small changes in the activities of PI and PIP kinases can have large but different effects on the level of IP3 and diacylglycerol following GTP gamma S addition. These results argue that regulation of PI and PIP kinases may be important for determining both cellular IP3 and diacylglycerol levels.

  4. 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.

  5. The histone H3 N-terminal tail: a computational analysis of the free energy landscape and kinetics.

    PubMed

    Zheng, Yuqing; Cui, Qiang

    2015-05-28

    Histone tails are the short peptide protrusions outside of the nucleosome core particle and they play a critical role in regulating chromatin dynamics and gene activity. A histone H3 N-terminal tail, like other histone tails, can be covalently modified on different residues to activate or repress gene expression. Previous studies have indicated that, despite its intrinsically disordered nature, the histone H3 N-terminal tail has regions of notable secondary structural propensities. To further understand the structure-dynamics-function relationship in this system, we have carried out 75.6 μs long implicit solvent simulations and 29.3 μs long explicit solvent simulations. The extensive samplings allow us to better characterize not only the underlying free energy landscape but also kinetic properties through Markov state models (MSM). Dihedral principal component analysis (dPCA) and locally scaled diffusion map (LSDMap) analysis yield consistent results that indicate an overall flat free energy surface with several shallow basins that correspond to conformations with a high α-helical propensity in two regions of the peptide. Kinetic information extracted from Markov state models reveals rapid transitions between different metastable states with mean first passage times spanning from several hundreds of nanoseconds to hundreds of microseconds. These findings shed light on how the dynamical nature of the histone H3 N-terminal tail is related to its function. The complementary nature of dPCA, LSDMap and MSM for the analysis of biomolecules is also discussed.

  6. 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

  7. Kinetic equations and mechanisms for activation and inhibition in enzyme systems.

    PubMed

    Laidler, K J

    1983-11-01

    The rates of enzyme reactions that are activated or inhibited by added modifiers can in some cases be expressed as a rational function of the first degree, v = (alpha 0 + alpha 1[Q] )/(beta 0 + beta 1 [Q] ) where [Q] is the concentration of the modifier and alpha 0, alpha 1, beta 0, and beta 1 are functions of rate constants and sometimes of the enzyme and substrate concentrations; the behaviour is then said to be linear. Three simple mechanisms that give rise to linear kinetics are examined, and the conditions under which there is activation or inhibition are determined. Sometimes there is a transition from activation to inhibition as the substrate concentration is varied. Definitions of competitive, uncompetitive, and noncompetitive activation are suggested, by analogy with the generally accepted definitions for inhibition. In second-degree activation or inhibition the rate can be expressed as the ratio of two quadratic polynomials with positive coefficients. Ten patterns are then possible for plots of v against [Q], and they may be classified with respect to (i) overall activation or inhibition, (ii) initial (at [Q] leads to 0) activation or inhibition, (iii) terminal (at [Q] leads to oo) activation or inhibition, and (iv) whether there is an initial inflexion. The general case of an n:n rational function is also discussed.

  8. Measurement of fatigue crack growth kinetics of Copper-Kapton laminates by dynamic mechanical thermal analysis

    SciTech Connect

    Pickard, J.M.; Walters, R.R.

    1986-01-01

    Copper-Kapton laminates fabricated with epoxy and Du Pont WA acrylic adhesives are used in printed circuit applications that are of current interest to the Department of Energy. Kinetics for fatigue crack growth at the Cu-epoxy interface were measured under a helium atmosphere over the temperature range of 473 to 563 K by dynamic mechanical thermal analysis (DMTA). A least squares treatment of data derived on the basis of a first-order fatigue mechanism resulted in: log(k(T)/s/sup -1/ = (14.6 +- 0.4) - (175.4 +- 3.8)/2.303RT, where k(T) is the rate coefficient for thermal fatigue, T is absolute temperature, and R is the ideal gas law constant (R = 0.00831 kJ/K mol). Error estimates for the pre-exponential factor and activation energy correspond to one standard deviation. Arguments are presented which indicate that the upper temperature limit for continuous use of the laminate is 85/sup 0/C. It is concluded that the laminate will meet and possibly exceed the 27-y shelf life required by the DOE.

  9. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay.

    PubMed

    Dölken, Lars; Ruzsics, Zsolt; Rädle, Bernd; Friedel, Caroline C; Zimmer, Ralf; Mages, Jörg; Hoffmann, Reinhard; Dickinson, Paul; Forster, Thorsten; Ghazal, Peter; Koszinowski, Ulrich H

    2008-09-01

    RNA levels in a cell are determined by the relative rates of RNA synthesis and decay. State-of-the-art transcriptional analyses only employ total cellular RNA. Therefore, changes in RNA levels cannot be attributed to RNA synthesis or decay, and temporal resolution is poor. Recently, it was reported that newly transcribed RNA can be biosynthetically labeled for 1-2 h using thiolated nucleosides, purified from total cellular RNA and subjected to microarray analysis. However, in order to study signaling events at molecular level, analysis of changes occurring within minutes is required. We developed an improved approach to separate total cellular RNA into newly transcribed and preexisting RNA following 10-15 min of metabolic labeling. Employing new computational tools for array normalization and half-life determination we simultaneously study short-term RNA synthesis and decay as well as their impact on cellular transcript levels. As an example we studied the response of fibroblasts to type I and II interferons (IFN). Analysis of RNA transcribed within 15-30 min at different times during the first three hours of interferon-receptor activation resulted in a >10-fold increase in microarray sensitivity and provided a comprehensive profile of the kinetics of IFN-mediated changes in gene expression. We identify a previously undisclosed highly connected network of short-lived transcripts selectively down-regulated by IFNgamma in between 30 and 60 min after IFN treatment showing strong associations with cell cycle and apoptosis, indicating novel mechanisms by which IFNgamma affects these pathways.

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

    PubMed

    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

    2016-07-19

    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.

  11. 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. PMID:24218864

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

    PubMed

    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 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.

  13. 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.

  14. RCAN1 regulates vesicle recycling and quantal release kinetics via effects on calcineurin activity.

    PubMed

    Zanin, Mark P; Mackenzie, Kimberly D; Peiris, Heshan; Pritchard, Melanie A; Keating, Damien J

    2013-02-01

    We have previously shown that Regulator of Calcineurin 1 (RCAN1) regulates multiple stages of vesicle exocytosis. However, the mechanisms by which RCAN1 affects secretory vesicle exocytosis and quantal release kinetics remain unknown. Here, we use carbon fibre amperometry to detect exocytosis from chromaffin cells and identify these underlying mechanisms. We observe reduced exocytosis with repeated stimulations in chromaffin cells over-expressing RCAN1 (RCAN1(ox)), but not in wild-type (WT) cells, indicating a negative effect of RCAN1 on vesicle recycling and endocytosis. Acute exposure to calcineurin inhibitors, cyclosporine A and FK-506, replicates this effect in WT cells but has no additional effect in RCAN1(ox) cells. When we chronically expose WT cells to cyclosporine A and FK-506 we find that catecholamine release per vesicle and pre-spike foot (PSF) signal parameters are decreased, similar to that in RCAN1(ox) cells. Inhibiting calcineurin activity in RCAN1(ox) cells has no additional effect on the amount of catecholamine release per vesicle but further reduces PSF signal parameters. Although electron microscopy studies indicate these changes are not because of altered vesicle number or distribution in RCAN1(ox) cells, the smaller vesicle and dense core size we observe in RCAN1(ox) cells may underlie the reduced quantal release in these cells. Thus, our results indicate that RCAN1 most likely affects vesicle recycling and quantal release kinetics via the inhibition of calcineurin activity.

  15. The kinetics and QSAR of abiotic reduction of mononitro aromatic compounds catalyzed by activated carbon.

    PubMed

    Gong, Wenwen; Liu, Xinhui; Gao, Ding; Yu, Yanjun; Fu, Wenjun; Cheng, Dengmiao; Cui, Baoshan; Bai, Junhong

    2015-01-01

    The kinetics of abiotic reduction of mono-nitro aromatic compounds (mono-NACs) catalyzed by activated carbon (AC) in an anaerobic system were examined. There were 6 types of substituent groups on nitrobenzene, including methyl, chlorine, amino, carboxyl, hydroxyl and cyanogen groups, at the ortho, meta or para positions. Our results showed that reduction followed pseudo-first order reaction kinetics, and that the rate constant (logkSA) varied widely, ranging between -4.77 and -2.82, depending upon the type and position of the substituent. A quantitative structure-activity relationship (QSAR) model using 15 theoretical molecular descriptors and partial-least-squares (PLS) regression was developed for the reduction rates of mono-NACs catalyzed by AC. The cross-validated regression coefficient (Qcum(2), 0.861) and correlation coefficient (R(2), 0.898) indicated significantly high robustness of the model. The VIP (variable importance in the projection) values of energy of the lowest unoccupied molecular orbital (ELUMO) and the maximum net atomic charge on the aromatic carbon bound to the nitro group (QC(-)) were 1.15 and 1.01, respectively. These values indicated that the molecular orbital energies and the atomic net charges might play important roles in the reduction of mono-NACs catalyzed by AC in anaerobic systems.

  16. Ultrasonic effects on the degradation kinetics, preliminary characterization and antioxidant activities of polysaccharides from Phellinus linteus mycelia.

    PubMed

    Yan, Jing-Kun; Wang, Yao-Yao; Ma, Hai-Le; Wang, Zhen-Bin

    2016-03-01

    In this study, a high-molecular-weight polysaccharide PL-N isolated from the alkaline extract of Phellinus linteus mycelia was degraded by ultrasound. Results showed that ultrasound treatment at different ultrasonic intensities decreased the intrinsic viscosity and molecular weight of PL-N, as well as narrowed the molecular weight distribution. A larger reduction in intrinsic viscosity and molecular weight was caused by a higher ultrasonic intensity. The degradation kinetics model was fitted to (1/Mt-1/M0)=k·t, and the reaction rate constant (k) increased with increasing ultrasonic intensity. Ultrasound degradation did not change the primary structure of PL-N, and scanning electron microscopy analysis indicated that the morphology of the original PL-N was different from that of degraded PL-N fractions. Antioxidant activity assays in vitro indicated that the degraded PL-N fraction with low molecular weight had stronger hydroxyl radical scavenging capacity and higher TEAC and FRAP values.

  17. Kinetic and equilibrium studies on the removal of acid dyes from aqueous solutions by adsorption onto activated carbon cloth.

    PubMed

    Hoda, Numan; Bayram, Edip; Ayranci, Erol

    2006-09-01

    Removal of acid dyes Acid Blue 45, Acid Blue 92, Acid Blue 120 and Acid Blue 129 from aqueous solutions by adsorption onto high area activated carbon cloth (ACC) was investigated. Kinetics of adsorption was followed by in situ UV-spectroscopy and the data were treated according to pseudo-first-order, pseudo-second-order and intraparticle diffusion models. It was found that the adsorption process of these dyes onto ACC follows the pseudo-second-order model. Adsorption isotherms were derived at 25 degrees C on the basis of batch analysis. Isotherm data were treated according to Langmuir and Freundlich models. The fits of experimental data to these equations were examined. PMID:16563617

  18. BRIEF COMMUNICATIONS: Analysis of the excitation kinetics of a CO2:N2:He mixture using refined models of the vibrational temperatures

    NASA Astrophysics Data System (ADS)

    Agalakov, Yu G.; Gulamov, É. N.; Islamov, R. Sh; Rubinov, Yu A.

    1989-04-01

    An analysis is made of the excitation kinetics of the active medium of a TEA CO2 laser using different theoretical models: a temperature model, either taking into account or neglecting anharmonicity in the ν3 modes of CO2 and N2, and a model taking into account the level kinetics in the ν3 modes of CO2 and N2. A comparison is made of the results of a calculation with the experimental dependence of the laser output energy on the specific input energy in the range up to 2 J/cm3. The calculated and experimental data are found to agree for a vibrational temperature model taking anharmonicity into account and using a relatively high value, known from the literature, of the constant of the intramode exchange in nitrogen, and for a model taking into account the level kinetics and assuming accumulation of strong relaxants of the upper active level.

  19. Matrix rigidity regulates spatiotemporal dynamics of Cdc42 activity and vacuole formation kinetics of endothelial colony forming cells.

    PubMed

    Kim, Seung Joon; Wan, Qiaoqiao; Cho, Eunhye; Han, Bumsoo; Yoder, Mervin C; Voytik-Harbin, Sherry L; Na, Sungsoo

    2014-01-24

    Recent evidence has shown that endothelial colony forming cells (ECFCs) may serve as a cell therapy for improving blood vessel formation in subjects with vascular injury, largely due to their robust vasculogenic potential. The Rho family GTPase Cdc42 is known to play a primary role in this vasculogenesis process, but little is known about how extracellular matrix (ECM) rigidity affects Cdc42 activity during the process. In this study, we addressed two questions: Does matrix rigidity affect Cdc42 activity in ECFC undergoing early vacuole formation? How is the spatiotemporal activation of Cdc42 related to ECFC vacuole formation? A fluorescence resonance energy transfer (FRET)-based Cdc42 biosensor was used to examine the effects of the rigidity of three-dimensional (3D) collagen matrices on spatiotemporal activity of Cdc42 in ECFCs. Collagen matrix stiffness was modulated by varying the collagen concentration and therefore fibril density. The results showed that soft (150 Pa) matrices induced an increased level of Cdc42 activity compared to stiff (1 kPa) matrices. Time-course imaging and colocalization analysis of Cdc42 activity and vacuole formation revealed that Cdc42 activity was colocalized to the periphery of cytoplasmic vacuoles. Moreover, soft matrices generated faster and larger vacuoles than stiff matrices. The matrix-driven vacuole formation was enhanced by a constitutively active Cdc42 mutant, but significantly inhibited by a dominant-negative Cdc42 mutant. Collectively, the results suggest that matrix rigidity is a strong regulator of Cdc42 activity and vacuole formation kinetics, and that enhanced activity of Cdc42 is an important step in early vacuole formation in ECFCs.

