Sample records for accurate kinetic parameters

  1. Application of lab derived kinetic biodegradation parameters at the field scale

    NASA Astrophysics Data System (ADS)

    Schirmer, M.; Barker, J. F.; Butler, B. J.; Frind, E. O.

    2003-04-01

    Estimating the intrinsic remediation potential of an aquifer typically requires the accurate assessment of the biodegradation kinetics, the level of available electron acceptors and the flow field. Zero- and first-order degradation rates derived at the laboratory scale generally overpredict the rate of biodegradation when applied to the field scale, because limited electron acceptor availability and microbial growth are typically not considered. On the other hand, field estimated zero- and first-order rates are often not suitable to forecast plume development because they may be an oversimplification of the processes at the field scale and ignore several key processes, phenomena and characteristics of the aquifer. This study uses the numerical model BIO3D to link the laboratory and field scale by applying laboratory derived Monod kinetic degradation parameters to simulate a dissolved gasoline field experiment at Canadian Forces Base (CFB) Borden. All additional input parameters were derived from laboratory and field measurements or taken from the literature. The simulated results match the experimental results reasonably well without having to calibrate the model. An extensive sensitivity analysis was performed to estimate the influence of the most uncertain input parameters and to define the key controlling factors at the field scale. It is shown that the most uncertain input parameters have only a minor influence on the simulation results. Furthermore it is shown that the flow field, the amount of electron acceptor (oxygen) available and the Monod kinetic parameters have a significant influence on the simulated results. Under the field conditions modelled and the assumptions made for the simulations, it can be concluded that laboratory derived Monod kinetic parameters can adequately describe field scale degradation processes, if all controlling factors are incorporated in the field scale modelling that are not necessarily observed at the lab scale. In this way

  2. Inverse modeling approach for evaluation of kinetic parameters of a biofilm reactor using tabu search.

    PubMed

    Kumar, B Shiva; Venkateswarlu, Ch

    2014-08-01

    The complex nature of biological reactions in biofilm reactors often poses difficulties in analyzing such reactors experimentally. Mathematical models could be very useful for their design and analysis. However, application of biofilm reactor models to practical problems proves somewhat ineffective due to the lack of knowledge of accurate kinetic models and uncertainty in model parameters. In this work, we propose an inverse modeling approach based on tabu search (TS) to estimate the parameters of kinetic and film thickness models. TS is used to estimate these parameters as a consequence of the validation of the mathematical models of the process with the aid of measured data obtained from an experimental fixed-bed anaerobic biofilm reactor involving the treatment of pharmaceutical industry wastewater. The results evaluated for different modeling configurations of varying degrees of complexity illustrate the effectiveness of TS for accurate estimation of kinetic and film thickness model parameters of the biofilm process. The results show that the two-dimensional mathematical model with Edward kinetics (with its optimum parameters as mu(max)rho(s)/Y = 24.57, Ks = 1.352 and Ki = 102.36) and three-parameter film thickness expression (with its estimated parameters as a = 0.289 x 10(-5), b = 1.55 x 10(-4) and c = 15.2 x 10(-6)) better describes the biofilm reactor treating the industry wastewater.

  3. One-step global parameter estimation of kinetic inactivation parameters for Bacillus sporothermodurans spores under static and dynamic thermal processes.

    PubMed

    Cattani, F; Dolan, K D; Oliveira, S D; Mishra, D K; Ferreira, C A S; Periago, P M; Aznar, A; Fernandez, P S; Valdramidis, V P

    2016-11-01

    Bacillus sporothermodurans produces highly heat-resistant endospores, that can survive under ultra-high temperature. High heat-resistant sporeforming bacteria are one of the main causes for spoilage and safety of low-acid foods. They can be used as indicators or surrogates to establish the minimum requirements for heat processes, but it is necessary to understand their thermal inactivation kinetics. The aim of the present work was to study the inactivation kinetics under both static and dynamic conditions in a vegetable soup. Ordinary least squares one-step regression and sequential procedures were applied for estimating these parameters. Results showed that multiple dynamic heating profiles, when analyzed simultaneously, can be used to accurately estimate the kinetic parameters while significantly reducing estimation errors and data collection. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

    PubMed Central

    Liu, Fei; Heiner, Monika; Yang, Ming

    2016-01-01

    Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830

  5. qPIPSA: Relating enzymatic kinetic parameters and interaction fields

    PubMed Central

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

    2007-01-01

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

  6. Parameter Balancing in Kinetic Models of Cell Metabolism†

    PubMed Central

    2010-01-01

    Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

  7. Effect of experimental and sample factors on dehydration kinetics of mildronate dihydrate: mechanism of dehydration and determination of kinetic parameters.

    PubMed

    Bērziņš, Agris; Actiņš, Andris

    2014-06-01

    The dehydration kinetics of mildronate dihydrate [3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propionate dihydrate] was analyzed in isothermal and nonisothermal modes. The particle size, sample preparation and storage, sample weight, nitrogen flow rate, relative humidity, and sample history were varied in order to evaluate the effect of these factors and to more accurately interpret the data obtained from such analysis. It was determined that comparable kinetic parameters can be obtained in both isothermal and nonisothermal mode. However, dehydration activation energy values obtained in nonisothermal mode showed variation with conversion degree because of different rate-limiting step energy at higher temperature. Moreover, carrying out experiments in this mode required consideration of additional experimental complications. Our study of the different sample and experimental factor effect revealed information about changes of the dehydration rate-limiting step energy, variable contribution from different rate limiting steps, as well as clarified the dehydration mechanism. Procedures for convenient and fast determination of dehydration kinetic parameters were offered. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  8. Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method.

    PubMed

    Jia, Gengjie; Stephanopoulos, Gregory N; Gunawan, Rudiyanto

    2011-07-15

    Time-series measurements of metabolite concentration have become increasingly more common, providing data for building kinetic models of metabolic networks using ordinary differential equations (ODEs). In practice, however, such time-course data are usually incomplete and noisy, and the estimation of kinetic parameters from these data is challenging. Practical limitations due to data and computational aspects, such as solving stiff ODEs and finding global optimal solution to the estimation problem, give motivations to develop a new estimation procedure that can circumvent some of these constraints. In this work, an incremental and iterative parameter estimation method is proposed that combines and iterates between two estimation phases. One phase involves a decoupling method, in which a subset of model parameters that are associated with measured metabolites, are estimated using the minimization of slope errors. Another phase follows, in which the ODE model is solved one equation at a time and the remaining model parameters are obtained by minimizing concentration errors. The performance of this two-phase method was tested on a generic branched metabolic pathway and the glycolytic pathway of Lactococcus lactis. The results showed that the method is efficient in getting accurate parameter estimates, even when some information is missing.

  9. Hindered rotor models with variable kinetic functions for accurate thermodynamic and kinetic predictions

    NASA Astrophysics Data System (ADS)

    Reinisch, Guillaume; Leyssale, Jean-Marc; Vignoles, Gérard L.

    2010-10-01

    We present an extension of some popular hindered rotor (HR) models, namely, the one-dimensional HR (1DHR) and the degenerated two-dimensional HR (d2DHR) models, allowing for a simple and accurate treatment of internal rotations. This extension, based on the use of a variable kinetic function in the Hamiltonian instead of a constant reduced moment of inertia, is extremely suitable in the case of rocking/wagging motions involved in dissociation or atom transfer reactions. The variable kinetic function is first introduced in the framework of a classical 1DHR model. Then, an effective temperature and potential dependent constant is proposed in the cases of quantum 1DHR and classical d2DHR models. These methods are finally applied to the atom transfer reaction SiCl3+BCl3→SiCl4+BCl2. We show, for this particular case, that a proper accounting of internal rotations greatly improves the accuracy of thermodynamic and kinetic predictions. Moreover, our results confirm (i) that using a suitably defined kinetic function appears to be very adapted to such problems; (ii) that the separability assumption of independent rotations seems justified; and (iii) that a quantum mechanical treatment is not a substantial improvement with respect to a classical one.

  10. Determining Kinetic Parameters for Isothermal Crystallization of Glasses

    NASA Technical Reports Server (NTRS)

    Ray, C. S.; Zhang, T.; Reis, S. T.; Brow, R. K.

    2006-01-01

    Non-isothermal crystallization techniques are frequently used to determine the kinetic parameters for crystallization in glasses. These techniques are experimentally simple and quick compared to the isothermal techniques. However, the analytical models used for non-isothermal data analysis, originally developed for describing isothermal transformation kinetics, are fundamentally flawed. The present paper describes a technique for determining the kinetic parameters for isothermal crystallization in glasses, which eliminates most of the common problems that generally make the studies of isothermal crystallization laborious and time consuming. In this technique, the volume fraction of glass that is crystallized as a function of time during an isothermal hold was determined using differential thermal analysis (DTA). The crystallization parameters for the lithium-disilicate (Li2O.2SiO2) model glass were first determined and compared to the same parameters determined by other techniques to establish the accuracy and usefulness of the present technique. This technique was then used to describe the crystallization kinetics of a complex Ca-Sr-Zn-silicate glass developed for sealing solid oxide fuel cells.

  11. Estimating the kinetic parameters of activated sludge storage using weighted non-linear least-squares and accelerating genetic algorithm.

    PubMed

    Fang, Fang; Ni, Bing-Jie; Yu, Han-Qing

    2009-06-01

    In this study, weighted non-linear least-squares analysis and accelerating genetic algorithm are integrated to estimate the kinetic parameters of substrate consumption and storage product formation of activated sludge. A storage product formation equation is developed and used to construct the objective function for the determination of its production kinetics. The weighted least-squares analysis is employed to calculate the differences in the storage product concentration between the model predictions and the experimental data as the sum of squared weighted errors. The kinetic parameters for the substrate consumption and the storage product formation are estimated to be the maximum heterotrophic growth rate of 0.121/h, the yield coefficient of 0.44 mg CODX/mg CODS (COD, chemical oxygen demand) and the substrate half saturation constant of 16.9 mg/L, respectively, by minimizing the objective function using a real-coding-based accelerating genetic algorithm. Also, the fraction of substrate electrons diverted to the storage product formation is estimated to be 0.43 mg CODSTO/mg CODS. The validity of our approach is confirmed by the results of independent tests and the kinetic parameter values reported in literature, suggesting that this approach could be useful to evaluate the product formation kinetics of mixed cultures like activated sludge. More importantly, as this integrated approach could estimate the kinetic parameters rapidly and accurately, it could be applied to other biological processes.

  12. Parameter estimation and order selection for an empirical model of VO2 on-kinetics.

    PubMed

    Alata, O; Bernard, O

    2007-04-27

    In humans, VO2 on-kinetics are noisy numerical signals that reflect the pulmonary oxygen exchange kinetics at the onset of exercise. They are empirically modelled as a sum of an offset and delayed exponentials. The number of delayed exponentials; i.e. the order of the model, is commonly supposed to be 1 for low-intensity exercises and 2 for high-intensity exercises. As no ground truth has ever been provided to validate these postulates, physiologists still need statistical methods to verify their hypothesis about the number of exponentials of the VO2 on-kinetics especially in the case of high-intensity exercises. Our objectives are first to develop accurate methods for estimating the parameters of the model at a fixed order, and then, to propose statistical tests for selecting the appropriate order. In this paper, we provide, on simulated Data, performances of Simulated Annealing for estimating model parameters and performances of Information Criteria for selecting the order. These simulated Data are generated with both single-exponential and double-exponential models, and noised by white and Gaussian noise. The performances are given at various Signal to Noise Ratio (SNR). Considering parameter estimation, results show that the confidences of estimated parameters are improved by increasing the SNR of the response to be fitted. Considering model selection, results show that Information Criteria are adapted statistical criteria to select the number of exponentials.

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

    PubMed

    Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

    2015-05-07

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

  14. Kinetic determinations of accurate relative oxidation potentials of amines with reactive radical cations.

    PubMed

    Gould, Ian R; Wosinska, Zofia M; Farid, Samir

    2006-01-01

    Accurate oxidation potentials for organic compounds are critical for the evaluation of thermodynamic and kinetic properties of their radical cations. Except when using a specialized apparatus, electrochemical oxidation of molecules with reactive radical cations is usually an irreversible process, providing peak potentials, E(p), rather than thermodynamically meaningful oxidation potentials, E(ox). In a previous study on amines with radical cations that underwent rapid decarboxylation, we estimated E(ox) by correcting the E(p) from cyclic voltammetry with rate constants for decarboxylation obtained using laser flash photolysis. Here we use redox equilibration experiments to determine accurate relative oxidation potentials for the same amines. We also describe an extension of these experiments to show how relative oxidation potentials can be obtained in the absence of equilibrium, from a complete kinetic analysis of the reversible redox kinetics. The results provide support for the previous cyclic voltammetry/laser flash photolysis method for determining oxidation potentials.

  15. Simultaneous versus sequential optimal experiment design for the identification of multi-parameter microbial growth kinetics as a function of temperature.

    PubMed

    Van Derlinden, E; Bernaerts, K; Van Impe, J F

    2010-05-21

    Optimal experiment design for parameter estimation (OED/PE) has become a popular tool for efficient and accurate estimation of kinetic model parameters. When the kinetic model under study encloses multiple parameters, different optimization strategies can be constructed. The most straightforward approach is to estimate all parameters simultaneously from one optimal experiment (single OED/PE strategy). However, due to the complexity of the optimization problem or the stringent limitations on the system's dynamics, the experimental information can be limited and parameter estimation convergence problems can arise. As an alternative, we propose to reduce the optimization problem to a series of two-parameter estimation problems, i.e., an optimal experiment is designed for a combination of two parameters while presuming the other parameters known. Two different approaches can be followed: (i) all two-parameter optimal experiments are designed based on identical initial parameter estimates and parameters are estimated simultaneously from all resulting experimental data (global OED/PE strategy), and (ii) optimal experiments are calculated and implemented sequentially whereby the parameter values are updated intermediately (sequential OED/PE strategy). This work exploits OED/PE for the identification of the Cardinal Temperature Model with Inflection (CTMI) (Rosso et al., 1993). This kinetic model describes the effect of temperature on the microbial growth rate and encloses four parameters. The three OED/PE strategies are considered and the impact of the OED/PE design strategy on the accuracy of the CTMI parameter estimation is evaluated. Based on a simulation study, it is observed that the parameter values derived from the sequential approach deviate more from the true parameters than the single and global strategy estimates. The single and global OED/PE strategies are further compared based on experimental data obtained from design implementation in a bioreactor

  16. Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

    PubMed

    Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

    2016-10-01

    Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  17. Estimation of beech pyrolysis kinetic parameters by Shuffled Complex Evolution.

    PubMed

    Ding, Yanming; Wang, Changjian; Chaos, Marcos; Chen, Ruiyu; Lu, Shouxiang

    2016-01-01

    The pyrolysis kinetics of a typical biomass energy feedstock, beech, was investigated based on thermogravimetric analysis over a wide heating rate range from 5K/min to 80K/min. A three-component (corresponding to hemicellulose, cellulose and lignin) parallel decomposition reaction scheme was applied to describe the experimental data. The resulting kinetic reaction model was coupled to an evolutionary optimization algorithm (Shuffled Complex Evolution, SCE) to obtain model parameters. To the authors' knowledge, this is the first study in which SCE has been used in the context of thermogravimetry. The kinetic parameters were simultaneously optimized against data for 10, 20 and 60K/min heating rates, providing excellent fits to experimental data. Furthermore, it was shown that the optimized parameters were applicable to heating rates (5 and 80K/min) beyond those used to generate them. Finally, the predicted results based on optimized parameters were contrasted with those based on the literature. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Quantitative evaluation of dual-flip-angle T1 mapping on DCE-MRI kinetic parameter estimation in head and neck

    PubMed Central

    Chow, Steven Kwok Keung; Yeung, David Ka Wai; Ahuja, Anil T; King, Ann D

    2012-01-01

    Purpose To quantitatively evaluate the kinetic parameter estimation for head and neck (HN) dynamic contrast-enhanced (DCE) MRI with dual-flip-angle (DFA) T1 mapping. Materials and methods Clinical DCE-MRI datasets of 23 patients with HN tumors were included in this study. T1 maps were generated based on multiple-flip-angle (MFA) method and different DFA combinations. Tofts model parameter maps of kep, Ktrans and vp based on MFA and DFAs were calculated and compared. Fitted parameter by MFA and DFAs were quantitatively evaluated in primary tumor, salivary gland and muscle. Results T1 mapping deviations by DFAs produced remarkable kinetic parameter estimation deviations in head and neck tissues. In particular, the DFA of [2º, 7º] overestimated, while [7º, 12º] and [7º, 15º] underestimated Ktrans and vp, significantly (P<0.01). [2º, 15º] achieved the smallest but still statistically significant overestimation for Ktrans and vp in primary tumors, 32.1% and 16.2% respectively. kep fitting results by DFAs were relatively close to the MFA reference compared to Ktrans and vp. Conclusions T1 deviations induced by DFA could result in significant errors in kinetic parameter estimation, particularly Ktrans and vp, through Tofts model fitting. MFA method should be more reliable and robust for accurate quantitative pharmacokinetic analysis in head and neck. PMID:23289084

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

    PubMed

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

    2017-03-01

    Anaerobic co-digestion has a potential to improve biogas production, but limited kinetic information is available for co-digestion. This study introduced regression-based models to estimate the kinetic parameters for the co-digestion of microalgae and Waste Activated Sludge (WAS). The models were developed using the ratios of co-substrates and the kinetic parameters for the single substrate as indicators. The models were applied to the modified first-order kinetics and Monod model to determine the rate of hydrolysis and methanogenesis for the co-digestion. The results showed that the model using a hyperbola function was better for the estimation of the first-order kinetic coefficients, while the model using inverse tangent function closely estimated the Monod kinetic parameters. The models can be used for estimating kinetic parameters for not only microalgae-WAS co-digestion but also other substrates' co-digestion such as microalgae-swine manure and WAS-aquatic plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Estimation of kinetic parameters from list-mode data using an indirect apporach

    NASA Astrophysics Data System (ADS)

    Ortiz, Joseph Christian

    This dissertation explores the possibility of using an imaging approach to model classical pharmacokinetic (PK) problems. The kinetic parameters which describe the uptake rates of a drug within a biological system, are parameters of interest. Knowledge of the drug uptake in a system is useful in expediting the drug development process, as well as providing a dosage regimen for patients. Traditionally, the uptake rate of a drug in a system is obtained via sampling the concentration of the drug in a central compartment, usually the blood, and fitting the data to a curve. In a system consisting of multiple compartments, the number of kinetic parameters is proportional to the number of compartments, and in classical PK experiments, the number of identifiable parameters is less than the total number of parameters. Using an imaging approach to model classical PK problems, the support region of each compartment within the system will be exactly known, and all the kinetic parameters are uniquely identifiable. To solve for the kinetic parameters, an indirect approach, which is a two part process, was used. First the compartmental activity was obtained from data, and next the kinetic parameters were estimated. The novel aspect of the research is using listmode data to obtain the activity curves from a system as opposed to a traditional binned approach. Using techniques from information theoretic learning, particularly kernel density estimation, a non-parametric probability density function for the voltage outputs on each photo-multiplier tube, for each event, was generated on the fly, which was used in a least squares optimization routine to estimate the compartmental activity. The estimability of the activity curves for varying noise levels as well as time sample densities were explored. Once an estimate for the activity was obtained, the kinetic parameters were obtained using multiple cost functions, and the compared to each other using the mean squared error as the figure

  1. Breakdown parameter for kinetic modeling of multiscale gas flows.

    PubMed

    Meng, Jianping; Dongari, Nishanth; Reese, Jason M; Zhang, Yonghao

    2014-06-01

    Multiscale methods built purely on the kinetic theory of gases provide information about the molecular velocity distribution function. It is therefore both important and feasible to establish new breakdown parameters for assessing the appropriateness of a fluid description at the continuum level by utilizing kinetic information rather than macroscopic flow quantities alone. We propose a new kinetic criterion to indirectly assess the errors introduced by a continuum-level description of the gas flow. The analysis, which includes numerical demonstrations, focuses on the validity of the Navier-Stokes-Fourier equations and corresponding kinetic models and reveals that the new criterion can consistently indicate the validity of continuum-level modeling in both low-speed and high-speed flows at different Knudsen numbers.

  2. Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

    PubMed

    Cotten, Cameron; Reed, Jennifer L

    2013-01-30

    Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the

  3. Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

    PubMed Central

    2013-01-01

    Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential

  4. Methods for Calibration of Prout-Tompkins Kinetics Parameters Using EZM Iteration and GLO

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

    Wemhoff, A P; Burnham, A K; de Supinski, B

    2006-11-07

    This document contains information regarding the standard procedures used to calibrate chemical kinetics parameters for the extended Prout-Tompkins model to match experimental data. Two methods for calibration are mentioned: EZM calibration and GLO calibration. EZM calibration matches kinetics parameters to three data points, while GLO calibration slightly adjusts kinetic parameters to match multiple points. Information is provided regarding the theoretical approach and application procedure for both of these calibration algorithms. It is recommended that for the calibration process, the user begin with EZM calibration to provide a good estimate, and then fine-tune the parameters using GLO. Two examples have beenmore » provided to guide the reader through a general calibrating process.« less

  5. Curcumin and kaempferol prevent lysozyme fibril formation by modulating aggregation kinetic parameters.

    PubMed

    Borana, Mohanish S; Mishra, Pushpa; Pissurlenkar, Raghuvir R S; Hosur, Ramakrishna V; Ahmad, Basir

    2014-03-01

    Interaction of small molecule inhibitors with protein aggregates has been studied extensively, but how these inhibitors modulate aggregation kinetic parameters is little understood. In this work, we investigated the ability of two potential aggregation inhibiting drugs, curcumin and kaempferol, to control the kinetic parameters of aggregation reaction. Using thioflavin T fluorescence and static light scattering, the kinetic parameters such as amplitude, elongation rate constant and lag time of guanidine hydrochloride-induced aggregation reactions of hen egg white lysozyme were studied. We observed a contrasting effect of inhibitors on the kinetic parameters when aggregation reactions were measured by these two probes. The interactions of these inhibitors with hen egg white lysozyme were investigated using fluorescence quench titration method and molecular dynamics simulations coupled with binding free energy calculations. We conclude that both the inhibitors prolong nucleation of amyloid aggregation through binding to region of the protein which is known to form the core of the protein fibril, but once the nucleus is formed the rate of elongation is not affected by the inhibitors. This work would provide insight into the mechanism of aggregation inhibition by these potential drug molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Estimating kinetic mechanisms with prior knowledge I: Linear parameter constraints.

    PubMed

    Salari, Autoosa; Navarro, Marco A; Milescu, Mirela; Milescu, Lorin S

    2018-02-05

    To understand how ion channels and other proteins function at the molecular and cellular levels, one must decrypt their kinetic mechanisms. Sophisticated algorithms have been developed that can be used to extract kinetic parameters from a variety of experimental data types. However, formulating models that not only explain new data, but are also consistent with existing knowledge, remains a challenge. Here, we present a two-part study describing a mathematical and computational formalism that can be used to enforce prior knowledge into the model using constraints. In this first part, we focus on constraints that enforce explicit linear relationships involving rate constants or other model parameters. We develop a simple, linear algebra-based transformation that can be applied to enforce many types of model properties and assumptions, such as microscopic reversibility, allosteric gating, and equality and inequality parameter relationships. This transformation converts the set of linearly interdependent model parameters into a reduced set of independent parameters, which can be passed to an automated search engine for model optimization. In the companion article, we introduce a complementary method that can be used to enforce arbitrary parameter relationships and any constraints that quantify the behavior of the model under certain conditions. The procedures described in this study can, in principle, be coupled to any of the existing methods for solving molecular kinetics for ion channels or other proteins. These concepts can be used not only to enforce existing knowledge but also to formulate and test new hypotheses. © 2018 Salari et al.

  7. 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.

  8. Kinetic and temporospatial gait parameters in a heterogeneous group of dogs.

    PubMed

    Kano, Washington T; Rahal, Sheila C; Agostinho, Felipe S; Mesquita, Luciane R; Santos, Rogerio R; Monteiro, Frederico O B; Castilho, Maira S; Melchert, Alessandra

    2016-01-04

    A prime concern of the gait analysis in a heterogeneous group of dogs is the potential influence of factors such as individual body size, body mass, type of gait, and velocity. Thus, this study aimed to evaluate in a heterogeneous group of dogs a possible correlation of the stride frequency with kinetic and temporospatial variables, as well as the percentage of body weight distribution (%BWD), and compare symmetry index (SI) between trotting and walking dogs. Twenty-nine clinically healthy dogs moving in a controlled velocity were used. The dogs were organized into two groups based on duty factor. Group 1 comprised 15 walking dogs, aged from 9 months to 8 years and weighing about 22.3 kg. Group 2 had 14 trotting dogs, aged from 1 to 6 years and weighing about 6.5 kg. The kinetic data and temporospatial parameters were obtained using a pressure-sensing walkway. The velocity was 0.9-1.1 m/s. The peak vertical force (PVF), vertical impulse (VI), gait cycle time, stance time, swing time, stride length, and percentages of body weight distribution among the four limbs were determined. For each variable, the SIs were calculated. Pearson's coefficient was used to evaluate correlation between stride frequency and other variables, initially in each group and after including all animals. Except for the %BWD (approximately 60% for the forelimbs and 40% for the hind limbs), all other parameters differed between groups. Considering each Group individually a strong correlation was observed for most of the temporospatial parameters, but no significant correlation occurred between stride frequency and PVF, and stride frequency and %BWD. However, including all dogs a strong correlation was observed in all temporospatial parameters, and moderate correlation between stride frequency and VI, and weak correlation between stride frequency and PVF. There was no correlation between stride frequency and %BWD. Groups 1 and 2 did not differ statistically in SIs. In a heterogeneous group of

  9. Blind identification of the kinetic parameters in three-compartment models

    NASA Astrophysics Data System (ADS)

    Riabkov, Dmitri Y.; Di Bella, Edward V. R.

    2004-03-01

    Quantified knowledge of tissue kinetic parameters in the regions of the brain and other organs can offer information useful in clinical and research applications. Dynamic medical imaging with injection of radioactive or paramagnetic tracer can be used for this measurement. The kinetics of some widely used tracers such as [18F]2-fluoro-2-deoxy-D-glucose can be described by a three-compartment physiological model. The kinetic parameters of the tissue can be estimated from dynamically acquired images. Feasibility of estimation by blind identification, which does not require knowledge of the blood input, is considered analytically and numerically in this work for the three-compartment type of tissue response. The non-uniqueness of the two-region case for blind identification of kinetic parameters in three-compartment model is shown; at least three regions are needed for the blind identification to be unique. Numerical results for the accuracy of these blind identification methods in different conditions were considered. Both a separable variables least-squares (SLS) approach and an eigenvector-based algorithm for multichannel blind deconvolution approach were used. The latter showed poor accuracy. Modifications for non-uniform time sampling were also developed. Also, another method which uses a model for the blood input was compared. Results for the macroparameter K, which reflects the metabolic rate of glucose usage, using three regions with noise showed comparable accuracy for the separable variables least squares method and for the input model-based method, and slightly worse accuracy for SLS with the non-uniform sampling modification.

  10. Kinetic approach to degradation mechanisms in polymer solar cells and their accurate lifetime predictions

    NASA Astrophysics Data System (ADS)

    Arshad, Muhammad Azeem; Maaroufi, AbdelKrim

    2018-07-01

    A beginning has been made in the present study regarding the accurate lifetime predictions of polymer solar cells. Certain reservations about the conventionally employed temperature accelerated lifetime measurements test for its unworthiness of predicting reliable lifetimes of polymer solar cells are brought into light. Critical issues concerning the accelerated lifetime testing include, assuming reaction mechanism instead of determining it, and relying solely on the temperature acceleration of a single property of material. An advanced approach comprising a set of theoretical models to estimate the accurate lifetimes of polymer solar cells is therefore suggested in order to suitably alternate the accelerated lifetime testing. This approach takes into account systematic kinetic modeling of various possible polymer degradation mechanisms under natural weathering conditions. The proposed kinetic approach is substantiated by its applications on experimental aging data-sets of polymer solar materials/solar cells including, P3HT polymer film, bulk heterojunction (MDMO-PPV:PCBM) and dye-sensitized solar cells. Based on the suggested approach, an efficacious lifetime determination formula for polymer solar cells is derived and tested on dye-sensitized solar cells. Some important merits of the proposed method are also pointed out and its prospective applications are discussed.

  11. Enzyme Kinetics Experiment with the Multienzyme Complex Viscozyme L and Two Substrates for the Accurate Determination of Michaelian Parameters

    ERIC Educational Resources Information Center

    Guerra, Nelson Pérez

    2017-01-01

    A laboratory experiment in which students study the kinetics of the Viscozyme-L-catalyzed hydrolysis of cellulose and starch comparatively was designed for an upper-division biochemistry laboratory. The main objective of this experiment was to provide an opportunity to perform enhanced enzyme kinetics data analysis using appropriate informatics…

  12. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

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

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-05-12

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  13. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  14. Determination of Kinetic Parameters for the Thermal Decomposition of Parthenium hysterophorus

    NASA Astrophysics Data System (ADS)

    Dhaundiyal, Alok; Singh, Suraj B.; Hanon, Muammel M.; Rawat, Rekha

    2018-02-01

    A kinetic study of pyrolysis process of Parthenium hysterophorous is carried out by using thermogravimetric analysis (TGA) equipment. The present study investigates the thermal degradation and determination of the kinetic parameters such as activation E and the frequency factor A using model-free methods given by Flynn Wall and Ozawa (FWO), Kissinger-Akahira-Sonuse (KAS) and Kissinger, and model-fitting (Coats Redfern). The results derived from thermal decomposition process demarcate decomposition of Parthenium hysterophorous among the three main stages, such as dehydration, active and passive pyrolysis. It is shown through DTG thermograms that the increase in the heating rate caused temperature peaks at maximum weight loss rate to shift towards higher temperature regime. The results are compared with Coats Redfern (Integral method) and experimental results have shown that values of kinetic parameters obtained from model-free methods are in good agreement. Whereas the results obtained through Coats Redfern model at different heating rates are not promising, however, the diffusion models provided the good fitting with the experimental data.

  15. Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

    NASA Astrophysics Data System (ADS)

    Pineda, M.; Stamatakis, M.

    2017-07-01

    Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks.

  16. Thermodynamic criteria for estimating the kinetic parameters of catalytic reactions

    NASA Astrophysics Data System (ADS)

    Mitrichev, I. I.; Zhensa, A. V.; Kol'tsova, E. M.

    2017-01-01

    Kinetic parameters are estimated using two criteria in addition to the traditional criterion that considers the consistency between experimental and modeled conversion data: thermodynamic consistency and the consistency with entropy production (i.e., the absolute rate of the change in entropy due to exchange with the environment is consistent with the rate of entropy production in the steady state). A special procedure is developed and executed on a computer to achieve the thermodynamic consistency of a set of kinetic parameters with respect to both the standard entropy of a reaction and the standard enthalpy of a reaction. A problem of multi-criterion optimization, reduced to a single-criterion problem by summing weighted values of the three criteria listed above, is solved. Using the reaction of NO reduction with CO on a platinum catalyst as an example, it is shown that the set of parameters proposed by D.B. Mantri and P. Aghalayam gives much worse agreement with experimental values than the set obtained on the basis of three criteria: the sum of the squares of deviations for conversion, the thermodynamic consistency, and the consistency with entropy production.

  17. Comparison Of A Neutron Kinetics Parameter For A Polyethylene Moderated Highly Enriched Uranium System

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

    McKenzie, IV, George Espy; Goda, Joetta Marie; Grove, Travis Justin

    This paper examines the comparison of MCNP® code’s capability to calculate kinetics parameters effectively for a thermal system containing highly enriched uranium (HEU). The Rossi-α parameter was chosen for this examination because it is relatively easy to measure as well as easy to calculate using MCNP®’s kopts card. The Rossi-α also incorporates many other parameters of interest in nuclear kinetics most of which are more difficult to precisely measure. The comparison looks at two different nuclear data libraries for comparison to the experimental data. These libraries are ENDF/BVI (.66c) and ENDF/BVII (.80c).

  18. Determination of kinetic parameters for 123-I thyroid uptake in healthy Japanese

    NASA Astrophysics Data System (ADS)

    Kusuhara, Hiroyuki; Maeda, Kazuya

    2017-09-01

    The purpose of this study was to compare the kinetic parameters for iodide thyroid accumulation in Japanese today with previously reported values. We determined the thyroid uptake of 123-I at 24 hours after the oral administration in healthy male Japanese without any diet restriction. The mean value was 16.1±5.4%, which was similar or rather lower than those previously reported in Japan (1958-1972). Kinetic model analysis was conducted to obtain the clearance for thyroid uptake from the blood circulation. The thyroid uptake clearance of 123-I was 0.540±0.073 ml/min, which was almost similar to those reported previously. There is no obvious difference in the thyroid uptake for 24 hours, and kinetic parameters in healthy Japanese for these 50 years. The fraction of distributed to the thyroid gland is lower than the ICRP reference man, and such difference must be taken into consideration to estimate the radiation exposure upon Fukushima accident in Japan.