  20. Kinetic analysis of thermal stability of human low density lipoproteins: a model for LDL fusion in atherogenesis.

    PubMed

    Lu, Mengxiao; Gantz, Donald L; Herscovitz, Haya; Gursky, Olga

    2012-10-01

    Fusion of modified LDL in the arterial wall promotes atherogenesis. Earlier we showed that thermal denaturation mimics LDL remodeling and fusion, and revealed kinetic origin of LDL stability. Here we report the first quantitative analysis of LDL thermal stability. Turbidity data show sigmoidal kinetics of LDL heat denaturation, which is unique among lipoproteins, suggesting that fusion is preceded by other structural changes. High activation energy of denaturation, E(a) = 100 ± 8 kcal/mol, indicates disruption of extensive packing interactions in LDL. Size-exclusion chromatography, nondenaturing gel electrophoresis, and negative-stain electron microscopy suggest that LDL dimerization is an early step in thermally induced fusion. Monoclonal antibody binding suggests possible involvement of apoB N-terminal domain in early stages of LDL fusion. LDL fusion accelerates at pH < 7, which may contribute to LDL retention in acidic atherosclerotic lesions. Fusion also accelerates upon increasing LDL concentration in near-physiologic range, which likely contributes to atherogenesis. Thermal stability of LDL decreases with increasing particle size, indicating that the pro-atherogenic properties of small dense LDL do not result from their enhanced fusion. Our work provides the first kinetic approach to measuring LDL stability and suggests that lipid-lowering therapies that reduce LDL concentration but increase the particle size may have opposite effects on LDL fusion.

  1. Comparison of the growth kinetics and proteolytic activities of Chryseobacterium species and Pseudomonas fluorescens.

    PubMed

    Bekker, A; Steyn, L; Charimba, G; Jooste, P; Hugo, C

    2015-12-01

    The effect of temperature on the growth kinetics and proteolytic activity of Chryseobacterium joostei and Chryseobacterium bovis was determined during this study. The results were compared with the activities of Pseudomonas fluorescens, which is regarded to be a major food spoilage psychrotolerant microorganism. For the growth studies, cultures were incubated in nutrient broth in a temperature gradient incubator (from 9 to 50 °C) and separately at 4 °C, and the optical density was measured at different time intervals. Growth temperature profiles for each organism were constructed. For determination of proteolytic activity, the cultures were incubated in fat-free ultra-high temperature processed milk in the temperature gradient incubator for 72 h (temperature range as above). Cell-free extracts were used to determine the proteolytic activity using the azocasein method. Results of the growth studies showed that C. joostei had the ability to grow over a wider temperature range than C. bovis and P. fluorescens without being affected by changes in the temperature. For the proteolytic activity, C. joostei had significantly (p < 0.001) higher activity per milligram of protein at 15.5 °C, followed by C. bovis and P. fluorescens. The results showed that C. joostei potentially has an even greater spoilage capacity in milk on the basis of growth rate and proteolytic activity than did P. fluorescens.

  2. 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

  3. 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

  4. 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

  5. Activation of protein kinase C accelerates contraction kinetics of airway smooth muscle.

    PubMed

    Peiper, U; Knipp, S C; Thies, B; Henke, R

    1996-01-01

    Contraction kinetics of isolated rat tracheal smooth muscle were studied by analysing the increase of force subsequent to force-inhibiting passive length changes lasting 1 s (100 Hz, sinus, 5% of muscle length). Compared with carbachol activation, phorboldibutyrate (PDBu)-induced stimulation of protein kinase C (PKC) demonstrated no significant difference in the extent of force development in the polarized preparation [mean peak force 9.16 +/- 0.37 mN (carbachol) vs. 9.12 +/- 0.37 mN (PDBu)]. However, the time constant calculated for the slow component of post-vibration force recovery was 6.40 +/- 0.29 s after addition of PDBu vs. 22.39 +/- 1.40 s during carbachol activation, indicating a significant phorbol ester-induced acceleration of the cross-bridge cycling rate. In the K-depolarized preparation, treatment with 26.4 microM indolactam (IL) to activate PKC produced muscle relaxation (9.94 +/- 0.16 mN measured 0-30 min after the onset of depolarization vs. 4.13 +/- 0.05 mN measured during 30-60 min of IL treatment). Again, even in the presence of high sarcoplasmic Ca2+ resulting from tonic depolarization, PKC activation was associated with a distinct diminution of the time constant (25.99 +/- 0.79 s during the first 30 min of depolarization vs. 10.32 +/- 0.21 s during 30-60 min of IL treatment). In contrast, addition of 0.035 microM verapamil, 1.5 microM isoproterenol, and 32 microM dibutyryl-cAMP to the bathing medium induced relaxation without affecting the rate of post-vibration force recovery. The results suggest that the calcium-dependent signal cascade (agonist receptor/inositol trisphosphate/ Ca(2+)-calmodulin/myosin light chain kinase) hardly affects the regulation of contraction kinetics in the tonically activated intact smooth muscle preparation. PKC stimulation, however, accelerates actin/myosin interaction kinetics, possibly by inhibition of phosphatase(s).

  6. Compartmental analysis of technetium-99m-teboroxime kinetics employing fast dynamic SPECT at rest and stress

    SciTech Connect

    Chiao, P.C.; Ficaro, E.P.; Dayaniki, F.

    1994-08-01

    The authors have examined the feasibility of compartmental analysis of {sup 99m}Tc-teboroxime kinetics in measuring physiological changes in response to adenosine-induced coronary vasodilation. To evaluate the effect of tracer recirculation on {sup 99m}Tc-teboroxime kinetics in the myocardium, they also compared compartmental analysis with washout analysis (monoexponertial fitting), which does not account for this effect. Eight healthy male volunteers were imaged using fast dynamic SPECT protocols (5 sec per tomographic image) at rest and during adenosine infusion. A two-compartment model was used and compartmental parameters K1 and k2 (characterizing the diffusion of {sup 99m}Tc-teboroxime from the blood to the myocardium and from the myocardium to the blood, respectively) were fitted from myocardial time-activity curves and left ventricular input functions. Both K1 and washout estimates for the whole left ventricular myocardium changed significantly in response to coronary vasodilation. Mean stress-to-rest (S/R) ratios were almost two times higher for K1 (S/R = 2.7 {plus_minus} 1.1) than for washout estimates (S/R = 1.5 {plus_minus} 0.3). Estimation of K1 for all local regions, except the septal wall, is feasible because variations in K1 estimates for all local regions, except the septum during stress, are comparable with those for the global region. The authors conclude that quantitative compartmental analysis of {sup 99m}Tc-teboroxime kinetics provides a sensitive indicator for changes in response to adenosine-induced coronary vasodilation. 39 refs., 7 figs., 1 tab.

  7. 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.

  8. Differences in Muscle Activities of the Infraspinatus and Posterior Deltoid during Shoulder External Rotation in Open Kinetic Chain and Closed Kinetic Chain Exercises.

    PubMed

    Kang, Min-Hyeok; Oh, Jae-Seop; Jang, Jun-Hyeok

    2014-06-01

    [Purpose] This study investigated the changes in electromyographic (EMG) activities of the infraspinatus and posterior deltoid muscles during shoulder external rotation under open kinetic chain (OKC) and closed kinetic chain (CKC) exercise conditions. [Subjects] In total, 15 healthy males participated in this study. [Methods] Subjects performed shoulder external rotations under CKC and OKC conditions while standing with and without weight support provided by a height-adjustable table. Pressure biofeedback was used to ensure a constant amount of weight support. The activities of the infraspinatus and posterior deltoid muscles during shoulder external rotation were measured using a wireless surface EMG system. The paired t-test was used to compare the EMG activities of the infraspinatus and the posterior deltoid muscles and the ratio of the infraspinatus to the posterior deltoid during shoulder external rotation under OKC and CKC conditions. [Results] The EMG activity of the infraspinatus and the ratio of the infraspinatus to the posterior deltoid activities were significantly increased, whereas the posterior deltoid activity was significantly decreased under the CKC condition compared to the OKC condition. [Conclusion] Clinicians should consider the CKC shoulder external rotation exercise when they wish to selectively strengthen the infraspinatus. PMID:25013291

  9. Coupling of chemical kinetics, gas dynamics, and charged particle kinetics models for the analysis of NO reduction from flue gases

    SciTech Connect

    Eichwald, O.; Yousfi, M.; Hennad, A.; Benabdessadok, M.D.

    1997-11-01

    A chemical kinetics model is developed to analyze the time evolution of the different main species involved in a flue gas initially stressed by a pulsed corona discharge at the atmospheric pressure and including N{sub 2}, O{sub 2}, H{sub 2}O, and CO{sub 2} with a few ppm of NO. The present chemical kinetics model is coupled to a gas dynamics model used to analyze the radial expansion of the gas in the ionized channel created during the discharge phase. It is also meant to analyze the gas heating due to the Joule effect. This chemical kinetics model is also coupled to charged particle kinetics models based on a Boltzmann equation model to calculate the electron-molecule reaction coefficients in the flue gas and on a Monte Carlo code to estimate the energy and momentum transfer terms relative to ion-molecule collisions which are the input data for the gas dynamics model. It is shown, in particular, that the evolution of the radicals and the oxides is substantially affected by the gas temperature rise (from the initial value of 300 K up to 750 K near the anode) thus emphasizing the present coupling between gas dynamics, charged particle, and chemical kinetics models. {copyright} {ital 1997 American Institute of Physics.}

  10. Coupling of chemical kinetics, gas dynamics, and charged particle kinetics models for the analysis of NO reduction from flue gases

    NASA Astrophysics Data System (ADS)

    Eichwald, O.; Yousfi, M.; Hennad, A.; Benabdessadok, M. D.

    1997-11-01

    A chemical kinetics model is developed to analyze the time evolution of the different main species involved in a flue gas initially stressed by a pulsed corona discharge at the atmospheric pressure and including N2, O2, H2O, and CO2 with a few ppm of NO. The present chemical kinetics model is coupled to a gas dynamics model used to analyze the radial expansion of the gas in the ionized channel created during the discharge phase. It is also meant to analyze the gas heating due to the Joule effect. This chemical kinetics model is also coupled to charged particle kinetics models based on a Boltzmann equation model to calculate the electron-molecule reaction coefficients in the flue gas and on a Monte Carlo code to estimate the energy and momentum transfer terms relative to ion-molecule collisions which are the input data for the gas dynamics model. It is shown, in particular, that the evolution of the radicals and the oxides is substantially affected by the gas temperature rise (from the initial value of 300 K up to 750 K near the anode) thus emphasizing the present coupling between gas dynamics, charged particle, and chemical kinetics models.

  11. 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.

  12. Gain and kinetics of activation in the G-protein cascade of phototransduction.

    PubMed Central

    Lamb, T D

    1996-01-01

    The guanine nucleotide binding protein (G protein) cascade underlying phototransduction is one of the best understood of all signaling pathways. The diffusional interactions of the proteins underlying the cascade have been analyzed, both at a macroscopic level and also in terms of the stochastic nature of the molecular contacts. In response to a single activated rhodopsin (R*) formed as a result of a single photon hit, it can be shown that molecules of the G-protein transducin will be activated approximately linearly with time. This, in turn, will cause the number of activated molecules of the effector protein (the phosphodiesterase) also to increase linearly with time. These kinetics of protein activation provide an accurate description of the time course of the rising phase of the photoreceptor's electrical response over a wide range of flash intensities. Recent estimates indicate that at room temperature each R* triggers activation of the phosphodiesterase at a rate of 1000-2000 subunits.s-1. Now that a quantitative description of the activation steps in transduction has been obtained, perhaps the greatest challenge for the future is to provide a comprehensive description of the shutoff reactions, so that a complete account of the photoreceptor's response to light can be achieved. Images Fig. 1 Fig. 2 PMID:8570596

  13. 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.

  14. 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

    2012-03-01

    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.

  15. 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.

  16. Theoretical analysis of kinetic effects on the quantitative comparison of K(d) values and contaminant retardation factors.

    PubMed

    Tinnacher, Ruth M; Honeyman, Bruce D

    2010-10-21

    Distribution coefficients (K(d) values) describe contaminant partitioning between liquids and solids for linear sorption at equilibrium conditions. If experimentally-determined K(d) values do not represent sorption equilibria, errors are introduced in contaminant transport models. These errors may be further propagated when K(d) values are used to compare contaminant mobility under different chemical solution conditions. Our theoretical analysis based on pseudo-first order sorption kinetics shows that, independent if two systems have the same or different sorption kinetics, relative comparisons of K(d) values and retardation factors are always affected by sorption times under non-equilibrium conditions. The time-frames required for attaining constant K(d) values are not only dependent on kinetic sorption characteristics, but also the equilibrium K(d) values approached. The type of kinetic errors introduced is affected by the specific differences in sorption kinetics and equilibrium K(d) values between the two systems. For systems with the same sorption kinetics, relative increases or decreases in contaminant velocities are always underestimated. In case of different kinetics, either an under- or overestimation of relative differences seems possible. Experimental sorption times should aim to equilibrate the system with the highest K(d) value for systems with comparable kinetics, and the system with the slowest sorption kinetics for different kinetics. PMID:20864208

  17. 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.

  18. Devolatilization Characteristics and Kinetic Analysis of Lump Coal from China COREX3000 Under High Temperature

    NASA Astrophysics Data System (ADS)

    Xu, Runsheng; Zhang, Jianliang; Wang, Guangwei; Zuo, Haibin; Liu, Zhengjian; Jiao, Kexin; Liu, Yanxiang; Li, Kejiang

    2016-08-01

    A devolatilization study of two lump coals used in China COREX3000 was carried out in a self-developed thermo-gravimetry at four temperature conditions [1173 K, 1273 K, 1373 K, and 1473 K (900 °C, 1000 °C, 1100 °C, and 1200 °C)] under N2. This study reveals that the working temperature has a strong impact on the devolatilization rate of the lump coal: the reaction rate increases with the increasing temperature. However, the temperature has little influence on the maximum mass loss. The conversion rate curve shows that the reaction rate of HY lump coal is higher than KG lump coal. The lump coals were analyzed by XRD, FTIR, and optical microscopy to explore the correlation between devolatilization rate and properties of lump coal. The results show that the higher reaction rate of HY lump coal attributes to its more active maceral components, less aromaticity and orientation degree of the crystallite, and more oxygenated functional groups. The random nucleation and nuclei growth model (RNGM), volume model (VM), and unreacted shrinking core model (URCM) were employed to describe the reaction behavior of lump coal. It was concluded from kinetics analysis that RNGM model was the best model for describing the devolatilization of lump coals. The apparent activation energies of isothermal devolatilization of HY lump coal and KG lump coal are 42.35 and 45.83 kJ/mol, respectively. This study has implications for the characteristics and mechanism modeling of devolatilization of lump coal in COREX gasifier.

  19. Accounting for unintended binding events in the analysis of quartz crystal microbalance kinetic data.

    PubMed

    Heller, Gabriella T; Zwang, Theodore J; Sarapata, Elizabeth A; Haber, Michael A; Sazinsky, Matthew H; Radunskaya, Ami E; Johal, Malkiat S

    2014-05-01

    Previous methods for analyzing protein-ligand binding events using the quartz crystal microbalance with dissipation monitoring (QCM-D) fail to account for unintended binding that inevitably occurs during surface measurements and obscure kinetic information. In this article, we present a system of differential equations that accounts for both reversible and irreversible unintended interactions. This model is tested on three protein-ligand systems, each of which has different features, to establish the feasibility of using the QCM-D for protein binding analysis. Based on this analysis, we were able to obtain kinetic information for the intended interaction that is consistent with those obtained in literature via bulk-phase methods. In the appendix, we include a method for decoupling these from the intended binding events and extracting relevant affinity information.

  20. High-throughput method for a kinetics analysis of the high-pressure inactivation of microorganisms using microplates.

    PubMed

    Hasegawa, Toshimi; Hayashi, Manabu; Nomura, Kazuki; Hayashi, Mayumi; Kido, Miyuki; Ohmori, Tsuneo; Fukuda, Masao; Iguchi, Akinori; Ueno, Shigeaki; Shigematsu, Toru; Hirayama, Masao; Fujii, Tomoyuki

    2012-06-01

    Using microplates as pressure and cultivation vessels, a high-throughput method was developed for analyzing the high-pressure inactivation kinetics of microorganisms. The loss of viability from a high-pressure treatment, measured based on the growth delay during microplate cultivation, showed reproducibility with the conventional agar plate method and was applicable for the kinetics analysis.

  1. Thermochemistry and Kinetic Analysis of the Unimolecular Oxiranyl Radical Dissociation Reaction: A Theoretical Study.

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-07-01

    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. PMID:26990491

  2. Thermochemistry and Kinetic Analysis of the Unimolecular Oxiranyl Radical Dissociation Reaction: A Theoretical Study.

    PubMed

    Wang, Heng; Bozzelli, Joseph W

    2016-07-01

    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.

  3. 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.

  4. Quantitative Förster resonance energy transfer analysis for kinetic determinations of SUMO-specific protease.

    PubMed

    Liu, Yan; Song, Yang; Madahar, Vipul; Liao, Jiayu

    2012-03-01

    Förster resonance energy transfer (FRET) technology has been widely used in biological and biomedical research, and it is a very powerful tool for elucidating protein interactions in either dynamic or steady state. SUMOylation (the process of SUMO [small ubiquitin-like modifier] conjugation to substrates) is an important posttranslational protein modification with critical roles in multiple biological processes. Conjugating SUMO to substrates requires an enzymatic cascade. Sentrin/SUMO-specific proteases (SENPs) act as an endopeptidase to process the pre-SUMO or as an isopeptidase to deconjugate SUMO from its substrate. To fully understand the roles of SENPs in the SUMOylation cycle, it is critical to understand their kinetics. Here, we report a novel development of a quantitative FRET-based protease assay for SENP1 kinetic parameter determination. The assay is based on the quantitative analysis of the FRET signal from the total fluorescent signal at acceptor emission wavelength, which consists of three components: donor (CyPet-SUMO1) emission, acceptor (YPet) emission, and FRET signal during the digestion process. Subsequently, we developed novel theoretical and experimental procedures to determine the kinetic parameters, k(cat), K(M), and catalytic efficiency (k(cat)/K(M)) of catalytic domain SENP1 toward pre-SUMO1. Importantly, the general principles of this quantitative FRET-based protease kinetic determination can be applied to other proteases.

  5. The cellular metabolism of lead and calcium: A kinetic analysis in cultured osteoclastic bone cells

    SciTech Connect

    Rosen, J.F.; Pounds, J.G.

    1986-01-01

    Characterization of lead metabolism in bone is necessary to understand the role of skeletal lead, an endogenous source of this toxic metal, in the expression of adverse effects of lead intoxication in concert with external sources. Moreover, it has been postulated that an early manifestation of lead toxicity common to diverse cell types may be pertubations in intracellular calcium homeostasis. Furthermore, it has been suggested that calciotropic hormones may express their actions on bone cells by modulating the messenger functions of intracellular Ca. Before these postulates can be more fully tested, the homeostasis of intracellular Pb and Ca must be understood more clearly. We have designed experiments to characterize the steady-state kinetic distribution and behavior of /sup 210/Pb and /sup 45/Ca in osteoclastic bone cells and to identify biological structures or functions associated with the kinetic pools. Cultures were labeled with /sup 210/Pb or /sup 45/Ca and the kinetic parameters were obtained by analysis of isotope washout curves. Cellular metabolism was defined by three kinetic pools of intracellular Pb and Ca. The largest and slowest exchanging pool was characterized as a mitochondrial compartment for both metals. These data indicate that Pb and Ca share similar intracellular pathways in osteoclastic bone cells and that both metals are readily exchangeable in this in vitro system. The results of other experiments have revealed that lead, at relatively low medium concentrations, produces a marked increase in all three intracellular Ca compartments. 18 refs., 2 figs.

  6. Raman mapping for kinetic analysis of crystallization of amorphous drug based on distributional images.

    PubMed

    Ueda, Hiroshi; Ida, Yasuo; Kadota, Kazunori; Tozuka, Yuichi

    2014-02-28

    The feasibility of Raman mapping for understanding the crystallization mechanism of an amorphous drug was investigated using described images. The crystallization tendency of amorphous indomethacin under dry condition at 30 °C was kinetically evaluated by means of Raman mapping and X-ray powder diffraction (XRPD) with change in the calculated crystallinities. Raman images directly revealed the occurrence of particle size-dependent non-uniform crystallization; slow crystallization of large particles, but fast crystallization of small particles. Kinetic analysis by fitting to the Kolmogorov-Johnson-Mehl-Avrami equation was performed for the crystallization profiles of both Raman mapping and XRPD data. For the Raman mapping data, the distribution of large particles was characterized and examined. The kinetic parameters calculated from the whole Raman image area agreed well with those of XRPD, suggesting accurate prediction of both techniques for the entire crystallization. Raman images revealed the change in the crystallization mechanism for the focused area; the large particles showed a reduced crystallization rate constant and an increase in the dimensional crystal growth exponent. Raman mapping is an attractive tool for quantitative and kinetic investigation of the crystallization mechanism with distributional images.

  7. Synthetic spectral analysis of a kinetic model for slow-magnetosonic waves in solar corona

    NASA Astrophysics Data System (ADS)

    Ruan, Wenzhi; He, Jiansen; Zhang, Lei; Vocks, Christian; Marsch, Eckart; Tu, Chuanyi; Peter, Hardi; Wang, Linghua

    2016-03-01

    We propose a kinetic model of slow-magnetosonic waves to explain various observational features associated with the propagating intensity disturbances (PIDs) occurring in the solar corona. The characteristics of slow mode waves, e.g, inphase oscillations of density, velocity, and thermal speed, are reproduced in this kinetic model. Moreover, the red-blue (R-B) asymmetry of the velocity distribution as self-consistently generated in the model is found to be contributed from the beam component, as a result of the competition between Landau resonance and Coulomb collisions. Furthermore, we synthesize the spectral lines and make the spectral analysis, based on the kinetic simulation data of the flux tube plasmas and the hypothesis of the surrounding background plasmas. It is found that the fluctuations of parameters of the synthetic spectral lines are basically consistent with the observations: (1) the line intensity, Doppler shift, and line width are fluctuating in phase; (2) the R-B asymmetry usually oscillate out of phase with the former three parameters; (3) the blueward asymmetry is more evident than the redward asymmetry in the R-B fluctuations. The oscillations of line parameters become weakened for the case with denser surrounding background plasmas. Similar to the observations, there is no doubled-frequency oscillation of the line width for the case with flux-tube plasmas flowing bulkly upward among the static background plasmas. Therefore, we suggest that the "wave + beam flow" kinetic model may be a viable interpretation for the PIDs observed in the solar corona.

  8. 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.

  9. Quantification of DNA repair protein kinetics after γ-irradiation using number and brightness analysis

    NASA Astrophysics Data System (ADS)

    Abdisalaam, Salim; Poudel, Milan; Chen, David J.; Alexandrakis, George

    2011-03-01

    The kinetics of most proteins involved in DNA damage sensing, signaling and repair following ionizing radiation exposure cannot be quantified by current live cell fluorescence microscopy methods. This is because most of these proteins, with only few notable exceptions, do not attach in large numbers at DNA damage sites to form easily detectable foci in microscopy images. As a result a high fluorescence background from freely moving and immobile fluorescent proteins in the nucleus masks the aggregation of proteins at sparse DNA damage sites. Currently, the kinetics of these repair proteins are studied by laser-induced damage and Fluorescence Recovery After Photobleaching that rely on the detectability of high fluorescence intensity spots of clustered DNA damage. We report on the use of Number and Brightness (N&B) analysis methods as a means to monitor kinetics of DNA repair proteins during sparse DNA damage created by γ-irradiation, which is more relevant to cancer treatment than laser-induced clustered damage. We use two key double strand break repair proteins, namely Ku 70/80 and the DNA-dependent protein kinase catalytic subunit (DNA-PKCS), as specific examples to showcase the feasibility of the proposed methods to quantify dose-dependent kinetics for DNA repair proteins after exposure to γ-rays.

  10. 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. PMID:26488499

  11. Activation analysis using Cornell TRIGA

    SciTech Connect

    Hossain, Tim Z.

    1994-07-01

    A major use of the Cornell TRIGA is for activation analysis. Over the years many varieties of samples have been analyzed from a number of fields of interest ranging from geology, archaeology and textiles. More recently the analysis has been extended to high technology materials for applications in optical and semiconductor devices. Trace analysis in high purity materials like Si wafers has been the focus in many instances, while in others analysis of major/minor components were the goals. These analysis has been done using the delayed mode. Results from recent measurements in semiconductors and other materials will be presented. In addition the near future capability of using prompt gamma activation analysis using the Cornell cold neutron beam will be discussed. (author)

  12. Antibacterial activity and kinetics of Litsea cubeba oil on Escherichia coli.

    PubMed

    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

  13. 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.

  14. Hydrolytic Activation Kinetics of the Herbicide Benzobicyclon in Simulated Aquatic Systems.

    PubMed

    Williams, Katryn L; Tjeerdema, Ronald S

    2016-06-22

    Herbicide resistance is a growing concern for weeds in California rice fields. Benzobicyclon (BZB; 3-(2-chloro-4-(methylsulfonyl)benzoyl)-2-phenylthiobicyclo[3.2.1]oct-2-en-4-one) has proven successful against resistant rice field weeds in Asia. A pro-herbicide, BZB forms the active agent, benzobicyclon hydrolysate (BH), in water; however, the transformation kinetics are not understood for aquatic systems, particularly flooded California rice fields. A quantitative experiment was performed to assess the primary mechanism and kinetics of BZB hydrolysis to BH. Complete conversion to BH was observed for all treatments. Basic conditions (pH 9) enhanced the reaction, with half-lives ranging from 5 to 28 h. Dissolved organic carbon (DOC) hindered transformation, which is consistent with other base-catalyzed hydrolysis reactions. BH was relatively hydrolytically stable, with 18% maximum loss after 5 days. Results indicate BZB is an efficient pro-herbicide under aqueous conditions such as those of a California rice field, although application may be best suited for fields with recirculating tailwater systems. PMID:27248841

  15. 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

  16. 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.

  17. Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2015-04-01

    This study evaluated the chronic impact of tetracycline on biomass with enriched nitrifying community sustained in a lab-scale activated sludge system. For this purpose, a fill and draw reactor fed with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia was sustained at a sludge age of 15 days. At steady-state, the reactor operation was continued with a daily tetracycline dosing of 50 mg/L for more than 40 days, with periodic monitoring of the microbial composition, the nitrifying bacteria abundance, as well as the amoA and 16S rRNA gene activity, using molecular techniques. Changes in the kinetics of nitrification were quantified by modelling concentration profiles of major nitrogen fractions and oxygen uptake rate profiles derived from parallel batch experiments. Activated sludge modeling results indicated inhibitory impact of tetracycline on the growth of nitrifiers with a significant increase of the half saturation coefficients in corresponding rate equations. Tetracycline also inactivated biomass components of the enriched culture at a gradually increasing rate with time of exposure, leading to total collapse of nitrification. Molecular analyses revealed significant changes in the composition of the microbial community throughout the observation period. They also showed that continuous exposure to tetracycline inflicted significant reduction in amoA mRNA and 16S rRNA levels directly affecting nitrification. The chronic impact was much more pronounced on the ammonia oxidizing bacteria (AOB) community. These observations explained the basis of numerical changes identified in the growth kinetics of nitrifiers under stress conditions.