  19. Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

    NASA Astrophysics Data System (ADS)

    Zhang, Hong; Zuo, Ran; Zhang, Guoyi

    2017-11-01

    In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

  20. An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.

    PubMed

    Ismail, Ahmad Muhaimin; Mohamad, Mohd Saberi; Abdul Majid, Hairudin; Abas, Khairul Hamimah; Deris, Safaai; Zaki, Nazar; Mohd Hashim, Siti Zaiton; Ibrahim, Zuwairie; Remli, Muhammad Akmal

    2017-12-01

    Mathematical modelling is fundamental to understand the dynamic behavior and regulation of the biochemical metabolisms and pathways that are found in biological systems. Pathways are used to describe complex processes that involve many parameters. It is important to have an accurate and complete set of parameters that describe the characteristics of a given model. However, measuring these parameters is typically difficult and even impossible in some cases. Furthermore, the experimental data are often incomplete and also suffer from experimental noise. These shortcomings make it challenging to identify the best-fit parameters that can represent the actual biological processes involved in biological systems. Computational approaches are required to estimate these parameters. The estimation is converted into multimodal optimization problems that require a global optimization algorithm that can avoid local solutions. These local solutions can lead to a bad fit when calibrating with a model. Although the model itself can potentially match a set of experimental data, a high-performance estimation algorithm is required to improve the quality of the solutions. This paper describes an improved hybrid of particle swarm optimization and the gravitational search algorithm (IPSOGSA) to improve the efficiency of a global optimum (the best set of kinetic parameter values) search. The findings suggest that the proposed algorithm is capable of narrowing down the search space by exploiting the feasible solution areas. Hence, the proposed algorithm is able to achieve a near-optimal set of parameters at a fast convergence speed. The proposed algorithm was tested and evaluated based on two aspartate pathways that were obtained from the BioModels Database. The results show that the proposed algorithm outperformed other standard optimization algorithms in terms of accuracy and near-optimal kinetic parameter estimation. Nevertheless, the proposed algorithm is only expected to work well in

  1. Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments

    NASA Astrophysics Data System (ADS)

    Aioanei, Daniel; Samorì, Bruno; Brucale, Marco

    2009-12-01

    Single molecule force spectroscopy (SMFS) is extensively used to characterize the mechanical unfolding behavior of individual protein domains under applied force by pulling chimeric polyproteins consisting of identical tandem repeats. Constant velocity unfolding SMFS data can be employed to reconstruct the protein unfolding energy landscape and kinetics. The methods applied so far require the specification of a single stretching force increase function, either theoretically derived or experimentally inferred, which must then be assumed to accurately describe the entirety of the experimental data. The very existence of a suitable optimal force model, even in the context of a single experimental data set, is still questioned. Herein, we propose a maximum likelihood (ML) framework for the estimation of protein kinetic parameters which can accommodate all the established theoretical force increase models. Our framework does not presuppose the existence of a single force characteristic function. Rather, it can be used with a heterogeneous set of functions, each describing the protein behavior in the stretching time range leading to one rupture event. We propose a simple way of constructing such a set of functions via piecewise linear approximation of the SMFS force vs time data and we prove the suitability of the approach both with synthetic data and experimentally. Additionally, when the spontaneous unfolding rate is the only unknown parameter, we find a correction factor that eliminates the bias of the ML estimator while also reducing its variance. Finally, we investigate which of several time-constrained experiment designs leads to better estimators.

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

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

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

    2013-12-14

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

  3. Kinetic Parameter Measurements in the MINERVE Reactor

    NASA Astrophysics Data System (ADS)

    Perret, Grégory; Geslot, Benoit; Gruel, Adrien; Blaise, Patrick; Di-Salvo, Jacques; De Izarra, Grégoire; Jammes, Christian; Hursin, Mathieu; Pautz, Andréas

    2017-01-01

    In the framework of an international collaboration, teams of the PSI and CEA research institutes measure the critical decay constant (α0 = β/A), delayed neutron fraction (β) and generation time (A) of the Minerve reactor using the Feynman-α, Power Spectral Density and Rossi-α neutron noise measurement techniques. These measurements contribute to the experimental database of kinetic parameters used to improve nuclear data files and validate modern methods in Monte Carlo codes. Minerve is a zero-power pool reactor composed of a central experimental test lattice surrounded by a large aluminum buffer and four high-enriched driver regions. Measurements are performed in three slightly subcritical configurations (-2 cents to -30 cents) using two high-efficiency 235U fission chambers in the driver regions. Measurement of α0 and β obtained by the two institutes and with the different techniques are consistent for the configurations envisaged. Slight increases of the β values are observed with the subcriticality level. Best estimate values are obtained with the Cross-Power Spectral Density technique at -2 cents, and are worth: β = 716.9±9.0 pcm, α0 = 79.0±0.6 s-1 and A = 90.7±1.4 μs. The kinetic parameters are predicted with MCNP5-v1.6 and TRIPOLI4.9 and the JEFF-3.1/3.1.1 and ENDF/B-VII.1 nuclear data libraries. The predictions for β and α0 overestimate the experimental results by 3-5% and 10-12%, respectively; that for A underestimate the experimental result by 6-7%. The discrepancies are suspected to come from the driven system nature of Minerve and the location of the detectors in the driver regions, which prevent accounting for the full reactor.

  4. Modification of the kinetic parameters of aldolase on binding to the actin-containing filaments of skeletal muscle.

    PubMed Central

    Walsh, T P; Clarke, F M; Masters, C J

    1977-01-01

    The kinetic parameters of fructose bisphosphate aldolase (EC 4.1.2.13) were shown to be modified on binding of the enzyme to the actin-containing filaments of skeletal muscle. Although binding to F-actin or F-actin-tropomyosin filaments results in relative minor changes in kinetic properties, binding to F-actin-tropomyosin-troponin filaments produces major alterations in the kinetic parameters, and, in addition, renders them Ca2+-sensitive. These observations may be relevant to an understanding of the function of this enzyme within the muscle fibre. PMID:889571

  5. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models

    PubMed Central

    2011-01-01

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison. PMID:21989173

  6. iSCHRUNK--In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks.

    PubMed

    Andreozzi, Stefano; Miskovic, Ljubisa; Hatzimanikatis, Vassily

    2016-01-01

    Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-based metabolic flux analysis contribute to improved understanding of steady-state properties of metabolism. However, knowledge about kinetics and enzyme activities though essential for quantitative understanding of metabolic dynamics remains scarce and involves uncertainty. Here, we present a computational methodology that allow us to determine and quantify the kinetic parameters that correspond to a certain physiology as it is described by a given metabolic flux profile and a given metabolite concentration vector. Though we initially determine kinetic parameters that involve a high degree of uncertainty, through the use of kinetic modeling and machine learning principles we are able to obtain more accurate ranges of kinetic parameters, and hence we are able to reduce the uncertainty in the model analysis. We computed the distribution of kinetic parameters for glucose-fed E. coli producing 1,4-butanediol and we discovered that the observed physiological state corresponds to a narrow range of kinetic parameters of only a few enzymes, whereas the kinetic parameters of other enzymes can vary widely. Furthermore, this analysis suggests which are the enzymes that should be manipulated in order to engineer the reference state of the cell in a desired way. The proposed approach also sets up the foundations of a novel type of approaches for efficient, non-asymptotic, uniform sampling of solution spaces. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  7. Dynamic identification of growth and survival kinetic parameters of microorganisms in foods

    USDA-ARS?s Scientific Manuscript database

    Inverse analysis is a mathematical method used in predictive microbiology to determine the kinetic parameters of microbial growth and survival in foods. The traditional approach in inverse analysis relies on isothermal experiments that are time-consuming and labor-intensive, and errors are accumula...

  8. Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

    PubMed

    Chiang, Austin W T; Liu, Wei-Chung; Charusanti, Pep; Hwang, Ming-Jing

    2014-01-15

    A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

  9. Kinetic parameters and structural variations in Cu-Al-Mn and Cu-Al-Mn-Mg shape memory alloys

    NASA Astrophysics Data System (ADS)

    Canbay, Canan Aksu

    2017-02-01

    In this work polycrystalline Cu-Al-Mn and Cu-Al-Mn-Mg SMAs were fabricated by arc melting. The thermal analysis was made to determine the characteristic transformation temperatures of the samples and kinetic parameters. Also the effect of Mg on transformation temperatures and kinetic parameters detected. The structural analysis was made to designate the diffraction planes of martensite phase at room temperature and this was supported by optical measurement observations.

  10. TU-C-12A-11: Comparisons Between Cu-ATSM PET and DCE-CT Kinetic Parameters in Canine Sinonasal Tumors

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

    La Fontaine, M; Bradshaw, T; Kubicek, L

    2014-06-15

    Purpose: Regions of poor perfusion within tumors may be associated with higher hypoxic levels. This study aimed to test this hypothesis by comparing measurements of hypoxia from Cu-ATSM PET to vasculature kinetic parameters from DCE-CT kinetic analysis. Methods: Ten canine patients with sinonasal tumors received one Cu-ATSM PET/CT scan and three DCE-CT scans prior to treatment. Cu-ATSM PET/CT and DCE-CT scans were registered and resampled to matching voxel dimensions. Kinetic analysis was performed on DCE-CT scans and for each patient, the resulting kinetic parameter values from the three DCE-CT scans were averaged together. Cu-ATSM SUVs were spatially correlated (r{sub spatial})more » on a voxel-to-voxel basis against the following DCE-CT kinetic parameters: transit time (t{sub 1}), blood flow (F), vasculature fraction (v{sub 1}), and permeability (PS). In addition, whole-tumor comparisons were performed by correlating (r{sub ROI}) the mean Cu-ATSM SUV (SUV{sub mean}) with median kinetic parameter values. Results: The spatial correlations (r{sub spatial}) were poor and ranged from -0.04 to 0.21 for all kinetic parameters. These low spatial correlations may be due to high variability in the DCE-CT kinetic parameter voxel values between scans. In our hypothesis, t{sub 1} was expected to have a positive correlation, while F was expected to have a negative correlation to hypoxia. However, in wholetumor analysis the opposite was found for both t{sub 1} (r{sub ROI} = -0.25) and F (r{sub ROI} = 0.56). PS and v{sub 1} may depict angiogenic responses to hypoxia and found positive correlations to Cu-ATSM SUV for PS (r{sub ROI} = 0.41), and v{sub 1} (r{sub ROI} = 0.57). Conclusion: Low spatial correlations were found between Cu-ATSM uptake and DCE-CT vasculature parameters, implying that poor perfusion is not associated with higher hypoxic regions. Across patients, the most hypoxic tumors tended to have higher blood flow values, which is contrary to our initial hypothesis

  11. 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.

  12. An efficient and accurate two-stage fourth-order gas-kinetic scheme for the Euler and Navier-Stokes equations

    NASA Astrophysics Data System (ADS)

    Pan, Liang; Xu, Kun; Li, Qibing; Li, Jiequan

    2016-12-01

    For computational fluid dynamics (CFD), the generalized Riemann problem (GRP) solver and the second-order gas-kinetic scheme (GKS) provide a time-accurate flux function starting from a discontinuous piecewise linear flow distributions around a cell interface. With the adoption of time derivative of the flux function, a two-stage Lax-Wendroff-type (L-W for short) time stepping method has been recently proposed in the design of a fourth-order time accurate method for inviscid flow [21]. In this paper, based on the same time-stepping method and the second-order GKS flux function [42], a fourth-order gas-kinetic scheme is constructed for the Euler and Navier-Stokes (NS) equations. In comparison with the formal one-stage time-stepping third-order gas-kinetic solver [24], the current fourth-order method not only reduces the complexity of the flux function, but also improves the accuracy of the scheme. In terms of the computational cost, a two-dimensional third-order GKS flux function takes about six times of the computational time of a second-order GKS flux function. However, a fifth-order WENO reconstruction may take more than ten times of the computational cost of a second-order GKS flux function. Therefore, it is fully legitimate to develop a two-stage fourth order time accurate method (two reconstruction) instead of standard four stage fourth-order Runge-Kutta method (four reconstruction). Most importantly, the robustness of the fourth-order GKS is as good as the second-order one. In the current computational fluid dynamics (CFD) research, it is still a difficult problem to extend the higher-order Euler solver to the NS one due to the change of governing equations from hyperbolic to parabolic type and the initial interface discontinuity. This problem remains distinctively for the hypersonic viscous and heat conducting flow. The GKS is based on the kinetic equation with the hyperbolic transport and the relaxation source term. The time-dependent GKS flux function

  13. Optimization of kinetic parameters for the degradation of plasmid DNA in rat plasma

    NASA Astrophysics Data System (ADS)

    Chaudhry, Q. A.

    2014-12-01

    Biotechnology is a rapidly growing area of research work in the field of pharmaceutical sciences. The study of pharmacokinetics of plasmid DNA (pDNA) is an important area of research work. It has been observed that the process of gene delivery faces many troubles on the transport of pDNA towards their target sites. The topoforms of pDNA has been termed as super coiled (S-C), open circular (O-C) and linear (L), the kinetic model of which will be presented in this paper. The kinetic model gives rise to system of ordinary differential equations (ODEs), the exact solution of which has been found. The kinetic parameters, which are responsible for the degradation of super coiled, and the formation of open circular and linear topoforms have a great significance not only in vitro but for modeling of further processes as well, therefore need to be addressed in great detail. For this purpose, global optimization techniques have been adopted, thus finding the optimal results for the said model. The results of the model, while using the optimal parameters, were compared against the measured data, which gives a nice agreement.

  14. Numerically accurate computational techniques for optimal estimator analyses of multi-parameter models

    NASA Astrophysics Data System (ADS)

    Berger, Lukas; Kleinheinz, Konstantin; Attili, Antonio; Bisetti, Fabrizio; Pitsch, Heinz; Mueller, Michael E.

    2018-05-01

    Modelling unclosed terms in partial differential equations typically involves two steps: First, a set of known quantities needs to be specified as input parameters for a model, and second, a specific functional form needs to be defined to model the unclosed terms by the input parameters. Both steps involve a certain modelling error, with the former known as the irreducible error and the latter referred to as the functional error. Typically, only the total modelling error, which is the sum of functional and irreducible error, is assessed, but the concept of the optimal estimator enables the separate analysis of the total and the irreducible errors, yielding a systematic modelling error decomposition. In this work, attention is paid to the techniques themselves required for the practical computation of irreducible errors. Typically, histograms are used for optimal estimator analyses, but this technique is found to add a non-negligible spurious contribution to the irreducible error if models with multiple input parameters are assessed. Thus, the error decomposition of an optimal estimator analysis becomes inaccurate, and misleading conclusions concerning modelling errors may be drawn. In this work, numerically accurate techniques for optimal estimator analyses are identified and a suitable evaluation of irreducible errors is presented. Four different computational techniques are considered: a histogram technique, artificial neural networks, multivariate adaptive regression splines, and an additive model based on a kernel method. For multiple input parameter models, only artificial neural networks and multivariate adaptive regression splines are found to yield satisfactorily accurate results. Beyond a certain number of input parameters, the assessment of models in an optimal estimator analysis even becomes practically infeasible if histograms are used. The optimal estimator analysis in this paper is applied to modelling the filtered soot intermittency in large eddy

  15. Ammonium Removal from Aqueous Solutions by Clinoptilolite: Determination of Isotherm and Thermodynamic Parameters and Comparison of Kinetics by the Double Exponential Model and Conventional Kinetic Models

    PubMed Central

    Tosun, İsmail

    2012-01-01

    The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R2) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients. PMID:22690177

  16. Ammonium removal from aqueous solutions by clinoptilolite: determination of isotherm and thermodynamic parameters and comparison of kinetics by the double exponential model and conventional kinetic models.

    PubMed

    Tosun, Ismail

    2012-03-01

    The adsorption isotherm, the adsorption kinetics, and the thermodynamic parameters of ammonium removal from aqueous solution by using clinoptilolite in aqueous solution was investigated in this study. Experimental data obtained from batch equilibrium tests have been analyzed by four two-parameter (Freundlich, Langmuir, Tempkin and Dubinin-Radushkevich (D-R)) and four three-parameter (Redlich-Peterson (R-P), Sips, Toth and Khan) isotherm models. D-R and R-P isotherms were the models that best fitted to experimental data over the other two- and three-parameter models applied. The adsorption energy (E) from the D-R isotherm was found to be approximately 7 kJ/mol for the ammonium-clinoptilolite system, thereby indicating that ammonium is adsorbed on clinoptilolite by physisorption. Kinetic parameters were determined by analyzing the nth-order kinetic model, the modified second-order model and the double exponential model, and each model resulted in a coefficient of determination (R(2)) of above 0.989 with an average relative error lower than 5%. A Double Exponential Model (DEM) showed that the adsorption process develops in two stages as rapid and slow phase. Changes in standard free energy (∆G°), enthalpy (∆H°) and entropy (∆S°) of ammonium-clinoptilolite system were estimated by using the thermodynamic equilibrium coefficients.

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

    ERIC Educational Resources Information Center

    Ribas, Joan; And Others

    1988-01-01

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

  18. Improved Parameter-Estimation With MRI-Constrained PET Kinetic Modeling: A Simulation Study

    NASA Astrophysics Data System (ADS)

    Erlandsson, Kjell; Liljeroth, Maria; Atkinson, David; Arridge, Simon; Ourselin, Sebastien; Hutton, Brian F.

    2016-10-01

    Kinetic analysis can be applied both to dynamic PET and dynamic contrast enhanced (DCE) MRI data. We have investigated the potential of MRI-constrained PET kinetic modeling using simulated [ 18F]2-FDG data for skeletal muscle. The volume of distribution, Ve, for the extra-vascular extra-cellular space (EES) is the link between the two models: It can be estimated by DCE-MRI, and then used to reduce the number of parameters to estimate in the PET model. We used a 3 tissue-compartment model with 5 rate constants (3TC5k), in order to distinguish between EES and the intra-cellular space (ICS). Time-activity curves were generated by simulation using the 3TC5k model for 3 different Ve values under basal and insulin stimulated conditions. Noise was added and the data were fitted with the 2TC3k model and with the 3TC5k model with and without Ve constraint. One hundred noise-realisations were generated at 4 different noise-levels. The results showed reductions in bias and variance with Ve constraint in the 3TC5k model. We calculated the parameter k3", representing the combined effect of glucose transport across the cellular membrane and phosphorylation, as an extra outcome measure. For k3", the average coefficient of variation was reduced from 52% to 9.7%, while for k3 in the standard 2TC3k model it was 3.4%. The accuracy of the parameters estimated with our new modeling approach depends on the accuracy of the assumed Ve value. In conclusion, we have shown that, by utilising information that could be obtained from DCE-MRI in the kinetic analysis of [ 18F]2-FDG-PET data, it is in principle possible to obtain better parameter estimates with a more complex model, which may provide additional information as compared to the standard model.

  19. Fast pyrolysis kinetics of alkali lignin: Evaluation of apparent rate parameters and product time evolution.

    PubMed

    Ojha, Deepak Kumar; Viju, Daniel; Vinu, R

    2017-10-01

    In this study, the apparent kinetics of fast pyrolysis of alkali lignin was evaluated by obtaining isothermal mass loss data in the timescale of 2-30s at 400-700°C in an analytical pyrolyzer. The data were analyzed using different reaction models to determine the rate constants and apparent rate parameters. First order and one dimensional diffusion models resulted in good fits with experimental data with apparent activation energy of 23kJmol -1 . Kinetic compensation effect was established using a large number of kinetic parameters reported in the literature for pyrolysis of different lignins. The time evolution of the major functional groups in the pyrolysate was analyzed using in situ Fourier transform infrared spectroscopy. Maximum production of the volatiles occurred around 10-12s. A clear transformation of guaiacols to phenol, catechol and their derivatives, and aromatic hydrocarbons was observed with increasing temperature. The plausible reaction steps involved in various transformations are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Reliability of spatiotemporal and kinetic gait parameters determined by a new instrumented treadmill system.

    PubMed

    Reed, Lloyd F; Urry, Stephen R; Wearing, Scott C

    2013-08-21

    Despite the emerging use of treadmills integrated with pressure platforms as outcome tools in both clinical and research settings, published evidence regarding the measurement properties of these new systems is limited. This study evaluated the within- and between-day repeatability of spatial, temporal and vertical ground reaction force parameters measured by a treadmill system instrumented with a capacitance-based pressure platform. Thirty three healthy adults (mean age, 21.5 ± 2.8 years; height, 168.4 ± 9.9 cm; and mass, 67.8 ± 18.6 kg), walked barefoot on a treadmill system (FDM-THM-S, Zebris Medical GmbH) on three separate occasions. For each testing session, participants set their preferred pace but were blinded to treadmill speed. Spatial (foot rotation, step width, stride and step length), temporal (stride and step times, duration of stance, swing and single and double support) and peak vertical ground reaction force variables were collected over a 30-second capture period, equating to an average of 52 ± 5 steps of steady-state walking. Testing was repeated one week following the initial trial and again, for a third time, 20 minutes later. Repeated measures ANOVAs within a generalized linear modelling framework were used to assess between-session differences in gait parameters. Agreement between gait parameters measured within the same day (session 2 and 3) and between days (session 1 and 2; 1 and 3) were evaluated using the 95% repeatability coefficient. There were statistically significant differences in the majority (14/16) of temporal, spatial and kinetic gait parameters over the three test sessions (P < .01). The minimum change that could be detected with 95% confidence ranged between 3% and 17% for temporal parameters, 14% and 33% for spatial parameters, and 4% and 20% for kinetic parameters between days. Within-day repeatability was similar to that observed between days. Temporal and kinetic gait parameters were typically more

  1. Data Mining for Efficient and Accurate Large Scale Retrieval of Geophysical Parameters

    NASA Astrophysics Data System (ADS)

    Obradovic, Z.; Vucetic, S.; Peng, K.; Han, B.

    2004-12-01

    Our effort is devoted to developing data mining technology for improving efficiency and accuracy of the geophysical parameter retrievals by learning a mapping from observation attributes to the corresponding parameters within the framework of classification and regression. We will describe a method for efficient learning of neural network-based classification and regression models from high-volume data streams. The proposed procedure automatically learns a series of neural networks of different complexities on smaller data stream chunks and then properly combines them into an ensemble predictor through averaging. Based on the idea of progressive sampling the proposed approach starts with a very simple network trained on a very small chunk and then gradually increases the model complexity and the chunk size until the learning performance no longer improves. Our empirical study on aerosol retrievals from data obtained with the MISR instrument mounted at Terra satellite suggests that the proposed method is successful in learning complex concepts from large data streams with near-optimal computational effort. We will also report on a method that complements deterministic retrievals by constructing accurate predictive algorithms and applying them on appropriately selected subsets of observed data. The method is based on developing more accurate predictors aimed to catch global and local properties synthesized in a region. The procedure starts by learning the global properties of data sampled over the entire space, and continues by constructing specialized models on selected localized regions. The global and local models are integrated through an automated procedure that determines the optimal trade-off between the two components with the objective of minimizing the overall mean square errors over a specific region. Our experimental results on MISR data showed that the combined model can increase the retrieval accuracy significantly. The preliminary results on various

  2. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji

    2018-04-01

    In molecular dynamics (MD) simulations, a proper definition of kinetic energy is essential for controlling pressure as well as temperature in the isothermal-isobaric condition. The virial theorem provides an equation that connects the average kinetic energy with the product of particle coordinate and force. In this paper, we show that the theorem is satisfied in MD simulations with a larger time step and holonomic constraints of bonds, only when a proper definition of kinetic energy is used. We provide a novel definition of kinetic energy, which is calculated from velocities at the half-time steps (t - Δt/2 and t + Δt/2) in the velocity Verlet integration method. MD simulations of a 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer and a water box using the kinetic energy definition could reproduce the physical properties in the isothermal-isobaric condition properly. We also develop a multiple time step (MTS) integration scheme with the kinetic energy definition. MD simulations with the MTS integration for the DPPC and water box systems provided the same quantities as the velocity Verlet integration method, even when the thermostat and barostat are updated less frequently.

  3. Kinetic energy definition in velocity Verlet integration for accurate pressure evaluation.

    PubMed

    Jung, Jaewoon; Kobayashi, Chigusa; Sugita, Yuji

    2018-04-28

    In molecular dynamics (MD) simulations, a proper definition of kinetic energy is essential for controlling pressure as well as temperature in the isothermal-isobaric condition. The virial theorem provides an equation that connects the average kinetic energy with the product of particle coordinate and force. In this paper, we show that the theorem is satisfied in MD simulations with a larger time step and holonomic constraints of bonds, only when a proper definition of kinetic energy is used. We provide a novel definition of kinetic energy, which is calculated from velocities at the half-time steps (t - Δt/2 and t + Δt/2) in the velocity Verlet integration method. MD simulations of a 1,2-dispalmitoyl-sn-phosphatidylcholine (DPPC) lipid bilayer and a water box using the kinetic energy definition could reproduce the physical properties in the isothermal-isobaric condition properly. We also develop a multiple time step (MTS) integration scheme with the kinetic energy definition. MD simulations with the MTS integration for the DPPC and water box systems provided the same quantities as the velocity Verlet integration method, even when the thermostat and barostat are updated less frequently.

  4. Bayesian parameter estimation of a k-ε model for accurate jet-in-crossflow simulations

    DOE PAGES

    Ray, Jaideep; Lefantzi, Sophia; Arunajatesan, Srinivasan; ...

    2016-05-31

    Reynolds-averaged Navier–Stokes models are not very accurate for high-Reynolds-number compressible jet-in-crossflow interactions. The inaccuracy arises from the use of inappropriate model parameters and model-form errors in the Reynolds-averaged Navier–Stokes model. In this study, the hypothesis is pursued that Reynolds-averaged Navier–Stokes predictions can be significantly improved by using parameters inferred from experimental measurements of a supersonic jet interacting with a transonic crossflow.

  5. Automated Transition State Theory Calculations for High-Throughput Kinetics.

    PubMed

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

    2017-09-21

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

  6. Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling

    NASA Astrophysics Data System (ADS)

    Sutton, Jonathan E.; Guo, Wei; Katsoulakis, Markos A.; Vlachos, Dionisios G.

    2016-04-01

    Kinetic models based on first principles are becoming common place in heterogeneous catalysis because of their ability to interpret experimental data, identify the rate-controlling step, guide experiments and predict novel materials. To overcome the tremendous computational cost of estimating parameters of complex networks on metal catalysts, approximate quantum mechanical calculations are employed that render models potentially inaccurate. Here, by introducing correlative global sensitivity analysis and uncertainty quantification, we show that neglecting correlations in the energies of species and reactions can lead to an incorrect identification of influential parameters and key reaction intermediates and reactions. We rationalize why models often underpredict reaction rates and show that, despite the uncertainty being large, the method can, in conjunction with experimental data, identify influential missing reaction pathways and provide insights into the catalyst active site and the kinetic reliability of a model. The method is demonstrated in ethanol steam reforming for hydrogen production for fuel cells.

  7. Kinetics of suicide substrates. Practical procedures for determining parameters.

    PubMed Central

    Waley, S G

    1985-01-01

    Many clinically important or mechanistically interesting inhibitors react with enzymes by a branched pathway in which inactivation of the enzyme and formation of product are competing reactions. The steady-state kinetics for this pathway [Waley (1980) Biochem. J. 185, 771-773] gave equations for progress curves that were cumbersome. A convenient linear plot is now described. The time (t1/2) for 50% inactivation of the enzyme (this is also the time for 50% formation of product), or for 50% loss of substrate, is measured in a series of experiments in which the concentration of inhibitor, [I]0, is varied; in these experiments the ratio of the concentration of enzyme to the concentration of inhibitor is kept fixed. Then a plot of [I]0 X t1/2 against [I]0 is linear, and the kinetic parameters can be found from the slope and intercept. Furthermore, simplifications of the equations for progress curves are described that are valid when the concentration of inhibitors is high, or is low, or when the extent of reaction is low. The use of simulated data has shown that the recommended methods are not unduly sensitive to experimental error. PMID:4004802

  8. Two-order parameters theory of the metal-insulator phase transition kinetics in the magnetic field

    NASA Astrophysics Data System (ADS)

    Dubovskii, L. B.

    2018-05-01

    The metal-insulator phase transition is considered within the framework of the Ginzburg-Landau approach for the phase transition described with two coupled order parameters. One of the order parameters is the mass density which variation is responsible for the origin of nonzero overlapping of the two different electron bands and the appearance of free electron carriers. This transition is assumed to be a first-order phase one. The free electron carriers are described with the vector-function representing the second-order parameter responsible for the continuous phase transition. This order parameter determines mostly the physical properties of the metal-insulator transition and leads to a singularity of the surface tension at the metal-insulator interface. The magnetic field is involved into the consideration of the system. The magnetic field leads to new singularities of the surface tension at the metal-insulator interface and results in a drastic variation of the phase transition kinetics. A strong singularity in the surface tension results from the Landau diamagnetism and determines anomalous features of the metal-insulator transition kinetics.

  9. Inter-trial and test–retest reliability of kinematic and kinetic gait parameters among subjects with adolescent idiopathic scoliosis

    PubMed Central

    Nadeau, Sylvie; Labelle, Hubert

    2007-01-01

    Gait analysis is actually used in subjects with scoliosis to determine the change in lower limb parameters after surgery, but the reliability of these parameters still remained unknown. The purpose of this study was to assess the repeatability of traditional gait parameters in subjects with adolescent idiopathic scoliosis (AIS) and to estimate the associated standard error of measurement (SEM). A test–retest design was used to assess the reliability of gait parameters at self-selected and fast speeds. A convenience sample of 20 girls aged from 12 to 17 years, with an idiopathic scoliosis (King classification: types I, II or III; Cobb angle 17–50°) participated in the study. Five good trials were recorded on two occasions. The time-distance, kinematic, and kinetic gait parameters were recorded using foot-switches in combination with a three-dimensional motion analysis system (Optotrak) and Advanced Mechanical Technologies Inc., (AMTI) Watertown, MA, USA; force plates. The coefficients of dependability and SEM derived from the generalizability theory were used to assess the reliability. Inter-trial reliability was good for time-distance, kinematic, and kinetic (absolute and normalized) gait parameters except for the medio-lateral ground reaction force (GRF) component and the ankle dorsiflexor moment (ϕ = 0.60–0.77). Test–retest reliability was higher for the kinetic than for the kinematic parameters. These coefficients ranged from 0.42 to 0.58 for the time-distance parameters; from 0.55 to 0.88 for the angular displacements and from 0.25 to 0.99 for the kinetic parameters. The SEMs were lower than 3.3° for the angular displacements and lower than 8 Nm (0.15 Nm/kg) and 36 W (0.54 W/Kg) for the joint moments and powers regardless of the speed. Several gait parameters are reliable among subjects with AIS and can be used to assess the evolution of the spinal modifications and the impact of treatment on their lower limb gait pattern. PMID:17891424

  10. Determination of kinetic parameters of 1,3-propanediol fermentation by Clostridium diolis using statistically optimized medium.

    PubMed

    Kaur, Guneet; Srivastava, Ashok K; Chand, Subhash

    2012-09-01

    1,3-propanediol (1,3-PD) is a chemical compound of immense importance primarily used as a raw material for fiber and textile industry. It can be produced by the fermentation of glycerol available abundantly as a by-product from the biodiesel plant. The present study was aimed at determination of key kinetic parameters of 1,3-PD fermentation by Clostridium diolis. Initial experiments on microbial growth inhibition were followed by optimization of nutrient medium recipe by statistical means. Batch kinetic data from studies in bioreactor using optimum concentration of variables obtained from statistical medium design was used for estimation of kinetic parameters of 1,3-PD production. Direct use of raw glycerol from biodiesel plant without any pre-treatment for 1,3-PD production using this strain investigated for the first time in this work gave results comparable to commercial glycerol. The parameter values obtained in this study would be used to develop a mathematical model for 1,3-PD to be used as a guide for designing various reactor operating strategies for further improving 1,3-PD production. An outline of protocol for model development has been discussed in the present work.

  11. Classical nucleation theory of homogeneous freezing of water: thermodynamic and kinetic parameters.

    PubMed

    Ickes, Luisa; Welti, André; Hoose, Corinna; Lohmann, Ulrike

    2015-02-28

    The probability of homogeneous ice nucleation under a set of ambient conditions can be described by nucleation rates using the theoretical framework of Classical Nucleation Theory (CNT). This framework consists of kinetic and thermodynamic parameters, of which three are not well-defined (namely the interfacial tension between ice and water, the activation energy and the prefactor), so that any CNT-based parameterization of homogeneous ice formation is less well-constrained than desired for modeling applications. Different approaches to estimate the thermodynamic and kinetic parameters of CNT are reviewed in this paper and the sensitivity of the calculated nucleation rate to the choice of parameters is investigated. We show that nucleation rates are very sensitive to this choice. The sensitivity is governed by one parameter - the interfacial tension between ice and water, which determines the energetic barrier of the nucleation process. The calculated nucleation rate can differ by more than 25 orders of magnitude depending on the choice of parameterization for this parameter. The second most important parameter is the activation energy of the nucleation process. It can lead to a variation of 16 orders of magnitude. By estimating the nucleation rate from a collection of droplet freezing experiments from the literature, the dependence of these two parameters on temperature is narrowed down. It can be seen that the temperature behavior of these two parameters assumed in the literature does not match with the predicted nucleation rates from the fit in most cases. Moreover a comparison of all possible combinations of theoretical parameterizations of the dominant two free parameters shows that one combination fits the fitted nucleation rates best, which is a description of the interfacial tension coming from a molecular model [Reinhardt and Doye, J. Chem. Phys., 2013, 139, 096102] in combination with the activation energy derived from self-diffusion measurements [Zobrist

  12. Kinetic study of corn straw pyrolysis: comparison of two different three-pseudocomponent models.

    PubMed

    Li, Zhengqi; Zhao, Wei; Meng, Baihong; Liu, Chunlong; Zhu, Qunyi; Zhao, Guangbo

    2008-11-01

    With heating rates of 20, 50 and 100 K min(-1), the thermal decomposition of corn straw samples (corn stalks skins, corn stalks cores, corn bracts and corn leaves) were studied using thermogravimetric analysis. The maximum pyrolysis rates increased with the heating rate increasing and the temperature at the peak pyrolysis rate also increased. Assuming the addition of three independent parallel reactions, corresponding to three pseudocomponents linked to the hemicellulose, cellulose and lignin, two different three-pseudocomponent models were used to simulate the corn straw pyrolysis. Model parameters of pyrolysis were given. It was found that the three-pseudocomponent model with n-order kinetics was more accurate than the model with first-order kinetics at most cases. It showed that the model with n-order kinetics was more accurate to describe the pyrolysis of the hemicellulose.