  18. Chronic impact of tetracycline on nitrification kinetics and the activity of enriched nitrifying microbial culture.

    PubMed

    Katipoglu-Yazan, Tugce; Merlin, Christophe; Pons, Marie-Noëlle; Ubay-Cokgor, Emine; Orhon, Derin

    2015-04-01

    This study evaluated the chronic impact of tetracycline on biomass with enriched nitrifying community sustained in a lab-scale activated sludge system. For this purpose, a fill and draw reactor fed with 100 mg COD/L of peptone mixture and 50 mg N/L of ammonia was sustained at a sludge age of 15 days. At steady-state, the reactor operation was continued with a daily tetracycline dosing of 50 mg/L for more than 40 days, with periodic monitoring of the microbial composition, the nitrifying bacteria abundance, as well as the amoA and 16S rRNA gene activity, using molecular techniques. Changes in the kinetics of nitrification were quantified by modelling concentration profiles of major nitrogen fractions and oxygen uptake rate profiles derived from parallel batch experiments. Activated sludge modeling results indicated inhibitory impact of tetracycline on the growth of nitrifiers with a significant increase of the half saturation coefficients in corresponding rate equations. Tetracycline also inactivated biomass components of the enriched culture at a gradually increasing rate with time of exposure, leading to total collapse of nitrification. Molecular analyses revealed significant changes in the composition of the microbial community throughout the observation period. They also showed that continuous exposure to tetracycline inflicted significant reduction in amoA mRNA and 16S rRNA levels directly affecting nitrification. The chronic impact was much more pronounced on the ammonia oxidizing bacteria (AOB) community. These observations explained the basis of numerical changes identified in the growth kinetics of nitrifiers under stress conditions. PMID:25616640

  19. Standardizing Activation Analysis: New Software for Photon Activation Analysis

    SciTech Connect

    Sun, Z. J.; Wells, D.; Green, J.; Segebade, C.

    2011-06-01

    Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

  20. 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.

  1. Kinetic characterization of high-activity mutants of human butyrylcholinesterase for the cocaine metabolite norcocaine.

    PubMed

    Zhan, Max; Hou, Shurong; Zhan, Chang-Guo; Zheng, Fang

    2014-01-01

    It has been known that cocaine produces its toxic and physiological effects through not only cocaine itself, but also norcocaine formed from cocaine oxidation catalysed by microsomal CYP (cytochrome P450) 3A4 in the human liver. The catalytic parameters (kcat and Km) of human BChE (butyrylcholinesterase) and its three mutants (i.e. A199S/S287G/A328W/Y332G, A199S/F227A/S287G/A328W/E441D and A199S/F227A/S287G/A328W/Y332G) for norcocaine have been characterized in the present study for the first time and compared with those for cocaine. On the basis of the obtained kinetic data, wild-type human BChE has a significantly lower catalytic activity for norcocaine (kcat=2.8 min(-1), Km=15 μM and kcat/Km=1.87 × 10(5) M(-1)·min(-1)) compared with its catalytic activity for (-)-cocaine. The BChE mutants examined in the present study have considerably improved catalytic activities against both cocaine and norcocaine compared with the wild-type enzyme. Within the enzymes examined in the present study, the A199S/F227A/S287G/A328W/Y332G mutant (CocH3) is identified as the most efficient enzyme for hydrolysing both cocaine and norcocaine. CocH3 has a 1080-fold improved catalytic efficiency for norcocaine (kcat=2610 min(-1), Km=13 μM and kcat/Km=2.01 × 10(8) M(-1)·min(-1)) and a 2020-fold improved catalytic efficiency for cocaine. It has been demonstrated that CocH3 as an exogenous enzyme can rapidly metabolize norcocaine, in addition to cocaine, in rats. Further kinetic modelling has suggested that CocH3 with an identical concentration with that of the endogenous BChE in human plasma can effectively eliminate both cocaine and norcocaine in a simplified kinetic model of cocaine abuse.

  2. Kinetic Characterization of High-Activity Mutants of Human Butyrylcholinesterase for Cocaine Metabolite Norcocaine

    PubMed Central

    Zhan, Max; Hou, Shurong; Zhan, Chang-Guo; Zheng, Fang

    2015-01-01

    It has been known that cocaine produces the toxic and physiological effects through not only cocaine itself but also norcocaine formed from cocaine oxidation catalyzed by microsomal cytochrome P450 3A4 in the human liver. The catalytic parameters (kcat and KM) of human butyrylcholinesterase (BChE) and its three mutants (i.e. the A199S/S287G/A328W/Y332G, A199S/F227A/S287G/A328W/E441D, and A199S/F227A/S287G/A328W/Y332G mutants) for norcocaine have been characterized in the present study, for the first time, in comparison with those for cocaine. Based on the obtained kinetic data, wild-type human BChE has a significantly lower catalytic activity for norcocaine (kcat = 2.8 min−1, KM = 15 μM, and kcat/KM = 1.87 × 105 M−1 min−1) compared to its catalytic activity for (−)-cocaine. The BChE mutants examined in this study have considerably improved catalytic activities against both cocaine and norcocaine compared to the wild-type enzyme. Within the enzymes examined in this study, the A199S/F227A/S287G/A328W/Y332G mutant (CocH3) is identified as the most efficient enzyme for hydrolyzing both cocaine and norcocaine. CocH3 has a 1080-fold improved catalytic efficiency for norcocaine (kcat = 2610 min−1, KM = 13 μM, and kcat/KM = 2.01 × 108 M−1 min−1) and a 2020-fold improved catalytic efficiency for cocaine. It has been demonstrated that CocH3 as an exogenous enzyme can rapidly metabolize norcocaine, in addition to cocaine, in rats. Further kinetic modeling has suggested that CocH3 with an identical concentration as that of the endogenous BChE in human plasma can effectively eliminate both cocaine and norcocaine in a simplified kinetic model of cocaine abuse. PMID:24125115

  3. The effects of closed kinetic chain exercises and open kinetic chain exercises using elastic bands on electromyographic activity in degenerative gonarthritis.

    PubMed

    Cho, Igsoo; Hwangbo, Gak; Lee, Daehee; Lee, Sangyong

    2014-09-01

    [Purpose] The purpose of this study was to examine the effects of closed kinetic chain exercises (CKCEs) and open kinetic chain exercises (OKCEs) with elastic bands on the electromyographic activity of patients with degenerative gonarthritis. [Subjects] The study subjects were 30 degenerative gonarthritis patients who were divided into a CKCE group (CKCEG, n=10), an OKCE group (OKCEG, n=10), and a control group (CG, n=10). [Methods] The CKCEG and the OKCEG performed exercises with elastic bands, and the CG took part in a quadriceps strengthening exercise. All three groups performed the exercises three times per week for four weeks. The electromyographic activities of the subjects' vastus medialis (VM), rectus femoris (RF), vastus lateralis (VL), semitendinosus (ST), and biceps femoris (BF) muscles were measured and compared. [Results] Within-group comparisons revealed that the electromyographic activities of the VM, RF, VL, ST, and BF muscles increased significantly in the CKCEG. The OKCEG displayed significant increases in the electromyographic activity of the VM, RF, ST, and BF muscles, and the CG showed significant increases in the electromyographic activities of the RF, VL, ST, and BF muscles. In between-group comparisons after the intervention, the electromyographic activities of the VM, RF, and VL muscles of the CKCEG were significantly higher than those of the CG. The electromyographic activities of the VM, RF, and ST muscles of the OKCEG were significantly higher than those of the CG. [Conclusion] We consider CKCEs with elastic bands are an effective intervention for increasing the electromyographic activities of the VM, RF, VL, ST, and BF muscles of degenerative gonarthritis patients, and OKCEs with elastic bands are an effective intervention for increasing the electromyographic activities of the VM, RF, ST, and BF muscles of degenerative gonarthritis patients. PMID:25276041

  4. 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.

  5. Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum.

    PubMed

    Moxley, Michael A; Beard, Daniel A; Bazil, Jason N

    2016-02-01

    Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD(+)/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD(+) activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat. PMID:26644471

  6. 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.

  7. 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

  8. Amyloid-β probes: Review of structure-activity and brain-kinetics relationships.

    PubMed

    Eckroat, Todd J; Mayhoub, Abdelrahman S; Garneau-Tsodikova, Sylvie

    2013-01-01

    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. Adsorption equilibrium and kinetics for multiple trace impurities in various gas streams on activated carbon

    SciTech Connect

    Golden, T.C.; Kumar, R. )

    1993-01-01

    Equilibrium and kinetic adsorption data for seven trace impurities (propylene, Freon-12 (CF[sub 2]Cl[sub 2]), n-butane, methylene chloride, acetone, n-hexane, toluene, and Freon-22 (CHFCl[sub 2])) from various carrier gases (helium, nitrogen, methane, carbon dioxide, and a mixture of methane and carbon dioxide) are provided. Activated carbon at several temperatures and pressures is used as the adsorbent. Two empirical characteristic curves, one relating equilibrium isotherms of trace impurities with their physical properties and the other relating mass-transfer coefficients with equilibrium properties, are generated. These can be used to predict equilibrium capacities and mass-transfer zone lengths for multiple trace impurities from a carrier gas and design a thermal swing adsorption clean-up system.

  10. 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

  11. 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.

  12. Oxidation of flavonoids by hypochlorous acid: reaction kinetics and antioxidant activity studies.

    PubMed

    Krych-Madej, Justyna; Stawowska, Katarzyna; Gebicka, Lidia

    2016-08-01

    Flavonoids, plant polyphenols, ubiquitous components of human diet, are excellent antioxidants. Hypochlorous acid (HOCl), produced by activated neutrophils, is highly reactive chlorinating and oxidizing species. It has been reported earlier that flavonoids are chlorinated by HOCl. Here we show that flavonoids from flavonol subclass are also oxidized by HOCl, but only if the latter is in a large molar excess (≥ 10). The kinetics of this reaction was studied by stopped-flow spectrophotometry, at different pH. We found that flavonols were oxidized by HOCl with the rate constants of the order of 10(4)-10(5) M(-1) s(-1) at pH 7.5. Antioxidant activity of HOCl-modified flavonoids was measured by 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) method. Slightly higher antioxidant activity, compared to parent compounds, was observed for flavonols after their reaction with equimolar or moderate excess of HOCl whereas flavonols treated with high molar excess of HOCl exhibited decrease in antioxidant activity. The mechanism of flavonoid reaction with HOCl at physiological pH is proposed, and biological consequences of this reaction are discussed. PMID:27225705

  13. Inhibitory effect of ebselen on cerebral acetylcholinesterase activity in vitro: kinetics and reversibility of inhibition.

    PubMed

    Martini, Franciele; Bruning, César Augusto; Soares, Suelen Mendonca; Nogueira, Cristina Wayne; Zeni, Gilson

    2015-01-01

    Ebselen is a synthetic organoselenium compound that has been considered a potential pharmacological agent with low toxicity, showing antioxidant, anti-inflammatory and neuroprotective effects. It is bioavailable, blood-brain barrier permeant and safe based on cellular toxicity and Phase I-III clinical trials. There is evidence that ebselen inhibits acetylcholinesterase (AChE) activity, an enzyme that plays a key role in the cholinergic system by hydrolyzing acetylcholine (ACh), in vitro and ex vivo. This system has a well-known relationship with cognitive process, and AChE inhibitors, such as donepezil and galantamine, have been used to treat cognitive deficits, mainly in the Alzheimer's Disease (AD). However, these drugs have poor bioavailability and a number of side effects, including gastrointestinal upsets and hepatotoxicity. In this way, this study aimed to evaluate the effect of ebselen on cerebral AChE activity in vitro and to determine the kinetic profile and the reversibility of inhibition by dialysis. Ebselen inhibited the cerebral AChE activity with an IC50 of 29 µM, similar to IC50 found with pure AChE from electric eel, demonstrating a mixed and reversible inhibition of AChE, since it increased Km and decreased Vmax. The AChE activity was recovered within 60 min of dialysis. Therefore, the use of ebselen as a therapeutic agent for treatment of AD should be considered, although memory behavior tasks are needed to support such hypothesis. PMID:25312723

  14. 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. PMID:25262554

  15. 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.

  16. Graph-based analysis of kinetics on multidimensional potential-energy surfaces

    NASA Astrophysics Data System (ADS)

    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.

  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. PMID:19905185

  18. Development of patient collation system by kinetic analysis for chest dynamic radiogram with flat panel detector

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Yuichiro; Kodera, Yoshie

    2006-03-01

    In the picture archiving and communication system (PACS) environment, it is important that all images be stored in the correct location. However, if information such as the patient's name or identification number has been entered incorrectly, it is difficult to notice the error. The present study was performed to develop a system of patient collation automatically for dynamic radiogram examination by a kinetic analysis, and to evaluate the performance of the system. Dynamic chest radiographs during respiration were obtained by using a modified flat panel detector system. Our computer algorithm developed in this study was consisted of two main procedures, kinetic map imaging processing, and collation processing. Kinetic map processing is a new algorithm to visualize a movement for dynamic radiography; direction classification of optical flows and intensity-density transformation technique was performed. Collation processing consisted of analysis with an artificial neural network (ANN) and discrimination for Mahalanobis' generalized distance, those procedures were performed to evaluate a similarity of combination for the same person. Finally, we investigated the performance of our system using eight healthy volunteers' radiographs. The performance was shown as a sensitivity and specificity. The sensitivity and specificity for our system were shown 100% and 100%, respectively. This result indicated that our system has excellent performance for recognition of a patient. Our system will be useful in PACS management for dynamic chest radiography.

  19. Kinetic analysis of mechanochemical chain scission of linear poly(phthalaldehyde).

    PubMed

    Peterson, Gregory I; Boydston, Andrew J

    2014-09-01

    The kinetics of mechanochemical chain scission of poly(phthalaldehyde) (PPA) are investigated. Ultrasound-induced cavitation is capable of causing chain scission in the PPA backbone that ultimately leads to rapid depolymerization of each resulting polymer fragment when above the polymer's ceiling temperature (Tc ). An interesting feature of the mechanochemical breakdown of PPA is that "half-chain" daughter fragments are not observed, since the depolymerization is rapid following chain scission. These features facilitate the determination of rate constants of activation for multiple molecular weights from a single sonication experiment. Additionally, the degradation kinetics are modified with chain-end trapping agents through variation of the nature and amount of small molecule nucleophile or electrophile.

  20. Kinetic analysis of free-radical reactions in the low-temperature autoxidation of triglycerides

    SciTech Connect

    Zhu, Jingmin; Sevilla, M.D. )

    1990-02-22

    The kinetics of the low-temperature autoxidation of triglycerides has been investigated by electron spin resonance spectroscopy. After initial radical production, four reaction stages are found in the overall autoxidation of unsaturated lipids: (1) formation of peroxyl radicals by addition of molecular oxygen to the initial carbon radicals, (2) consumption of oxygen in the autoxidation cycle, (3) decay of the lipid peroxyl radical into allylic and pentadienyl radicals, and (4) recombination of the carbon-centered radicals. Peroxyl radical decay in saturated lipids follows second-order kinetics with an apparent activation energy of ca. 50 kJ/mol. The authors find that, for polyunsaturated lipids, even at quite low temperatures (120 K), the autoxidation process occurs readily and must be considered in the storage of biological samples.