  13. Effective potential kinetic theory for strongly coupled plasmas

    NASA Astrophysics Data System (ADS)

    Baalrud, Scott D.; Daligault, Jérôme

    2016-11-01

    The effective potential theory (EPT) is a recently proposed method for extending traditional plasma kinetic and transport theory into the strongly coupled regime. Validation from experiments and molecular dynamics simulations have shown it to be accurate up to the onset of liquid-like correlation parameters (corresponding to Γ ≃ 10-50 for the one-component plasma, depending on the process of interest). Here, this theory is briefly reviewed along with comparisons between the theory and molecular dynamics simulations for self-diffusivity and viscosity of the one-component plasma. A number of new results are also provided, including calculations of friction coefficients, energy exchange rates, stopping power, and mobility. The theory is also cast in the Landau and Fokker-Planck kinetic forms, which may prove useful for enabling efficient kinetic computations.

  14. Plyometric Long Jump Training With Progressive Loading Improves Kinetic and Kinematic Swimming Start Parameters.

    PubMed

    Rebutini, Vanessa Z; Pereira, Gleber; Bohrer, Roberta C D; Ugrinowitsch, Carlos; Rodacki, André L F

    2016-09-01

    Rebutini, VZ, Pereira, G, Bohrer, RCD, Ugrinowitsch, C, and Rodacki, ALF. Plyometric long jump training with progressive loading improves kinetic and kinematic swimming start parameters. J Strength Cond Res 30(9): 2392-2398, 2016-This study was aimed to determine the effects of a plyometric long jump training program on torque around the lower limb joints and kinetic and kinematics parameters during the swimming jump start. Ten swimmers performed 3 identical assessment sessions, measuring hip and knee muscle extensors during maximal voluntary isometric contraction and kinetic and kinematics parameters during the swimming jump start, at 3 instants: INI (2 weeks before the training program, control period), PRE (2 weeks after INI measurements), and POST (24-48 hours after 9 weeks of training). There were no significant changes from INI to PRE measurements. However, the peak torque and rate of torque development increased significantly from PRE to POST measurements for both hip (47 and 108%) and knee (24 and 41%) joints. There were significant improvements to the horizontal force (7%), impulse (9%), and angle of resultant force (19%). In addition, there were significant improvements to the center of mass displacement (5%), horizontal takeoff velocity (16%), horizontal velocity at water entrance (22%), and peak angle velocity for the knee (15%) and hip joints (16%). Therefore, the plyometric long jump training protocol was effective to enhance torque around the lower limb joints and to control the resultant vector direction, to increase the swimming jump start performance. These findings suggest that coaches should use long jump training instead of vertical jump training to improve swimming start performance.

  15. Estimation of fundamental kinetic parameters of polyhydroxybutyrate fermentation process of Azohydromonas australica using statistical approach of media optimization.

    PubMed

    Gahlawat, Geeta; Srivastava, Ashok K

    2012-11-01

    Polyhydroxybutyrate or PHB is a biodegradable and biocompatible thermoplastic with many interesting applications in medicine, food packaging, and tissue engineering materials. The present study deals with the enhanced production of PHB by Azohydromonas australica using sucrose and the estimation of fundamental kinetic parameters of PHB fermentation process. The preliminary culture growth inhibition studies were followed by statistical optimization of medium recipe using response surface methodology to increase the PHB production. Later on batch cultivation in a 7-L bioreactor was attempted using optimum concentration of medium components (process variables) obtained from statistical design to identify the batch growth and product kinetics parameters of PHB fermentation. A. australica exhibited a maximum biomass and PHB concentration of 8.71 and 6.24 g/L, respectively in bioreactor with an overall PHB production rate of 0.75 g/h. Bioreactor cultivation studies demonstrated that the specific biomass and PHB yield on sucrose was 0.37 and 0.29 g/g, respectively. The kinetic parameters obtained in the present investigation would be used in the development of a batch kinetic mathematical model for PHB production which will serve as launching pad for further process optimization studies, e.g., design of several bioreactor cultivation strategies to further enhance the biopolymer production.

  16. Computer-Aided Construction of Chemical Kinetic Models

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

    Green, William H.

    2014-12-31

    The combustion chemistry of even simple fuels can be extremely complex, involving hundreds or thousands of kinetically significant species. The most reasonable way to deal with this complexity is to use a computer not only to numerically solve the kinetic model, but also to construct the kinetic model in the first place. Because these large models contain so many numerical parameters (e.g. rate coefficients, thermochemistry) one never has sufficient data to uniquely determine them all experimentally. Instead one must work in “predictive” mode, using theoretical rather than experimental values for many of the numbers in the model, and as appropriatemore » refining the most sensitive numbers through experiments. Predictive chemical kinetics is exactly what is needed for computer-aided design of combustion systems based on proposed alternative fuels, particularly for early assessment of the value and viability of proposed new fuels before those fuels are commercially available. This project was aimed at making accurate predictive chemical kinetics practical; this is a challenging goal which requires a range of science advances. The project spanned a wide range from quantum chemical calculations on individual molecules and elementary-step reactions, through the development of improved rate/thermo calculation procedures, the creation of algorithms and software for constructing and solving kinetic simulations, the invention of methods for model-reduction while maintaining error control, and finally comparisons with experiment. Many of the parameters in the models were derived from quantum chemistry calculations, and the models were compared with experimental data measured in our lab or in collaboration with others.« less

  17. The influence of pH adjustment on kinetics parameters in tapioca wastewater treatment using aerobic sequencing batch reactor system

    NASA Astrophysics Data System (ADS)

    Mulyani, Happy; Budianto, Gregorius Prima Indra; Margono, Kaavessina, Mujtahid

    2018-02-01

    The present investigation deals with the aerobic sequencing batch reactor system of tapioca wastewater treatment with varying pH influent conditions. This project was carried out to evaluate the effect of pH on kinetics parameters of system. It was done by operating aerobic sequencing batch reactor system during 8 hours in many tapioca wastewater conditions (pH 4.91, pH 7, pH 8). The Chemical Oxygen Demand (COD) and Mixed Liquor Volatile Suspended Solids (MLVSS) of the aerobic sequencing batch reactor system effluent at steady state condition were determined at interval time of two hours to generate data for substrate inhibition kinetics parameters. Values of the kinetics constants were determined using Monod and Andrews models. There was no inhibition constant (Ki) detected in all process variation of aerobic sequencing batch reactor system for tapioca wastewater treatment in this study. Furthermore, pH 8 was selected as the preferred aerobic sequencing batch reactor system condition in those ranging pH investigated due to its achievement of values of kinetics parameters such µmax = 0.010457/hour and Ks = 255.0664 mg/L COD.

  18. Kinetic characterisation of primer mismatches in allele-specific PCR: a quantitative assessment.

    PubMed

    Waterfall, Christy M; Eisenthal, Robert; Cobb, Benjamin D

    2002-12-20

    A novel method of estimating the kinetic parameters of Taq DNA polymerase during rapid cycle PCR is presented. A model was constructed using a simplified sigmoid function to represent substrate accumulation during PCR in combination with the general equation describing high substrate inhibition for Michaelis-Menten enzymes. The PCR progress curve was viewed as a series of independent reactions where initial rates were accurately measured for each cycle. Kinetic parameters were obtained for allele-specific PCR (AS-PCR) amplification to examine the effect of mismatches on amplification. A high degree of correlation was obtained providing evidence of substrate inhibition as a major cause of the plateau phase that occurs in the later cycles of PCR.

  19. Technical Note: Using experimentally determined proton spot scanning timing parameters to accurately model beam delivery time.

    PubMed

    Shen, Jiajian; Tryggestad, Erik; Younkin, James E; Keole, Sameer R; Furutani, Keith M; Kang, Yixiu; Herman, Michael G; Bues, Martin

    2017-10-01

    To accurately model the beam delivery time (BDT) for a synchrotron-based proton spot scanning system using experimentally determined beam parameters. A model to simulate the proton spot delivery sequences was constructed, and BDT was calculated by summing times for layer switch, spot switch, and spot delivery. Test plans were designed to isolate and quantify the relevant beam parameters in the operation cycle of the proton beam therapy delivery system. These parameters included the layer switch time, magnet preparation and verification time, average beam scanning speeds in x- and y-directions, proton spill rate, and maximum charge and maximum extraction time for each spill. The experimentally determined parameters, as well as the nominal values initially provided by the vendor, served as inputs to the model to predict BDTs for 602 clinical proton beam deliveries. The calculated BDTs (T BDT ) were compared with the BDTs recorded in the treatment delivery log files (T Log ): ∆t = T Log -T BDT . The experimentally determined average layer switch time for all 97 energies was 1.91 s (ranging from 1.9 to 2.0 s for beam energies from 71.3 to 228.8 MeV), average magnet preparation and verification time was 1.93 ms, the average scanning speeds were 5.9 m/s in x-direction and 19.3 m/s in y-direction, the proton spill rate was 8.7 MU/s, and the maximum proton charge available for one acceleration is 2.0 ± 0.4 nC. Some of the measured parameters differed from the nominal values provided by the vendor. The calculated BDTs using experimentally determined parameters matched the recorded BDTs of 602 beam deliveries (∆t = -0.49 ± 1.44 s), which were significantly more accurate than BDTs calculated using nominal timing parameters (∆t = -7.48 ± 6.97 s). An accurate model for BDT prediction was achieved by using the experimentally determined proton beam therapy delivery parameters, which may be useful in modeling the interplay effect and patient throughput. The model may

  20. Metastable Solution Thermodynamic Properties and Crystal Growth Kinetics

    NASA Technical Reports Server (NTRS)

    Kim, Soojin; Myerson, Allan S.

    1996-01-01

    The crystal growth rates of NH4H2PO4, KH2PO4, (NH4)2SO4, KAl(SO4)2 central dot 12H2O, NaCl, and glycine and the nucleation rates of KBr, KCl, NaBr central dot 2H2O, (NH4)2Cl, and (NH4)2SO4 were expressed in terms of the fundamental driving force of crystallization calculated from the activity of supersaturated solutions. The kinetic parameters were compared with those from the commonly used kinetic expression based on the concentration difference. From the viewpoint of thermodynamics, rate expressions based on the chemical potential difference provide accurate kinetic representation over a broad range of supersaturation. The rates estimated using the expression based on the concentration difference coincide with the true rates of crystallization only in the concentration range of low supersaturation and deviate from the true kinetics as the supersaturation increases.

  1. A BAYESIAN METHOD OF ESTIMATING KINETIC PARAMETERS FOR THE INACTIVATION OF CRYPTOSPORIDIUM PARVUM OOCYSTS WITH CHLORINE DIOXIDE AND OZONE

    EPA Science Inventory

    The main objective of this paper is to use Bayesian methods to estimate the kinetic parameters for the inactivation kinetics of Cryptosporidium parvum oocysts with chlorine dioxide or ozone which are characterized by the delayed Chick-Watson model, i.e., a lag phase or shoulder f...

  2. Fuzzy C-mean clustering on kinetic parameter estimation with generalized linear least square algorithm in SPECT

    NASA Astrophysics Data System (ADS)

    Choi, Hon-Chit; Wen, Lingfeng; Eberl, Stefan; Feng, Dagan

    2006-03-01

    Dynamic Single Photon Emission Computed Tomography (SPECT) has the potential to quantitatively estimate physiological parameters by fitting compartment models to the tracer kinetics. The generalized linear least square method (GLLS) is an efficient method to estimate unbiased kinetic parameters and parametric images. However, due to the low sensitivity of SPECT, noisy data can cause voxel-wise parameter estimation by GLLS to fail. Fuzzy C-Mean (FCM) clustering and modified FCM, which also utilizes information from the immediate neighboring voxels, are proposed to improve the voxel-wise parameter estimation of GLLS. Monte Carlo simulations were performed to generate dynamic SPECT data with different noise levels and processed by general and modified FCM clustering. Parametric images were estimated by Logan and Yokoi graphical analysis and GLLS. The influx rate (K I), volume of distribution (V d) were estimated for the cerebellum, thalamus and frontal cortex. Our results show that (1) FCM reduces the bias and improves the reliability of parameter estimates for noisy data, (2) GLLS provides estimates of micro parameters (K I-k 4) as well as macro parameters, such as volume of distribution (Vd) and binding potential (BP I & BP II) and (3) FCM clustering incorporating neighboring voxel information does not improve the parameter estimates, but improves noise in the parametric images. These findings indicated that it is desirable for pre-segmentation with traditional FCM clustering to generate voxel-wise parametric images with GLLS from dynamic SPECT data.

  3. Accurate estimation of motion blur parameters in noisy remote sensing image

    NASA Astrophysics Data System (ADS)

    Shi, Xueyan; Wang, Lin; Shao, Xiaopeng; Wang, Huilin; Tao, Zhong

    2015-05-01

    The relative motion between remote sensing satellite sensor and objects is one of the most common reasons for remote sensing image degradation. It seriously weakens image data interpretation and information extraction. In practice, point spread function (PSF) should be estimated firstly for image restoration. Identifying motion blur direction and length accurately is very crucial for PSF and restoring image with precision. In general, the regular light-and-dark stripes in the spectrum can be employed to obtain the parameters by using Radon transform. However, serious noise existing in actual remote sensing images often causes the stripes unobvious. The parameters would be difficult to calculate and the error of the result relatively big. In this paper, an improved motion blur parameter identification method to noisy remote sensing image is proposed to solve this problem. The spectrum characteristic of noisy remote sensing image is analyzed firstly. An interactive image segmentation method based on graph theory called GrabCut is adopted to effectively extract the edge of the light center in the spectrum. Motion blur direction is estimated by applying Radon transform on the segmentation result. In order to reduce random error, a method based on whole column statistics is used during calculating blur length. Finally, Lucy-Richardson algorithm is applied to restore the remote sensing images of the moon after estimating blur parameters. The experimental results verify the effectiveness and robustness of our algorithm.

  4. Novel methods to estimate the enantiomeric ratio and the kinetic parameters of enantiospecific enzymatic reactions.

    PubMed

    Machado, G D.C.; Paiva, L M.C.; Pinto, G F.; Oestreicher, E G.

    2001-03-08

    1The Enantiomeric Ratio (E) of the enzyme, acting as specific catalysts in resolution of enantiomers, is an important parameter in the quantitative description of these chiral resolution processes. In the present work, two novel methods hereby called Method I and II, for estimating E and the kinetic parameters Km and Vm of enantiomers were developed. These methods are based upon initial rate (v) measurements using different concentrations of enantiomeric mixtures (C) with several molar fractions of the substrate (x). Both methods were tested using simulated "experimental data" and actual experimental data. Method I is easier to use than Method II but requires that one of the enantiomers is available in pure form. Method II, besides not requiring the enantiomers in pure form shown better results, as indicated by the magnitude of the standard errors of estimates. The theoretical predictions were experimentally confirmed by using the oxidation of 2-butanol and 2-pentanol catalyzed by Thermoanaerobium brockii alcohol dehydrogenase as reaction models. The parameters E, Km and Vm were estimated by Methods I and II with precision and were not significantly different from those obtained experimentally by direct estimation of E from the kinetic parameters of each enantiomer available in pure form.

  5. Thermodynamic, Kinetic, and Equilibrium Parameters for the Removal of Lead and Cadmium from Aqueous Solutions with Calcium Alginate Beads

    PubMed Central

    Alfaro-Cuevas-Villanueva, Ruth; Hidalgo-Vázquez, Aura Roxana; Cortés Penagos, Consuelo de Jesús; Cortés-Martínez, Raúl

    2014-01-01

    The sorption of cadmium (Cd) and lead (Pb) by calcium alginate beads (CAB) from aqueous solutions in batch systems was investigated. The kinetic and thermodynamic parameters, as well as the sorption capacities of CAB in each system at different temperatures, were evaluated. The rate of sorption for both metals was rapid in the first 10 minutes and reached a maximum in 50 minutes. Sorption kinetic data were fitted to Lagergren, pseudo-second-order and Elovich models and it was found that the second-order kinetic model describes these data for the two metals; comparing kinetic parameters for Cd and Pb sorption a higher kinetic rate (K 2) for Pb was observed, indicating that the interaction between lead cations and alginate beads was faster than for cadmium. Similarly, isotherm data were fitted to different models reported in literature and it was found that the Langmuir-Freundlich (L-F) and Dubinin-Radushkevich (D-R) models describe the isotherms in all cases. CAB sorption capacity for cadmium was 27.4 mg/g and 150.4 mg/g for lead, at 25°C. Sorption capacities of Cd and Pb increase as temperature rises. According to the thermodynamic parameters, the cadmium and lead adsorption process was spontaneous and endothermic. It was also found that pH has an important effect on the adsorption of these metals by CAB, as more were removed at pH values between 6 and 7. PMID:24587740

  6. Measurement of the Kinetic Energy of a Body by Means of a Deformation.

    ERIC Educational Resources Information Center

    Perez, Pedro J.; And Others

    1996-01-01

    Describes a technique that measures the deformation produced in a plastic material by a falling ball in order to compute the ball's kinetic energy. Varying the parameters produces accurate results and gives students a good understanding of the measurement of energy. Combines various mechanical concepts that students have learned separately in…

  7. Nonlinear saturation of the slab ITG instability and zonal flow generation with fully kinetic ions

    NASA Astrophysics Data System (ADS)

    Miecnikowski, Matthew T.; Sturdevant, Benjamin J.; Chen, Yang; Parker, Scott E.

    2018-05-01

    Fully kinetic turbulence models are of interest for their potential to validate or replace gyrokinetic models in plasma regimes where the gyrokinetic expansion parameters are marginal. Here, we demonstrate fully kinetic ion capability by simulating the growth and nonlinear saturation of the ion-temperature-gradient instability in shearless slab geometry assuming adiabatic electrons and including zonal flow dynamics. The ion trajectories are integrated using the Lorentz force, and the cyclotron motion is fully resolved. Linear growth and nonlinear saturation characteristics show excellent agreement with analogous gyrokinetic simulations across a wide range of parameters. The fully kinetic simulation accurately reproduces the nonlinearly generated zonal flow. This work demonstrates nonlinear capability, resolution of weak gradient drive, and zonal flow physics, which are critical aspects of modeling plasma turbulence with full ion dynamics.

  8. Determination of char combustion kinetics parameters: Comparison of point detector and imaging-based particle-sizing pyrometry

    NASA Astrophysics Data System (ADS)

    Schiemann, Martin; Geier, Manfred; Shaddix, Christopher R.; Vorobiev, Nikita; Scherer, Viktor

    2014-07-01

    In this study, the char burnout characteristics of two German coals (a lignite and a high-volatile bituminous coal) were investigated using two different experimental configurations and optical techniques in two distinct laboratories for measurement of temperature and size of burning particles. The optical diagnostic hardware is quite different in the two systems, but both perform two-color pyrometry and optical sizing measurements on individual particles burning in isolation from each other in high-temperature laminar flows to characterize the char consumption kinetics. The performance of the specialized systems is compared for two different combustion atmospheres (with 6.6 and 12 vol.% O2) and gas temperatures between 1700 and 1800 K. The measured particle temperatures and diameters are converted to char burning rate parameters for several residence times during the course of the particles' burnout. The results confirm that comparable results are obtained with the two configurations, although higher levels of variability in the measured data were observed in the imaging-based pyrometer setup. Corresponding uncertainties in kinetics parameters were larger, and appear to be more sensitive to systematic measurement errors when lower oxygen contents are used in the experiments. Consequently, burnout experiments in environments with sufficiently high O2 contents may be used to measure reliable char burning kinetics rates. Based on simulation results for the two coals, O2 concentrations in the range 10%-30% are recommended for kinetic rate measurements on 100 μm particles.

  9. Improved accuracy and precision of tracer kinetic parameters by joint fitting to variable flip angle and dynamic contrast enhanced MRI data.

    PubMed

    Dickie, Ben R; Banerji, Anita; Kershaw, Lucy E; McPartlin, Andrew; Choudhury, Ananya; West, Catharine M; Rose, Chris J

    2016-10-01

    To improve the accuracy and precision of tracer kinetic model parameter estimates for use in dynamic contrast enhanced (DCE) MRI studies of solid tumors. Quantitative DCE-MRI requires an estimate of precontrast T1 , which is obtained prior to fitting a tracer kinetic model. As T1 mapping and tracer kinetic signal models are both a function of precontrast T1 it was hypothesized that its joint estimation would improve the accuracy and precision of both precontrast T1 and tracer kinetic model parameters. Accuracy and/or precision of two-compartment exchange model (2CXM) parameters were evaluated for standard and joint fitting methods in well-controlled synthetic data and for 36 bladder cancer patients. Methods were compared under a number of experimental conditions. In synthetic data, joint estimation led to statistically significant improvements in the accuracy of estimated parameters in 30 of 42 conditions (improvements between 1.8% and 49%). Reduced accuracy was observed in 7 of the remaining 12 conditions. Significant improvements in precision were observed in 35 of 42 conditions (between 4.7% and 50%). In clinical data, significant improvements in precision were observed in 18 of 21 conditions (between 4.6% and 38%). Accuracy and precision of DCE-MRI parameter estimates are improved when signal models are fit jointly rather than sequentially. Magn Reson Med 76:1270-1281, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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

    NASA Astrophysics Data System (ADS)

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

    2017-10-01

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

  11. Combined Yamamoto approach for simultaneous estimation of adsorption isotherm and kinetic parameters in ion-exchange chromatography.

    PubMed

    Rüdt, Matthias; Gillet, Florian; Heege, Stefanie; Hitzler, Julian; Kalbfuss, Bernd; Guélat, Bertrand

    2015-09-25

    Application of model-based design is appealing to support the development of protein chromatography in the biopharmaceutical industry. However, the required efforts for parameter estimation are frequently perceived as time-consuming and expensive. In order to speed-up this work, a new parameter estimation approach for modelling ion-exchange chromatography in linear conditions was developed. It aims at reducing the time and protein demand for the model calibration. The method combines the estimation of kinetic and thermodynamic parameters based on the simultaneous variation of the gradient slope and the residence time in a set of five linear gradient elutions. The parameters are estimated from a Yamamoto plot and a gradient-adjusted Van Deemter plot. The combined approach increases the information extracted per experiment compared to the individual methods. As a proof of concept, the combined approach was successfully applied for a monoclonal antibody on a cation-exchanger and for a Fc-fusion protein on an anion-exchange resin. The individual parameter estimations for the mAb confirmed that the new approach maintained the accuracy of the usual Yamamoto and Van Deemter plots. In the second case, offline size-exclusion chromatography was performed in order to estimate the thermodynamic parameters of an impurity (high molecular weight species) simultaneously with the main product. Finally, the parameters obtained from the combined approach were used in a lumped kinetic model to simulate the chromatography runs. The simulated chromatograms obtained for a wide range of gradient lengths and residence times showed only small deviations compared to the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Kinetic and thermodynamic parameters for heat denaturation of human recombinant lactoferrin from rice.

    PubMed

    Castillo, Eduardo; Pérez, María Dolores; Franco, Indira; Calvo, Miguel; Sánchez, Lourdes

    2012-06-01

    Heat denaturation of recombinant human lactoferrin (rhLf) from rice with 3 different iron-saturation degrees, holo rhLf (iron-saturated), AsIs rhLf (60% iron saturation), and apo rhLf (iron-depleted), was studied. The 3 forms of rhLf were subjected to heat treatment, and the kinetic and thermodynamic parameters of the denaturation process were determined. Thermal denaturation of rhLf was assessed by measuring the loss of reactivity against specific antibodies. D(t) values (time to reduce 90% of immunoreactivity) decreased with increasing temperature of treatment for apo and holo rhLf, those values being higher for the iron-saturated form, which indicates that iron confers thermal stability to rhLf. However, AsIs rhLf showed a different behaviour with an increase in resistance to heat between 79 °C and 84 °C, so that the kinetic parameters could not be calculated. The heat denaturation process for apo and holo rhLf was best described assuming a reaction order of 1.5. The activation energy of the denaturation process was 648.20 kJ/mol for holo rhLf and 406.94 kJ/mol for apo rhLf, confirming that iron-depleted rhLf is more sensitive to heat treatment than iron-saturated rhLf.

  13. A global resource allocation strategy governs growth transition kinetics of Escherichia coli

    PubMed Central

    Erickson, David W; Schink, Severin J.; Patsalo, Vadim; Williamson, James R.; Gerland, Ulrich; Hwa, Terence

    2018-01-01

    A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms1–3 and they remain a topic of active investigation4–11. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations12–17, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models15,18–20 from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions. PMID:29072300

  14. Kinetic Parameters for the Noncatalyzed and Enzyme-Catalyzed Mutarotation of Glucose Using a Blood Glucometer

    ERIC Educational Resources Information Center

    Hardee, John R.; Delgado, Bryan; Jones, Wray

    2011-01-01

    The kinetic parameters for the conversion of alpha-D-glucose to beta-D-glucose were measured using a blood glucometer. The reaction order, rate constant, and Arrhenius activation energy are reported for the noncatalyzed reaction and turnover number and Michaelis constant are reported for the reaction catalyzed by porcine kidney mutarotase. The…

  15. Kinetics of nickel electrodeposition from low electrolyte concentration and at a narrow interelectrode gap

    NASA Astrophysics Data System (ADS)

    Widayatno, Tri

    2015-12-01

    Electrodeposition of nickel onto copper in a system of low Ni2+ concentration and at a narrow interelectrode gap has been carried out. This electrochemical system was required for maskless pattern transfer through electroplating (Enface technique). Kinetics of Electrochemical reaction of Nickel is relatively slow, where such electrochemical system has never been used in this technology. Study on the kinetics of the electrochemical reaction of nickel in such system is essential due to the fact that the quality of an electrodeposited nickel is affected by kinetics. Analytical and graphical methods were utilised to determine kinetic parameters. The kinetic model was approximated by Butler-Volmer and j-η equation. Kinetic parameters such as exchange current density (j0) and charge transfer coefficient (α) were also graphically determined using the plot of η vs. log|j| known as Tafel plot. The polarisation data for an unstirred 0.19 M nickel sulfamate solution at 0.5 mV/s scan rate and RDE system was used. The results indicate that both methods are fairly accurate. For the analytical, the Tafel slope, the exchange current density, and charge transfer coefficient were found to be 149 mV/dec, 1.60 × 10-4 mA/cm2, and 0.39 respectively, whilst for the graphical method were 159 mV/dec, 3.16 × 10-4 mA/cm2, and 0.37. The kinetics parameters in this current study were also compared to those in literature. Significant differences were observed which might be due to the effect of composition and concentration of the electrolytes, operating temperature, and pH leading to the different reaction mechanism. However, the results obtained in this work are in the range of acceptable values. These kinetic parameters will then be used in further study of nickel deposition by modelling and simulation

  16. Does Vibration Warm-up Enhance Kinetic and Temporal Sprint Parameters?

    PubMed

    Cochrane, D J; Cronin, M J; Fink, P W

    2015-08-01

    The aim of this study was to investigate the efficacy of vibration warm-up to enhance sprint performance. 12 males involved in representative team sports performed 4 warm-up conditions in a randomised order performed at least 24 h apart; VbX warm-up (VbX-WU); Neural activation warm-up (Neu-WU); Dynamic warm-up (Dyn-WU) and Control (No VbX). Participants completed 5 m sprint at 30 s, 2:30 min and 5 min post warm-up where sprint time, kinetics, and temporal components were recorded. There was no significant (p>0.05) main effect or interaction effect between the split sprint times of 1 m, 2.5 m, and 5 m. There was a condition effect where vertical mean force was significantly higher (p<0.05) in Dyn-WU and Control compared to Neu-WU. No other significant (p>0.05) main and interaction effects in sprint kinetic and temporal parameters existed. Overall, all 4 warm-up conditions produced comparable results for sprint performance, and there was no detrimental effect on short-duration sprint performance using VbX-WU. Therefore, VbX could be useful for adding variety to the training warm-up or be included into the main warm-up routine as a supplementary modality. © Georg Thieme Verlag KG Stuttgart · New York.

  17. Enhanced von Weizsäcker Wang-Govind-Carter kinetic energy density functional for semiconductors

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

    Shin, Ilgyou; Carter, Emily A., E-mail: eac@princeton.edu

    2014-05-14

    We propose a new form of orbital-free (OF) kinetic energy density functional (KEDF) for semiconductors that is based on the Wang-Govind-Carter (WGC99) nonlocal KEDF. We enhance within the latter the semi-local von Weizsäcker KEDF term, which is exact for a single orbital. The enhancement factor we introduce is related to the extent to which the electron density is localized. The accuracy of the new KEDF is benchmarked against Kohn-Sham density functional theory (KSDFT) by comparing predicted energy differences between phases, equilibrium volumes, and bulk moduli for various semiconductors, along with metal-insulator phase transition pressures. We also compare point defect andmore » (100) surface energies in silicon for a broad test of its applicability. This new KEDF accurately reproduces the exact non-interacting kinetic energy of KSDFT with only one additional adjustable parameter beyond the three parameters in the WGC99 KEDF; it exhibits good transferability between semiconducting to metallic silicon phases and between various III-V semiconductors without parameter adjustment. Overall, this KEDF is more accurate than previously proposed OF KEDFs (e.g., the Huang-Carter (HC) KEDF) for semiconductors, while the computational efficiency remains at the level of the WGC99 KEDF (several hundred times faster than the HC KEDF). This accurate, fast, and transferable new KEDF holds considerable promise for large-scale OFDFT simulations of metallic through semiconducting materials.« less

  18. Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models

    PubMed Central

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

    2013-01-01

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

  19. Estimation of Transport and Kinetic Parameters of Vanadium Redox Batteries Using Static Cells

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

    Lee, Seong Beom; Pratt, III, Harry D.; Anderson, Travis M.

    Mathematical models of Redox Flow Batteries (RFBs) can be used to analyze cell performance, optimize battery operation, and control the energy storage system efficiently. Among many other models, physics-based electrochemical models are capable of predicting internal states of the battery, such as temperature, state-of-charge, and state-of-health. In the models, estimating parameters is an important step that can study, analyze, and validate the models using experimental data. A common practice is to determine these parameters either through conducting experiments or based on the information available in the literature. However, it is not easy to investigate all proper parameters for the modelsmore » through this way, and there are occasions when important information, such as diffusion coefficients and rate constants of ions, has not been studied. Also, the parameters needed for modeling charge-discharge are not always available. In this paper, an efficient way to estimate parameters of physics-based redox battery models will be proposed. Furthermore, this paper also demonstrates that the proposed approach can study and analyze aspects of capacity loss/fade, kinetics, and transport phenomena of the RFB system.« less

  20. Estimation of Transport and Kinetic Parameters of Vanadium Redox Batteries Using Static Cells

    DOE PAGES

    Lee, Seong Beom; Pratt, III, Harry D.; Anderson, Travis M.; ...

    2018-03-27

    Mathematical models of Redox Flow Batteries (RFBs) can be used to analyze cell performance, optimize battery operation, and control the energy storage system efficiently. Among many other models, physics-based electrochemical models are capable of predicting internal states of the battery, such as temperature, state-of-charge, and state-of-health. In the models, estimating parameters is an important step that can study, analyze, and validate the models using experimental data. A common practice is to determine these parameters either through conducting experiments or based on the information available in the literature. However, it is not easy to investigate all proper parameters for the modelsmore » through this way, and there are occasions when important information, such as diffusion coefficients and rate constants of ions, has not been studied. Also, the parameters needed for modeling charge-discharge are not always available. In this paper, an efficient way to estimate parameters of physics-based redox battery models will be proposed. Furthermore, this paper also demonstrates that the proposed approach can study and analyze aspects of capacity loss/fade, kinetics, and transport phenomena of the RFB system.« less

  1. Dry mechanochemical synthesis of hydroxyapatites from DCPD and CaO: influence of instrumental parameters on the reaction kinetics.