  1. An application of high performance liquid chromatographic assay for the kinetic analysis of degradation of faropenem.

    PubMed

    Cielecka-Piontek, J; Krause, A; Paczkowska, M

    2012-11-01

    An isocratic RP-HPLC-DAD procedure was developed and validated for kinetic analysis of degradation of faropenem in bulk drug substance and in tablets. It involved the use of a C-18 analytical column (5 microm particle size, 250 mm x 4.6 mm), flow rate 1.3 ml/min and 50 microl injection volume. The mobile phase consisted of acetate buffer (pH 3.5) - acetonitrile (70:30 v/v). The determination was carried out at the wavelength of 323 nm. Kinetic studies of faropenem degradation in aqueous solutions included hydrolysis, oxidation, photolysis and thermal degradation. A derivative spectrophotometry was used as an alternative method to compare the observed rate constants. PMID:23210240

  2. 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.

  3. 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.

  4. 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. PMID:11992536

  5. 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.

  6. First-order kinetics analysis of monomer composition dependent polyhydroxyalkanoic acid degradation in Pseudomonas spp.

    PubMed

    Choi, Mun Hwan; Rho, Jong Kook; Lee, Ho-Joo; Song, Jae Jun; Yoon, Sung Chul; Lee, Sang Yeol

    2003-01-01

    The intracellular degradation of polyhydroxyalkanoic acid (PHA) in pseudomonads was investigated by first-order kinetics analysis using the initial rate method. One type of PHA was accumulated in five Pseudomonas spp., P. oleovorans, P. aeruginosa, P. fluorescens, P. citronellolis, and P. putida, by growing them on octanoic acid. The monomer compositions of the five PHA were not significantly different from one another: 85-90 mol % 3-hydroxyoctanoic acid (3HO), 7-12 mol % 3-hydorxycaproic acid (3HC), and 3-6 mol % 3-hydroxydecanoic acid (3HD). The first-order degradation rate constants (k(1)) for the octanoate-derived PHA (designated P(3HO)) in the five species were in a similar range between 0.060 and 0.088 h(-1). This may indicate the similar specificities of the five intracellular depolymerases. In addition, the similar k(1) among the different species may correlate with the high degree of amino acid sequence identities (over 85%) among the intracellular PHA depolymerase phaZ genes. Six other chemically different types of PHA were accumulated in P. putida from n-nonanoic acid, n-decanoic acid, 5-phenyvaleric acid, or 11-phenoxyundecanoic acid as a single or a mixed carbon source. The calculated k(1) values were characteristic to each PHA, reflecting their chemical structures. In comparison with P(3HO), an increase in the levels of the two minor monomers 3HC and 3HD as in P(21 mol % 3HC-co-56 mol % 3HO-co-23 mol % 3HD) significantly slowed the rate of intracellular degradation. From the comparison of k(1) values, it is suggested that the P. putida intracellular depolymerase is most active against P(3HO). PMID:12625741

  7. 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

  8. Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function

    DOE PAGES

    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 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

  9. 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

  10. The Interaction of the Chemotherapeutic Drug Chlorambucil with Human Glutathione Transferase A1-1: Kinetic and Structural Analysis

    PubMed Central

    Karpusas, Michael; Axarli, Irine; Chiniadis, Lykourgos; Papakyriakou, Athanasios; Bethanis, Kostas; Scopelitou, Katholiki; Clonis, Yannis D.; Labrou, Nikolaos E.

    2013-01-01

    Glutathione transferases (GSTs) are enzymes that contribute to cellular detoxification by catalysing the nucleophilic attack of glutathione (GSH) on the electrophilic centre of a number of xenobiotic compounds, including several chemotherapeutic drugs. In the present work we investigated the interaction of the chemotherapeutic drug chlorambucil (CBL) with human GSTA1-1 (hGSTA1-1) using kinetic analysis, protein crystallography and molecular dynamics. In the presence of GSH, CBL behaves as an efficient substrate for hGSTA1-1. The rate-limiting step of the catalytic reaction between CBL and GSH is viscosity-dependent and kinetic data suggest that product release is rate-limiting. The crystal structure of the hGSTA1-1/CBL-GSH complex was solved at 2.1 Å resolution by molecular replacement. CBL is bound at the H-site attached to the thiol group of GSH, is partially ordered and exposed to the solvent, making specific interactions with the enzyme. Molecular dynamics simulations based on the crystal structure indicated high mobility of the CBL moiety and stabilization of the C-terminal helix due to the presence of the adduct. In the absence of GSH, CBL is shown to be an alkylating irreversible inhibitor for hGSTA1-1. Inactivation of the enzyme by CBL followed a biphasic pseudo-first-order saturation kinetics with approximately 1 mol of CBL per mol of dimeric enzyme being incorporated. Structural analysis suggested that the modifying residue is Cys112 which is located at the entrance of the H-site. The results are indicative of a structural communication between the subunits on the basis of mutually exclusive modification of Cys112, indicating that the two enzyme active sites are presumably coordinated. PMID:23460799

  11. The interaction of the chemotherapeutic drug chlorambucil with human glutathione transferase A1-1: kinetic and structural analysis.

    PubMed

    Karpusas, Michael; Axarli, Irine; Chiniadis, Lykourgos; Papakyriakou, Athanasios; Bethanis, Kostas; Scopelitou, Katholiki; Clonis, Yannis D; Labrou, Nikolaos E

    2013-01-01

    Glutathione transferases (GSTs) are enzymes that contribute to cellular detoxification by catalysing the nucleophilic attack of glutathione (GSH) on the electrophilic centre of a number of xenobiotic compounds, including several chemotherapeutic drugs. In the present work we investigated the interaction of the chemotherapeutic drug chlorambucil (CBL) with human GSTA1-1 (hGSTA1-1) using kinetic analysis, protein crystallography and molecular dynamics. In the presence of GSH, CBL behaves as an efficient substrate for hGSTA1-1. The rate-limiting step of the catalytic reaction between CBL and GSH is viscosity-dependent and kinetic data suggest that product release is rate-limiting. The crystal structure of the hGSTA1-1/CBL-GSH complex was solved at 2.1 Å resolution by molecular replacement. CBL is bound at the H-site attached to the thiol group of GSH, is partially ordered and exposed to the solvent, making specific interactions with the enzyme. Molecular dynamics simulations based on the crystal structure indicated high mobility of the CBL moiety and stabilization of the C-terminal helix due to the presence of the adduct. In the absence of GSH, CBL is shown to be an alkylating irreversible inhibitor for hGSTA1-1. Inactivation of the enzyme by CBL followed a biphasic pseudo-first-order saturation kinetics with approximately 1 mol of CBL per mol of dimeric enzyme being incorporated. Structural analysis suggested that the modifying residue is Cys112 which is located at the entrance of the H-site. The results are indicative of a structural communication between the subunits on the basis of mutually exclusive modification of Cys112, indicating that the two enzyme active sites are presumably coordinated.

  12. Development of kinetic analysis technique for PACS management and a screening examination in dynamic radiography

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Yuichiro; Kodera, Yoshie

    2005-04-01

    The purpose of this study was to develop of kinetic analysis method for PACS management and computer-aided diagnosis. We obtained dynamic chest radiographs (512x512, 8bit, 4fps, and 1344x1344, 12bit, 3fps) of five healthy volunteers during respiration using an I.I. system twice, and one healthy volunteer using dynamic FPD system. Optical flows of images were obtained using customized block matching technique, and were divided into a direction, and transformed into the RGB color. Density was determined by the sum pixel length of movement during respiration phase. The made new static image was defined as the "kinetic map". The evaluation of patient's collation was performed with a template matching to the three colors. The same person's each correlation value and similar-coefficient which is defined in this study were statistically significant high (P<0.01). We used the artificial neural network (ANN) for the judgment of the same person. Five volunteers were divided into two groups, three volunteers and two volunteers became a training signal and unknown signal. Correlation value and similar-coefficient was used for the input signal, and ANN was designed so that the same person's probability might be outputted. The average of the specificity of the unknown signal obtained 98.2%. The kinetic map including the imitation tumor was used for the simulation. The tumor was detected by temporal subtraction of kinetic map, and then the superior sensitivity was obtained. Our analysis method was useful in risk management and computer-aided diagnosis.

  13. 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.

  14. 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. PMID:27138167

  15. 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.

  16. 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

  17. 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

  18. Steady-State Kinetic Mechanism of the Proline:Ubiquinone Oxidoreductase Activity of Proline Utilization A (PutA) from Escherichia coli

    PubMed Central

    Moxley, Michael A.; Tanner, John J.; Becker, Donald F.

    2011-01-01

    The multifunctional proline utilization A (PutA) flavoenzyme from Escherichia coli performs the oxidation of proline to glutamate in two catalytic steps using separate proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate (P5C) dehydrogenase domains. In the first reaction, the oxidation of proline is coupled to the reduction of ubiquinone (CoQ) by the PRODH domain, which has a β8α8-barrel structure that is conserved in bacterial and eukaryotic PRODH enzymes. The structural requirements of the benzoquinone moiety were examined by steady-state kinetics using CoQ analogs. PutA displayed activity with all the analogs tested; the highest kcat/Km was obtained with CoQ2. The kinetic mechanism of the PRODH reaction was investigated use a variety of steady-state approaches. Initial velocity patterns measured using proline and CoQ1, combined with dead-end and product inhibition studies, suggested a two-site ping-pong mechanism for PutA. The kinetic parameters for PutA were not strongly influenced by solvent viscosity suggesting that diffusive steps do not significantly limit the overall reaction rate. In summary, the kinetic data reported here, along with analysis of the crystal structure data for the PRODH domain, suggest that the proline:ubiquinone oxidoreductase reaction of PutA occurs via a rapid equilibrium ping-pong mechanism with proline and ubiquinone binding at two distinct sites. PMID:22040654

  19. 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

  20. Viral Decay Kinetics in the Highly Active Antiretroviral Therapy-Treated Rhesus Macaque Model of AIDS

    PubMed Central

    Deere, Jesse D.; Higgins, Joanne; Cannavo, Elda; Villalobos, Andradi; Adamson, Lourdes; Fromentin, Emilie; Schinazi, Raymond F.; Luciw, Paul A.; North, Thomas W.

    2010-01-01

    To prevent progression to AIDS, persons infected with human immunodeficiency virus type 1 (HIV-1) must remain on highly active antiretroviral therapy (HAART) indefinitely since this modality does not eradicate the virus. The mechanisms involved in viral persistence during HAART are poorly understood, but an animal model of HAART could help elucidate these mechanisms and enable studies of HIV-1 eradication strategies. Due to the specificity of non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) for HIV-1, we have used RT-SHIV, a chimeric virus of simian immunodeficiency virus with RT from HIV-1. This virus is susceptible to NNRTIs and causes an AIDS-like disease in rhesus macaques. In this study, two groups of HAART-treated, RT-SHIV-infected macaques were analyzed to determine viral decay kinetics. In the first group, viral loads were monitored with a standard TaqMan RT-PCR assay with a limit of detection of 50 viral RNA copies per mL. Upon initiation of HAART, viremia decayed in a bi-phasic manner with half-lives of 1.7 and 8.5 days, respectively. A third phase was observed with little further decay. In the second group, the macaques were followed longitudinally with a more sensitive assay utilizing ultracentrifugation to concentrate virus from plasma. Bi-phasic decay of viral RNA was also observed in these animals with half-lives of 1.8 and 5.8 days. Viral loads in these animals during a third phase ranged from 2–58 RNA copies/mL, with little decay over time. The viral decay kinetics observed in these macaques are similar to those reported for HIV-1 infected humans. These results demonstrate that low-level viremia persists in RT-SHIV-infected macaques despite a HAART regimen commonly used in humans. PMID:20668516

  1. Kinetics of Ion Transport in Perovskite Active Layers and Its Implications for Active Layer Stability.

    PubMed

    Bag, Monojit; Renna, Lawrence A; Adhikari, Ramesh Y; Karak, Supravat; Liu, Feng; Lahti, Paul M; Russell, Thomas P; Tuominen, Mark T; Venkataraman, D

    2015-10-14

    Solar cells fabricated using alkyl ammonium metal halides as light absorbers have the right combination of high power conversion efficiency and ease of fabrication to realize inexpensive but efficient thin film solar cells. However, they degrade under prolonged exposure to sunlight. Herein, we show that this degradation is quasi-reversible, and that it can be greatly lessened by simple modifications of the solar cell operating conditions. We studied perovskite devices using electrochemical impedance spectroscopy (EIS) with methylammonium (MA)-, formamidinium (FA)-, and MA(x)FA(1-x) lead triiodide as active layers. From variable temperature EIS studies, we found that the diffusion coefficient using MA ions was greater than when using FA ions. Structural studies using powder X-ray diffraction (PXRD) show that for MAPbI3 a structural change and lattice expansion occurs at device operating temperatures. On the basis of EIS and PXRD studies, we postulate that in MAPbI3 the predominant mechanism of accelerated device degradation under sunlight involves thermally activated fast ion transport coupled with a lattice-expanding phase transition, both of which are facilitated by absorption of the infrared component of the solar spectrum. Using these findings, we show that the devices show greatly improved operation lifetimes and stability under white-light emitting diodes, or under a solar simulator with an infrared cutoff filter or with cooling. PMID:26414066

  2. 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.

  3. The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

    PubMed Central

    Kim, Jiho; Doose, Sören; Neuweiler, Hannes; Sauer, Markus

    2006-01-01

    Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides. PMID:16687657

  4. 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.

  5. Selective removal of dibenzothiophene from commercial diesel using manganese dioxide-modified activated carbon: a kinetic study.