    PubMed

    Mochales, Carolina; El Briak-BenAbdeslam, Hassane; Ginebra, Maria Pau; Terol, Alain; Planell, Josep A; Boudeville, Philippe

    2004-01-01

    Mechanochemistry is a possible route to synthesize calcium deficient hydroxyapatite (CDHA) with an expected molar calcium-to-phosphate (Ca/P) ratio +/-0.01. To optimize the experimental conditions of CDHA preparation from dicalcium phosphate dihydrate (DCPD) and calcium oxide by dry mechanosynthesis reaction, we performed the kinetic study varying some experimental parameters. This kinetic study was carried out with two different planetary ball mills (Retsch or Fritsch Instuments). Results obtained with the two mills led to the same conclusions although the values of the rate constants of DCPD disappearance and times for complete reaction were very different. Certainly, the origin of these differences was from the mills used, thus we investigated the influence of instrumental parameters such as the mass and the surface area of the balls or the rotation velocity on the mechanochemical reaction kinetics of DCPD with CaO. Results show that the DCPD reaction rate constant and the inverse of the time for complete disappearance of CaO both vary linearly with (i) the square of the rotation velocity, (ii) the square of eccentricity of the vial on the rotating disc and (iii) the product of the mass by the surface area of the balls. These observations comply with theoretical models developed for mechanical alloying. The consideration of these four parameters allows the transposition of experimental conditions from one mill to another or the comparison between results obtained with different planetary ball mills. These instrumental parameters have to be well described in papers concerning mechanochemistry or when grinding is an important stage in a process.

  2. Derivation of hydrous pyrolysis kinetic parameters from open-system pyrolysis

    NASA Astrophysics Data System (ADS)

    Tseng, Yu-Hsin; Huang, Wuu-Liang

    2010-05-01

    Kinetic information is essential to predict the temperature, timing or depth of hydrocarbon generation within a hydrocarbon system. The most common experiments for deriving kinetic parameters are mainly by open-system pyrolysis. However, it has been shown that the conditions of open-system pyrolysis are deviant from nature by its low near-ambient pressure and high temperatures. Also, the extrapolation of heating rates in open-system pyrolysis to geological conditions may be questionable. Recent study of Lewan and Ruble shows hydrous-pyrolysis conditions can simulate the natural conditions better and its applications are supported by two case studies with natural thermal-burial histories. Nevertheless, performing hydrous pyrolysis experiment is really tedious and requires large amount of sample, while open-system pyrolysis is rather convenient and efficient. Therefore, the present study aims at the derivation of convincing distributed hydrous pyrolysis Ea with only routine open-system Rock-Eval data. Our results unveil that there is a good correlation between open-system Rock-Eval parameter Tmax and the activation energy (Ea) derived from hydrous pyrolysis. The hydrous pyrolysis single Ea can be predicted from Tmax based on the correlation, while the frequency factor (A0) is estimated based on the linear relationship between single Ea and log A0. Because the Ea distribution is more rational than single Ea, we modify the predicted single hydrous pyrolysis Ea into distributed Ea by shifting the pattern of Ea distribution from open-system pyrolysis until the weight mean Ea distribution equals to the single hydrous pyrolysis Ea. Moreover, it has been shown that the shape of the Ea distribution is very much alike the shape of Tmax curve. Thus, in case of the absence of open-system Ea distribution, we may use the shape of Tmax curve to get the distributed hydrous pyrolysis Ea. The study offers a new approach as a simple method for obtaining distributed hydrous pyrolysis

  3. Non-Isothermic Chemical Kinetics in the Undergraduate Laboratory: Arrhenius Parameters from Experiments with Hyperbolic Temperature Variation.

    ERIC Educational Resources Information Center

    Salvador, F.; And Others

    1984-01-01

    Describes a method which adapts itself to the characteristics of the kinetics of a chemical reaction in solution, enabling students to determine the Arrhenius parameters with satisfactory accuracy by means of a single non-isothermic experiment. Both activation energy and the preexponential factor values can be obtained by the method. (JN)

  4. Effect of heating rate on kinetic parameters of β-irradiated Li2B4O7:Cu,Ag,P in TSL measurements

    NASA Astrophysics Data System (ADS)

    Türkler Ege, A.; Ekdal, E.; Karali, T.; Can, N.; Prokic, M.

    2007-03-01

    The effect of heating rate on the thermally stimulated luminescence (TSL) emission due to the temperature lag (TLA) between the TSL material and the heating element has been investigated using Li2B4O7:Cu,Ag,P dosimetric materials. The TLA becomes significant when the material is heated at high heating rates. TSL glow curves of Li2B4O7:Cu,Ag,P material showed two main peaks after β-irradiation. The kinetic parameters, namely activation energy (E) and frequency factor (s) associated with the high temperature main peak of Li2B4O7:Cu,Ag,P were determined using the method of various heating rates (VHR), in which heating rates from 1 to 40 K s-1 were used. It is assumed that non-ideal heat transfer between the heater and the material may cause significant inconsistency of kinetic parameter values obtained with different methods. The effect of TLA on kinetic parameters of the dosimeter was examined.

  5. Estimation of kinetics parameters for the adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes by piezoelectric quartz crystal impedance analysis.

    PubMed

    Tian, Lu; Wei, Wan-Zhi; Mao, You-An

    2004-04-01

    The adsorption of human serum albumin onto hydroxyapatite-modified silver electrodes has been in situ investigated by utilizing the piezoelectric quartz crystal impedance technique. The changes of equivalent circuit parameters were used to interpret the adsorption process. A kinetic model of two consecutive steps was derived to describe the process and compared with a first-order kinetic model by using residual analysis. The experimental data of frequency shift fitted to the model and kinetics parameters, k1, k2, psi1, psi2 and qr, were obtained. All fitted results were in reasonable agreement with the corresponding experimental results. Two adsorption constants (7.19 kJ mol(-1) and 22.89 kJ mol(-1)) were calculated according to the Arrhenius formula.

  6. Fundamental electrode kinetics

    NASA Technical Reports Server (NTRS)

    Elder, J. P.

    1968-01-01

    Report presents the fundamentals of electrode kinetics and the methods used in evaluating the characteristic parameters of rapid-charge transfer processes at electrode-electrolyte interfaces. The concept of electrode kinetics is outlined, followed by the principles underlying the experimental techniques for the investigation of electrode kinetics.

  7. Analysis of blind identification methods for estimation of kinetic parameters in dynamic medical imaging

    NASA Astrophysics Data System (ADS)

    Riabkov, Dmitri

    Compartment modeling of dynamic medical image data implies that the concentration of the tracer over time in a particular region of the organ of interest is well-modeled as a convolution of the tissue response with the tracer concentration in the blood stream. The tissue response is different for different tissues while the blood input is assumed to be the same for different tissues. The kinetic parameters characterizing the tissue responses can be estimated by blind identification methods. These algorithms use the simultaneous measurements of concentration in separate regions of the organ; if the regions have different responses, the measurement of the blood input function may not be required. In this work it is shown that the blind identification problem has a unique solution for two-compartment model tissue response. For two-compartment model tissue responses in dynamic cardiac MRI imaging conditions with gadolinium-DTPA contrast agent, three blind identification algorithms are analyzed here to assess their utility: Eigenvector-based Algorithm for Multichannel Blind Deconvolution (EVAM), Cross Relations (CR), and Iterative Quadratic Maximum Likelihood (IQML). Comparisons of accuracy with conventional (not blind) identification techniques where the blood input is known are made as well. The statistical accuracies of estimation for the three methods are evaluated and compared for multiple parameter sets. The results show that the IQML method gives more accurate estimates than the other two blind identification methods. A proof is presented here that three-compartment model blind identification is not unique in the case of only two regions. It is shown that it is likely unique for the case of more than two regions, but this has not been proved analytically. For the three-compartment model the tissue responses in dynamic FDG PET imaging conditions are analyzed with the blind identification algorithms EVAM and Separable variables Least Squares (SLS). A method of

  8. Numerical methods for solving moment equations in kinetic theory of neuronal network dynamics

    NASA Astrophysics Data System (ADS)

    Rangan, Aaditya V.; Cai, David; Tao, Louis

    2007-02-01

    Recently developed kinetic theory and related closures for neuronal network dynamics have been demonstrated to be a powerful theoretical framework for investigating coarse-grained dynamical properties of neuronal networks. The moment equations arising from the kinetic theory are a system of (1 + 1)-dimensional nonlinear partial differential equations (PDE) on a bounded domain with nonlinear boundary conditions. The PDEs themselves are self-consistently specified by parameters which are functions of the boundary values of the solution. The moment equations can be stiff in space and time. Numerical methods are presented here for efficiently and accurately solving these moment equations. The essential ingredients in our numerical methods include: (i) the system is discretized in time with an implicit Euler method within a spectral deferred correction framework, therefore, the PDEs of the kinetic theory are reduced to a sequence, in time, of boundary value problems (BVPs) with nonlinear boundary conditions; (ii) a set of auxiliary parameters is introduced to recast the original BVP with nonlinear boundary conditions as BVPs with linear boundary conditions - with additional algebraic constraints on the auxiliary parameters; (iii) a careful combination of two Newton's iterates for the nonlinear BVP with linear boundary condition, interlaced with a Newton's iterate for solving the associated algebraic constraints is constructed to achieve quadratic convergence for obtaining the solutions with self-consistent parameters. It is shown that a simple fixed-point iteration can only achieve a linear convergence for the self-consistent parameters. The practicability and efficiency of our numerical methods for solving the moment equations of the kinetic theory are illustrated with numerical examples. It is further demonstrated that the moment equations derived from the kinetic theory of neuronal network dynamics can very well capture the coarse-grained dynamical properties of

  9. 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

  10. Use of extant kinetic parameters to predict effluent concentrations of specific organic compounds at full-scale facilities.

    PubMed

    Ellis, Timothy G; Eliosov, Boris

    2004-01-01

    To use the results of kinetic tests to predict effluent concentrations of specific contaminants in activated sludge systems, the fraction of the biomass that has an ability to degrade the test compound (i.e., competent biomass) must be estimated. A calibration procedure was developed to assess the competent biomass concentration because the chemical oxygen demand (COD) fraction tended to underestimate the degrading fraction for three of the four test compounds. Acetone, for instance, had a measured influent COD fraction of 0.08%, and the actual competent fraction was estimated to be 2.3%, based on the model calibration. Once the competent biomass fraction in the mixed liquor was determined, the extant kinetic parameters were subsequently used to predict activated sludge system performance. Predicted effluent concentrations were within 2, 5, and 16% of the average measured concentrations for acetone, linear alkylbenzene sulfonate, and furfural, respectively. Day-to-day predictions for these compounds were less accurate, possibly because of the non-steady-state nature of the activated sludge systems studied. The difference between the fraction of the influent COD contributed by the target compounds and the competent biomass fraction in the mixed liquor was found to be more significant when the target compound contributed less than 1% of the influent organic matter. The chemical structure of the target compound and chemical composition of the influent likely had an effect on the resulting competent biomass concentration. The total maximum growth rate, microX, was observed to be independent of the influent concentration of acetone and furfural, thus suggesting that the competent biomass concentration for these compounds was not affected by the changes in their influent concentrations. Consequently, a majority of competent biomass growth resulted from the degradation of other substrates, resulting in a competent biomass concentration significantly higher than predicted

  11. Temperature-Dependent Kinetic Model for Nitrogen-Limited Wine Fermentations▿

    PubMed Central

    Coleman, Matthew C.; Fish, Russell; Block, David E.

    2007-01-01

    A physical and mathematical model for wine fermentation kinetics was adapted to include the influence of temperature, perhaps the most critical factor influencing fermentation kinetics. The model was based on flask-scale white wine fermentations at different temperatures (11 to 35°C) and different initial concentrations of sugar (265 to 300 g/liter) and nitrogen (70 to 350 mg N/liter). The results show that fermentation temperature and inadequate levels of nitrogen will cause stuck or sluggish fermentations. Model parameters representing cell growth rate, sugar utilization rate, and the inactivation rate of cells in the presence of ethanol are highly temperature dependent. All other variables (yield coefficient of cell mass to utilized nitrogen, yield coefficient of ethanol to utilized sugar, Monod constant for nitrogen-limited growth, and Michaelis-Menten-type constant for sugar transport) were determined to vary insignificantly with temperature. The resulting mathematical model accurately predicts the observed wine fermentation kinetics with respect to different temperatures and different initial conditions, including data from fermentations not used for model development. This is the first wine fermentation model that accurately predicts a transition from sluggish to normal to stuck fermentations as temperature increases from 11 to 35°C. Furthermore, this comprehensive model provides insight into combined effects of time, temperature, and ethanol concentration on yeast (Saccharomyces cerevisiae) activity and physiology. PMID:17616615

  12. Optimization of a direct spectrophotometric method to investigate the kinetics and inhibition of sialidases

    PubMed Central

    2012-01-01

    Backgrounds Streptococcus pneumoniae expresses three distinct sialidases, NanA, NanB, and NanC, that are believed to be key virulence factors and thus, potential important drug targets. We previously reported that the three enzymes release different products from sialosides, but could share a common catalytic mechanism before the final step of product formation. However, the kinetic investigations of the three sialidases have not been systematically done thus far, due to the lack of an easy and steady measurement of sialidase reaction rate. Results In this work, we present further kinetic characterization of pneumococcal sialidases by using a direct spectrophotometric method with the chromogenic substrate p-nitrophenyl-N-acetylneuraminic acid (p-NP-Neu5Ac). Using our assay, the measured kinetic parameters of the three purified pneumococcal sialidase, NanA, NanB and NanC, were obtained and were in perfect agreement with the previously published data. The major advantage of this alternative method resides in the direct measurement of the released product, allowing to readily determine of initial reaction rates and record complete hydrolysis time courses. Conclusion We developed an accurate, fast and sensitive spectrophotometric method to investigate the kinetics of sialidase-catalyzed reactions. This fast, sensitive, inexpensive and accurate method could benefit the study of the kinetics and inhibition of sialidases in general. PMID:23031230

  13. Non-Isothermal Kinetics.

    ERIC Educational Resources Information Center

    Brown, M. E.; Phillpotts, C. A. R.

    1978-01-01

    Discusses the principle of nonisothermal kinetics and some of the factors involved in such reactions, especially when considering the reliability of the kinetic parameters, compared to those of isothermal conditions. (GA)

  14. The combination of kinetic and flow cytometric semen parameters as a tool to predict fertility in cryopreserved bull semen.

    PubMed

    Gliozzi, T M; Turri, F; Manes, S; Cassinelli, C; Pizzi, F

    2017-11-01

    Within recent years, there has been growing interest in the prediction of bull fertility through in vitro assessment of semen quality. A model for fertility prediction based on early evaluation of semen quality parameters, to exclude sires with potentially low fertility from breeding programs, would therefore be useful. The aim of the present study was to identify the most suitable parameters that would provide reliable prediction of fertility. Frozen semen from 18 Italian Holstein-Friesian proven bulls was analyzed using computer-assisted semen analysis (CASA) (motility and kinetic parameters) and flow cytometry (FCM) (viability, acrosomal integrity, mitochondrial function, lipid peroxidation, plasma membrane stability and DNA integrity). Bulls were divided into two groups (low and high fertility) based on the estimated relative conception rate (ERCR). Significant differences were found between fertility groups for total motility, active cells, straightness, linearity, viability and percentage of DNA fragmented sperm. Correlations were observed between ERCR and some kinetic parameters, and membrane instability and some DNA integrity indicators. In order to define a model with high relation between semen quality parameters and ERCR, backward stepwise multiple regression analysis was applied. Thus, we obtained a prediction model that explained almost half (R 2=0.47, P<0.05) of the variation in the conception rate and included nine variables: five kinetic parameters measured by CASA (total motility, active cells, beat cross frequency, curvilinear velocity and amplitude of lateral head displacement) and four parameters related to DNA integrity evaluated by FCM (degree of chromatin structure abnormality Alpha-T, extent of chromatin structure abnormality (Alpha-T standard deviation), percentage of DNA fragmented sperm and percentage of sperm with high green fluorescence representative of immature cells). A significant relationship (R 2=0.84, P<0.05) was observed between

  15. Development of an ESI-LC-MS-based assay for kinetic evaluation of Mycobacterium tuberculosis shikimate kinase activity and inhibition.

    PubMed

    Simithy, Johayra; Gill, Gobind; Wang, Yu; Goodwin, Douglas C; Calderón, Angela I

    2015-02-17

    A simple and reliable liquid chromatography-mass spectrometry (LC-MS) assay has been developed and validated for the kinetic characterization and evaluation of inhibitors of shikimate kinase from Mycobacterium tuberculosis (MtSK), a potential target for the development of novel antitubercular drugs. This assay is based on the direct determination of the reaction product shikimate-3-phosphate (S3P) using electrospray ionization (ESI) and a quadrupole time-of-flight (Q-TOF) detector. A comparative analysis of the kinetic parameters of MtSK obtained by the LC-MS assay with those obtained by a conventional UV-assay was performed. Kinetic parameters determined by LC-MS were in excellent agreement with those obtained from the UV assay, demonstrating the accuracy, and reliability of this method. The validated assay was successfully applied to the kinetic characterization of a known inhibitor of shikimate kinase; inhibition constants and mode of inhibition were accurately delineated with LC-MS.

  16. The influence of inertial sensor sampling frequency on the accuracy of measurement parameters in rearfoot running.

    PubMed

    Mitschke, Christian; Zaumseil, Falk; Milani, Thomas L

    2017-11-01

    Increasingly, inertial sensors are being used for running analyses. The aim of this study was to systematically investigate the influence of inertial sensor sampling frequencies (SF) on the accuracy of kinematic, spatio-temporal, and kinetic parameters. We hypothesized that running analyses at lower SF result in less signal information and therefore the inability to sufficiently interpret measurement data. Twenty-one subjects participated in this study. Rearfoot strikers ran on an indoor running track at a velocity of 3.5 ± 0.1 ms -1 . A uniaxial accelerometer was attached at the tibia and an inertial measurement unit was mounted at the heel of the right shoe. All sensors were synchronized at the start and data was measured with 1000 Hz (reference SF). Datasets were reduced to 500, 333, 250, 200, and 100 Hz in post-processing. The results of this study showed that a minimum SF of 500 Hz should be used to accurately measure kinetic parameters (e.g. peak heel acceleration). In contrast, stride length showed accurate results even at 333 Hz. 200 Hz were required to calculate parameters accurately for peak tibial acceleration, stride duration, and all kinematic measurements. The information from this study is necessary to correctly interpret measurement data of existing investigations and to plan future studies.

  17. Sampling the kinetic pathways of a micelle fusion and fission transition.

    PubMed

    Pool, René; Bolhuis, Peter G

    2007-06-28

    The mechanism and kinetics of micellar breakup and fusion in a dilute solution of a model surfactant are investigated by path sampling techniques. Analysis of the path ensemble gives insight in the mechanism of the transition. For larger, less stable micelles the fission/fusion occurs via a clear neck formation, while for smaller micelles the mechanism is more direct. In addition, path analysis yields an appropriate order parameter to evaluate the fusion and fission rate constants using stochastic transition interface sampling. For the small, stable micelle (50 surfactants) the computed fission rate constant is a factor of 10 lower than the fusion rate constant. The procedure opens the way for accurate calculation of free energy and kinetics for, e.g., membrane fusion, and wormlike micelle endcap formation.

  18. Intrinsic kinetic parameters of Thermococcus onnurineus NA1 strains and prediction of optimum carbon monoxide level for ideal bioreactor operation.

    PubMed

    Jeong, Yeseul; Jang, Nulee; Yasin, Muhammad; Park, Shinyoung; Chang, In Seop

    2016-02-01

    This study determines and compares the intrinsic kinetic parameters (Ks and Ki) of selected Thermococcus onnurineus NA1 strains (wild-type (WT), and mutants MC01, MC02, and WTC156T) using the substrate inhibition model. Ks and Ki values were used to find the optimum dissolved CO (CL) conditions inside the reactor. The results showed that in terms of the maximum specific CO consumption rates (qCO(max)) of WT, MC01, MC02, and WTC156T the optimum activities can be achieved by maintaining the CL levels at 0.56mM, 0.52mM, 0.58mM, and 0.75mM, respectively. The qCO(max) value of WTC156T at 0.75mM was found to be 1.5-fold higher than for the WT strain, confirming its superiority. Kinetic modeling was then used to predict the conditions required to maintain the optimum CL levels and high cell concentrations in the reactor, based on the kinetic parameters of the WTC156T strain. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Kinetic modelling of non-enzymatic browning and changes of physio-chemical parameters of peach juice during storage.

    PubMed

    Lyu, Jian; Liu, Xuan; Bi, Jinfeng; Wu, Xinye; Zhou, Linyan; Ruan, Weihong; Zhou, Mo; Jiao, Yi

    2018-03-01

    Kinetics of non-enzymatic browning and loss of free amino acids during different storage temperature (4, 25, 37 °C) were investigated. Changes of browning degree ( A 420 ), color parameters, Vitamin C ( V c ), free amino acids and 5-hydroxymethylfurfural (5-HMF) were analyzed to evaluate the non-enzymatic browning reactions, which were significantly affected by storage temperature. The lower temperature (4 °C) decreased the loss of V c and the generation of 5-HMF, but induce the highest loss of serine. At the end of storage, loss of serine, alanine and aspartic acid were mainly lost. Results showed that zero-order kinetic model ( R 2  > 0.859), the first-order model ( R 2  > 0.926) and the combined kinetic model ( R 2  > 0.916) were the most appropriate to describe the changes of a * and b * values, the degradation of V c and the changes of A 420 , L * and 5-HMF during different storage temperatures. These kinetic models can be applied for predicting and minimizing the non-enzymatic browning of fresh peach juice during storage.

  20. Parameters and kinetics of olive mill wastewater dephenolization by immobilized Rhodotorula glutinis cells.

    PubMed

    Bozkoyunlu, Gaye; Takaç, Serpil

    2014-01-01

    Olive mill wastewater (OMW) with total phenol (TP) concentration range of 300-1200 mg/L was treated with alginate-immobilized Rhodotorula glutinis cells in batch system. The effects of pellet properties (diameter, alginate concentration and cell loading (CL)) and operational parameters (initial TP concentration, agitation rate and reusability of pellets) on dephenolization of OMW were studied. Up to 87% dephenolization was obtained after 120 h biodegradations. The utilization number of pellets increased with the addition of calcium ions into the biodegradation medium. The overall effectiveness factors calculated for different conditions showed that diffusional limitations arising from pellet size and pellet composition could be neglected. Mass transfer limitations appeared to be more effective at high substrate concentrations and low agitation rates. The parameters of logistic model for growth kinetics of R. glutinis in OMW were estimated at different initial phenol concentrations of OMW by curve-fitting of experimental data with the model.

  1. Impact of process parameters on the breakage kinetics of poorly water-soluble drugs during wet stirred media milling: a microhydrodynamic view.

    PubMed

    Afolabi, Afolawemi; Akinlabi, Olakemi; Bilgili, Ecevit

    2014-01-23

    Wet stirred media milling has proven to be a robust process for producing nanoparticle suspensions of poorly water-soluble drugs. As the process is expensive and energy-intensive, it is important to study the breakage kinetics, which determines the cycle time and production rate for a desired fineness. Although the impact of process parameters on the properties of final product suspensions has been investigated, scant information is available regarding their impact on the breakage kinetics. Here, we elucidate the impact of stirrer speed, bead concentration, and drug loading on the breakage kinetics via a microhydrodynamic model for the bead-bead collisions. Suspensions of griseofulvin, a model poorly water-soluble drug, were prepared in the presence of two stabilizers: hydroxypropyl cellulose and sodium dodecyl sulfate. Laser diffraction, scanning electron microscopy, and rheometry were used to characterize them. Various microhydrodynamic parameters including a newly defined milling intensity factor was calculated. An increase in either the stirrer speed or the bead concentration led to an increase in the specific energy and the milling intensity factor, consequently faster breakage. On the other hand, an increase in the drug loading led to a decrease in these parameters and consequently slower breakage. While all microhydrodynamic parameters provided significant physical insight, only the milling intensity factor was capable of explaining the influence of all parameters directly through its strong correlation with the process time constant. Besides guiding process optimization, the analysis rationalizes the preparation of a single high drug-loaded batch (20% or higher) instead of multiple dilute batches. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Pixel-based approach to assess contrast-enhanced ultrasound kinetics parameters for differential diagnosis of rheumatoid arthritis.

    PubMed

    Rizzo, Gaia; Raffeiner, Bernd; Coran, Alessandro; Ciprian, Luca; Fiocco, Ugo; Botsios, Costantino; Stramare, Roberto; Grisan, Enrico

    2015-07-01

    Inflammatory rheumatic diseases are the leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity, and increased mortality. The standard for diagnosing and differentiating arthritis is based on clinical examination, laboratory exams, and imaging findings, such as synovitis, bone edema, or joint erosions. Contrast-enhanced ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. Quantitative assessment is mostly performed at the region of interest level, where the mean intensity curve is fitted with an exponential function. We showed that using a more physiologically motivated perfusion curve, and by estimating the kinetic parameters separately pixel by pixel, the quantitative information gathered is able to more effectively characterize the different perfusion patterns. In particular, we demonstrated that a random forest classifier based on pixelwise quantification of the kinetic contrast agent perfusion features can discriminate rheumatoid arthritis from different arthritis forms (psoriatic arthritis, spondyloarthritis, and arthritis in connective tissue disease) with an average accuracy of 97%. On the contrary, clinical evaluation (DAS28), semiquantitative CEUS assessment, serological markers, or region-based parameters do not allow such a high diagnostic accuracy.

  3. Pixel-based approach to assess contrast-enhanced ultrasound kinetics parameters for differential diagnosis of rheumatoid arthritis

    PubMed Central

    Rizzo, Gaia; Raffeiner, Bernd; Coran, Alessandro; Ciprian, Luca; Fiocco, Ugo; Botsios, Costantino; Stramare, Roberto; Grisan, Enrico

    2015-01-01

    Abstract. Inflammatory rheumatic diseases are the leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity, and increased mortality. The standard for diagnosing and differentiating arthritis is based on clinical examination, laboratory exams, and imaging findings, such as synovitis, bone edema, or joint erosions. Contrast-enhanced ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. Quantitative assessment is mostly performed at the region of interest level, where the mean intensity curve is fitted with an exponential function. We showed that using a more physiologically motivated perfusion curve, and by estimating the kinetic parameters separately pixel by pixel, the quantitative information gathered is able to more effectively characterize the different perfusion patterns. In particular, we demonstrated that a random forest classifier based on pixelwise quantification of the kinetic contrast agent perfusion features can discriminate rheumatoid arthritis from different arthritis forms (psoriatic arthritis, spondyloarthritis, and arthritis in connective tissue disease) with an average accuracy of 97%. On the contrary, clinical evaluation (DAS28), semiquantitative CEUS assessment, serological markers, or region-based parameters do not allow such a high diagnostic accuracy. PMID:27014713

  4. Predicting heavy metals' adsorption edges and adsorption isotherms on MnO2 with the parameters determined from Langmuir kinetics.

    PubMed

    Hu, Qinghai; Xiao, Zhongjin; Xiong, Xinmei; Zhou, Gongming; Guan, Xiaohong

    2015-01-01

    Although surface complexation models have been widely used to describe the adsorption of heavy metals, few studies have verified the feasibility of modeling the adsorption kinetics, edge, and isotherm data with one pH-independent parameter. A close inspection of the derivation process of Langmuir isotherm revealed that the equilibrium constant derived from the Langmuir kinetic model, KS-kinetic, is theoretically equivalent to the adsorption constant in Langmuir isotherm, KS-Langmuir. The modified Langmuir kinetic model (MLK model) and modified Langmuir isotherm model (MLI model) incorporating pH factor were developed. The MLK model was employed to simulate the adsorption kinetics of Cu(II), Co(II), Cd(II), Zn(II) and Ni(II) on MnO2 at pH3.2 or 3.3 to get the values of KS-kinetic. The adsorption edges of heavy metals could be modeled with the modified metal partitioning model (MMP model), and the values of KS-Langmuir were obtained. The values of KS-kinetic and KS-Langmuir are very close to each other, validating that the constants obtained by these two methods are basically the same. The MMP model with KS-kinetic constants could predict the adsorption edges of heavy metals on MnO2 very well at different adsorbent/adsorbate concentrations. Moreover, the adsorption isotherms of heavy metals on MnO2 at various pH levels could be predicted reasonably well by the MLI model with the KS-kinetic constants. Copyright © 2014. Published by Elsevier B.V.

  5. Accurate evaluation for the biofilm-activated sludge reactor using graphical techniques

    NASA Astrophysics Data System (ADS)

    Fouad, Moharram; Bhargava, Renu

    2018-05-01

    A complete graphical solution is obtained for the completely mixed biofilm-activated sludge reactor (hybrid reactor). The solution consists of a series of curves deduced from the principal equations of the hybrid system after converting them in dimensionless form. The curves estimate the basic parameters of the hybrid system such as suspended biomass concentration, sludge residence time, wasted mass of sludge, and food to biomass ratio. All of these parameters can be expressed as functions of hydraulic retention time, influent substrate concentration, substrate concentration in the bulk, stagnant liquid layer thickness, and the minimum substrate concentration which can maintain the biofilm growth in addition to the basic kinetics of the activated sludge process in which all these variables are expressed in a dimensionless form. Compared to other solutions of such system these curves are simple, easy to use, and provide an accurate tool for analyzing such system based on fundamental principles. Further, these curves may be used as a quick tool to get the effect of variables change on the other parameters and the whole system.

  6. A second-order accurate kinetic-theory-based method for inviscid compressible flows

    NASA Technical Reports Server (NTRS)

    Deshpande, Suresh M.

    1986-01-01

    An upwind method for the numerical solution of the Euler equations is presented. This method, called the kinetic numerical method (KNM), is based on the fact that the Euler equations are moments of the Boltzmann equation of the kinetic theory of gases when the distribution function is Maxwellian. The KNM consists of two phases, the convection phase and the collision phase. The method is unconditionally stable and explicit. It is highly vectorizable and can be easily made total variation diminishing for the distribution function by a suitable choice of the interpolation strategy. The method is applied to a one-dimensional shock-propagation problem and to a two-dimensional shock-reflection problem.

  7. Compost mixture influence of interactive physical parameters on microbial kinetics and substrate fractionation.

    PubMed

    Mohajer, Ardavan; Tremier, Anne; Barrington, Suzelle; Teglia, Cecile

    2010-01-01

    Composting is a feasible biological treatment for the recycling of wastewater sludge as a soil amendment. The process can be optimized by selecting an initial compost recipe with physical properties that enhance microbial activity. The present study measured the microbial O(2) uptake rate (OUR) in 16 sludge and wood residue mixtures to estimate the kinetics parameters of maximum growth rate mu(m) and rate of organic matter hydrolysis K(h), as well as the initial biodegradable organic matter fractions present. The starting mixtures consisted of a wide range of moisture content (MC), waste to bulking agent (BA) ratio (W/BA ratio) and BA particle size, which were placed in a laboratory respirometry apparatus to measure their OUR over 4 weeks. A microbial model based on the activated sludge process was used to calculate the kinetic parameters and was found to adequately reproduced OUR curves over time, except for the lag phase and peak OUR, which was not represented and generally over-estimated, respectively. The maximum growth rate mu(m), was found to have a quadratic relationship with MC and a negative association with BA particle size. As a result, increasing MC up to 50% and using a smaller BA particle size of 8-12 mm was seen to maximize mu(m). The rate of hydrolysis K(h) was found to have a linear association with both MC and BA particle size. The model also estimated the initial readily biodegradable organic matter fraction, MB(0), and the slower biodegradable matter requiring hydrolysis, MH(0). The sum of MB(0) and MH(0) was associated with MC, W/BA ratio and the interaction between these two parameters, suggesting that O(2) availability was a key factor in determining the value of these two fractions. The study reinforced the idea that optimization of the physical characteristics of a compost mixture requires a holistic approach. 2010 Elsevier Ltd. All rights reserved.

  8. A three-time-point method for assessing kinetic parameters of 64Cu-labeled Ramucirumab trapping in VEGFR-2 positive lung tumors.

    PubMed

    Laffon, Eric; Marthan, Roger

    2017-11-01

    To describe a three-time-point method for estimating kinetic parameters involved in 64 Cu-labeled Ramucirumab ( 64 Cu-NOTA-RamAb) trapping of VEGFR-2 positive lung tumors. Positron emission tomography (microPET) data of tumor-bearing mice for 64 Cu-NOTA-RamAb trapping in VEGFR-2 positive HCC4006 tumor were used, involving tissue activity measurements acquired at 3, 24 and 48 h post-injection, without and with administration of RamAb blocking dose. A kinetic model provided an analytical formula describing the tissue time-activity-curve, involving 64 Cu-NOTA-RamAb uptake (Ki), release rate constant (k R ) and fraction of free tracer in blood and interstitial volume (F). Fitting analytical formula outcomes on mean microPET data yielded values of the kinetic parameters: Ki = 0.0314/0.0123 gram of blood per hour per gram of tissue, k R  = 0.0387/0.0313 h -1 and F = 0.2075/0.2007 gram of blood per gram of tissue, without/with RamAb blocking dose, respectively (R = 0.99999 for the graph displaying microPET versus theoretical data; P < .01). Three independent kinetic parameters (Ki, k R and F) can be assessed from three data points acquired at early, mid and late imaging, i.e., at 3, 24 and 48 h post-injection, for further characterization of 64 Cu-NOTA-RamAb trapping in VEGFR-2 positive lung tumors. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  9. Estimation of kinetic parameters of anthocyanins and color degradation in vitamin C fortified cranberry juice during storage.