    PubMed

    Safieh, Kayed A Abu; Al-Degs, Yahya S; Sunjuk, Mahmoud S; Saleh, Abdullah I; Al-Ghouti, Mohammad A

    2015-01-01

    With a total concentration of 7055 mgS/kgfuel, the content of organosulphur compounds (OSCs) in local diesel is 20 times higher than the regulated value. Analysis revealed that 30% of OSC is originated from dibenzothiophene (DBT). It is known that DBT is a hardly removable compound and selective adsorbents are often needed for its removal with low affinity for other diesel components. In this work, a selective adsorbent based on surface modification of activated carbon (AC) by MnO2 is prepared for DBT removal from diesel. The porous nature of AC enabled carrying large amounts of MnO2 particles to end up with a selective adsorber for DBT. The best performance was observed at a surface loading of 26.8% of Mn and DBT is favourably removed over mono- and diaromatics hydrocarbons in diesel. Adsorption kinetics of DBT is studied under a high initial concentration of 835-11,890 mg/kg and at a ratio of 11 cm3/g (diesel:carbon). The results indicated a fast removal process after surface modification where 96% of the surface is occupied within 30 min of interaction. Kinetic data were best presented by reaction-based models with low prediction error sum of squares values 0.5-47.0, while, diffusion-based models showed limited application for modelling DBT adsorption. Accordingly, adsorption process is controlled by surface reactions and pore diffusion has a minor role in the overall process. The modified adsorbent is satisfactorily regenerated using n-hexane at 65°C.

  6. 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.

  7. 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

  8. 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.

  9. Evidence of Negative Cooperativity and Half-Site Reactivity within an F420-Dependent Enzyme: Kinetic Analysis of F420H2:NADP(+) Oxidoreductase.

    PubMed

    Joseph, Ebenezer; Le, Cuong Quang; Nguyen, Toan; Oyugi, Mercy; Hossain, Mohammad Shawkat; Foss, Frank W; Johnson-Winters, Kayunta

    2016-02-23

    Here, we report the very first example of half-site reactivity and negative cooperativity involving an important F420 cofactor-dependent enzyme. F420H2:NADP(+) oxidoreductase (Fno) is an F420 cofactor-dependent enzyme that catalyzes the reversible reduction of NADP(+) through the transfer of a hydride from the reduced F420 cofactor. These catalytic processes are of major significance in numerous biochemical processes. While the steady-state kinetic analysis showed classic Michaelis-Menten kinetics with varying concentrations of the F420 redox moiety, FO, such plots revealed non-Michaelis-Menten kinetic behavior when NADPH was varied. The double reciprocal plot of the varying concentrations of NADPH displays a downward concave shape, suggesting that negative cooperativity occurs between the two identical monomers. The transient state kinetic data show a burst prior to entering steady-state turnover. The burst suggests that product release is rate-limiting, and the amplitude of the burst phase corresponds to production of product in only one of the active sites of the functional dimer. These results suggest either half-site reactivity or an alternate sites model wherein the reduction of the cofactor, FO occurs at one active site at a time followed by reduction at the second active site. Thus, the data imply that Fno may be a functional regulatory enzyme.

  10. Analysis of the kinetics of diffraction efficiency during the holographic grating recording in azobenzene functionalized polymers.

    PubMed

    Sobolewska, Anna; Miniewicz, Andrzej

    2007-02-22

    The laser-assisted holographic grating recording process in films of azobenzene functionalized polymers is usually studied by observation of the efficiency of light scattering on a developing in time diffraction grating. Various possible mechanisms contributing to grating formation as well as the bulk or surface origin (bulk refractive index and/or relief grating) of light scattering make the analysis of kinetics of grating recording, from the light scattering data only, difficult and ambiguous. To fully explain experimentally observed various and complex (frequently nonexponential) kinetics of the first-order light diffraction intensity, we considered a simple single-exponential growth of the two phase gratings in the same polymer film. In modeling we assumed that the bulk refractive index grating Deltan(t) and the surface relief grating Deltad(t) differ considerably in their growth rates and we allowed for a nonstationary phase shift Deltaphi(t) between them which was experimentally observed during the recording process. The origin of the nonstationary phase shift is a result of a slow shift of interference pattern due to delicate symmetry breaking in illumination conditions (e.g., difference in beam intensities and deviation of exact symmetrical beam incidence angles on the sample). Changing only such parameters as stationary amplitudes of refractive index and relief gratings for a span of phase shifts (0-pi) between them, we obtained a series of kinetic responses which we discuss and interpret. The various examples of temporal evolution of diffraction efficiency for the same grating formation kinetics, modeled in our work, supply evidence that great care must be taken to properly interpret the experimental results. PMID:17263574

  11. 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.

  12. 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. PMID:24231380

  13. 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.

  14. Kinetic and mechanistic investigations of the degradation of sulfamethazine in heat-activated persulfate oxidation process.

    PubMed

    Fan, Yan; Ji, Yuefei; Kong, Deyang; Lu, Junhe; Zhou, Quansuo

    2015-12-30

    Sulfamethazine (SMZ) is widely used in livestock feeding and aquaculture as an antibiotic agent and growth promoter. Widespread occurrence of SMZ in surface water, groundwater, soil and sediment has been reported. In this study, degradation of SMZ by heat-activated persulfate (PS) oxidation was investigated in aqueous solution. Experimental results demonstrated that SMZ degradation followed pseudo-first-order reaction kinetics. The pseudo-first-order rate constant (kobs) was increased markedly with increasing concentration of PS and temperature. Radical scavenging tests revealed that the predominant oxidizing species was SO4·(-) with HO playing a less important role. Aniline moiety in SMZ molecule was confirmed to be the reactive site for SO4·(-) attack by comparison with substructural analogs. Nontarget natural water constituents affected SMZ removal significantly, e.g., Cl(-) and HCO3(-) improved the degradation while fulvic acid reduced it. Reaction products were enriched by solid phase extraction (SPE) and analyzed by liquid chromatography-electrospray ionization-triple quadrupole mass spectrometry (LC-ESI-MS/MS). 6 products derived from sulfonamide S--N bond cleavage, aniline moiety oxidation and Smiles-type rearrangement were identified, and transformation pathways of SMZ oxidation were proposed. Results reveal that heat-activated PS oxidation could be an efficient approach for remediation of water contaminated by SMZ and related sulfonamides.

  15. Kinetics, equilibrium, and thermodynamics investigation on the adsorption of lead(II) by coal-based activated carbon.

    PubMed

    Yi, Zhengji; Yao, Jun; Zhu, Mijia; Chen, Huilun; Wang, Fei; Liu, Xing

    2016-01-01

    The goal of this research is to investigate the feasibility of using activated coal-based activated carbon (CBAC) to adsorb Pb(II) from aqueous solutions through batch tests. Effects of contact time, pH, temperature and initial Pb(II) concentration on the Pb(II) adsorption were examined. The Pb(II) adsorption is strongly dependent on pH, but insensitive to temperature. The best pH for Pb(II) removal is in the range of 5.0-5.5 with more than 90 % of Pb(II) removed. The equilibrium time was found to be 60 min and the adsorption data followed the pseudo-second-order kinetics. Isotherm data followed Langmuir isotherm model with a maximum adsorption capacity of 162.33 mg/g. The adsorption was exothermic and spontaneous in nature. The Fourier transform infrared spectroscopy and scanning electron microscopy analysis suggested that CBAC possessed a porous structure and was rich in carboxyl and hydroxyl groups on its surface, which might play a major role in Pb(II) adsorption. These findings indicated that CBAC has great potential as an alternative adsorbent for Pb(II) removal. PMID:27504258

  16. 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.

  17. Mechanistic insight into sono-enzymatic degradation of organic pollutants with kinetic and thermodynamic analysis.

    PubMed

    Malani, Ritesh S; Khanna, Swati; Chakma, Sankar; Moholkar, Vijayanand S

    2014-07-01

    In this paper, we have attempted to get a physical insight into process of sono-enzymatic treatment for degradation of recalcitrant organic pollutants. Decolourization of an azo dye has been used as model reaction with different experimental protocols that alter characteristics of ultrasound and cavitation phenomena in the system. Experimental data is analyzed to determine kinetic and thermodynamic parameters of decolorization process. The trends observed in kinetic and thermodynamic parameters of decolourization are essentially manifestations of the dominating mechanism of the decolorization of the textile dye (or nature of prevalent chemical reaction in the system), viz. either molecular reaction due to enzyme or radical reaction due to transient cavitation. The activation energy for sonochemical protocol is negative, which indicates instantaneity of the radical reactions. The frequency factor is also low, which is attributed to high instability of radicals. For enzymatic and sono-enzymatic protocols, activation energy is positive with higher frequency factor. Enthalpy change for sonochemical protocol is negative, while that for enzymatic and sono-enzymatic protocols is positive. The net entropy change for sonochemical protocol is more negative than enzymatic or sono-enzymatic protocol due to differences in prevalent chemical mechanism of dye decolorization. Due to inverse variations of frequency factor and activation energy, marginal rise in reaction kinetics is seen for sono-enzymatic protocol, as compared to enzymatic treatment alone. Due to inverse variations of enthalpy and entropy change, net Gibbs energy change in all experimental protocols shows little variation indicating synergism of the mechanism of ultrasound and enzyme. PMID:24548544

  18. New library of aminosulfonyl-tagged Hoveyda–Grubbs type complexes: Synthesis, kinetic studies and activity in olefin metathesis transformations

    PubMed Central

    Borré, Etienne; Caijo, Frederic

    2010-01-01

    Summary Seven novel Hoveyda–Grubbs precatalysts bearing an aminosulfonyl function are reported. Kinetic studies indicate an activity enhancement compared to Hoveyda’s precatalyst. A selection of these catalysts was investigated with various substrates in ring-closing metathesis of dienes or enynes and cross metathesis. The results demonstrate that these catalysts show a good tolerance to various chemical functions. PMID:21165173

  19. A Detailed Chemical Kinetic Analysis of Low Temperature Non-Sooting Diesel Combustion

    SciTech Connect

    Aceves, S M; Flowers, D L

    2004-10-01

    We have developed a model of the diesel fuel injection process for application to analysis of low temperature non-sooting combustion. The model uses a simplified mixing correlation and detailed chemical kinetics, and analyzes a parcel of fuel as it moves along the fuel jet, from injection into evaporation and ignition. The model predicts chemical composition and soot precursors, and is applied at conditions that result in low temperature non-sooting combustion. Production of soot precursors is the first step toward production of soot, and modeling precursor production is expected to give insight into the overall evolution of soot inside the engine. The results of the analysis show that the model has been successful in describing many of the observed characteristics of low temperature combustion. The model predicts results that are qualitatively similar to those obtained for soot formation experiments at conditions in which the EGR rate is increased from zero to very high values as the fueling rate is kept constant. The model also describes the two paths to achieve non-sooting combustion. The first is smokeless rich combustion and the second is modulated kinetics (MK). The importance of the temperature after ignition and the equivalence ratio at the time of ignition is demonstrated, as these parameters can be used to collapse onto a single line all the results for soot precursors for multiple fueling rates. A parametric analysis indicates that precursor formation increases considerably as the gas temperature in the combustion chamber and the characteristic mixing time are increased. The model provides a chemical kinetic description of low temperature diesel combustion that improves the understanding of this clean and efficient regime of operation.

  20. Impact of spatial kinetics in severe accident analysis for a large HWR

    SciTech Connect

    Morris, E.E.

    1994-03-01

    The impact on spatial kinetics on the analysis of severe accidents initiated by the unprotected withdrawal of one or more control rods is investigated for a large heavy water reactor. Large inter- and intra-assembly power shifts are observed, and the importance of detailed geometrical modeling of fuel assemblies is demonstrated. Neglect of space-time effects is shown to lead to erroneous estimates of safety margins, and of accident consequences in the event safety margins are exceeded. The results and conclusions are typical of what would be expected for any large, loosely coupled core.

  1. 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.

  2. KINETIC ANALYSIS OF HIGH-NITROGEN ENERGETIC MATERIALS USING MULTIVARIATE NONLINEAR REGRESSION

    SciTech Connect

    Campbell, M. S.; Rabie, R. L.; Diaz-Acosta, I.; Pulay, P.

    2001-01-01

    New high-nitrogen energetic materials were synthesized by Hiskey and Naud. J. Opfermann reported a new tool for finding the probable model of the complex reactions using multivariate non-linear regression analysis of DSC and TGA data from several measurements run at different heating rates. This study is to take the kinetic parameters from the different steps and discover which reaction step is responsible for the runaway reaction by comparing predicted results from the Frank-Kamenetsckii equation with the critical temperature found experimentally using the modified Henkin test.

  3. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics

    PubMed Central

    Tewari, Shivendra G.; Zhou, Yifan; Otto, Bradley J.; Dash, Ranjan K.; Kwok, Wai-Meng; Beard, Daniel A.

    2015-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  4. Markov chain Monte Carlo based analysis of post-translationally modified VDAC gating kinetics.

    PubMed

    Tewari, Shivendra G; Zhou, Yifan; Otto, Bradley J; Dash, Ranjan K; Kwok, Wai-Meng; Beard, Daniel A

    2014-01-01

    The voltage-dependent anion channel (VDAC) is the main conduit for permeation of solutes (including nucleotides and metabolites) of up to 5 kDa across the mitochondrial outer membrane (MOM). Recent studies suggest that VDAC activity is regulated via post-translational modifications (PTMs). Yet the nature and effect of these modifications is not understood. Herein, single channel currents of wild-type, nitrosated, and phosphorylated VDAC are analyzed using a generalized continuous-time Markov chain Monte Carlo (MCMC) method. This developed method describes three distinct conducting states (open, half-open, and closed) of VDAC activity. Lipid bilayer experiments are also performed to record single VDAC activity under un-phosphorylated and phosphorylated conditions, and are analyzed using the developed stochastic search method. Experimental data show significant alteration in VDAC gating kinetics and conductance as a result of PTMs. The effect of PTMs on VDAC kinetics is captured in the parameters associated with the identified Markov model. Stationary distributions of the Markov model suggest that nitrosation of VDAC not only decreased its conductance but also significantly locked VDAC in a closed state. On the other hand, stationary distributions of the model associated with un-phosphorylated and phosphorylated VDAC suggest a reversal in channel conformation from relatively closed state to an open state. Model analyses of the nitrosated data suggest that faster reaction of nitric oxide with Cys-127 thiol group might be responsible for the biphasic effect of nitric oxide on basal VDAC conductance. PMID:25628567

  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. 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…

  7. 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.

  8. 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.

  9. Two kinetically distinct components of hyperpolarization-activated current in rat superior colliculus-projecting neurons.

    PubMed Central

    Solomon, J S; Nerbonne, J M

    1993-01-01

    1. Whole-cell and perforated patch recording techniques were used to examine the activation, deactivation and inactivation of the time-dependent hyperpolarization-activated inward currents (Ih) in isolated superior colliculus-projecting (SCP) neurons from rat primary visual cortex. 2. Examination of inward current waveforms revealed the presence of two kinetically distinct components of Ih: one that activates with a time constant of the order of hundreds of milliseconds, and one that activates with a time constant of the order of seconds. We have termed these Ih,f and Ih,s, to denote the fast and slow components, respectively, of current activation. The time constants of activation of both Ih,f and Ih,s decrease with increasing membrane hyperpolarization. 3. Following the onset of hyperpolarizing voltage steps, a delay is evident prior to time-dependent inward current activation. This delay is voltage dependent and decreases with increasing membrane hyperpolarization. 4. The sigmoidal inward current waveforms are well fitted by the sum of two exponentials in which the faster term, corresponding to the activation of Ih,f, is raised to the power 1.34 +/- 0.26 (mean +/- S.D.). The non-integral exponent suggests that Ih,f activation involves at least two energetically non-equivalent gating transitions prior to channel opening. 5. Over a limited voltage range, tail currents could also be resolved into two distinct components. The faster component, which corresponds to the deactivation of Ih,f, decayed over a single exponential time course with a mean (+/- S.D.) time constant of 355 +/- 161 ms at -70 mV. Ih,s decay also followed a single exponential time course with a mean (+/- S.D.) time constant of 2428 +/- 1285 ms at -70 mV. Both deactivation time constants decreased with increasing depolarization. 6. The separation of inward current activation and deactivation into two distinct components and the lack of correlation between the relative amplitudes of these components

  10. Texture analysis as a tool to study the kinetics of wet agglomeration processes.

    PubMed

    Nalesso, Silvia; Codemo, Carlo; Franceschinis, Erica; Realdon, Nicola; Artoni, Riccardo; Santomaso, Andrea C

    2015-05-15

    In this work wet granulation experiments were carried out in a planetary mixer with the aim to develop a novel analytical tool based on surface texture analysis. The evolution of a simple formulation (300g of microcrystalline cellulose with a solid binders pre-dispersed in water) was monitored from the very beginning up to the end point and information on the kinetics of granulation as well as on the effect of liquid binder amount were collected. Agreement between texture analysis and granules particle size distribution obtained by sieving analysis was always found. The method proved to be robust enough to easily monitor the process and its use for more refined analyses on the different rate processes occurring during granulation is also suggested. PMID:25746734

  11. Exploring "one-shot" kinetics and small molecule analysis using the ProteOn XPR36 array biosensor.

    PubMed

    Bravman, Tsafrir; Bronner, Vered; Lavie, Kobi; Notcovich, Ariel; Papalia, Giuseppe A; Myszka, David G

    2006-11-15

    A ProteOn XPR36 parallel array biosensor was used to characterize the binding kinetics of a set of small molecule/enzyme interactions. Using one injection with the ProteOn's crisscrossing flow path system, we collected response data for six different concentrations of each analyte over six different target protein surfaces. This "one-shot" approach to kinetic analysis significantly improves throughput while generating high-quality data even for low-molecular-mass analytes. We found that the affinities determined for nine sulfonamide-based inhibitors of the enzyme carbonic anhydrase II were highly correlated with the values determined using isothermal titration calorimetry. We also measured the temperature dependence (from 15 to 35 degrees C) of the kinetics for four of the inhibitor/enzyme interactions. Our results illustrate the potential of this new parallel-processing biosensor to increase the speed of kinetic analysis in drug discovery and expand the applications of real-time protein interaction arrays.

  12. 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.

  13. Neutron Activation Analysis: Techniques and Applications

    NASA Astrophysics Data System (ADS)

    MacLellan, Ryan

    2011-04-01

    The role of neutron activation analysis in low-energy low-background experimentsis discussed in terms of comparible methods. Radiochemical neutron activation analysis is introduce. The procedure of instrumental neutron activation analysis is detailed especially with respect to the measurement of trace amounts of natural radioactivity. The determination of reactor neutron spectrum parameters required for neutron activation analysis is also presented.

  14. Neutron Activation Analysis: Techniques and Applications

    SciTech Connect

    MacLellan, Ryan

    2011-04-27

    The role of neutron activation analysis in low-energy low-background experimentsis discussed in terms of comparible methods. Radiochemical neutron activation analysis is introduce. The procedure of instrumental neutron activation analysis is detailed especially with respect to the measurement of trace amounts of natural radioactivity. The determination of reactor neutron spectrum parameters required for neutron activation analysis is also presented.

  15. 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.

  16. Quantitative analysis of the kinetics of denaturation and renaturation of barstar in the folding transition zone.

    PubMed Central

    Shastry, M. C.; Agashe, V. R.; Udgaonkar, J. B.

    1994-01-01

    The fluorescence-monitored kinetics of folding and unfolding of barstar by guanidine hydrochloride (GdnHCl) in the folding transition zone, at pH 7, 25 degrees C, have been quantitatively analyzed using a 3-state mechanism: U(S)<-->UF<-->N. U(S) and UF are slow-refolding and fast-refolding unfolded forms of barstar, and N is the native protein. U(S) and UF probably differ in possessing trans and cis conformations, respectively, of the Tyr 47-Pro 48 bond. The 3-state model could be used because the kinetics of folding and unfolding of barstar show 2 phases, a fast phase and a slow phase, and because the relative amplitudes of the 2 phases depend only on the final refolding conditions and not on the initial conditions. Analysis of the observed kinetics according to the 3-state model yields the values of the 4 microscopic rate constants that describe the transitions between the 3 states at different concentrations of GdnHCl. The value of the equilibrium unfolded ratio U(S):UF (K21) and the values of the rate constants of the U(S)-->UF and UF-->U(S) reactions, k12 and k21, respectively, are shown to be independent of the concentration of GdnHCl. K21 has a value of 2.1 +/- 0.1, and k12 and k21 have values of 5.3 x 10(-3) s-1 and 11.2 x 10(-3) s-1, respectively. Double-jump experiments that monitor reactions that are silent to fluorescence monitoring were used to confirm the values of K21, k12, and k21 obtained from the 3-state analysis and thereby the validity of the 3-state model.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7833803

  17. 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.

  18. 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.

  19. 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.

  20. Comment on "Single-point kinetic energy density functionals: A pointwise kinetic energy density analysis and numerical convergence investigation"

    NASA Astrophysics Data System (ADS)

    Trickey, S. B.; Karasiev, Valentin V.; Chakraborty, Debajit

    2015-09-01

    We suggest a more nuanced view of the merit and utility of generalized gradient approximations (GGAs) for the noninteracting kinetic energy (KE) than the critique of Xia and Carter (XC) [Phys. Rev. B 91, 045124 (2015), 10.1103/PhysRevB.91.045124]. Specifically, the multiple valuedness of the Pauli term enhancement factor (denoted G [n ] by XC) with respect to the inhomogeneity variable s can be excluded by enforcement of a bound on the Kohn-Sham KE to achieve universality of the functional along with enforcement of proper large-s behavior. This is physically sensible in that the excluded G values occur for s values that correspond to low densities. The behavior is exacerbated by peculiarities of pseudodensities. The VT84F KE GGA, constructed with these constraints, does not have the numerical instability in our older PBE2 functional analyzed by XC.

  1. 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.

  2. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis.

    PubMed

    Yonetani, Yoshiteru

    2015-07-28

    Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

  3. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis

    NASA Astrophysics Data System (ADS)

    Yonetani, Yoshiteru

    2015-07-01

    Different ion pairs exhibit different dissociation kinetics; however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant, following the trend kLiCl < kNaCl < kKCl < kCsCl. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.

  4. 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

  5. Evaluation of a novel accelerometer for kinetic gait analysis in dogs.

    PubMed

    Clark, Kyle; Caraguel, Charles; Leahey, Lorne; Béraud, Romain

    2014-07-01

    The objective of this study was to evaluate a novel accelerometer-based sensor system, the Walkabout Portable Gait Monitor (WPGM), for use in kinetic gait analysis of dogs. The accelerometer was compared to the common reference standard of force platform analysis. Fifteen client-owned, orthopedically sound dogs of various breeds underwent simultaneous force platform and accelerometer gait trials to measure peak vertical forces (PVFs). The agreement between PVF for the accelerometer and force platform was measured using concordance correlation coefficient (CCC) and was found, overall, to be moderate [CCC = 0.51; 95% confidence interval (CI): 0.46 to 0.56]. The agreement between PVF for the accelerometer and force platform for the forelimbs was positive and substantial (CCC = 0.79; 95% CI: 0.74 to 0.84) and for the hind limbs was positive and low (CCC = 0.34; 95% CI: 0.29 to 0.38). As measured by the accelerometer, PVF was systematically higher than as measured by the force platform (forelimbs 55.3 N, hind limbs 144.3 N). It was also found that, when positioned over the lumbar spine, the WPGM cannot measure PVF of the individual forelimbs and hind limbs, which limits its use as a clinical tool to measure kinetic variables in dogs. PMID:24982555

  6. Kinetic and Kinematic Analysis for Assessing the Differences in Countermovement Jump Performance in Rugby Players.

    PubMed

    Floría, Pablo; Gómez-Landero, Luis A; Suárez-Arrones, Luis; Harrison, Andrew J

    2016-09-01

    Floría, P, Gómez-Landero, LA, Suárez-Arrones, L, and Harrison, AJ. Kinetic and kinematic analysis for assessing the differences in countermovement jump performance in rugby players. J Strength Cond Res 30(9): 2533-2539, 2016-The aim of this study was to ascertain the differences in kinetic and kinematic profiles between better and poorer performers of the vertical jump within a homogeneous group of trained adults. Fifty rugby players were divided into low scoring (LOW) and high scoring (HIGH) groups based on their performance in the vertical jump. The force, velocity, displacement, and rate of force development (RFD)-time curves were analyzed to determine the differences between groups. The analysis of the data showed differences in all the patterns of the ensemble mean curves of the HIGH and LOW groups. During the eccentric phase, the differences in the HIGH group with respect to the LOW group were lower crouch position, higher downward velocity, and higher force and RFD during the braking of the downward movement. During the concentric phase, the HIGH group achieved higher upward velocity, higher force at the end of phase, and a higher position at takeoff. The higher jump performances seem to be related to a more effective stretch-shortening cycle function that is characterized by a deeper and faster countermovement with higher eccentric forces being applied to decelerate the downward movement leading to enhanced force generation during the concentric phase.

  7. 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.

  8. 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

  9. Engineering Substrate Preference in Subtilisin: Structural and Kinetic Analysis of a Specificity Mutant

    SciTech Connect

    Ruan, Biao; London, Viktoriya; Fisher, Kathryn E.; Gallagher, D. Travis; Bryan, Philip N.

    2008-08-06

    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{sub cat} for the reaction. This also leads to strong product inhibition of substrate

  10. Kinetic Analysis of [11C]McN5652: A Serotonin Transporter Radioligand

    PubMed Central

    Szabo, Zsolt; Scheffel, Ursula; Mathews, William B.; Ravert, Hayden T.; Szabo, Katalina; Kraut, Michael; Palmon, Sally; Ricaurte, George A.; Dannals, Robert F.

    2007-01-01

    Summary The impulse response function of a radioligand is the most fundamental way to describe its pharmacokinetics and to assess its tissue uptake and retention pattern. This study investigates the impulse response function of [11C](+)McN5652, a radioligand used for positron emission tomography (PET) imaging of the serotonin transporter (SERT) in the brain. Dynamic PET studies were performed in eight healthy volunteers injected with [11C](+)McN5652 and subsequently with its pharmacologically inactive enantiomer [11C](−)McN5652. The impulse response function was calculated by deconvolution analysis of regional time-activity curves, and its peak value (fmax), its retention value at 75 minutes (fT), and its normalized retention (frel = fr/fmax) were obtained. Alternatively, compartmental models were applied to calculate the apparent total distribution volume (DVT) and its specific binding component (DVS). Both the noncompartmental (fT, frel) and the compartmental parameters (DV) were investigated with and without correction for nonspecific binding by simple subtraction of the corresponding value obtained with [11C](−)McN5652. The impulse response function obtained by deconvolution analysis demonstrated high tracer extraction followed by a slow decline in the form of a monoexponential function. Statistical analysis revealed that the best compartmental model in terms of analysis of variance F and condition number of the parameter variance-covariance matrix was the one that was based on a single tissue compartment with parameters k1and k2 and that also included the parameter of regional cerebral blood volume (BV). The parameter frel demonstrated low between-subject variance (coefficient of variation [CV] = 19%), a midbrain to cerebellum ratio of 1.85, and high correlation with the known density of SERT (r = 0.787 where r is the coefficient of linear correlation between the parameter and the known density of SERT). After correction for nonspecific binding, frel

  11. 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.

  12. 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. PMID:25766013

  13. A green approach towards adoption of chemical reaction model on 2,5-dimethyl-2,5-di-(tert-butylperoxy)hexane decomposition by differential isoconversional kinetic analysis.

    PubMed

    Das, Mitali; Shu, Chi-Min

    2016-01-15

    This study investigated the thermal degradation products of 2,5-dimethyl-2,5-di-(tert-butylperoxy) hexane (DBPH), by TG/GC/MS to identify runaway reaction and thermal safety parameters. It also included the determination of time to maximum rate under adiabatic conditions (TMR(ad)) and self-accelerating decomposition temperature obtained through Advanced Kinetics and Technology Solutions. The apparent activation energy (Ea) was calculated from differential isoconversional kinetic analysis method using differential scanning calorimetry experiments. The Ea value obtained by Friedman analysis is in the range of 118.0-149.0 kJ mol(-1). The TMR(ad) was 24.0 h with an apparent onset temperature of 82.4°C. This study has also established an efficient benchmark for a thermal hazard assessment of DBPH that can be applied to assure safer storage conditions.

  14. 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.

  15. Anticancer activity of rhamnoallosan against DU-145 cells is kinetically complementary to coexisting Polyphenolics in Psidium guajava budding leaves.