    PubMed

    Roidoung, Sunisa; Dolan, Kirk D; Siddiq, Muhammad

    2017-04-01

    Color degradation in cranberry juice during storage is the most common consumer complaint. To enhance nutritional quality, juice is typically fortified with vitamin C. This study determined effect of gallic acid, a natural antioxidant, for the preservation of anthocyanins (ACYs) and color, and estimated kinetics of ACYs and color degradation. Juice, fortified with 40-80mg/100mL vitamin C and 0-320mg/100mL gallic acid, was pasteurized at 85°C for 1min and stored at 23°C for 16days. Total monomeric anthocyanins and red color intensity were evaluated spectrophotometrically and data were used to determine degradation rate constants (k values) and order of reaction (n) of ACYs and color. Due to high correlation, k and n could not be estimated simultaneously. To overcome this difficulty, both n and k were held at different constant values in separate analyses to allow accurate estimation of each. Parameters n and k were modeled empirically as functions of vitamin C, and of vitamin C and gallic acid, respectively. Reaction order n ranged from 1.2 to 4.4, and decreased with increasing vitamin C concentration. The final model offers an effective tool that could be used for predicting ACYs and color retention in cranberry juice during storage. Copyright © 2017. Published by Elsevier Ltd.

  10. Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data.

    PubMed

    Tesmar, Aleksandra; Wyrzykowski, Dariusz; Muñoz, Eva; Pilarski, Bogusław; Pranczk, Joanna; Jacewicz, Dagmara; Chmurzyński, Lech

    2017-04-01

    The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co 2 + and Ni 2 + ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N-(2-hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2-(N-morpholino)ethanesulfonic acid hydrate (2-(N-morpholino) ethanesulfonic acid), piperazine-N,N'-bis(2-ethanesulfonic acid), and dimethylarsenic acid buffers (0.1 mol L -1 , pH 6) at 298.15 K. The quantification of the metal-buffer interactions and their incorporation into the ITC data analysis enabled to obtain the pH-independent and buffer-independent thermodynamic parameters (K, ΔG, ΔH, and ΔS) for the reactions under study. Furthermore, the kinITC method was applied to obtain kinetic information on complexation reactions from the ITC data. Correlations, based on kinetic and thermodynamic data, between the kinetics of formation of Co 2 + and Ni 2 + complexes and their thermodynamic stabilities are discussed. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    PubMed

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  12. Comment on ‘Information hidden in the velocity distribution of ions and the exact kinetic Bohm criterion’

    NASA Astrophysics Data System (ADS)

    Mustafaev, A. S.; Sukhomlinov, V. S.; Timofeev, N. A.

    2018-03-01

    This Comment is devoted to some mathematical inaccuracies made by the authors of the paper ‘Information hidden in the velocity distribution of ions and the exact kinetic Bohm criterion’ (Plasma Sources Science and Technology 26 055003). In the Comment, we show that the diapason of plasma parameters for the validity of the theoretical results obtained by the authors was defined incorrectly; we made a more accurate definition of this diapason. As a result, we show that it is impossible to confirm or refute the feasibility of the Bohm kinetic criterion on the basis of the data of the cited paper.

  13. Esterification of fatty acids using nylon-immobilized lipase in n-hexane: kinetic parameters and chain-length effects.

    PubMed

    Zaidi, A; Gainer, J L; Carta, G; Mrani, A; Kadiri, T; Belarbi, Y; Mir, A

    2002-02-28

    The esterification of long-chain fatty acids in n-hexane catalyzed by nylon-immobilized lipase from Candida rugosa has been investigated. Butyl oleate (22 carbon atoms), oleyl butyrate (22 carbon atoms) and oleyl oleate (36 carbon atoms) were produced at maximum reaction rates of approximately equal to 60 mmol h(-1) g(-1) immobilized enzyme when the substrates were present in equimolar proportions at an initial concentration of 0.6 mol l(-1). The observed kinetic behavior of all the esterification reactions is found to follow a ping-pong bi-bi mechanism with competitive inhibition by both substrates. The effect of the chain-length of the fatty acids and the alcohols could be correlated to some mechanistic models, in accordance with the calculated kinetic parameters.

  14. Testing the nonlocal kinetic energy functional of an inhomogeneous, two-dimensional degenerate Fermi gas within the average density approximation

    NASA Astrophysics Data System (ADS)

    Towers, J.; van Zyl, B. P.; Kirkby, W.

    2015-08-01

    In a recent paper [B. P. van Zyl et al., Phys. Rev. A 89, 022503 (2014), 10.1103/PhysRevA.89.022503], the average density approximation (ADA) was implemented to develop a parameter-free, nonlocal kinetic energy functional to be used in the orbital-free density functional theory of an inhomogeneous, two-dimensional (2D) Fermi gas. In this work, we provide a detailed comparison of self-consistent calculations within the ADA with the exact results of the Kohn-Sham density functional theory and the elementary Thomas-Fermi (TF) approximation. We demonstrate that the ADA for the 2D kinetic energy functional works very well under a wide variety of confinement potentials, even for relatively small particle numbers. Remarkably, the TF approximation for the kinetic energy functional, without any gradient corrections, also yields good agreement with the exact kinetic energy for all confining potentials considered, although at the expense of the spatial and kinetic energy densities exhibiting poor pointwise agreement, particularly near the TF radius. Our findings illustrate that the ADA kinetic energy functional yields accurate results for both the local and global equilibrium properties of an inhomogeneous 2D Fermi gas, without the need for any fitting parameters.

  15. A comparison of region-based and pixel-based CEUS kinetics parameters in the assessment of arthritis

    NASA Astrophysics Data System (ADS)

    Grisan, E.; Raffeiner, B.; Coran, A.; Rizzo, G.; Ciprian, L.; Stramare, R.

    2014-03-01

    Inflammatory rheumatic diseases are leading causes of disability and constitute a frequent medical disorder, leading to inability to work, high comorbidity and increased mortality. The gold-standard for diagnosing and differentiating arthritis is based on patient conditions and radiographic findings, as joint erosions or decalcification. However, early signs of arthritis are joint effusion, hypervascularization and synovial hypertrophy. In particular, vascularization has been shown to correlate with arthritis' destructive behavior, more than clinical assessment. Contrast Enhanced Ultrasound (CEUS) examination of the small joints is emerging as a sensitive tool for assessing vascularization and disease activity. The evaluation of perfusion pattern rely on subjective semi-quantitative scales, that are able to capture the macroscopic degree of vascularization, but are unable to detect the subtler differences in kinetics perfusion parameters that might lead to a deeper understanding of disease progression and a better management of patients. Quantitative assessment is mostly performed by means of the Qontrast software package, that requires the user to define a region of interest, whose mean intensity curve is fitted with an exponential function. We show that using a more physiologically motivated perfusion curve, and by estimating the kinetics parameters separately pixel per pixel, the quantitative information gathered is able to differentiate more effectively different perfusion patterns. In particular, we will show that a pixel-based analysis is able to provide significant markers differentiating rheumatoid arthritis from simil-rheumatoid psoriatic arthritis, that have non-significant differences in clinical evaluation (DAS28), serological markers, or region-based parameters.

  16. Incorporation of MRI-AIF Information For Improved Kinetic Modelling of Dynamic PET Data

    NASA Astrophysics Data System (ADS)

    Sari, Hasan; Erlandsson, Kjell; Thielemans, Kris; Atkinson, David; Ourselin, Sebastien; Arridge, Simon; Hutton, Brian F.

    2015-06-01

    In the analysis of dynamic PET data, compartmental kinetic analysis methods require an accurate knowledge of the arterial input function (AIF). Although arterial blood sampling is the gold standard of the methods used to measure the AIF, it is usually not preferred as it is an invasive method. An alternative method is the simultaneous estimation method (SIME), where physiological parameters and the AIF are estimated together, using information from different anatomical regions. Due to the large number of parameters to estimate in its optimisation, SIME is a computationally complex method and may sometimes fail to give accurate estimates. In this work, we try to improve SIME by utilising an input function derived from a simultaneously obtained DSC-MRI scan. With the assumption that the true value of one of the six parameter PET-AIF model can be derived from an MRI-AIF, the method is tested using simulated data. The results indicate that SIME can yield more robust results when the MRI information is included with a significant reduction in absolute bias of Ki estimates.

  17. Associations between timing in the baseball pitch and shoulder kinetics, elbow kinetics, and ball speed.

    PubMed

    Urbin, M A; Fleisig, Glenn S; Abebe, Asheber; Andrews, James R

    2013-02-01

    A baseball pitcher's ability to maximize ball speed while avoiding shoulder and elbow injuries is an important determinant of a successful career. Pitching injuries are attributed to microtrauma brought about by the repetitive stress of high-magnitude shoulder and elbow kinetics. Over a number of pitches, variations in timing peak angular velocities of trunk segment rotations will be significantly associated with ball speed and upper extremity kinetic parameters. Descriptive laboratory study. Kinematic and kinetic data were derived from 9 to 15 fastball pitches performed by 16 active, healthy collegiate (n = 8) and professional (n = 8) pitchers via 3-dimensional motion capture (240 Hz). Each pitch was decomposed into 4 phases corresponding to the time between peak angular velocities of sequential body segment rotations. Four mixed models were used to evaluate which phases varied significantly in relation to ball speed, peak shoulder proximal force, peak shoulder internal rotation torque, and peak elbow varus torque. Mixed-model parameter coefficient estimates were used to quantify the influence of these variations in timing on ball speed and upper extremity kinetics. All 4 mixed models were significant (P < .05). The time from stride-foot contact to peak pelvis angular velocity varied significantly in relation to all upper extremity kinetic parameters and ball speed. Increased time in this phase correlated with decreases in all parameters. Decreased ball speed also correlated with increased time between peak upper torso and elbow extension angular velocities. Decreased shoulder proximal force also correlated with increased time between peak pelvis and upper torso angular velocities. There are specific phases that vary in relation to ball speed and upper extremity kinetic parameters, reinforcing the importance of effectively and consistently timing segmental interactions. For the specific interactions that varied significantly, increased phase times were associated

  18. Optimization of magnetization transfer measurements: statistical analysis by stochastic simulation. Application to creatine kinase kinetics.

    PubMed

    Rydzy, M; Deslauriers, R; Smith, I C; Saunders, J K

    1990-08-01

    A systematic study was performed to optimize the accuracy of kinetic parameters derived from magnetization transfer measurements. Three techniques were investigated: time-dependent saturation transfer (TDST), saturation recovery (SRS), and inversion recovery (IRS). In the last two methods, one of the resonances undergoing exchange is saturated throughout the experiment. The three techniques were compared with respect to the accuracy of the kinetic parameters derived from experiments performed in a given, fixed, amount of time. Stochastic simulation of magnetization transfer experiments was performed to optimize experimental design. General formulas for the relative accuracies of the unidirectional rate constant (k) were derived for each of the three experimental methods. It was calculated that for k values between 0.1 and 1.0 s-1, T1 values between 1 and 10 s, and relaxation delays appropriate for the creatine kinase reaction, the SRS method yields more accurate values of k than does the IRS method. The TDST method is more accurate than the SRS method for reactions where T1 is long and k is large, within the range of k and T1 values examined. Experimental verification of the method was carried out on a solution in which the forward (PCr----ATP) rate constant (kf) of the creatine kinase reaction was measured.

  19. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Kinetics of Germination of Bacillus Spores1

    PubMed Central

    Vary, J. C.; Halvorson, H. O.

    1965-01-01

    Vary, J. C. (University of Wisconsin, Madison), and H. O. Halvorson. Kinetics or germination of Bacillus spores. J. Bacteriol. 89:1340–1347. 1965.—The kinetics of germination of Bacillus cereus strain T spores was accurately described by McCormick. To study the mechanism of germination, it is necessary to correlate the characteristic changes in a population of germinating spores with the behavior of the individual spores in the same population. Two microscopic events are apparent during germination: microlag, the time interval between the addition of l-alanine to heat-activated spores and the beginning of loss in refractility, and microgermination time, the time for the actual change in refractility to occur. The frequency distributions of both events are skewed, and appear to be independent. The effects of l-alanine concentration, heat activation, and temperature of germination on three parameters, microlag, microgermination, and per cent germination, were microscopically studied. The data are discussed in relation to the mechanism of germination, and a correlation between microlag and microgermination times with the constants of McCormick's equation has been suggested. Images PMID:14293008

  1. Optimization of tissue physical parameters for accurate temperature estimation from finite-element simulation of radiofrequency ablation.

    PubMed

    Subramanian, Swetha; Mast, T Douglas

    2015-10-07

    Computational finite element models are commonly used for the simulation of radiofrequency ablation (RFA) treatments. However, the accuracy of these simulations is limited by the lack of precise knowledge of tissue parameters. In this technical note, an inverse solver based on the unscented Kalman filter (UKF) is proposed to optimize values for specific heat, thermal conductivity, and electrical conductivity resulting in accurately simulated temperature elevations. A total of 15 RFA treatments were performed on ex vivo bovine liver tissue. For each RFA treatment, 15 finite-element simulations were performed using a set of deterministically chosen tissue parameters to estimate the mean and variance of the resulting tissue ablation. The UKF was implemented as an inverse solver to recover the specific heat, thermal conductivity, and electrical conductivity corresponding to the measured area of the ablated tissue region, as determined from gross tissue histology. These tissue parameters were then employed in the finite element model to simulate the position- and time-dependent tissue temperature. Results show good agreement between simulated and measured temperature.

  2. Droplet Growth Kinetics in Various Environments

    NASA Astrophysics Data System (ADS)

    Raatikainen, T. E.; Lathem, T. L.; Moore, R.; Lin, J. J.; Cerully, K. M.; Padro, L.; Lance, S.; Cozic, J.; Anderson, B. E.; Nenes, A.

    2012-12-01

    The largest uncertainties in the effects of atmospherics aerosols on the global radiation budget are related to their indirect effects on cloud properties (IPCC, the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, 2007). Cloud formation is a kinetic process where the resulting cloud properties depend on aerosol properties and meteorological parameters such as updraft velocity (e.g. McFiggans et al., Atmos. Chem. Phys., 6, 2593-2649, 2006). Droplet growth rates are limited by the water vapor diffusion, but additional kinetic limitations, e.g., due to organic surface films, slow solute dissociation or highly viscous or glassy aerosol states have been hypothesized. Significant additional kinetic limitations can lead to increased cloud droplet number concentration, thus the effect is similar to those of increased aerosol number concentration or changes in vertical velocity (e.g. Nenes et al., Geophys. Res. Lett., 29, 1848, 2002). There are a few studies where slow droplet growth has been observed (e.g. Ruehl et al., Geophys. Res. Lett., 36, L15814, 2009), however, little is currently known about their global occurrence and magnitude. Cloud micro-physics models often describe kinetic limitations by an effective water vapor uptake coefficient or similar parameter. Typically, determining aerosol water vapor uptake coefficients requires experimental observations of droplet growth which are interpreted by a numerical droplet growth model where the uptake coefficient is an adjustable parameter (e.g. Kolb et al., Atmos. Chem. Phys., 10, 10561-10605, 2010). Such methods have not been practical for high time-resolution or long term field measurements, until a model was recently developed for analyzing Droplet Measurement Technologies (DMT) cloud condensation nuclei (CCN) counter data (Raatikainen et al., Atmos. Chem. Phys., 12, 4227-4243, 2012). Model verification experiments showed that the calibration aerosol droplet size can be predicted accurately

  3. Intrinsic kinetic parameters of substrate utilization by immobilized anaerobic sludge.

    PubMed

    Zaiat, M; Vieira, L G; Foresti, E

    1997-01-20

    This article presents a method for evaluating the intrinsic kinetic parameters of the specific substrate utilization rate (r) equation and discusses the results obtained for anaerobic sludge-bed samples taken from a horizontal-flow anaerobic immobilized sludge (HAIS) reactor. This method utilizes a differential reactor filled with polyurethane foam matrices containing immobilized anaerobic sludge which is subjected to a range of feeding substrate flow rates. The range of liquid superficial velocities thus obtained are used for generating data of observed specific substrate utilization rates (r(obs)) under a diversity of external mass transfer resistance conditions. The r(obs) curves are then adjusted to permit their extrapolation for the condition of no external mass transfer resistance, and the values determined are used as a test for the condition of absence of limitation of internal mass transfer. The intrinsic parameters r(max), the maximum specific substrate utilization rate, and K(s), the half-velocity coefficient, are evaluated from the r values under no external mass transfer resistance and no internal mass transfer limitation. The application of such a method for anaerobic sludge immobilized in polyurethane foam particles treating a glucose substrate at 30 degrees C resulted in intrinsic r(max) and K(s), respectively, of 0.330 mg chemical oxygen demand (COD) . mg(-1) volatile suspended solids (VSS) . h(-1) and 72 mg COD . L(-1). In comparison with the values found in the literature, intrinsic r(max) is significantly high and intrinsic K(s) is relatively low. (c) 1997 John Wiley & Sons, Inc.

  4. Deposition kinetics of colloidal particles at high ionic strengths

    NASA Astrophysics Data System (ADS)

    Cejas, Cesare; Monti, Fabrice; Truchet, Marine; Burnouf, Jean-Pierre; Tabeling, Patrick

    Using microfluidic experiments, we describe the deposition of a fluid suspension of weakly brownian particles transported in a straight channel at small Reynolds numbers under conditions of high ionic strengths. Our studies fall in a regime where electrostatic interactions are neglected and particle-wall van der Waals interactions govern the deposition mechanism on channel walls. We calculate the deposition kinetics analytically for a wide range of physical parameters. We find that the theory agrees with numerical Langevin simulations, which both confirm the experimental results. From this analysis, we demonstrate a universal dimensionless deposition function described by contributions from advection-diffusion transport and adhesion interactions (Hamaker constant). Results show that we accurately confirm the theoretical expression for the deposition kinetics. From a surface science perspective, working in the van der Waals regime enables to measure the Hamaker constant, a task that would take much longer to perform with the standard AFM. Funding from Sanofi Recherche and ESPCI.

  5. Reliability and Validity of Kinetic and Kinematic Parameters Determined With Force Plates Embedded Under a Soil-Filled Baseball Mound.

    PubMed

    Yanai, Toshimasa; Matsuo, Akifumi; Maeda, Akira; Nakamoto, Hiroki; Mizutani, Mirai; Kanehisa, Hiroaki; Fukunaga, Tetsuo

    2017-08-01

    We developed a force measurement system in a soil-filled mound for measuring ground reaction forces (GRFs) acting on baseball pitchers and examined the reliability and validity of kinetic and kinematic parameters determined from the GRFs. Three soil-filled trays of dimensions that satisfied the official baseball rules were fixed onto 3 force platforms. Eight collegiate pitchers wearing baseball shoes with metal cleats were asked to throw 5 fastballs with maximum effort from the mound toward a catcher. The reliability of each parameter was determined for each subject as the coefficient of variation across the 5 pitches. The validity of the measurements was tested by comparing the outcomes either with the true values or the corresponding values computed from a motion capture system. The coefficients of variation in the repeated measurements of the peak forces ranged from 0.00 to 0.17, and were smaller for the pivot foot than the stride foot. The mean absolute errors in the impulses determined over the entire duration of pitching motion were 5.3 N˙s, 1.9 N˙s, and 8.2 N˙s for the X-, Y-, and Z-directions, respectively. These results suggest that the present method is reliable and valid for determining selected kinetic and kinematic parameters for analyzing pitching performance.

  6. Differential effects on enzyme stability and kinetic parameters of mutants related to human triosephosphate isomerase deficiency.

    PubMed

    Cabrera, Nallely; Torres-Larios, Alfredo; García-Torres, Itzhel; Enríquez-Flores, Sergio; Perez-Montfort, Ruy

    2018-06-01

    Human triosephosphate isomerase (TIM) deficiency is a very rare disease, but there are several mutations reported to be causing the illness. In this work, we produced nine recombinant human triosephosphate isomerases which have the mutations reported to produce TIM deficiency. These enzymes were characterized biophysically and biochemically to determine their kinetic and stability parameters, and also to substitute TIM activity in supporting the growth of an Escherichia coli strain lacking the tim gene. Our results allowed us to rate the deleteriousness of the human TIM mutants based on the type and severity of the alterations observed, to classify four "unknown severity mutants" with altered residues in positions 62, 72, 122 and 154 and to explain in structural terms the mutation V231M, the most affected mutant from the kinetic point of view and the only homozygous mutation reported besides E104D. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Predicting DNA hybridization kinetics from sequence

    NASA Astrophysics Data System (ADS)

    Zhang, Jinny X.; Fang, John Z.; Duan, Wei; Wu, Lucia R.; Zhang, Angela W.; Dalchau, Neil; Yordanov, Boyan; Petersen, Rasmus; Phillips, Andrew; Zhang, David Yu

    2018-01-01

    Hybridization is a key molecular process in biology and biotechnology, but so far there is no predictive model for accurately determining hybridization rate constants based on sequence information. Here, we report a weighted neighbour voting (WNV) prediction algorithm, in which the hybridization rate constant of an unknown sequence is predicted based on similarity reactions with known rate constants. To construct this algorithm we first performed 210 fluorescence kinetics experiments to observe the hybridization kinetics of 100 different DNA target and probe pairs (36 nt sub-sequences of the CYCS and VEGF genes) at temperatures ranging from 28 to 55 °C. Automated feature selection and weighting optimization resulted in a final six-feature WNV model, which can predict hybridization rate constants of new sequences to within a factor of 3 with ∼91% accuracy, based on leave-one-out cross-validation. Accurate prediction of hybridization kinetics allows the design of efficient probe sequences for genomics research.

  8. Laser diode absorption spectroscopy for accurate CO(2) line parameters at 2 microm: consequences for space-based DIAL measurements and potential biases.

    PubMed

    Joly, Lilian; Marnas, Fabien; Gibert, Fabien; Bruneau, Didier; Grouiez, Bruno; Flamant, Pierre H; Durry, Georges; Dumelie, Nicolas; Parvitte, Bertrand; Zéninari, Virginie

    2009-10-10

    Space-based active sensing of CO(2) concentration is a very promising technique for the derivation of CO(2) surface fluxes. There is a need for accurate spectroscopic parameters to enable accurate space-based measurements to address global climatic issues. New spectroscopic measurements using laser diode absorption spectroscopy are presented for the preselected R30 CO(2) absorption line ((20(0)1)(III)<--(000) band) and four others. The line strength, air-broadening halfwidth, and its temperature dependence have been investigated. The results exhibit significant improvement for the R30 CO(2) absorption line: 0.4% on the line strength, 0.15% on the air-broadening coefficient, and 0.45% on its temperature dependence. Analysis of potential biases of space-based DIAL CO(2) mixing ratio measurements associated to spectroscopic parameter uncertainties are presented.

  9. Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

    PubMed

    Mollica, Luca; Theret, Isabelle; Antoine, Mathias; Perron-Sierra, Françoise; Charton, Yves; Fourquez, Jean-Marie; Wierzbicki, Michel; Boutin, Jean A; Ferry, Gilles; Decherchi, Sergio; Bottegoni, Giovanni; Ducrot, Pierre; Cavalli, Andrea

    2016-08-11

    Ligand-target residence time is emerging as a key drug discovery parameter because it can reliably predict drug efficacy in vivo. Experimental approaches to binding and unbinding kinetics are nowadays available, but we still lack reliable computational tools for predicting kinetics and residence time. Most attempts have been based on brute-force molecular dynamics (MD) simulations, which are CPU-demanding and not yet particularly accurate. We recently reported a new scaled-MD-based protocol, which showed potential for residence time prediction in drug discovery. Here, we further challenged our procedure's predictive ability by applying our methodology to a series of glucokinase activators that could be useful for treating type 2 diabetes mellitus. We combined scaled MD with experimental kinetics measurements and X-ray crystallography, promptly checking the protocol's reliability by directly comparing computational predictions and experimental measures. The good agreement highlights the potential of our scaled-MD-based approach as an innovative method for computationally estimating and predicting drug residence times.

  10. Displacement cascades and defect annealing in tungsten, Part III: The sensitivity of cascade annealing in tungsten to the values of kinetic parameters

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

    Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

    2015-07-01

    Object kinetic Monte Carlo (OKMC) simulations have been performed to investigate various aspects of cascade aging in bulk tungsten and to determine the sensitivity of the results to the kinetic parameters. The primary focus is on how the kinetic parameters affect the initial recombination of defects in the first few ns of a simulation. The simulations were carried out using the object kinetic Monte Carlo (OKMC) code KSOME (kinetic simulations of microstructure evolution), using a database of cascades obtained from results of molecular dynamics (MD) simulations at various primary knock-on atom (PKA) energies and directions at temperatures of 300, 1025more » and 2050 K. The OKMC model was parameterized using defect migration barriers and binding energies from ab initio calculations. Results indicate that, due to the disparate mobilities of SIA and vacancy clusters in tungsten, annealing is dominated by SIA migration even at temperatures as high as 2050 K. For 100 keV cascades initiated at 300 K recombination is dominated by annihilation of large defect clusters. But for all other PKA energies and temperatures most of the recombination is due to the migration and rotation of small SIA clusters, while all the large SIA clusters escape the cubic simulation cell. The inverse U-shape behavior exhibited by the annealing efficiency as a function of temperature curve, especially for cascades of large PKA energies, is due to asymmetry in SIA and vacancy clustering assisted by the large difference in mobilities of SIAs and vacancies. This annealing behavior is unaffected by the dimensionality of SIA migration persists over a broad range of relative mobilities of SIAs and vacancies.« less

  11. Discussion of the Investigation Method on the Reaction Kinetics of Metallurgical Reaction Engineering

    NASA Astrophysics Data System (ADS)

    Du, Ruiling; Wu, Keng; Zhang, Jiazhi; Zhao, Yong

    Reaction kinetics of metallurgical physical chemistry which was successfully applied in metallurgy (as ferrous metallurgy, non-ferrous metallurgy) became an important theoretical foundation for subject system of traditional metallurgy. Not only the research methods were very perfect, but also the independent structures and systems of it had been formed. One of the important tasks of metallurgical reaction engineering was the simulation of metallurgical process. And then, the mechanism of reaction process and the conversion time points of different control links should be obtained accurately. Therefore, the research methods and results of reaction kinetics in metallurgical physical chemistry were not very suitable for metallurgical reaction engineering. In order to provide the definite conditions of transmission, reaction kinetics parameters and the conversion time points of different control links for solving the transmission and reaction equations in metallurgical reaction engineering, a new method for researching kinetics mechanisms in metallurgical reaction engineering was proposed, which was named stepwise attempt method. Then the comparison of results between the two methods and the further development of stepwise attempt method were discussed in this paper. As a new research method for reaction kinetics in metallurgical reaction engineering, stepwise attempt method could not only satisfy the development of metallurgical reaction engineering, but also provide necessary guarantees for establishing its independent subject system.

  12. Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

    PubMed Central

    2017-01-01

    Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

  13. Comparison of petroleum generation kinetics by isothermal hydrous and nonisothermal open-system pyrolysis

    USGS Publications Warehouse

    Lewan, M.D.; Ruble, T.E.

    2002-01-01

    This study compares kinetic parameters determined by open-system pyrolysis and hydrous pyrolysis using aliquots of source rocks containing different kerogen types. Kinetic parameters derived from these two pyrolysis methods not only differ in the conditions employed and products generated, but also in the derivation of the kinetic parameters (i.e., isothermal linear regression and non-isothermal nonlinear regression). Results of this comparative study show that there is no correlation between kinetic parameters derived from hydrous pyrolysis and open-system pyrolysis. Hydrous-pyrolysis kinetic parameters determine narrow oil windows that occur over a wide range of temperatures and depths depending in part on the organic-sulfur content of the original kerogen. Conversely, open-system kinetic parameters determine broad oil windows that show no significant differences with kerogen types or their organic-sulfur contents. Comparisons of the kinetic parameters in a hypothetical thermal-burial history (2.5 ??C/my) show open-system kinetic parameters significantly underestimate the extent and timing of oil generation for Type-US kerogen and significantly overestimate the extent and timing of petroleum formation for Type-I kerogen compared to hydrous pyrolysis kinetic parameters. These hypothetical differences determined by the kinetic parameters are supported by natural thermal-burial histories for the Naokelekan source rock (Type-IIS kerogen) in the Zagros basin of Iraq and for the Green River Formation (Type-I kerogen) in the Uinta basin of Utah. Differences in extent and timing of oil generation determined by open-system pyrolysis and hydrous pyrolysis can be attributed to the former not adequately simulating natural oil generation conditions, products, and mechanisms.

  14. Characterization of the cytochrome P450 enzymes and enzyme kinetic parameters for metabolism of BVT.2938 using different in vitro systems.

    PubMed

    Baranczewski, Pawel; Edlund, Per Olof; Postlind, Hans

    2006-03-18

    An important step in the drug development process is identification of enzymes responsible for metabolism of drug candidates and determination of enzyme kinetic parameters. These data are used to increase understanding of the pharmacokinetics and possible metabolic-based drug interactions of drug candidates. The aim of the present study was to characterize the cytochrome P450 enzymes and enzyme kinetic parameters for metabolism of BVT.2938 [1-(3-{2-[(2-ethoxy-3-pyridinyl)oxy]ethoxy}-2-pyrazinyl)-2(R)-methylpiperazine], a potent and selective 5HT2c-receptor agonist. The enzyme kinetic parameters were determined for formation of three main metabolites of BVT.2938 using human liver microsomes and expressed cytochrome P450 (CYP) isoforms. The major metabolite was formed by hydroxylation of the pyridine ring (CL(int)=27 microl/mgmin), and was catalysed by both CYP2D6*1 and CYP1A1, with K(m) values corresponding to 1.4 and 2.7 microM, respectively. The results from enzyme kinetic studies were confirmed by incubation of BVT.2938 in the presence of the chemical inhibitor of CYP2D6*1, quinidine. Quinidine inhibited the formation of the major metabolite by approximately 90%. Additionally, studies with recombinant expressed CYP isoforms from rat indicated that formation of the major metabolite of BVT.2938 was catalysed by CYP2D2. This result was further confirmed by experiments with liver slices from different rat strains, where the formation of the metabolite correlated with phenotype of CYP2D2 isoform (Sprague-Dawley male, extensive; Dark Agouti male, intermediate; Dark Agouti female, poor metabolizer). The present study showed that the major metabolite of BVT.2938 is formed by hydroxylation of the pyridine ring and catalysed by CYP2D6*1. CYP1A1 is also involved in this reaction and its role in extra-hepatic metabolism of BVT.2938 might be significant.

  15. Revealing the physical insight of a length-scale parameter in metamaterials by exploiting the variational formulation

    NASA Astrophysics Data System (ADS)

    Abali, B. Emek

    2018-04-01

    For micro-architectured materials with a substructure, called metamaterials, we can realize a direct numerical simulation in the microscale by using classical mechanics. This method is accurate, however, computationally costly. Instead, a solution of the same problem in the macroscale is possible by means of the generalized mechanics. In this case, no detailed modeling of the substructure is necessary; however, new parameters emerge. A physical interpretation of these metamaterial parameters is challenging leading to a lack of experimental strategies for their determination. In this work, we exploit the variational formulation based on action principles and obtain a direct relation between a parameter used in the kinetic energy and a metamaterial parameter in the case of a viscoelastic model.

  16. A Kinetic Model for Calcium Dynamics in RAW 264.7 Cells: 1. Mechanisms, Parameters, and Subpopulational Variability

    PubMed Central

    Maurya, Mano Ram; Subramaniam, Shankar

    2007-01-01

    Calcium (Ca2+) is an important second messenger and has been the subject of numerous experimental measurements and mechanistic studies in intracellular signaling. Calcium profile can also serve as a useful cellular phenotype. Kinetic models of calcium dynamics provide quantitative insights into the calcium signaling networks. We report here the development of a complex kinetic model for calcium dynamics in RAW 264.7 cells stimulated by the C5a ligand. The model is developed using the vast number of measurements of in vivo calcium dynamics carried out in the Alliance for Cellular Signaling (AfCS) Laboratories. Ligand binding, phospholipase C-β (PLC-β) activation, inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) dynamics, and calcium exchange with mitochondria and extracellular matrix have all been incorporated into the model. The experimental data include data from both native and knockdown cell lines. Subpopulational variability in measurements is addressed by allowing nonkinetic parameters to vary across datasets. The model predicts temporal response of Ca2+ concentration for various doses of C5a under different initial conditions. The optimized parameters for IP3R dynamics are in agreement with the legacy data. Further, the half-maximal effect concentration of C5a and the predicted dose response are comparable to those seen in AfCS measurements. Sensitivity analysis shows that the model is robust to parametric perturbations. PMID:17483174

  17. Evaluation of oxygen reduction activity by the thin-film rotating disk electrode methodology: The effects of potentiodynamic parameters

    DOE PAGES

    Chen, Guangyu; Li, Meng; Kuttiyiel, Kurian A.; ...

    2016-04-11

    Here, an accurate and efficient assessment of activity is critical for the research and development of electrocatalysts for oxygen reduction reaction (ORR). Currently, the methodology combining the thin-film rotating disk electrode (TF-RDE) and potentiodynamic polarization is the most commonly used to pre-evaluate ORR activity, acquire kinetic data (i.e., kinetic current, Tafel slope, etc.), and gain understanding of the ORR mechanism. However, it is often neglected that appropriate potentiodynamic parameters have to be chosen to obtain reliable results. We first evaluate the potentiodynamic and potentiostatic polarization measurements with TF-RDE to examine the ORR activity of Pt nanoelectrocatalyst. Furthermore, our results demonstratemore » that besides depending on the nature of electrocatalyst, the apparent ORR kinetics also strongly depends on the associated potentiodynamic parameters, such as scan rate and scan region, which have a great effect on the coverage of adsorbed OH ad/O ad on Pt surface, thereby affecting the ORR activities of both nanosized and bulk Pt. However, the apparent Tafel slopes remained nearly the same, indicating that the ORR mechanism in all the measurements was not affected by different potentiodynamic parameters.« less

  18. Anoxic denitrification of BTEX: Biodegradation kinetics and pollutant interactions.

    PubMed

    Carvajal, Andrea; Akmirza, Ilker; Navia, Daniel; Pérez, Rebeca; Muñoz, Raúl; Lebrero, Raquel

    2018-05-15

    Anoxic mineralization of BTEX represents a promising alternative for their abatement from O 2 -deprived emissions. However, the kinetics of anoxic BTEX biodegradation and the interactions underlying the treatment of BTEX mixtures are still unknown. An activated sludge inoculum was used for the anoxic abatement of single, dual and quaternary BTEX mixtures, being acclimated prior performing the biodegradation kinetic tests. The Monod model and a Modified Gompertz model were then used for the estimation of the biodegradation kinetic parameters. Results showed that both toluene and ethylbenzene are readily biodegradable under anoxic conditions, whereas the accumulation of toxic metabolites resulted in partial xylene and benzene degradation when present both as single components or in mixtures. Moreover, the supplementation of an additional pollutant always resulted in an inhibitory competition, with xylene inducing the highest degree of inhibition. The Modified Gompertz model provided an accurate fitting for the experimental data for single and dual substrate experiments, satisfactorily representing the antagonistic pollutant interactions. Finally, microbial analysis suggested that the degradation of the most biodegradable compounds required a lower microbial specialization and diversity, while the presence of the recalcitrant compounds resulted in the selection of a specific group of microorganisms. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Probabilistic parameter estimation in a 2-step chemical kinetics model for n-dodecane jet autoignition

    NASA Astrophysics Data System (ADS)

    Hakim, Layal; Lacaze, Guilhem; Khalil, Mohammad; Sargsyan, Khachik; Najm, Habib; Oefelein, Joseph

    2018-05-01

    This paper demonstrates the development of a simple chemical kinetics model designed for autoignition of n-dodecane in air using Bayesian inference with a model-error representation. The model error, i.e. intrinsic discrepancy from a high-fidelity benchmark model, is represented by allowing additional variability in selected parameters. Subsequently, we quantify predictive uncertainties in the results of autoignition simulations of homogeneous reactors at realistic diesel engine conditions. We demonstrate that these predictive error bars capture model error as well. The uncertainty propagation is performed using non-intrusive spectral projection that can also be used in principle with larger scale computations, such as large eddy simulation. While the present calibration is performed to match a skeletal mechanism, it can be done with equal success using experimental data only (e.g. shock-tube measurements). Since our method captures the error associated with structural model simplifications, we believe that the optimised model could then lead to better qualified predictions of autoignition delay time in high-fidelity large eddy simulations than the existing detailed mechanisms. This methodology provides a way to reduce the cost of reaction kinetics in simulations systematically, while quantifying the accuracy of predictions of important target quantities.

  20. Investigation of thermoluminescence and kinetic parameters of CaMgB{sub 2}O{sub 5}: Dy{sup 3+} nanophosphor

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

    Manhas, M.; Kumar, Vinay, E-mail: vinaykumar@smvdu.ac.in; Department of Physics, University of the Free State, P.O. Box 339, Bloemfontein ZA9300

    2016-05-06

    In this paper, thermoluminescence (TL) properties of Dy{sup 3+} (1.5 mol %) doped CaMgB{sub 2}O{sub 5} nanophosphor after being exposed to ultraviolet (UV) radiations (λ=254nm) were investigated. In UV exposed samples, the thermoluminescence glow curve consists of a broad glow peak located at 380 K with a small shoulder at 507 K. A shift in glow peak temperature from 367 K to 380 K after the UV exposure for 80 min was observed, which clearly shows that glow peaks follow the second order kinetics. The TL intensity of the peaks increases with an increase in the exposure time of UV rays (10-180 min). The TL Anal programmore » was used to analyze the glow curve. The kinetic parameters such as activation energy (E), the frequency factor (s) and the order of kinetics (b) were calculated for CaMgB{sub 2}O{sub 5}: Dy{sup 3+} nanophosphors.« less

  1. [Analysis of hydrodynamics parameters of runoff erosion and sediment-yielding on unpaved road].

    PubMed

    Huang, Peng-Fei; Wang, Wen-Long; Luo, Ting; Wang, Zhen; Wang, Zheng-Li; Li, Ren

    2013-02-01

    By the method of field runoff washout experiment, a simulation study was conducted on the relationships between the soil detachment rate and the hydrodynamic parameters on unpaved road, and the related quantitative formulas were established. Under the conditions of different flow discharges and road gradients, the averaged soil detachment rate increased with increasing flow discharge and road gradient, and the relationships between them could be described by a power function. As compared with road gradient, flow discharge had greater effects on the soil detachment rate. The soil detachment rate had a power relation with water flow velocity and runoff kinetic energy, and the runoff kinetic energy was of importance to the soil detachment rate. The soil detachment rate was linearly correlated with the unit runoff kinetic energy. The averaged soil erodibility was 0.120 g m-1.J-F-1, and the averaged critical unit runoff kinetic energy was 2.875 g.m-1.J-1. Flow discharge, road gradient, and unit runoff kinetic energy could be used to accurately describe the soil erosion process and calculate the soil erosion rate on unpaved road.

  2. Kinetic study of the anaerobic biodegradation of alkyl polyglucosides and the influence of their structural parameters.

    PubMed

    Ríos, Francisco; Fernández-Arteaga, Alejandro; Lechuga, Manuela; Jurado, Encarnación; Fernández-Serrano, Mercedes

    2016-05-01

    This paper reports a study of the anaerobic biodegradation of non-ionic surfactants alkyl polyglucosides applying the method by measurement of the biogas production in digested sludge. Three alkyl polyglucosides with different length alkyl chain and degree of polymerization of the glucose units were tested. The influence of their structural parameters was evaluated, and the characteristics parameters of the anaerobic biodegradation were determined. Results show that alkyl polyglucosides, at the standard initial concentration of 100 mgC L(-1), are not completely biodegradable in anaerobic conditions because they inhibit the biogas production. The alkyl polyglucoside having the shortest alkyl chain showed the fastest biodegradability and reached the higher percentage of final mineralization. The anaerobic process was well adjusted to a pseudo first-order equation using the carbon produced as gas during the test; also, kinetics parameters and a global rate constant for all the involved metabolic process were determined. This modeling is helpful to evaluate the biodegradation or the persistence of alkyl polyglucosides under anaerobic conditions in the environment and in the wastewater treatment.

  3. Petermann I and II spot size: Accurate semi analytical description involving Nelder-Mead method of nonlinear unconstrained optimization and three parameter fundamental modal field

    NASA Astrophysics Data System (ADS)

    Roy Choudhury, Raja; Roy Choudhury, Arundhati; Kanti Ghose, Mrinal

    2013-01-01

    A semi-analytical model with three optimizing parameters and a novel non-Gaussian function as the fundamental modal field solution has been proposed to arrive at an accurate solution to predict various propagation parameters of graded-index fibers with less computational burden than numerical methods. In our semi analytical formulation the optimization of core parameter U which is usually uncertain, noisy or even discontinuous, is being calculated by Nelder-Mead method of nonlinear unconstrained minimizations as it is an efficient and compact direct search method and does not need any derivative information. Three optimizing parameters are included in the formulation of fundamental modal field of an optical fiber to make it more flexible and accurate than other available approximations. Employing variational technique, Petermann I and II spot sizes have been evaluated for triangular and trapezoidal-index fibers with the proposed fundamental modal field. It has been demonstrated that, the results of the proposed solution identically match with the numerical results over a wide range of normalized frequencies. This approximation can also be used in the study of doped and nonlinear fiber amplifier.

  4. Kinetic and temporospatial parameters in male and female cats walking over a pressure sensing walkway.

    PubMed

    Verdugo, Mirela R; Rahal, Sheila C; Agostinho, Felipe S; Govoni, Verônica M; Mamprim, Maria J; Monteiro, Frederico O B

    2013-06-27

    Several factors may influence kinetic data measurements, including body conformation and body mass. In addition, gender differences in gait pattern have been observed in healthy humans. Therefore, the aim of this study was to compare the kinetic and temporospatial parameters in clinically healthy male and female cats using a pressure-sensitive walkway. Eighteen crossbreed adult cats were divided into two groups: G1 had ten male cats (nine neutered) aged from 1 to 4 years and body mass 3.1-6.8 kg; G2 had eight spayed female cats, aged from 1 to 6 years and body mass 3.3-4.75 kg. The data from the first five valid trials were collected for each cat. A trial was considered valid if the cat maintained a velocity between 0.54-0.74 m/s and acceleration from -0.20 to 0.20 m/s2. The peak vertical force (PVF), vertical impulse (VI), gait cycle time, stance time, swing time, stride length, and percentage body weight distribution among the four limbs were determined. In addition, the lengths of each forelimb and each hind limb were measured using a tape with the animal standing. No significant differences were observed in each group in either the forelimbs or the hind limbs or between the left and right sides for any of the variables. For both groups, the PVF (%BW), the VI, and the percentage body weight distribution were higher at the forelimbs than the hind limbs. The stride length was larger for males; however, the other kinetic and temporospatial variables did not show any statistically significant differences between the groups. The lengths of the forelimbs and hind limbs were larger in the male cats. There was a significant moderate positive correlation between the stride length and the length of the limbs. In conclusion, the only difference observed between male and female cats was the stride length, and this was due to the greater body size of male cats. This difference did not affect other temporospatial or kinetics variables.

  5. Estimating parameters from rotating ring disc electrode measurements

    DOE PAGES

    Santhanagopalan, Shriram; White, Ralph E.

    2017-10-21

    Rotating ring disc electrode (RRDE) experiments are a classic tool for investigating kinetics of electrochemical reactions. Several standardized methods exist for extracting transport parameters and reaction rate constants using RRDE measurements. Here in this work, we compare some approximate solutions to the convective diffusion used popularly in the literature to a rigorous numerical solution of the Nernst-Planck equations coupled to the three dimensional flow problem. In light of these computational advancements, we explore design aspects of the RRDE that will help improve sensitivity of our parameter estimation procedure to experimental data. We use the oxygen reduction in acidic media involvingmore » three charge transfer reactions and a chemical reaction as an example, and identify ways to isolate reaction currents for the individual processes in order to accurately estimate the exchange current densities.« less

  6. A kinetic model of municipal sludge degradation during non-catalytic wet oxidation.

    PubMed

    Prince-Pike, Arrian; Wilson, David I; Baroutian, Saeid; Andrews, John; Gapes, Daniel J

    2015-12-15

    Wet oxidation is a successful process for the treatment of municipal sludge. In addition, the resulting effluent from wet oxidation is a useful carbon source for subsequent biological nutrient removal processes in wastewater treatment. Owing to limitations with current kinetic models, this study produced a kinetic model which predicts the concentrations of key intermediate components during wet oxidation. The model was regressed from lab-scale experiments and then subsequently validated using data from a wet oxidation pilot plant. The model was shown to be accurate in predicting the concentrations of each component, and produced good results when applied to a plant 500 times larger in size. A statistical study was undertaken to investigate the validity of the regressed model parameters. Finally the usefulness of the model was demonstrated by suggesting optimum operating conditions such that volatile fatty acids were maximised. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Mammalian cell culture process for monoclonal antibody production: nonlinear modelling and parameter estimation.

    PubMed

    Selişteanu, Dan; Șendrescu, Dorin; Georgeanu, Vlad; Roman, Monica

    2015-01-01

    Monoclonal antibodies (mAbs) are at present one of the fastest growing products of pharmaceutical industry, with widespread applications in biochemistry, biology, and medicine. The operation of mAbs production processes is predominantly based on empirical knowledge, the improvements being achieved by using trial-and-error experiments and precedent practices. The nonlinearity of these processes and the absence of suitable instrumentation require an enhanced modelling effort and modern kinetic parameter estimation strategies. The present work is dedicated to nonlinear dynamic modelling and parameter estimation for a mammalian cell culture process used for mAb production. By using a dynamical model of such kind of processes, an optimization-based technique for estimation of kinetic parameters in the model of mammalian cell culture process is developed. The estimation is achieved as a result of minimizing an error function by a particle swarm optimization (PSO) algorithm. The proposed estimation approach is analyzed in this work by using a particular model of mammalian cell culture, as a case study, but is generic for this class of bioprocesses. The presented case study shows that the proposed parameter estimation technique provides a more accurate simulation of the experimentally observed process behaviour than reported in previous studies.

  8. Mammalian Cell Culture Process for Monoclonal Antibody Production: Nonlinear Modelling and Parameter Estimation

    PubMed Central

    Selişteanu, Dan; Șendrescu, Dorin; Georgeanu, Vlad

    2015-01-01

    Monoclonal antibodies (mAbs) are at present one of the fastest growing products of pharmaceutical industry, with widespread applications in biochemistry, biology, and medicine. The operation of mAbs production processes is predominantly based on empirical knowledge, the improvements being achieved by using trial-and-error experiments and precedent practices. The nonlinearity of these processes and the absence of suitable instrumentation require an enhanced modelling effort and modern kinetic parameter estimation strategies. The present work is dedicated to nonlinear dynamic modelling and parameter estimation for a mammalian cell culture process used for mAb production. By using a dynamical model of such kind of processes, an optimization-based technique for estimation of kinetic parameters in the model of mammalian cell culture process is developed. The estimation is achieved as a result of minimizing an error function by a particle swarm optimization (PSO) algorithm. The proposed estimation approach is analyzed in this work by using a particular model of mammalian cell culture, as a case study, but is generic for this class of bioprocesses. The presented case study shows that the proposed parameter estimation technique provides a more accurate simulation of the experimentally observed process behaviour than reported in previous studies. PMID:25685797

  9. Oxidation characteristics of gasoline direct-injection (GDI) engine soot: Catalytic effects of ash and modified kinetic correlation

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

    Choi, Seungmok; Seong, Heeje

    In this paper, experimental analyses are conducted into the GDI soot oxidation characteristics as dependent on engine operating conditions. Soot is sampled at various engine operating conditions of a commercial 2.4 L GDI engine with a naturally aspirated, homogeneous, and stoichiometric operation strategy. The oxidation reactivity, ash composition, and carbon nanostructure of the GDI soot samples are analyzed using thermogravimetric analysis (TGA), scanning electron microscope–energy-dispersive spectroscopy (SEM-EDS), high-resolution transmission electron microscopy (HR-TEM), and Raman spectroscopy. Based on the analyses, a global GDI soot oxidation mechanism is proposed which includes the effects of soluble organic fractions (SOF)/weakly bonded carbon (WBC), andmore » three types of ash on GDI soot oxidation. The results show that GDI soot contains an order of magnitude higher ash fraction than does conventional diesel soot, and oxidation reactivity is significantly enhanced by the catalytic effects of ash, as a function of ash content in soot. A modified empirical kinetic correlation for GDI soot oxidation is suggested on the basis of the results, and the modified kinetic correlation predicts the GDI soot oxidation rate accurately for various engine operation points at wide ranges of soot conversion and temperature without modifying kinetic parameters. The kinetic parameters are determined from isothermal and non-isothermal thremogravimetric analysis (TGA) soot oxidation tests; the methods are elucidated in detail.« less

  10. Oxidation characteristics of gasoline direct-injection (GDI) engine soot: Catalytic effects of ash and modified kinetic correlation

    DOE PAGES

    Choi, Seungmok; Seong, Heeje

    2015-03-02

    In this paper, experimental analyses are conducted into the GDI soot oxidation characteristics as dependent on engine operating conditions. Soot is sampled at various engine operating conditions of a commercial 2.4 L GDI engine with a naturally aspirated, homogeneous, and stoichiometric operation strategy. The oxidation reactivity, ash composition, and carbon nanostructure of the GDI soot samples are analyzed using thermogravimetric analysis (TGA), scanning electron microscope–energy-dispersive spectroscopy (SEM-EDS), high-resolution transmission electron microscopy (HR-TEM), and Raman spectroscopy. Based on the analyses, a global GDI soot oxidation mechanism is proposed which includes the effects of soluble organic fractions (SOF)/weakly bonded carbon (WBC), andmore » three types of ash on GDI soot oxidation. The results show that GDI soot contains an order of magnitude higher ash fraction than does conventional diesel soot, and oxidation reactivity is significantly enhanced by the catalytic effects of ash, as a function of ash content in soot. A modified empirical kinetic correlation for GDI soot oxidation is suggested on the basis of the results, and the modified kinetic correlation predicts the GDI soot oxidation rate accurately for various engine operation points at wide ranges of soot conversion and temperature without modifying kinetic parameters. The kinetic parameters are determined from isothermal and non-isothermal thremogravimetric analysis (TGA) soot oxidation tests; the methods are elucidated in detail.« less

  11. The metallicity of M4: Accurate spectroscopic fundamental parameters for four giants

    NASA Technical Reports Server (NTRS)

    Drake, J. J.; Smith, V. V.; Suntzeff, N. B.

    1994-01-01

    High-quality spectra, covering the wavelength range 5480 to 7080 A, have been obtained for four giant stars in the intermediate-metallicity CN-bimodal globular cluster M4 (NGC 6121). We have employed a model atmosphere analysis that is entirely independent from cluster parameters, such as distance, age, and reddening, in order to derive accurate values for the stellar parameters effective temperature, surface gravity, and microturbulence, and for the abundance of iron relative to the Sun, (Fe/H), and of calcium, Ca/H, for each of the four stars. Detailed radiative transfer and statistical equilibrium calculations carried out for iron and calcium suggest that departures from local thermodynamic equilibrium are not significant for the purposes of our analysis. The spectroscopically derived effective temperatures for our program stars are hotter by about 200 K than existing photometric calibrations suggest. We conclude that this is due partly to the uncertain reddening of M4 and to the existing photometric temperature calibration for red giants being too cool by about 100 K. Comparison of our spectroscopic and existing photometric temperatures supports the prognosis of a significant east-west gradient in the reddening across M4. Our derived iron abundances are slightly higher than previous high-resolution studies suggested; the differences are most probably due to the different temperature scale and choice of microturbulent velocities adopted by earlier workers. The resulting value for the metallicity of M4 is (Fe/H )(sub M4) = -1.05 + or - 0.15. Based on this result, we suggest that metallicities derived in previous high-dispersion globular cluster abundance analyses could be too low by 0.2 to 0.3 dex. Our calcium abundances suggest an enhancement of calcium, an alpha element, over iron, relative to the Sun, in M4 of (Ca/H) = 0.23.

  12. Batch Tests To Determine Activity Distribution and Kinetic Parameters for Acetate Utilization in Expanded-Bed Anaerobic Reactors

    PubMed Central

    Fox, Peter; Suidan, Makram T.

    1990-01-01

    Batch tests to measure maximum acetate utilization rates were used to determine the distribution of acetate utilizers in expanded-bed sand and expanded-bed granular activated carbon (GAC) reactors. The reactors were fed a mixture of acetate and 3-ethylphenol, and they contained the same predominant aceticlastic methanogen, Methanothrix sp. Batch tests were performed both on the entire reactor contents and with media removed from the reactors. Results indicated that activity was evenly distributed within the GAC reactors, whereas in the sand reactor a sludge blanket on top of the sand bed contained approximately 50% of the activity. The Monod half-velocity constant (Ks) for the acetate-utilizing methanogens in two expanded-bed GAC reactors was searched for by combining steady-state results with batch test data. All parameters necessary to develop a model with Monod kinetics were experimentally determined except for Ks. However, Ks was a function of the effluent 3-ethylphenol concentration, and batch test results demonstrated that maximum acetate utilization rates were not a function of the effluent 3-ethylphenol concentration. Addition of a competitive inhibition term into the Monod expression predicted the dependence of Ks on the effluent 3-ethylphenol concentration. A two-parameter search determined a Ks of 8.99 mg of acetate per liter and a Ki of 2.41 mg of 3-ethylphenol per liter. Model predictions were in agreement with experimental observations for all effluent 3-ethylphenol concentrations. Batch tests measured the activity for a specific substrate and determined the distribution of activity in the reactor. The use of steady-state data in conjunction with batch test results reduced the number of unknown kinetic parameters and thereby reduced the uncertainty in the results and the assumptions made. PMID:16348175

  13. Batch tests to determine activity distribution and kinetic parameters for acetate utilization in expanded-bed anaerobic reactors.

    PubMed

    Fox, P; Suidan, M T

    1990-04-01

    Batch tests to measure maximum acetate utilization rates were used to determine the distribution of acetate utilizers in expanded-bed sand and expanded-bed granular activated carbon (GAC) reactors. The reactors were fed a mixture of acetate and 3-ethylphenol, and they contained the same predominant aceticlastic methanogen, Methanothrix sp. Batch tests were performed both on the entire reactor contents and with media removed from the reactors. Results indicated that activity was evenly distributed within the GAC reactors, whereas in the sand reactor a sludge blanket on top of the sand bed contained approximately 50% of the activity. The Monod half-velocity constant (K(s)) for the acetate-utilizing methanogens in two expanded-bed GAC reactors was searched for by combining steady-state results with batch test data. All parameters necessary to develop a model with Monod kinetics were experimentally determined except for K(s). However, K(s) was a function of the effluent 3-ethylphenol concentration, and batch test results demonstrated that maximum acetate utilization rates were not a function of the effluent 3-ethylphenol concentration. Addition of a competitive inhibition term into the Monod expression predicted the dependence of K(s) on the effluent 3-ethylphenol concentration. A two-parameter search determined a K(s) of 8.99 mg of acetate per liter and a K(i) of 2.41 mg of 3-ethylphenol per liter. Model predictions were in agreement with experimental observations for all effluent 3-ethylphenol concentrations. Batch tests measured the activity for a specific substrate and determined the distribution of activity in the reactor. The use of steady-state data in conjunction with batch test results reduced the number of unknown kinetic parameters and thereby reduced the uncertainty in the results and the assumptions made.

  14. ITC Recommendations for Transporter Kinetic Parameter Estimation and Translational Modeling of Transport-Mediated PK and DDIs in Humans

    PubMed Central

    Zamek-Gliszczynski, MJ; Lee, CA; Poirier, A; Bentz, J; Chu, X; Ellens, H; Ishikawa, T; Jamei, M; Kalvass, JC; Nagar, S; Pang, KS; Korzekwa, K; Swaan, PW; Taub, ME; Zhao, P; Galetin, A

    2013-01-01

    This white paper provides a critical analysis of methods for estimating transporter kinetics and recommendations on proper parameter calculation in various experimental systems. Rational interpretation of transporter-knockout animal findings and application of static and dynamic physiologically based modeling approaches for prediction of human transporter-mediated pharmacokinetics and drug–drug interactions (DDIs) are presented. The objective is to provide appropriate guidance for the use of in vitro, in vivo, and modeling tools in translational transporter science. PMID:23588311

  15. Combined TGA-MS kinetic analysis of multistep processes. Thermal decomposition and ceramification of polysilazane and polysiloxane preceramic polymers.

    PubMed

    García-Garrido, C; Sánchez-Jiménez, P E; Pérez-Maqueda, L A; Perejón, A; Criado, José M

    2016-10-26

    The polymer-to-ceramic transformation kinetics of two widely employed ceramic precursors, 1,3,5,7-tetramethyl-1,3,5,7-tetravinylcyclotetrasiloxane (TTCS) and polyureamethylvinylsilazane (CERASET), have been investigated using coupled thermogravimetry and mass spectrometry (TG-MS), Raman, XRD and FTIR. The thermally induced decomposition of the pre-ceramic polymer is the critical step in the synthesis of polymer derived ceramics (PDCs) and accurate kinetic modeling is key to attaining a complete understanding of the underlying process and to attempt any behavior predictions. However, obtaining a precise kinetic description of processes of such complexity, consisting of several largely overlapping physico-chemical processes comprising the cleavage of the starting polymeric network and the release of organic moieties, is extremely difficult. Here, by using the evolved gases detected by MS as a guide it has been possible to determine the number of steps that compose the overall process, which was subsequently resolved using a semiempirical deconvolution method based on the Frasier-Suzuki function. Such a function is more appropriate that the more usual Gaussian or Lorentzian functions since it takes into account the intrinsic asymmetry of kinetic curves. Then, the kinetic parameters of each constituent step were independently determined using both model-free and model-fitting procedures, and it was found that the processes obey mostly diffusion models which can be attributed to the diffusion of the released gases through the solid matrix. The validity of the obtained kinetic parameters was tested not only by the successful reconstruction of the original experimental curves, but also by predicting the kinetic curves of the overall processes yielded by different thermal schedules and by a mixed TTCS-CERASET precursor.

  16. Evaporation Kinetics of Polyol Droplets: Determination of Evaporation Coefficients and Diffusion Constants

    NASA Astrophysics Data System (ADS)

    Su, Yong-Yang; Marsh, Aleksandra; Haddrell, Allen E.; Li, Zhi-Ming; Reid, Jonathan P.

    2017-11-01

    In order to quantify the kinetics of mass transfer between the gas and condensed phases in aerosol, physicochemical properties of the gas and condensed phases and kinetic parameters (mass/thermal accommodation coefficients) are crucial for estimating mass fluxes over a wide size range from the free molecule to continuum regimes. In this study, we report measurements of the evaporation kinetics of droplets of 1-butanol, ethylene glycol (EG), diethylene glycol (DEG), and glycerol under well-controlled conditions (gas flow rates and temperature) using the previously developed cylindrical electrode electrodynamic balance technique. Measurements are compared with a model that captures the heat and mass transfer occurring at the evaporating droplet surface. The aim of these measurements is to clarify the discrepancy in the reported values of mass accommodation coefficient (αM, equals to evaporation coefficient based on microscopic reversibility) for 1-butanol, EG, and DEG and improve the accuracy of the value of the diffusion coefficient for glycerol in gaseous nitrogen. The uncertainties in the thermophysical and experimental parameters are carefully assessed, the literature values of the vapor pressures of these components are evaluated, and the plausible ranges of the evaporation coefficients for 1-butanol, EG, and DEG as well as uncertainty in diffusion coefficient for glycerol are reported. Results show that αM should be greater than 0.4, 0.2, and 0.4 for EG, DEG, and 1-butanol, respectively. The refined values are helpful for accurate prediction of the evaporation/condensation rates.

  17. Modeling the degradation kinetics of ascorbic acid.

    PubMed

    Peleg, Micha; Normand, Mark D; Dixon, William R; Goulette, Timothy R

    2018-06-13

    Most published reports on ascorbic acid (AA) degradation during food storage and heat preservation suggest that it follows first-order kinetics. Deviations from this pattern include Weibullian decay, and exponential drop approaching finite nonzero retention. Almost invariably, the degradation rate constant's temperature-dependence followed the Arrhenius equation, and hence the simpler exponential model too. A formula and freely downloadable interactive Wolfram Demonstration to convert the Arrhenius model's energy of activation, E a , to the exponential model's c parameter, or vice versa, are provided. The AA's isothermal and non-isothermal degradation can be simulated with freely downloadable interactive Wolfram Demonstrations in which the model's parameters can be entered and modified by moving sliders on the screen. Where the degradation is known a priori to follow first or other fixed order kinetics, one can use the endpoints method, and in principle the successive points method too, to estimate the reaction's kinetic parameters from considerably fewer AA concentration determinations than in the traditional manner. Freeware to do the calculations by either method has been recently made available on the Internet. Once obtained in this way, the kinetic parameters can be used to reconstruct the entire degradation curves and predict those at different temperature profiles, isothermal or dynamic. Comparison of the predicted concentration ratios with experimental ones offers a way to validate or refute the kinetic model and the assumptions on which it is based.

  18. Improving estimation of kinetic parameters in dynamic force spectroscopy using cluster analysis

    NASA Astrophysics Data System (ADS)

    Yen, Chi-Fu; Sivasankar, Sanjeevi

    2018-03-01

    Dynamic Force Spectroscopy (DFS) is a widely used technique to characterize the dissociation kinetics and interaction energy landscape of receptor-ligand complexes with single-molecule resolution. In an Atomic Force Microscope (AFM)-based DFS experiment, receptor-ligand complexes, sandwiched between an AFM tip and substrate, are ruptured at different stress rates by varying the speed at which the AFM-tip and substrate are pulled away from each other. The rupture events are grouped according to their pulling speeds, and the mean force and loading rate of each group are calculated. These data are subsequently fit to established models, and energy landscape parameters such as the intrinsic off-rate (koff) and the width of the potential energy barrier (xβ) are extracted. However, due to large uncertainties in determining mean forces and loading rates of the groups, errors in the estimated koff and xβ can be substantial. Here, we demonstrate that the accuracy of fitted parameters in a DFS experiment can be dramatically improved by sorting rupture events into groups using cluster analysis instead of sorting them according to their pulling speeds. We test different clustering algorithms including Gaussian mixture, logistic regression, and K-means clustering, under conditions that closely mimic DFS experiments. Using Monte Carlo simulations, we benchmark the performance of these clustering algorithms over a wide range of koff and xβ, under different levels of thermal noise, and as a function of both the number of unbinding events and the number of pulling speeds. Our results demonstrate that cluster analysis, particularly K-means clustering, is very effective in improving the accuracy of parameter estimation, particularly when the number of unbinding events are limited and not well separated into distinct groups. Cluster analysis is easy to implement, and our performance benchmarks serve as a guide in choosing an appropriate method for DFS data analysis.

  19. Evaluation of Thermal Evolution Profiles and Estimation of Kinetic Parameters for Pyrolysis of Coal/Corn Stover Blends Using Thermogravimetric Analysis

    DOE PAGES

    Bhagavatula, Abhijit; Huffman, Gerald; Shah, Naresh; ...

    2014-01-01

    The thermal evolution profiles and kinetic parameters for the pyrolysis of two Montana coals (DECS-38 subbituminous coal and DECS-25 lignite coal), one biomass sample (corn stover), and their blends (10%, 20%, and 30% by weight of corn stover) have been investigated at a heating rate of 5°C/min in an inert nitrogen atmosphere, using thermogravimetric analysis. The thermal evolution profiles of subbituminous coal and lignite coal display only one major peak over a wide temperature distribution, ~152–814°C and ~175–818°C, respectively, whereas the thermal decomposition profile for corn stover falls in a much narrower band than that of the coals, ~226–608°C. Themore » nonlinearity in the evolution of volatile matter with increasing percentage of corn stover in the blends verifies the possibility of synergistic behavior in the blends with subbituminous coal where deviations from the predicted yield ranging between 2% and 7% were observed whereas very little deviations (1%–3%) from predicted yield were observed in blends with lignite indicating no significant interactions with corn stover. In addition, a single first-order reaction model using the Coats-Redfern approximation was utilized to predict the kinetic parameters of the pyrolysis reaction. The kinetic analysis indicated that each thermal evolution profile may be represented as a single first-order reaction. Three temperature regimes were identified for each of the coals while corn stover and the blends were analyzed using two and four temperature regimes, respectively.« less

  20. Evaluation of Thermal Evolution Profiles and Estimation of Kinetic Parameters for Pyrolysis of Coal/Corn Stover Blends Using Thermogravimetric Analysis

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

    Bhagavatula, Abhijit; Huffman, Gerald; Shah, Naresh

    The thermal evolution profiles and kinetic parameters for the pyrolysis of two Montana coals (DECS-38 subbituminous coal and DECS-25 lignite coal), one biomass sample (corn stover), and their blends (10%, 20%, and 30% by weight of corn stover) have been investigated at a heating rate of 5°C/min in an inert nitrogen atmosphere, using thermogravimetric analysis. The thermal evolution profiles of subbituminous coal and lignite coal display only one major peak over a wide temperature distribution, ~152–814°C and ~175–818°C, respectively, whereas the thermal decomposition profile for corn stover falls in a much narrower band than that of the coals, ~226–608°C. Themore » nonlinearity in the evolution of volatile matter with increasing percentage of corn stover in the blends verifies the possibility of synergistic behavior in the blends with subbituminous coal where deviations from the predicted yield ranging between 2% and 7% were observed whereas very little deviations (1%–3%) from predicted yield were observed in blends with lignite indicating no significant interactions with corn stover. In addition, a single first-order reaction model using the Coats-Redfern approximation was utilized to predict the kinetic parameters of the pyrolysis reaction. The kinetic analysis indicated that each thermal evolution profile may be represented as a single first-order reaction. Three temperature regimes were identified for each of the coals while corn stover and the blends were analyzed using two and four temperature regimes, respectively.« less

  1. A comparison between a new model and current models for estimating trunk segment inertial parameters.

    PubMed

    Wicke, Jason; Dumas, Genevieve A; Costigan, Patrick A

    2009-01-05

    Modeling of the body segments to estimate segment inertial parameters is required in the kinetic analysis of human motion. A new geometric model for the trunk has been developed that uses various cross-sectional shapes to estimate segment volume and adopts a non-uniform density function that is gender-specific. The goal of this study was to test the accuracy of the new model for estimating the trunk's inertial parameters by comparing it to the more current models used in biomechanical research. Trunk inertial parameters estimated from dual X-ray absorptiometry (DXA) were used as the standard. Twenty-five female and 24 male college-aged participants were recruited for the study. Comparisons of the new model to the accepted models were accomplished by determining the error between the models' trunk inertial estimates and that from DXA. Results showed that the new model was more accurate across all inertial estimates than the other models. The new model had errors within 6.0% for both genders, whereas the other models had higher average errors ranging from 10% to over 50% and were much more inconsistent between the genders. In addition, there was little consistency in the level of accuracy for the other models when estimating the different inertial parameters. These results suggest that the new model provides more accurate and consistent trunk inertial estimates than the other models for both female and male college-aged individuals. However, similar studies need to be performed using other populations, such as elderly or individuals from a distinct morphology (e.g. obese). In addition, the effect of using different models on the outcome of kinetic parameters, such as joint moments and forces needs to be assessed.