    PubMed

    Chen, Kuan-Chou; Hsieh, Chiu-Lan; Huang, Kuan-Dar; Ker, Yaw-Bee; Chyau, Charng-Cherng; Peng, Robert Y

    2009-07-22

    Psidium guajava L. is a valuable farm fruit plant having many medicinal uses. Previously its budding leaves (PE) were shown to contain huge amounts of soluble polyphenolics (SP) including (in mg/g) gallic acid (348), catechin (102), epicatechin (60), rutin (100), quercetin (102), and rutin (100) and to exhibit potent anticancer activity. However, reconstitution of these polyphenolics recovered only 40% of the original bioactivity, and the soluble carbohydrate (SC) portion in PE was suspected to contribute the remaining. PE contained a novel rhamnoallosan, which had a carbohydrate/protein (w/w) ratio = 29.06%/10.27% (=2.83, average molecular mass of 5029 kDa), characteristically evidencing a peptidoglycan, consisting of a composition (mole % ratio) of rhamnose/allose/arabinose/tallose/xylose/fucose/glucose/mannose/galactose = 36.05:24.24:8.76:7.95:7.37:5.90:3.69:3.19:2.85 and of amino acid (in wt %) glycine/leucine/proline/alanine/methionine/isoleucine/valine/histidine/tyrosine/phenylalanine/cysteine/aspartic acid/lysine/glutamic acid = 37.12:12.68:10.05:8.97:5.99:4.89:4.83:4.25:4.05:2.78:1.86:1.10:0.73:0.70. Kinetic analysis showed comparable apparent cell-killing rate coefficients (k(app)) to be 4.03 x 10(3) and 2.92 x 10(3) cells mg(-1) h(-1), respectively, by SP and SC, evidencing the complementary anti-DU-145 bioactivity in nature.

  16. Effects of Juvenile Idiopathic Arthritis on Kinematics and Kinetics of the Lower Extremities Call for Consequences in Physical Activities Recommendations

    PubMed Central

    Hartmann, M.; Kreuzpointner, F.; Haefner, R.; Michels, H.; Schwirtz, A.; Haas, J. P.

    2010-01-01

    Juvenile idiopathic arthritis (JIA) patients (n = 36) with symmetrical polyarticular joint involvement of the lower extremities and healthy controls (n = 20) were compared concerning differences in kinematic, kinetic, and spatio-temporal parameters with 3D gait analysis. The aims of this study were to quantify the differences in gait between JIA patients and healthy controls and to provide data for more detailed sport activities recommendations. JIA-patients showed reduced walking speed and step length, strongly anterior tilted pelvis, reduced maximum hip extension, reduced knee extension during single support phase and reduced plantar flexion in push off. Additionally the roll-off procedure of the foot was slightly decelerated. The reduced push off motion in the ankle was confirmed by lower peaks in ankle moment and power. The gait of JIA-patients can be explained as a crouch-like gait with hyperflexion in hip and knee joints and less plantar flexion in the ankle. A preventive mobility workout would be recommendable to reduce these restrictions in the future. Advisable are sports with emphasis on extension in hip, knee, and ankle plantar flexion. PMID:20862334

  17. Kinetic analysis of photocatalytic oxidation of gas-phase formaldehyde over titanium dioxide.

    PubMed

    Liu, Hongmin; Lian, Zhiwei; Ye, Xiaojiang; Shangguan, Wenfeng

    2005-07-01

    Degradation of formaldehyde with different initial concentration over titanium dioxide was carried out in a photocatalytic reactor. Photocatalytic rates were well described by the simplified Langmuir-Hinshelwood model. The kinetic analysis shows that the apparent first-order reaction coefficient is lower and half-life of photocatalysis is longer for low concentration than for high concentration formaldehyde. A network formation model of the photocatalytic products was established. Experimental results and analysis demonstrate that carbon dioxide concentration and carbon monoxide concentration in gas phase vary exponentially with the illumination time and may be even higher than gas-phase formaldehyde concentration if there is much pre-adsorbed formaldehyde in adsorption equilibrium on catalysts before illumination. Carbon monoxide is found to be one of the by-products during formaldehyde photooxidation.

  18. 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.

  19. 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. PMID:22097045

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. Goal-oriented sensitivity analysis for lattice kinetic Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Arampatzis, Georgios; Katsoulakis, Markos A.

    2014-03-01

    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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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…

  10. A novel method for the synthesis of glyceryl monocaffeate by the enzymatic transesterification and kinetic analysis.

    PubMed

    Sun, Shangde; Hu, Bingxue

    2017-01-01

    A novel enzymatic method for glyceryl monocaffeate (GMC) preparation by the transesterification of ethyl caffeate (EC) was investigated. The effects of reaction variables (reaction pressure, temperature, reaction time, enzyme load, and substrate ratio) on the enzymatic transesterification were studied and optimized using response surface methodology. HPLC-ESI-MS and HPLC-UV were used to monitor the transesterification. Thermodynamics, kinetic analyses and reaction mechanism were also evaluated. Results showed that, GMC can be successfully prepared by the enzymatic transesterification of EC with glycerol. Under the optimal conditions (enzyme load 22.54%, EC:glycerol=1:12.75 (mol/mol), 72.5°C, and 10.5h), EC conversion and GMC yield were 97.9±0.7% and 95.8±1.0%, respectively. The activation energies (Ea) for EC conversion and GMC formation were 44.23 and 46.51kJ/mol, respectively. The kinetic values for Vmax, Km(') and KIA were 2.18×10(-3)mol/(Lmin), 0.086mol/L, and 0.52mol/L, respectively. The transesterification mechanism with EC inhibition was also proposed. PMID:27507465

  11. Simultaneous analysis of the equilibrium hygroscopicity and water transport kinetics of liquid aerosol.

    PubMed

    Davies, James F; Haddrell, Allen E; Rickards, Andrew M J; Reid, Jonathan P

    2013-06-18

    We demonstrate that the equilibrium hygroscopic response of an aerosol droplet and the kinetics of water condensation and evaporation can be retrieved with high accuracy, even close to saturation, through comparative measurements of probe and sample aerosol droplets. The experimental methodology is described and is based on an electrodynamic balance with a newly designed trapping chamber. Through use of a probe aerosol, composed of either pure water or a sodium chloride solution of known concentration, the gas-phase relative humidity (RH) can be accurately measured with an uncertainty of typically <0.005. By fast manipulation of the airflows into the chamber, a step-change in RH over a time scale of <0.5 s can be achieved. Using this approach, the kinetics of mass transfer are studied using the comparative procedure, and results are compared to theoretical mass flux predictions. The time-dependent measured mass fluxes for sodium chloride, ammonium sulfate, sorbitol, and galactose are used to calculate droplet water activities as a function of the droplet growth factor, allowing retrieval of a hygroscopic growth curve in a matter of seconds. Comparisons with both new and established thermodynamic predictions of hygroscopicity, as well as to optical tweezers measurements, are presented, demonstrating good agreement within the experimental uncertainties. PMID:23662676

  12. 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.

  13. 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. PMID:26512858

  14. Hg(II) binding to a weakly associated coiled coil nucleates an encoded metalloprotein fold: a kinetic analysis.

    PubMed

    Farrer, Brian T; Pecoraro, Vincent L

    2003-04-01

    A detailed kinetic analysis of metal encapsulation by a de novo-designed protein is described. The kinetic mechanism of Hg(II) encapsulation in the three-stranded coiled coil formed by the peptide CH(3)CO-G LKALEEK CKALEEK LKALEEK G-NH(2) (Baby L9C) is derived by global analysis. The mechanism involves rapid initial collapse of two peptides by Hg(II) forming Hg(Baby L9C(-H))(2) with a linear thiolato Hg(II) bound to the cysteine sulfur atoms. Here, Baby L9C(-H) denotes Baby L9C with the cysteine thiol deprotonated. Addition of the third peptide, forming the three-stranded coiled coil, is the rate-determining step and results in an intermediate state involving two separate species. One of the species, termed the properly folded intermediate, undergoes rapid deprotonation of the third cysteine thiol, yielding the desired three-stranded coiled coil with an encapsulated trigonal thiolato Hg(II). The other species, termed the misfolded intermediate, rearranges in an experimentally distinguishable step to the properly folded intermediate. The order of the reaction involving the addition of the third peptide with respect to the concentration of Baby L9C indicates that addition of the third helix only occurs through reaction of Hg(Baby L9C(-H))(2) and Baby L9C that is unassociated with a coiled coil. Temperature dependence of the reaction afforded activation parameters for both the addition of the third helix (deltaH = 20(2) kcalmol; deltaS= 40(5) calmol K) and the rearrangement of the misfolded intermediate steps (deltaH = 23(2) kcalmol; deltaS= 27(5) calmol K). The mechanism is discussed with regard to metalloprotein folding and metalloprotein design.

  15. Exploring the Role of Mechanotransduction Activation and Adaptation Kinetics in Hair Cell Filtering Using a Hodgkin-Huxley Approach

    NASA Astrophysics Data System (ADS)

    Wells, Gregg B.; Ricci, Anthony J.

    2011-11-01

    In the auditory system, mechanotransduction occurs in the hair cell sensory hair bundle and is the first major step in the translation of mechanical energy into electrical. Tonotopic variations in the activation kinetics of this process are posited to provide a low pass filter to the input. An adaptation process, also associated with mechanotransduction, is postulated to provide a high pass filter to the input in a tonotopic manner. Together a bandpass filter is created at the hair cell input. Corresponding mechanical components to both activation and adaptation are also suggested to be involved in generating cochlear amplification. A paradox to this story is that hair cells where the mechanotransduction properties are most robust possess an intrinsic electrical resonance mechanism proposed to account for all required tuning and amplification. A simple Hodgkin-Huxley type model is presented to attempt to determine the role of the activation and adaptation kinetics in further tuning hair cells that exhibit electrical resonance. Results further support that steady state mechanotransduction properties are critical for setting the resting potential of the hair cell while the kinetics of activation and adaptation are important for sharpening tuning around the characteristic frequency of the hair cell.

  16. Kinetic and Statistical Analysis of Primary Circuit Water Chemistry Data in a VVER Power Plant

    SciTech Connect

    Nagy, Gabor; Tilky, Peter; Horvath, Akos; Pinter, Tamas; Schiller, Robert

    2001-12-15

    The results of chemical and radiochemical analyses of the primary circuit coolant liquid, obtained between 1995 and 1999 at the four VVER-type blocks of the Paks (Hungary) nuclear power station, are assessed. A model has been developed regarding the pressure vessel with its auxiliary parts plus the fuel elements as the zone, with the six steam generators as one single unit. The stream from the steam generator is split, with its larger part returning to the zone through the main circulating pump and the smaller one passing through the purifier column. Based on this flowchart, the formation kinetics of corrosion products and of radioactive substances are evaluated. Correlation analysis is applied to reveal any eventual interdependence of the processes, whereas the range-per-scatter (R/S) method is used to characterize the random or deterministic nature of a process. The evaluation of the t {yields} {infinity} limits of the kinetic equations enables one to conclude that (a) the total amount of corrosion products per element during one cycle is almost always <15 kg and (b) the zone acts as a highly efficient filter with an efficiency of {approx}1. The R/S results show that the fluctuations in the concentrations of the corrosion products are persistent; this finding indicates that random effects play here little if any role and that the processes in the coolant are under control. Correlation analyses show that the variations of the concentrations are practically uncorrelated and that the processes are independent of each other.

  17. 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.

  18. Kinetic analysis and energy efficiency of phenol degradation in a plasma-photocatalysis system.

    PubMed

    Wang, Hui-juan; Chen, Xiao-yang

    2011-02-28

    Combination of two kinds of advanced oxidation processes (AOPs) is an effective approach to control wastewater pollution. In this research, a pulsed discharge plasma system with multi-point-to-plate electrode and an immobilized TiO(2) photocatalysis system is coupled to oxidize target pollutant in aqueous solution. Kinetic analysis (pseudo-first order kinetic constant, k) and energy efficiency (energy yield value at 50% phenol conversion, G(50)) of phenol oxidation in different reaction systems (plasma alone and plasma-photocatalysis) are reviewed to account for the synergistic mechanism of plasma and photocatalysis. The experimental results show that higher k and G(50) of phenol oxidation can be obtained in the plasma-photocatalysis system under the conditions of different gas bubbling varieties, initial solution pH and radical scavenger addition. Moreover, the investigation tested hydroxyl radical (OH) is the most important species for phenol removal in the synergistic system of plasma-photocatalysis as well as in the plasma alone system.

  19. 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

  20. Kinetic analysis of nitroxide radical formation under oxygenated photolysis: toward quantitative singlet oxygen topology.

    PubMed

    Zigler, David F; Ding, Eva Chuheng; Jarocha, Lauren E; Khatmullin, Renat R; DiPasquale, Vanessa M; Sykes, R Brendan; Tarasov, Valery F; Forbes, Malcolm D E

    2014-12-01

    Reaction kinetics for two sterically hindered secondary amines with singlet oxygen have been studied in detail. A water soluble porphyrin sensitizer, 5,10,15,20-tetrakis-(4-sulfunatophenyl)-21,23H-porphyrin (TPPS), was irradiated in oxygenated aqueous solutions containing either 2,2,6,6-tetramethylpiperidin-4-one (TMPD) or 4-[N,N,N-trimethyl-ammonium]-2,2,6,6-tetramethylpiperidinyl chloride (N-TMPCl). The resulting sensitization reaction produced singlet oxygen in high yield, ultimately leading to the formation of the corresponding nitroxide free radicals (R2NO) which were detected using steady-state electron paramagnetic resonance (EPR) spectroscopy. Careful actinometry and EPR calibration curves, coupled with a detailed kinetic analysis, led to a simple and compact expression relating the nitroxide quantum yield ΦR2NO (from the doubly-integrated EPR signal intensity) to the initial amine concentration [R2NH]i. With all other parameters held constant, a plot of ΦR2NOvs. [R2NH]i gave a straight line with a slope proportional to the rate constant for nitroxide formation, kR2NO. This establishment of a rigorous quantitative relationship between the EPR signal and the rate constant provides a mechanism for quantifying singlet oxygen production as a function of its topology in heterogeneous media. Implications for in vivo assessment of singlet oxygen topology are briefly discussed.