  2. On-rate based optimization of structure-kinetic relationship--surfing the kinetic map.

    PubMed

    Schoop, Andreas; Dey, Fabian

    2015-10-01

    In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Experimental and kinetic study for lead removal via photosynthetic consortia using genetic algorithms to parameter estimation.

    PubMed

    Hernández-Melchor, Dulce Jazmín; López-Pérez, Pablo A; Carrillo-Vargas, Sergio; Alberto-Murrieta, Alvaro; González-Gómez, Evanibaldo; Camacho-Pérez, Beni

    2017-09-06

    This work presents an experimental-theoretical strategy for a batch process for lead removal by photosynthetic consortium, conformed by algae and bacteria. Photosynthetic consortium, isolated from a treatment plant wastewater of Tecamac (Mexico), was used as inoculum in bubble column photobioreactors. The consortium was used to evaluate the kinetics of lead removal at different initial concentrations of metal (15, 30, 40, 50, and 60 mgL -1 ), carried out in batch culture with a hydraulic residence time of 14 days using Bold's Basal mineral medium. The photobioreactor was operated under the following conditions: aeration of 0.5 vvm, 80 μmol m -2  s -1 of photon flux density and a photoperiod light/dark 12:12. After determining the best growth kinetics of biomass and metal removal, they were tested under different ratios (30 and 60%) of wastewater-culture medium. Additionally, the biomass growth (X), nitrogen consumption (N), chemical oxygen demand (COD), and metal removal (Pb) were quantified. Achieved lead removal was 97.4% when the initial lead concentration was up to 50 mgL -1 using 60% of wastewater. Additionally, an unstructured-type mathematical model was developed to simulate COD, X, N, and lead removal. Furthermore, a comparison between the Levenberg-Marquardt (L-M) optimization approach and Genetic Algorithms (GA) was carried out for parameter estimation. Also, it was concluded that GA has a slightly better performance and possesses better convergence and computational time than L-M. Hence, the proposed method might be applied for parameter estimation of biological models and be used for the monitoring and control process.

  4. Thermal inactivation kinetics of β-galactosidase during bread baking.

    PubMed

    Zhang, Lu; Chen, Xiao Dong; Boom, Remko M; Schutyser, Maarten A I

    2017-06-15

    In this study, β-galactosidase was utilized as a model enzyme to investigate the mechanism of enzyme inactivation during bread baking. Thermal inactivation of β-galactosidase was investigated in a wheat flour/water system at varying temperature-moisture content combinations, and in bread during baking at 175 or 205°C. In the wheat flour/water system, the thermostability of β-galactosidase increased with decreased moisture content, and a kinetic model was accurately fitted to the corresponding inactivation data (R 2 =0.99). Interestingly, the residual enzyme activity in the bread crust (about 30%) was hundredfold higher than that in the crumb (about 0.3%) after baking, despite the higher temperature in the crust throughout baking. This result suggested that the reduced moisture content in the crust increased the thermostability of the enzyme. Subsequently, the kinetic model reasonably predicted the enzyme inactivation in the crumb using the same parameters derived from the wheat flour/water system. However, the model predicted a lower residual enzyme activity in the crust compared with the experimental result, which indicated that the structure of the crust may influence the enzyme inactivation mechanism during baking. The results reported can provide a quantitative understanding of the thermal inactivation kinetics of enzyme during baking, which is essential to better retain enzymatic activity in bakery products supplemented with heat-sensitive enzymes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Optimization of Process Parameters and Kinetic Model of Enzymatic Extraction of Polyphenols from Lonicerae Flos

    PubMed Central

    Kong, Fansheng; Yu, Shujuan; Bi, Yongguang; Huang, Xiaojun; Huang, Mengqian

    2016-01-01

    Objective: To optimize and verify the cellulase extraction of polyphenols from honeysuckle and provide a reference for enzymatic extracting polyphenols from honeysuckle. Materials and Methods: The uniform design was used According to Fick's first law and kinetic model, fitting analysis of the dynamic process of enzymatic extracting polyphenols was conducted. Results: The optimum enzymatic extraction parameters for polyphenols from honeysuckle are found to be 80% (v/v) of alcohol, 35:1 (mL/g) of liquid-solid ratio, 80°C of extraction temperature, 8.5 of pH, 6.0 mg of enzyme levels, and 130 min of extraction time. Under the optimal conditions, the extraction rate of polyphenols was 3.03%. The kinetic experiments indicated kinetic equation had a good linear relationship with t even under the conditions of different levels of enzyme and temperature, which means fitting curve tallies well with the experimental values. Conclusion: The results of quantification showed that the results provide a reference for enzymatic extracting polyphenols from honeysuckle. SUMMARY Lonicerae flos (Lonicera japonica Thunb.) is a material of traditional Chinese medicine and healthy drinks, of which active compounds mainly is polyphenols. At present, plant polyphenols are the hotspots centents of food, cosmetic and medicine, because it has strong bioactivity. Several traditional methods are available for the extraction of plant polyphenols including impregnation, solvent extraction, ultrasonic extraction, hot-water extraction, alkaline dilute alcohol or alkaline water extraction, microwave extraction and Supercritical CO2 extraction. But now, an increasing number of research on using cellulase to extract active ingredients from plants. Enzymatic method is widely used for enzyme have excellent properties of high reaction efficiency and specificity, moderate reaction conditions, shorter extraction time and easier to control, less damage to the active ingredient. At present, the enzymatic

  6. Does a foot-drop implant improve kinetic and kinematic parameters in the foot and ankle?

    PubMed

    Daniilidis, Kiriakos; Jakubowitz, Eike; Thomann, Anna; Ettinger, Sarah; Stukenborg-Colsman, Christina; Yao, Daiwei

    2017-04-01

    Unlike the drop foot therapy with ortheses, the therapeutic effect of an implantable peroneus nerve stimulator (iPNS) is not well described. IPNS is a dynamic therapy option which is placed directly to the motoric part of the peroneal nerve and evokes a dorsiflexion of the paralysed foot. This retrospective study evaluates the kinematics and kinetics in drop foot patients who were treated with an iPNS. 18 subjects (mean age 51.3 years) with a chronic stroke-related drop foot were treated with an implantable peroneal nerve stimulator. After a mean follow-up from 12.5 months, kinematics and kinetics as well as spatiotemporal parameters were evaluated and compared in activated and deactivated iPNS. Therefore, a gait analysis with motion capture system (Vicon Motion System Ltd®, Oxford, UK) and Plug-in-Gait model was performed. The study showed significantly improved results in ankle dorsiflexion from 6.8° to 1.8° at the initial contact and from -7.3° to 0.9° during swing phase (p ≤ 0.004 and p ≤ 0.005, respectively). Likewise, we could measure improved kinetics, i.a. with a statistically significant improvement in vertical ground reaction force at loading response from 99.76 to 106.71 N/kg (p = 0.043). Enhanced spatiotemporal results in cadence, douple support, stride length, and walking speed could also be achieved, but without statistical significance (p > 0.05). The results show statistically significant improvement in ankle dorsiflexion and vertical ground reaction forces. These facts indicate a more gait stability and gait efficacy. Therefore, the use of an iPNS appears an encouraging therapeutic option for patients with a stroke-related drop foot.

  7. Identifiability of sorption parameters in stirred flow-through reactor experiments and their identification with a Bayesian approach.

    PubMed

    Nicoulaud-Gouin, V; Garcia-Sanchez, L; Giacalone, M; Attard, J C; Martin-Garin, A; Bois, F Y

    2016-10-01

    This paper addresses the methodological conditions -particularly experimental design and statistical inference- ensuring the identifiability of sorption parameters from breakthrough curves measured during stirred flow-through reactor experiments also known as continuous flow stirred-tank reactor (CSTR) experiments. The equilibrium-kinetic (EK) sorption model was selected as nonequilibrium parameterization embedding the K d approach. Parameter identifiability was studied formally on the equations governing outlet concentrations. It was also studied numerically on 6 simulated CSTR experiments on a soil with known equilibrium-kinetic sorption parameters. EK sorption parameters can not be identified from a single breakthrough curve of a CSTR experiment, because K d,1 and k - were diagnosed collinear. For pairs of CSTR experiments, Bayesian inference allowed to select the correct models of sorption and error among sorption alternatives. Bayesian inference was conducted with SAMCAT software (Sensitivity Analysis and Markov Chain simulations Applied to Transfer models) which launched the simulations through the embedded simulation engine GNU-MCSim, and automated their configuration and post-processing. Experimental designs consisting in varying flow rates between experiments reaching equilibrium at contamination stage were found optimal, because they simultaneously gave accurate sorption parameters and predictions. Bayesian results were comparable to maximum likehood method but they avoided convergence problems, the marginal likelihood allowed to compare all models, and credible interval gave directly the uncertainty of sorption parameters θ. Although these findings are limited to the specific conditions studied here, in particular the considered sorption model, the chosen parameter values and error structure, they help in the conception and analysis of future CSTR experiments with radionuclides whose kinetic behaviour is suspected. Copyright © 2016 Elsevier Ltd. All

  8. Characterization of nicotinamidases: steady state kinetic parameters, classwide inhibition by nicotinaldehydes, and catalytic mechanism.

    PubMed

    French, Jarrod B; Cen, Yana; Vrablik, Tracy L; Xu, Ping; Allen, Eleanor; Hanna-Rose, Wendy; Sauve, Anthony A

    2010-12-14

    Nicotinamidases are metabolic enzymes that hydrolyze nicotinamide to nicotinic acid. These enzymes are widely distributed across biology, with examples found encoded in the genomes of Mycobacteria, Archaea, Eubacteria, Protozoa, yeast, and invertebrates, but there are none found in mammals. Although recent structural work has improved our understanding of these enzymes, their catalytic mechanism is still not well understood. Recent data show that nicotinamidases are required for the growth and virulence of several pathogenic microbes. The enzymes of Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans regulate life span in their respective organisms, consistent with proposed roles in the regulation of NAD(+) metabolism and organismal aging. In this work, the steady state kinetic parameters of nicotinamidase enzymes from C. elegans, Sa. cerevisiae, Streptococcus pneumoniae (a pathogen responsible for human pneumonia), Borrelia burgdorferi (the pathogen that causes Lyme disease), and Plasmodium falciparum (responsible for most human malaria) are reported. Nicotinamidases are generally efficient catalysts with steady state k(cat) values typically exceeding 1 s(-1). The K(m) values for nicotinamide are low and in the range of 2 -110 μM. Nicotinaldehyde was determined to be a potent competitive inhibitor of these enzymes, binding in the low micromolar to low nanomolar range for all nicotinamidases tested. A variety of nicotinaldehyde derivatives were synthesized and evaluated as inhibitors in kinetic assays. Inhibitions are consistent with reaction of the universally conserved catalytic Cys on each enzyme with the aldehyde carbonyl carbon to form a thiohemiacetal complex that is stabilized by a conserved oxyanion hole. The S. pneumoniae nicotinamidase can catalyze exchange of (18)O into the carboxy oxygens of nicotinic acid with H(2)(18)O. The collected data, along with kinetic analysis of several mutants, allowed us to propose a catalytic

  9. Influence of external mass transfer limitation on apparent kinetic parameters of penicillin G acylase immobilized on nonporous ultrafine silica particles.

    PubMed

    Kheirolomoom, Azadeh; Khorasheh, Farhad; Fazelinia, Hossein

    2002-01-01

    Immobilization of enzymes on nonporous supports provides a suitable model for investigating the effect of external mass transfer limitation on the reaction rate in the absence of internal diffusional resistance. In this study, deacylation of penicillin G was investigated using penicillin acylase immobilized on ultrafine silica particles. Kinetic studies were performed within the low-substrate-concentration region, where the external mass transfer limitation becomes significant. To predict the apparent kinetic parameters and the overall effectiveness factor, knowledge of the external mass transfer coefficient, k(L)a, is necessary. Although various correlations exist for estimation of k(L)a, in this study, an optimization scheme was utilized to obtain this coefficient. Using the optimum values of k(L)a, the initial reaction rates were predicted and found to be in good agreement with the experimental data.

  10. Evaluation of fermentation kinetics of acid-treated corn cob hydrolysate for xylose fermentation in the presence of acetic acid by Pichia stipitis.

    PubMed

    Kashid, Mohan; Ghosalkar, Anand

    2017-08-01

    The efficient utilization of lignocellulosic biomass for ethanol production depends on the fermentability of the biomass hydrolysate obtained after pretreatment. In this work we evaluated the kinetics of ethanol production from xylose using Pichia stipitis in acid-treated corn cob hydrolysate. Acetic acid is one of the main inhibitors in corn cob hydrolysate that negatively impacts kinetics of xylose fermentation by P. stipitis. Unstructured kinetic model has been formulated that describes cell mass growth and ethanol production as a function of xylose, oxygen, ethanol, and acetic acid concentration. Kinetic parameters were estimated under different operating conditions affecting xylose fermentation. This is the first report on kinetics of xylose fermentation by P. stipitis which includes inhibition of acetic acid on growth and product formation. In the presence of acetic acid in the hydrolysate, the model accurately predicted reduction in maximum specific growth rate (from 0.23 to 0.15 h -1 ) and increase in ethanol yield per unit biomass (from 3 to 6.2 gg -1 ), which was also observed during experimental trials. Presence of acetic acid in the fermentation led to significant reduction in the cell growth rate, reduction in xylose consumption and ethanol production rate. The developed model accurately described physiological state of P. stipitis during corn cob hydrolysate fermentation. Proposed model can be used to predict the influence of xylose, ethanol, oxygen, and acetic acid concentration on cell growth and ethanol productivity in industrial fermentation.

  11. Structural kinetic modeling of metabolic networks.

    PubMed

    Steuer, Ralf; Gross, Thilo; Selbig, Joachim; Blasius, Bernd

    2006-08-08

    To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

  12. Kinetics and yields of pesticide biodegradation at low substrate concentrations and under conditions restricting assimilable organic carbon.

    PubMed

    Helbling, Damian E; Hammes, Frederik; Egli, Thomas; Kohler, Hans-Peter E

    2014-02-01

    The fundamentals of growth-linked biodegradation occurring at low substrate concentrations are poorly understood. Substrate utilization kinetics and microbial growth yields are two critically important process parameters that can be influenced by low substrate concentrations. Standard biodegradation tests aimed at measuring these parameters generally ignore the ubiquitous occurrence of assimilable organic carbon (AOC) in experimental systems which can be present at concentrations exceeding the concentration of the target substrate. The occurrence of AOC effectively makes biodegradation assays conducted at low substrate concentrations mixed-substrate assays, which can have profound effects on observed substrate utilization kinetics and microbial growth yields. In this work, we introduce a novel methodology for investigating biodegradation at low concentrations by restricting AOC in our experiments. We modified an existing method designed to measure trace concentrations of AOC in water samples and applied it to systems in which pure bacterial strains were growing on pesticide substrates between 0.01 and 50 mg liter(-1). We simultaneously measured substrate concentrations by means of high-performance liquid chromatography with UV detection (HPLC-UV) or mass spectrometry (MS) and cell densities by means of flow cytometry. Our data demonstrate that substrate utilization kinetic parameters estimated from high-concentration experiments can be used to predict substrate utilization at low concentrations under AOC-restricted conditions. Further, restricting AOC in our experiments enabled accurate and direct measurement of microbial growth yields at environmentally relevant concentrations for the first time. These are critical measurements for evaluating the degradation potential of natural or engineered remediation systems. Our work provides novel insights into the kinetics of biodegradation processes and growth yields at low substrate concentrations.

  13. Kinetics of resid hydrodesulfurization reactions

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

    Mohammed, A.H.A.K.; Abbas, A.A.A.; Al'-Maiya, A.S.K.

    1987-07-01

    In this article the authors examine the results obtained in hydrodesulfurizing an atmospheric resis from Bai-Hassan crude on Ni-Mo/Al/sub 2/O/sub 3/ catalyst at 320-420/sup 0/C, feedstock space velocity 0.37-2.6 h/sup -1/, pressure 6.1 MPa, and hydrogen/feed ratio 300 liters/liter, in a single-pass downflow reactor with a stationary bed of catalyst. Also, they give certain thermodynamic characteristics for desulfurization, demetalization, and deasphalting of this resid. The kinetic model describing most accurately the kinetics of the different reactions will be examined.

  14. Improved parameter extraction and classification for dynamic contrast enhanced MRI of prostate

    NASA Astrophysics Data System (ADS)

    Haq, Nandinee Fariah; Kozlowski, Piotr; Jones, Edward C.; Chang, Silvia D.; Goldenberg, S. Larry; Moradi, Mehdi

    2014-03-01

    Magnetic resonance imaging (MRI), particularly dynamic contrast enhanced (DCE) imaging, has shown great potential in prostate cancer diagnosis and prognosis. The time course of the DCE images provides measures of the contrast agent uptake kinetics. Also, using pharmacokinetic modelling, one can extract parameters from the DCE-MR images that characterize the tumor vascularization and can be used to detect cancer. A requirement for calculating the pharmacokinetic DCE parameters is estimating the Arterial Input Function (AIF). One needs an accurate segmentation of the cross section of the external femoral artery to obtain the AIF. In this work we report a semi-automatic method for segmentation of the cross section of the femoral artery, using circular Hough transform, in the sequence of DCE images. We also report a machine-learning framework to combine pharmacokinetic parameters with the model-free contrast agent uptake kinetic parameters extracted from the DCE time course into a nine-dimensional feature vector. This combination of features is used with random forest and with support vector machine classi cation for cancer detection. The MR data is obtained from patients prior to radical prostatectomy. After the surgery, wholemount histopathology analysis is performed and registered to the DCE-MR images as the diagnostic reference. We show that the use of a combination of pharmacokinetic parameters and the model-free empirical parameters extracted from the time course of DCE results in improved cancer detection compared to the use of each group of features separately. We also validate the proposed method for calculation of AIF based on comparison with the manual method.

  15. A general moment expansion method for stochastic kinetic models

    NASA Astrophysics Data System (ADS)

    Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.

    2013-05-01

    Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.

  16. Kinetics of austenite-pearlite transformation in eutectoid carbon steel

    NASA Astrophysics Data System (ADS)

    Hawbolt, E. B.; Chau, B.; Brimacombe, J. K.

    1983-09-01

    The kinetics of the austenite-to-pearlite transformation have been measured under isothermal and continuous-cooling conditions on a eutectoid carbon (1080) steel using a diametral dilatometric technique. The isothermal transformation kinetics have been analyzed in terms of the Avrami Equation containing the two parameters n and b; the initiation of transformation was characterized by an empirically determined transformation-start time (tAv). The parameter n was found to be nearly constant; and neither n nor b was dependent on the cooling rate between T A1 and the test temperature. Continuous-cooling tests were performed with cooling rates ranging from 7.5 to 108 °C per second, and the initiation of transformation was determined. Comparison of this transformation-start time for different cooling rates with the measured slow cooling of a test coupon immersed in a salt bath indicates that, particularly at lower temperatures, the transformation in the traditional T-T-T test specimen may not be isothermal. The additivity rule was found to predict accurately the time taken, relative to tAv, to reach a given fraction of austenite transformed, even though there is some question that the isokinetic condition was met above 660 °C. However, the additivity rule does not hold for the pretransformation or incubation period, as originally proposed by Scheil, and seriously overestimates the incubation time. Application of the additivity rule to the prediction of transformation-finish time, based on transformation start at TA1, also leads to overestimates, but these are less serious. The isothermal parameters— n ( T), b ( T), and tAv ( T)—have been used to predict continuous-cooling transformation kinetics which are in close agreement with measurements at four cooling rates ranging from 7.5 to 64 °C per second.

  17. Direct recovery of regional tracer kinetics from temporally inconsistent dynamic ECT projections using dimension-reduced time-activity basis

    NASA Astrophysics Data System (ADS)

    Maltz, Jonathan S.

    2000-11-01

    We present an algorithm of reduced computational cost which is able to estimate kinetic model parameters directly from dynamic ECT sinograms made up of temporally inconsistent projections. The algorithm exploits the extreme degree of parameter redundancy inherent in linear combinations of the exponential functions which represent the modes of first-order compartmental systems. The singular value decomposition is employed to find a small set of orthogonal functions, the linear combinations of which are able to accurately represent all modes within the physiologically anticipated range in a given study. The reduced-dimension basis is formed as the convolution of this orthogonal set with a measured input function. The Moore-Penrose pseudoinverse is used to find coefficients of this basis. Algorithm performance is evaluated at realistic count rates using MCAT phantom and clinical 99mTc-teboroxime myocardial study data. Phantom data are modelled as originating from a Poisson process. For estimates recovered from a single slice projection set containing 2.5×105 total counts, recovered tissue responses compare favourably with those obtained using more computationally intensive methods. The corresponding kinetic parameter estimates (coefficients of the new basis) exhibit negligible bias, while parameter variances are low, falling within 30% of the Cramér-Rao lower bound.

  18. The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

    NASA Astrophysics Data System (ADS)

    Sharma, H. N.; McLean, W.; Maxwell, R. S.; Dinh, L. N.

    2016-09-01

    A silica-filled polydimethylsiloxane (PDMS) composite M9787 was investigated for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environment applications at room temperature (˜300 K). The main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (˜30 ppm by volume of H2O) for even a couple of days was the formation, on the silica surface fillers, of ˜60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. The presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.

  19. The moisture outgassing kinetics of a silica reinforced polydimethylsiloxane

    DOE PAGES

    Sharma, H. N.; McLean, W.; Maxwell, R. S.; ...

    2016-09-21

    We investigated a silica-filled polydimethylsiloxane (PDMS) composite M9787 for potential outgassing in a vacuum/dry environment with the temperature programmed desorption/reaction method. The outgassing kinetics of 463 K vacuum heat-treated samples, vacuum heat-treated samples which were subsequently re-exposed to moisture, and untreated samples were extracted using the isoconversional and constrained iterative regression methods in a complementary fashion. Density functional theory (DFT) calculations of water interactions with a silica surface were also performed to provide insight into the structural motifs leading to the obtained kinetic parameters. Kinetic analysis/model revealed that no outgassing occurs from the vacuum heat-treated samples in subsequent vacuum/dry environmentmore » applications at room temperature (~300 K). Moreover, the main effect of re-exposure of the vacuum heat-treated samples to a glove box condition (~30 ppm by volume of H 2O) for even a couple of days was the formation, on the silica surface fillers, of ~60 ppm by weight of physisorbed and loosely bonded moisture, which subsequently outgasses at room temperature in a vacuum/dry environment in a time span of 10 yr. However, without any vacuum heat treatment and even after 1 h of vacuum pump down, about 300 ppm by weight of H 2O would be released from the PDMS in the next few hours. Thereafter the outgassing rate slows down substantially. Our presented methodology of using the isoconversional kinetic analysis results and some appropriate nature of the reaction as the constraints for more accurate iterative regression analysis/deconvolution of complex kinetic spectra, and of checking the so-obtained results with first principle calculations such as DFT can serve as a template for treating other complex physical/chemical processes as well.« less

  20. Poster — Thur Eve — 44: Linearization of Compartmental Models for More Robust Estimates of Regional Hemodynamic, Metabolic and Functional Parameters using DCE-CT/PET Imaging

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

    Blais, AR; Dekaban, M; Lee, T-Y

    2014-08-15

    Quantitative analysis of dynamic positron emission tomography (PET) data usually involves minimizing a cost function with nonlinear regression, wherein the choice of starting parameter values and the presence of local minima affect the bias and variability of the estimated kinetic parameters. These nonlinear methods can also require lengthy computation time, making them unsuitable for use in clinical settings. Kinetic modeling of PET aims to estimate the rate parameter k{sub 3}, which is the binding affinity of the tracer to a biological process of interest and is highly susceptible to noise inherent in PET image acquisition. We have developed linearized kineticmore » models for kinetic analysis of dynamic contrast enhanced computed tomography (DCE-CT)/PET imaging, including a 2-compartment model for DCE-CT and a 3-compartment model for PET. Use of kinetic parameters estimated from DCE-CT can stabilize the kinetic analysis of dynamic PET data, allowing for more robust estimation of k{sub 3}. Furthermore, these linearized models are solved with a non-negative least squares algorithm and together they provide other advantages including: 1) only one possible solution and they do not require a choice of starting parameter values, 2) parameter estimates are comparable in accuracy to those from nonlinear models, 3) significantly reduced computational time. Our simulated data show that when blood volume and permeability are estimated with DCE-CT, the bias of k{sub 3} estimation with our linearized model is 1.97 ± 38.5% for 1,000 runs with a signal-to-noise ratio of 10. In summary, we have developed a computationally efficient technique for accurate estimation of k{sub 3} from noisy dynamic PET data.« less

  1. Modeling of chemical inhibition from amyloid protein aggregation kinetics.

    PubMed

    Vázquez, José Antonio

    2014-02-27

    The process of amyloid proteins aggregation causes several human neuropathologies. In some cases, e.g. fibrillar deposits of insulin, the problems are generated in the processes of production and purification of protein and in the pump devices or injectable preparations for diabetics. Experimental kinetics and adequate modelling of chemical inhibition from amyloid aggregation are of practical importance in order to study the viable processing, formulation and storage as well as to predict and optimize the best conditions to reduce the effect of protein nucleation. In this manuscript, experimental data of insulin, Aβ42 amyloid protein and apomyoglobin fibrillation from recent bibliography were selected to evaluate the capability of a bivariate sigmoid equation to model them. The mathematical functions (logistic combined with Weibull equation) were used in reparameterized form and the effect of inhibitor concentrations on kinetic parameters from logistic equation were perfectly defined and explained. The surfaces of data were accurately described by proposed model and the presented analysis characterized the inhibitory influence on the protein aggregation by several chemicals. Discrimination between true and apparent inhibitors was also confirmed by the bivariate equation. EGCG for insulin (working at pH = 7.4/T = 37°C) and taiwaniaflavone for Aβ42 were the compounds studied that shown the greatest inhibition capacity. An accurate, simple and effective model to investigate the inhibition of chemicals on amyloid protein aggregation has been developed. The equation could be useful for the clear quantification of inhibitor potential of chemicals and rigorous comparison among them.

  2. Higher adsorption capacity of Spirulina platensis alga for Cr(VI) ions removal: parameter optimisation, equilibrium, kinetic and thermodynamic predictions.

    PubMed

    Gunasundari, Elumalai; Senthil Kumar, Ponnusamy

    2017-04-01

    This study discusses about the biosorption of Cr(VI) ion from aqueous solution using ultrasonic assisted Spirulina platensis (UASP). The prepared UASP biosorbent was characterised by Fourier transform infrared spectroscopy, X-ray diffraction, Brunauer-Emmet-Teller, scanning electron spectroscopy and energy dispersive X-ray and thermogravimetric analyses. The optimum condition for the maximum removal of Cr(VI) ions for an initial concentration of 50 mg/l by UASP was measured as: adsorbent dose of 1 g/l, pH of 3.0, contact time of 30 min and temperature of 303 K. Adsorption isotherm, kinetics and thermodynamic parameters were calculated. Freundlich model provided the best results for the removal of Cr(VI) ions by UASP. The adsorption kinetics of Cr(VI) ions onto UASP showed that the pseudo-first-order model was well in line with the experimental data. In the thermodynamic study, the parameters like Gibb's free energy, enthalpy and entropy changes were evaluated. This result explains that the adsorption of Cr(VI) ions onto the UASP was exothermic and spontaneous in nature. Desorption of the biosorbent was done using different desorbing agents in which NaOH gave the best result. The prepared material showed higher affinity for the removal of Cr(VI) ions and this may be an alternative material to the existing commercial adsorbents.

  3. Analytical Expressions for the Mixed-Order Kinetics Parameters of TL Glow Peaks Based on the two Heating Rates Method.

    PubMed

    Maghrabi, Mufeed; Al-Abdullah, Tariq; Khattari, Ziad

    2018-03-24

    The two heating rates method (originally developed for first-order glow peaks) was used for the first time to evaluate the activation energy (E) from glow peaks obeying mixed-order (MO) kinetics. The derived expression for E has an insignificant additional term (on the scale of a few meV) when compared with the first-order case. Hence, the original expression for E using the two heating rates method can be used with excellent accuracy in the case of MO glow peaks. In addition, we derived a simple analytical expression for the MO parameter. The present procedure has the advantage that the MO parameter can now be evaluated using analytical expression instead of using the graphical representation between the geometrical factor and the MO parameter as given by the existing peak shape methods. The applicability of the derived expressions for real samples was demonstrated for the glow curve of Li 2 B 4 O 7 :Mn single crystal. The obtained parameters compare very well with those obtained by glow curve fitting and with the available published data.

  4. Modeling the growth kinetics of Bacillus cereus as a function of temperature, pH, sodium lactate and sodium chloride concentrations.

    PubMed

    Olmez, Hülya Kaptan; Aran, Necla

    2005-02-01

    Mathematical models describing the growth kinetic parameters (lag phase duration and growth rate) of Bacillus cereus as a function of temperature, pH, sodium lactate and sodium chloride concentrations were obtained in this study. In order to get a residual distribution closer to a normal distribution, the natural logarithm of the growth kinetic parameters were used in modeling. For reasons of parsimony, the polynomial models were reduced to contain only the coefficients significant at a level of pparameters. Predicted data were compared with the predictions from Pathogen Modeling Program (PMP-US Department of Agriculture-Agricultural Research Service) and validated against data extracted from the literature. The mean absolute relative error (MARE) and the median relative error (MRE) of the predicted generation times with the derived model were 25.6% and -16.7%, respectively, showing that the growth rate model accurately and safely predicted the growth kinetics of B. cereus. Results of the modeling study indicated that all of the studied factors had a significant effect on the growth of B. cereus in the experimental range studied.

  5. Kinetic operational models of agonism for G-protein-coupled receptors.

    PubMed

    Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

    2018-06-07

    The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics

  6. Development of a Kinetic Assay for Late Endosome Movement.

    PubMed

    Esner, Milan; Meyenhofer, Felix; Kuhn, Michael; Thomas, Melissa; Kalaidzidis, Yannis; Bickle, Marc

    2014-08-01

    Automated imaging screens are performed mostly on fixed and stained samples to simplify the workflow and increase throughput. Some processes, such as the movement of cells and organelles or measuring membrane integrity and potential, can be measured only in living cells. Developing such assays to screen large compound or RNAi collections is challenging in many respects. Here, we develop a live-cell high-content assay for tracking endocytic organelles in medium throughput. We evaluate the added value of measuring kinetic parameters compared with measuring static parameters solely. We screened 2000 compounds in U-2 OS cells expressing Lamp1-GFP to label late endosomes. All hits have phenotypes in both static and kinetic parameters. However, we show that the kinetic parameters enable better discrimination of the mechanisms of action. Most of the compounds cause a decrease of motility of endosomes, but we identify several compounds that increase endosomal motility. In summary, we show that kinetic data help to better discriminate phenotypes and thereby obtain more subtle phenotypic clustering. © 2014 Society for Laboratory Automation and Screening.

  7. Relativistic Kinetic Theory

    NASA Astrophysics Data System (ADS)

    Vereshchagin, Gregory V.; Aksenov, Alexey G.

    2017-02-01

    Preface; Acknowledgements; Acronyms and definitions; Introduction; Part I. Theoretical Foundations: 1. Basic concepts; 2. Kinetic equation; 3. Averaging; 4. Conservation laws and equilibrium; 5. Relativistic BBGKY hierarchy; 6. Basic parameters in gases and plasmas; Part II. Numerical Methods: 7. The basics of computational physics; 8. Direct integration of Boltzmann equations; 9. Multidimensional hydrodynamics; Part III. Applications: 10. Wave dispersion in relativistic plasma; 11. Thermalization in relativistic plasma; 12. Kinetics of particles in strong fields; 13. Compton scattering in astrophysics and cosmology; 14. Self-gravitating systems; 15. Neutrinos, gravitational collapse and supernovae; Appendices; Bibliography; Index.

  8. Thermal oxidative degradation kinetics of agricultural residues using distributed activation energy model and global kinetic model.

    PubMed

    Ren, Xiu'e; Chen, Jianbiao; Li, Gang; Wang, Yanhong; Lang, Xuemei; Fan, Shuanshi

    2018-08-01

    The study concerned the thermal oxidative degradation kinetics of agricultural residues, peanut shell (PS) and sunflower shell (SS). The thermal behaviors were evaluated via thermogravimetric analysis and the kinetic parameters were determined by using distributed activation energy model (DAEM) and global kinetic model (GKM). Results showed that thermal oxidative decomposition of two samples processed in three zones; the ignition, burnout, and comprehensive combustibility between two agricultural residues were of great difference; and the combustion performance could be improved by boosting heating rate. The activation energy ranges calculated by the DAEM for the thermal oxidative degradation of PS and SS were 88.94-145.30 kJ mol -1 and 94.86-169.18 kJ mol -1 , respectively. The activation energy obtained by the GKM for the oxidative decomposition of hemicellulose and cellulose was obviously lower than that for the lignin oxidation at identical heating rate. To some degree, the determined kinetic parameters could acceptably simulate experimental data. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Theoretical Investigation of Kinetic Processes in Small Radicals of Importance in Combustion

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

    Alexander, Millard; Dagdigian, Paul J.

    Our group studies inelastic and reactive collisions of small molecules, focusing on radicals important in combustion environments. The goal is the better understanding of kinetic processes that may be difficult to access experimentally. An essential component is the accurate determination and fitting of potential energy surfaces (PESs). After fitting the ab initio points to obtain global PESs, we treat the dynamics using time-independent (close-coupling) methods. Cross sections and rate constants for collisions of are determined with our Hibridon program suite . We have studied energy transfer (rotationally, vibrationally, and/or electronically inelastic) in small hydrocarbon radicals (CH 2 and CH 3)more » and the CN radical. We have made a comparison with experimental measurements of relevant rate constants for collisions of these radicals. Also, we have calculated accurate transport properties using state-of-the-art PESs and to investigate the sensitivity to these parameters in 1-dimensional flame simulations. Of particular interest are collision pairs involving the light H atom.« less

  10. Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

    PubMed Central

    Magnus, Carsten

    2013-01-01

    Antibodies binding to the surface of virions can lead to virus neutralisation. Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation. Early models are based on chemical binding kinetics. Applying these models lead to very low estimates of the number of antibodies needed for neutralisation. In contrast, according to the more conceptual approach of stoichiometries in virology a much higher number of antibodies is required for virus neutralisation by antibodies. Here, we combine chemical binding kinetics with (virological) stoichiometries to better explain virus neutralisation by antibody binding. This framework is in agreement with published data on the neutralisation of the human immunodeficiency virus. Knowing antibody reaction constants, our model allows us to estimate stoichiometrical parameters from kinetic neutralisation curves. In addition, we can identify important parameters that will make further analysis of kinetic neutralisation curves more valuable in the context of estimating stoichiometries. Our model gives a more subtle explanation of kinetic neutralisation curves in terms of single-hit and multi-hit kinetics. PMID:23468602

  11. Kinetic parameters of grinding media in ball mills with various liner design and mill speed based on DEM modeling

    NASA Astrophysics Data System (ADS)

    Khakhalev, P. A.; Bogdanov, VS; Kovshechenko, V. M.

    2018-03-01

    The article presents analysis of the experiments in the ball mill of 0.5x0.3 m with four different liner types based on DEM modeling. The numerical experiment always complements laboratory research and allow obtaining high accuracy output data. An important property of the numerical experiment is the possibility of visualization of the results. The EDEM software allows calculating trajectory of the grinding bodies and kinetic parameters of each ball for the relative mill speed and the different types of mill’s liners.

  12. Modelling the growth kinetics of Kocuria marina DAGII as a function of single and binary substrate during batch production of β-Cryptoxanthin.

    PubMed

    Mitra, Ruchira; Chaudhuri, Surabhi; Dutta, Debjani

    2017-01-01

    In the present investigation, growth kinetics of Kocuria marina DAGII during batch production of β-Cryptoxanthin (β-CRX) was studied by considering the effect of glucose and maltose as a single and binary substrate. The importance of mixed substrate over single substrate has been emphasised in the present study. Different mathematical models namely, the Logistic model for cell growth, the Logistic mass balance equation for substrate consumption and the Luedeking-Piret model for β-CRX production were successfully implemented. Model-based analyses for the single substrate experiments suggested that the concentrations of glucose and maltose higher than 7.5 and 10.0 g/L, respectively, inhibited the growth and β-CRX production by K. marina DAGII. The Han and Levenspiel model and the Luong product inhibition model accurately described the cell growth in glucose and maltose substrate systems with a R 2 value of 0.9989 and 0.9998, respectively. The effect of glucose and maltose as binary substrate was further investigated. The binary substrate kinetics was well described using the sum-kinetics with interaction parameters model. The results of production kinetics revealed that the presence of binary substrate in the cultivation medium increased the biomass and β-CRX yield significantly. This study is a first time detailed investigation on kinetic behaviours of K. marina DAGII during β-CRX production. The parameters obtained in the study might be helpful for developing strategies for commercial production of β-CRX by K. marina DAGII.

  13. Proton dissociation properties of arylphosphonates: Determination of accurate Hammett equation parameters.

    PubMed

    Dargó, Gergő; Bölcskei, Adrienn; Grün, Alajos; Béni, Szabolcs; Szántó, Zoltán; Lopata, Antal; Keglevich, György; Balogh, György T

    2017-09-05

    Determination of the proton dissociation constants of several arylphosphonic acid derivatives was carried out to investigate the accuracy of the Hammett equations available for this family of compounds. For the measurement of the pK a values modern, accurate methods, such as the differential potentiometric titration and NMR-pH titration were used. We found our results significantly different from the pK a values reported before (pK a1 : MAE = 0.16 pK a2 : MAE=0.59). Based on our recently measured pK a values, refined Hammett equations were determined that might be used for predicting highly accurate ionization constants of newly synthesized compounds (pK a1 =1.70-0.894σ, pK a2 =6.92-0.934σ). Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

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

    Parker, Stephen S.; White, Josh; Hosemann, Peter

    High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

  15. Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

    DOE PAGES

    Parker, Stephen S.; White, Josh; Hosemann, Peter; ...

    2017-11-03

    High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. We measured the oxidation kinetic constant (k) as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3–5 orders of magnitude lower across the experimental temperature range. Our results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

  16. Oxidation Kinetics of Ferritic Alloys in High-Temperature Steam Environments

    NASA Astrophysics Data System (ADS)

    Parker, Stephen S.; White, Josh; Hosemann, Peter; Nelson, Andrew

    2018-02-01

    High-temperature isothermal steam oxidation kinetic parameters of several ferritic alloys were determined by thermogravimetric analysis. The oxidation kinetic constant ( k) was measured as a function of temperature from 900°C to 1200°C. The results show a marked increase in oxidation resistance compared to reference Zircaloy-2, with kinetic constants 3-5 orders of magnitude lower across the experimental temperature range. The results of this investigation supplement previous findings on the properties of ferritic alloys for use as candidate cladding materials and extend kinetic parameter measurements to high-temperature steam environments suitable for assessing accident tolerance for light water reactor applications.

  17. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  18. Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method.

    PubMed

    Sinha, Debalina; Pavanello, Michele

    2015-08-28

    The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.

  19. Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method

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

    Sinha, Debalina; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

    2015-08-28

    The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term themore » Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.« less

  20. A new methodology to determine kinetic parameters for one- and two-step chemical models

    NASA Technical Reports Server (NTRS)

    Mantel, T.; Egolfopoulos, F. N.; Bowman, C. T.

    1996-01-01

    In this paper, a new methodology to determine kinetic parameters for simple chemical models and simple transport properties classically used in DNS of premixed combustion is presented. First, a one-dimensional code is utilized to performed steady unstrained laminar methane-air flame in order to verify intrinsic features of laminar flames such as burning velocity and temperature and concentration profiles. Second, the flame response to steady and unsteady strain in the opposed jet configuration is numerically investigated. It appears that for a well determined set of parameters, one- and two-step mechanisms reproduce the extinction limit of a laminar flame submitted to a steady strain. Computations with the GRI-mech mechanism (177 reactions, 39 species) and multicomponent transport properties are used to validate these simplified models. A sensitivity analysis of the preferential diffusion of heat and reactants when the Lewis number is close to unity indicates that the response of the flame to an oscillating strain is very sensitive to this number. As an application of this methodology, the interaction between a two-dimensional vortex pair and a premixed laminar flame is performed by Direct Numerical Simulation (DNS) using the one- and two-step mechanisms. Comparison with the experimental results of Samaniego et al. (1994) shows a significant improvement in the description of the interaction when the two-step model is used.

  1. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

    PubMed Central

    2014-01-01

    Background Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for accomplishing such tasks. While significant progress has been made, effective experimental strategies for parameter identification and for distinguishing among alternative network topologies remain unclear. We approached these questions in an unbiased manner using a unique community-based approach in the context of the DREAM initiative (Dialogue for Reverse Engineering Assessment of Methods). We created an in silico test framework under which participants could probe a network with hidden parameters by requesting a range of experimental assays; results of these experiments were simulated according to a model of network dynamics only partially revealed to participants. Results We proposed two challenges; in the first, participants were given the topology and underlying biochemical structure of a 9-gene regulatory network and were asked to determine its parameter values. In the second challenge, participants were given an incomplete topology with 11 genes and asked to find three missing links in the model. In both challenges, a budget was provided to buy experimental data generated in silico with the model and mimicking the features of different common experimental techniques, such as microarrays and fluorescence microscopy. Data could be bought at any stage, allowing participants to implement an iterative loop of experiments and computation. Conclusions A total of 19 teams participated in this competition. The results suggest that the combination of state-of-the-art parameter estimation and a varied set of experimental methods using a few datasets, mostly fluorescence imaging data, can accurately determine parameters of biochemical models of gene regulation. However, the task is considerably more difficult if the gene network topology is not completely

  2. Demon voltammetry and analysis software: Analysis of cocaine-induced alterations in dopamine signaling using multiple kinetic measures

    PubMed Central

    Yorgason, Jordan T.; España, Rodrigo A.; Jones, Sara R.

    2011-01-01

    The fast sampling rates of fast scan cyclic voltammetry make it a favorable method for measuring changes in brain monoamine release and uptake kinetics in slice, anesthetized, and freely moving preparations. The most common analysis technique for evaluating changes in dopamine signaling uses well-established Michaelis-Menten kinetic methods that can accurately model dopamine release and uptake parameters across multiple experimental conditions. Nevertheless, over the years, many researchers have turned to other measures to estimate changes in dopamine release and uptake, yet to our knowledge no systematic comparison amongst these measures has been conducted. To address this lack of uniformity in kinetic analyses, we have created the Demon Voltammetry and Analysis software suite, which is freely available to academic and non-profit institutions. Here we present an explanation of the Demon Acquisition and Analysis features, and demonstrate its utility for acquiring voltammetric data under in vitro, in vivo anesthetized, and freely moving conditions. Additionally, the software was used to compare the sensitivity of multiple kinetic measures of release and uptake to cocaine-induced changes in electrically evoked dopamine efflux in nucleus accumbens core slices. Specifically, we examined and compared tau, full width at half height, half-life, T20, T80, slope, peak height, calibrated peak dopamine concentration, and area under the curve to the well-characterized Michaelis-Menten parameters, dopamine per pulse, maximal uptake rate, and apparent affinity. Based on observed results we recommend tau for measuring dopamine uptake and calibrated peak dopamine concentration for measuring dopamine release. PMID:21392532

  3. An improved kinetics approach to describe the physical stability of amorphous solid dispersions.

    PubMed

    Yang, Jiao; Grey, Kristin; Doney, John

    2010-01-15

    The recrystallization of amorphous solid dispersions may lead to a loss in the dissolution rate, and consequently reduce bioavailability. The purpose of this work is to understand factors governing the recrystallization of amorphous drug-polymer solid dispersions, and develop a kinetics model capable of accurately predicting their physical stability. Recrystallization kinetics was measured using differential scanning calorimetry for initially amorphous efavirenz-polyvinylpyrrolidone solid dispersions stored at controlled temperature and relative humidity. The experimental measurements were fitted by a new kinetic model to estimate the recrystallization rate constant and microscopic geometry of crystal growth. The new kinetics model was used to illustrate the governing factors of amorphous solid dispersions stability. Temperature was found to affect efavirenz recrystallization in an Arrhenius manner, while recrystallization rate constant was shown to increase linearly with relative humidity. Polymer content tremendously inhibited the recrystallization process by increasing the crystallization activation energy and decreasing the equilibrium crystallinity. The new kinetic model was validated by the good agreement between model fits and experiment measurements. A small increase in polyvinylpyrrolidone resulted in substantial stability enhancements of efavirenz amorphous solid dispersion. The new established kinetics model provided more accurate predictions than the Avrami equation.

  4. A Comprehensive Enzyme Kinetic Exercise for Biochemistry

    ERIC Educational Resources Information Center

    Barton, Janice S.

    2011-01-01

    This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…

  5. Growth kinetic and fuel quality parameters as selective criterion for screening biodiesel producing cyanobacterial strains.

    PubMed

    Gayathri, Manickam; Shunmugam, Sumathy; Mugasundari, Arumugam Vanmathi; Rahman, Pattanathu K S M; Muralitharan, Gangatharan

    2018-01-01

    The efficiency of cyanobacterial strains as biodiesel feedstock varies with the dwelling habitat. Fourteen indigenous heterocystous cyanobacterial strains from rice field ecosystem were screened based on growth kinetic and fuel parameters. The highest biomass productivity was obtained in Nostoc punctiforme MBDU 621 (19.22mg/L/day) followed by Calothrix sp. MBDU 701 (13.43mg/L/day). While lipid productivity and lipid content was highest in Nostoc spongiaeforme MBDU 704 (4.45mg/L/day and 22.5%dwt) followed by Calothrix sp. MBDU 701 (1.54mg/L/day and 10.75%dwt). Among the tested strains, Nostoc spongiaeforme MBDU 704 and Nostoc punctiforme MBDU 621 were selected as promising strains for good quality biodiesel production by Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA) analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. An algorithm for the kinetics of tire pyrolysis under different heating rates.

    PubMed

    Quek, Augustine; Balasubramanian, Rajashekhar

    2009-07-15

    Tires exhibit different kinetic behaviors when pyrolyzed under different heating rates. A new algorithm has been developed to investigate pyrolysis behavior of scrap tires. The algorithm includes heat and mass transfer equations to account for the different extents of thermal lag as the tire is heated at different heating rates. The algorithm uses an iterative approach to fit model equations to experimental data to obtain quantitative values of kinetic parameters. These parameters describe the pyrolysis process well, with good agreement (r(2)>0.96) between the model and experimental data when the model is applied to three different brands of automobile tires heated under five different heating rates in a pure nitrogen atmosphere. The model agrees with other researchers' results that frequencies factors increased and time constants decreased with increasing heating rates. The model also shows the change in the behavior of individual tire components when the heating rates are increased above 30 K min(-1). This result indicates that heating rates, rather than temperature, can significantly affect pyrolysis reactions. This algorithm is simple in structure and yet accurate in describing tire pyrolysis under a wide range of heating rates (10-50 K min(-1)). It improves our understanding of the tire pyrolysis process by showing the relationship between the heating rate and the many components in a tire that depolymerize as parallel reactions.

  7. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    PubMed

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  8. Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures

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

    Guha, S.; Peters, C.A.; Jaffe, P.R.

    Biodegradation kinetics of naphthalene, phenanthrene and pyrene were studied in sole-substrate systems, and in binary and ternary mixtures to examine substrate interactions. The experiments were conducted in aerobic batch aqueous systems inoculated with a mixed culture that had been isolated from soils contaminated with polycyclic aromatic hydrocarbons (PAHs). Monod kinetic parameters and yield coefficients for the individual parameters and yield coefficients for the individual compounds were estimated from substrate depletion and CO{sub 2} evolution rate data in sole-substrate experiments. In all three binary mixture experiments, biodegradation kinetics were comparable to the sole-substrate kinetics. In the ternary mixture, biodegradation of naphthalenemore » was inhibited and the biodegradation rates of phenanthrene and pyrene were enhanced. A multisubstrate form of the Monod kinetic model was found to adequately predict substrate interactions in the binary and ternary mixtures using only the parameters derived from sole-substrate experiments. Numerical simulations of biomass growth kinetics explain the observed range of behaviors in PAH mixtures. In general, the biodegradation rates of the more degradable and abundant compounds are reduced due to competitive inhibition, but enhanced biodegradation of the more recalcitrant PAHs occurs due to simultaneous biomass growth on multiple substrates. In PAH-contaminated environments, substrate interactions may be very large due to additive effects from the large number of compounds present.« less

  9. TNT Prout-Tompkins Kinetics Calibration with PSUADE

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

    Wemhoff, A P; Hsieh, H

    2007-04-11

    We used the code PSUADE to calibrate Prout-Tompkins kinetic parameters for pure recrystallized TNT. The calibration was based on ALE3D simulations of a series of One Dimensional Time to Explosion (ODTX) experiments. The resultant kinetic parameters differed from TNT data points with an average error of 28%, which is slightly higher than the value of 23% previously calculated using a two-point optimization. The methodology described here provides a basis for future calibration studies using PSUADE. The files used in the procedure are listed in the Appendix.

  10. Combined Homogeneous Surface Diffusion Model - Design of experiments approach to optimize dye adsorption considering both equilibrium and kinetic aspects.

    PubMed

    Muthukkumaran, A; Aravamudan, K

    2017-12-15

    Adsorption, a popular technique for removing azo dyes from aqueous streams, is influenced by several factors such as pH, initial dye concentration, temperature and adsorbent dosage. Any strategy that seeks to identify optimal conditions involving these factors, should take into account both kinetic and equilibrium aspects since they influence rate and extent of removal by adsorption. Hence rigorous kinetics and accurate equilibrium models are required. In this work, the experimental investigations pertaining to adsorption of acid orange 10 dye (AO10) on activated carbon were carried out using Central Composite Design (CCD) strategy. The significant factors that affected adsorption were identified to be solution temperature, solution pH, adsorbent dosage and initial solution concentration. Thermodynamic analysis showed the endothermic nature of the dye adsorption process. The kinetics of adsorption has been rigorously modeled using the Homogeneous Surface Diffusion Model (HSDM) after incorporating the non-linear Freundlich adsorption isotherm. Optimization was performed for kinetic parameters (color removal time and surface diffusion coefficient) as well as the equilibrium affected response viz. percentage removal. Finally, the optimum conditions predicted were experimentally validated. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Quantitative Evaluation of the Total Magnetic Moments of Colloidal Magnetic Nanoparticles: A Kinetics-based Method.

    PubMed

    Liu, Haiyi; Sun, Jianfei; Wang, Haoyao; Wang, Peng; Song, Lina; Li, Yang; Chen, Bo; Zhang, Yu; Gu, Ning

    2015-06-08

    A kinetics-based method is proposed to quantitatively characterize the collective magnetization of colloidal magnetic nanoparticles. The method is based on the relationship between the magnetic force on a colloidal droplet and the movement of the droplet under a gradient magnetic field. Through computational analysis of the kinetic parameters, such as displacement, velocity, and acceleration, the magnetization of colloidal magnetic nanoparticles can be calculated. In our experiments, the values measured by using our method exhibited a better linear correlation with magnetothermal heating, than those obtained by using a vibrating sample magnetometer and magnetic balance. This finding indicates that this method may be more suitable to evaluate the collective magnetism of colloidal magnetic nanoparticles under low magnetic fields than the commonly used methods. Accurate evaluation of the magnetic properties of colloidal nanoparticles is of great importance for the standardization of magnetic nanomaterials and for their practical application in biomedicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation.

    PubMed

    Cha, Tae-Gon; Pan, Jing; Chen, Haorong; Robinson, Heather N; Li, Xiang; Mao, Chengde; Choi, Jong Hyun

    2015-07-29

    Dynamic DNA enzyme-based walkers complete their stepwise movements along the prescribed track through a series of reactions, including hybridization, enzymatic cleavage, and strand displacement; however, their overall translocation kinetics is not well understood. Here, we perform mechanistic studies to elucidate several key parameters that govern the kinetics and processivity of DNA enzyme-based walkers. These parameters include DNA enzyme core type and structure, upper and lower recognition arm lengths, and divalent metal cation species and concentration. A theoretical model is developed within the framework of single-molecule kinetics to describe overall translocation kinetics as well as each reaction step. A better understanding of kinetics and design parameters enables us to demonstrate a walker movement near 5 μm at an average speed of ∼1 nm s(-1). We also show that the translocation kinetics of DNA walkers can be effectively controlled by external light stimuli using photoisomerizable azobenzene moieties. A 2-fold increase in the cleavage reaction is observed when the hairpin stems of enzyme catalytic cores are open under UV irradiation. This study provides general design guidelines to construct highly processive, autonomous DNA walker systems and to regulate their translocation kinetics, which would facilitate the development of functional DNA walkers.

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

    PubMed

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

    2017-05-01

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

  14. Solar Fenton and solar TiO2 catalytic treatment of ofloxacin in secondary treated effluents: evaluation of operational and kinetic parameters.

    PubMed

    Michael, I; Hapeshi, E; Michael, C; Fatta-Kassinos, D

    2010-10-01

    Two different technical approaches based on advanced oxidation processes (AOPs), solar Fenton homogeneous photocatalysis (hv/Fe(2+)/H(2)O(2)) and heterogeneous photocatalysis with titanium dioxide (TiO(2)) suspensions were studied for the chemical degradation of the fluoroquinolone ofloxacin in secondary treated effluents. A bench-scale solar simulator in combination with an appropriate photochemical batch reactor was used to evaluate and select the optimal oxidation conditions of ofloxacin spiked in secondary treated domestic effluents. The concentration profile of the examined substrate during degradation was determined by UV/Vis spectrophotometry. Mineralization was monitored by measuring the dissolved organic carbon (DOC). The concentrations of Fe(2+) and H(2)O(2) were the key factors for the solar Fenton process, while the most important parameter of the heterogeneous photocatalysis was proved to be the catalyst loading. Kinetic analyses indicated that the photodegradation of ofloxacin can be described by a pseudo-first-order reaction. The rate constant (k) for the solar Fenton process was determined at different Fe(2+) and H(2)O(2) concentrations whereas the Langmuir-Hinshelwood (LH) kinetic expression was used to assess the kinetics of the heterogeneous photocatalytic process. The conversion of ofloxacin depends on several parameters based on the various experimental conditions, which were investigated. A Daphnia magna bioassay was used to evaluate the potential toxicity of the parent compound and its photo-oxidation by-products in different stages of oxidation. In the present study solar Fenton has been demonstrated to be more effective than the solar TiO(2) process, yielding complete degradation of the examined substrate and DOC reduction of about 50% in 30 min of the photocatalytic treatment. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. Errors in Sounding of the Atmosphere Using Broadband Emission Radiometry (SABER) Kinetic Temperature Caused by Non-Local Thermodynamic Equilibrium Model Parameters

    NASA Technical Reports Server (NTRS)

    Garcia-Comas, Maya; Lopez-Puertas, M.; Funke, B.; Bermejo-Pantaleon, D.; Marshall, Benjamin T.; Mertens, Christopher J.; Remsberg, Ellis E.; Mlynczak, Martin G.; Gordley, L. L.; Russell, James M.

    2008-01-01

    The vast set of near global and continuous atmospheric measurements made by the SABER instrument since 2002, including daytime and nighttime kinetic temperature (T(sub k)) from 20 to 105 km, is available to the scientific community. The temperature is retrieved from SABER measurements of the atmospheric 15 micron CO2 limb emission. This emission separates from local thermodynamic equilibrium (LTE) conditions in the rarefied mesosphere and thermosphere, making it necessary to consider the CO2 vibrational state non-LTE populations in the retrieval algorithm above 70 km. Those populations depend on kinetic parameters describing the rate at which energy exchange between atmospheric molecules take place, but some of these collisional rates are not well known. We consider current uncertainties in the rates of quenching of CO2 (v2 ) by N2 , O2 and O, and the CO2 (v2 ) vibrational-vibrational exchange to estimate their impact on SABER T(sub k) for different atmospheric conditions. The T(sub k) is more sensitive to the uncertainty in the latter two and their effects depend on altitude. The T(sub k) combined systematic error due to non-LTE kinetic parameters does not exceed +/- 1.5 K below 95 km and +/- 4-5 K at 100 km for most latitudes and seasons (except for polar summer) if the Tk profile does not have pronounced vertical structure. The error is +/- 3 K at 80 km, +/- 6 K at 84 km and +/- 18 K at 100 km under the less favourable polar summer conditions. For strong temperature inversion layers, the errors reach +/- 3 K at 82 km and +/- 8 K at 90 km. This particularly affects tide amplitude estimates, with errors of up to +/- 3 K.

  16. Parameter identification of thermophilic anaerobic degradation of valerate.

    PubMed

    Flotats, Xavier; Ahring, Birgitte K; Angelidaki, Irini

    2003-01-01

    The considered mathematical model of the decomposition of valerate presents three unknown kinetic parameters, two unknown stoichiometric coefficients, and three unknown initial concentrations for biomass. Applying a structural identifiability study, we concluded that it is necessary to perform simultaneous batch experiments with different initial conditions for estimating these parameters. Four simultaneous batch experiments were conducted at 55 degrees C, characterized by four different initial acetate concentrations. Product inhibition of valerate degradation by acetate was considered. Practical identification was done optimizing the sum of the multiple determination coefficients for all measured state variables and for all experiments simultaneously. The estimated values of kinetic parameters and stoichiometric coefficients were characterized by the parameter correlation matrix, the confidence interval, and the student's t-test at 5% significance level with positive results except for the saturation constant, for which more experiments for improving its identifiability should be conducted. In this article, we discuss kinetic parameter estimation methods.

  17. The Kinetics of Dissolution Revisited

    NASA Astrophysics Data System (ADS)

    Antonel, Paula S.; Hoijemberg, Pablo A.; Maiante, Leandro M.; Lagorio, M. Gabriela

    2003-09-01

    An experiment analyzing the kinetics of dissolution of a solid with cylindrical geometry in water is presented. The dissolution process is followed by measuring the solid mass and its size parameters (thickness and diameter) as a function of time. It is verified that the dissolution rate follows the Nernst model. Data treatment is compared with the dissolution of a spherical solid previously described. Kinetics, diffusion concepts, and polynomial fitting of experimental data are combined in this simple experiment.

  18. Kinetics of alkali-based photocathode degradation

    DOE PAGES

    Pavlenko, Vitaly; Liu, Fangze; Hoffbauer, Mark A.; ...

    2016-11-02

    Here, we report on a kinetic model that describes the degradation of the quantum efficiency (QE) of Cs 3Sb and negative electron affinity (NEA) GaAs photocathodes under UHV conditions. Additionally, the generally accepted irreversible chemical change of a photocathode’s surface due to reactions with residual gases, such as O 2, CO 2, and H 2O, the model incorporates an intermediate reversible physisorption step, similar to Langmuir adsorption. Moreover, this intermediate step is needed to satisfactorily describe the strongly non-exponential QE degradation curves for two distinctly different classes of photocathodes –surface-activated and “bulk,” indicating that in both systems the QE degradationmore » results from surface damage. The recovery of the QE upon improvement of vacuum conditions is also accurately predicted by this model with three parameters (rates of gas adsorption, desorption, and irreversible chemical reaction with the surface) comprising metrics to better characterize the lifetime of the cathodes, instead of time-pressure exposure expressed in Langmuir units.« less

  19. The initial value problem in Lagrangian drift kinetic theory

    NASA Astrophysics Data System (ADS)

    Burby, J. W.

    2016-06-01

    > Existing high-order variational drift kinetic theories contain unphysical rapidly varying modes that are not seen at low orders. These unphysical modes, which may be rapidly oscillating, damped or growing, are ushered in by a failure of conventional high-order drift kinetic theory to preserve the structure of its parent model's initial value problem. In short, the (infinite dimensional) system phase space is unphysically enlarged in conventional high-order variational drift kinetic theory. I present an alternative, `renormalized' variational approach to drift kinetic theory that manifestly respects the parent model's initial value problem. The basic philosophy underlying this alternate approach is that high-order drift kinetic theory ought to be derived by truncating the all-orders system phase-space Lagrangian instead of the usual `field particle' Lagrangian. For the sake of clarity, this story is told first through the lens of a finite-dimensional toy model of high-order variational drift kinetics; the analogous full-on drift kinetic story is discussed subsequently. The renormalized drift kinetic system, while variational and just as formally accurate as conventional formulations, does not support the troublesome rapidly varying modes.

  20. pyJac: Analytical Jacobian generator for chemical kinetics

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

    Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using py

  1. α-Phase transformation kinetics of U – 8 wt% Mo established by in situ neutron diffraction

    DOE PAGES

    Garlea, Elena; Steiner, M. A.; Calhoun, C. A.; ...

    2016-05-08

    The α-phase transformation kinetics of as-cast U - 8 wt% Mo below the eutectoid temperature have been established by in situ neutron diffraction. α-phase weight fraction data acquired through Rietveld refinement at five different isothermal hold temperatures can be modeled accurately utilizing a simple Johnson-Mehl-Avrami-Kolmogorov impingement-based theory, and the results are validated by a corresponding evolution in the γ-phase lattice parameter during transformation that follows Vegard’s law. Neutron diffraction data is used to produce a detailed Time-Temperature-Transformation diagram that improves upon inconsistencies in the current literature, exhibiting a minimum transformation start time of 40 min at temperatures between 500 °Cmore » and 510 °C. Lastly, the transformation kinetics of U – 8 wt% Mo can vary significantly from as-cast conditions after extensive heat treatments, due to homogenization of the typical dendritic microstructure which possesses non-negligible solute segregation.« less

  2. Significance of accurate diffraction corrections for the second harmonic wave in determining the acoustic nonlinearity parameter

    NASA Astrophysics Data System (ADS)

    Jeong, Hyunjo; Zhang, Shuzeng; Barnard, Dan; Li, Xiongbing

    2015-09-01

    The accurate measurement of acoustic nonlinearity parameter β for fluids or solids generally requires making corrections for diffraction effects due to finite size geometry of transmitter and receiver. These effects are well known in linear acoustics, while those for second harmonic waves have not been well addressed and therefore not properly considered in previous studies. In this work, we explicitly define the attenuation and diffraction corrections using the multi-Gaussian beam (MGB) equations which were developed from the quasilinear solutions of the KZK equation. The effects of making these corrections are examined through the simulation of β determination in water. Diffraction corrections are found to have more significant effects than attenuation corrections, and the β values of water can be estimated experimentally with less than 5% errors when the exact second harmonic diffraction corrections are used together with the negligible attenuation correction effects on the basis of linear frequency dependence between attenuation coefficients, α2 ≃ 2α1.

  3. A kinetics database and scripts for PHREEQC

    NASA Astrophysics Data System (ADS)

    Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

    2017-12-01

    Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

  4. Direct estimation of tracer-kinetic parameter maps from highly undersampled brain dynamic contrast enhanced MRI.

    PubMed

    Guo, Yi; Lingala, Sajan Goud; Zhu, Yinghua; Lebel, R Marc; Nayak, Krishna S

    2017-10-01

    The purpose of this work was to develop and evaluate a T 1 -weighted dynamic contrast enhanced (DCE) MRI methodology where tracer-kinetic (TK) parameter maps are directly estimated from undersampled (k,t)-space data. The proposed reconstruction involves solving a nonlinear least squares optimization problem that includes explicit use of a full forward model to convert parameter maps to (k,t)-space, utilizing the Patlak TK model. The proposed scheme is compared against an indirect method that creates intermediate images by parallel imaging and compressed sensing before to TK modeling. Thirteen fully sampled brain tumor DCE-MRI scans with 5-second temporal resolution are retrospectively undersampled at rates R = 20, 40, 60, 80, and 100 for each dynamic frame. TK maps are quantitatively compared based on root mean-squared-error (rMSE) and Bland-Altman analysis. The approach is also applied to four prospectively R = 30 undersampled whole-brain DCE-MRI data sets. In the retrospective study, the proposed method performed statistically better than indirect method at R ≥ 80 for all 13 cases. This approach provided restoration of TK parameter values with less errors in tumor regions of interest, an improvement compared to a state-of-the-art indirect method. Applied prospectively, the proposed method provided whole-brain, high-resolution TK maps with good image quality. Model-based direct estimation of TK maps from k,t-space DCE-MRI data is feasible and is compatible up to 100-fold undersampling. Magn Reson Med 78:1566-1578, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  5. General solutions for the oxidation kinetics of polymers

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

    Gillen, K.T.; Clough, R.L.; Wise, J.

    1996-08-01

    The simplest general kinetic schemes applicable to the oxidation of polymers are presented, discussed and analyzed in terms of the underlying kinetic assumptions. For the classic basic autoxidation scheme (BAS), which involves three bimolecular termination steps and is applicable mainly to unstabilized polymers, typical assumptions used singly or in groups include (1) long kinetic chain length, (2) a specific ratio of the termination rate constants and (3) insensitivity to the oxygen concentration (e.g., domination by a single termination step). Steady-state solutions for the rate of oxidation are given in terms of one, two, three, or four parameters, corresponding respectively tomore » three, two, one, or zero kinetic assumptions. The recently derived four-parameter solution predicts conditions yielding unusual dependencies of the oxidation rate on oxygen concentration and on initiation rate, as well as conditions leading to some unusual diffusion-limited oxidation profile shapes. For stabilized polymers, unimolecular termination schemes are typically more appropriate than bimolecular. Kinetics incorporating unimolecular termination reactions are shown to result in very simple oxidation expressions which have been experimentally verified for both radiation-initiated oxidation of an EPDM and thermoxidative degradation of nitrile and chloroprene elastomers.« less

  6. TRANSITION FROM KINETIC TO MHD BEHAVIOR IN A COLLISIONLESS PLASMA

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

    Parashar, Tulasi N.; Matthaeus, William H.; Shay, Michael A.

    The study of kinetic effects in heliospheric plasmas requires representation of dynamics at sub-proton scales, but in most cases the system is driven by magnetohydrodynamic (MHD) activity at larger scales. The latter requirement challenges available computational resources, which raises the question of how large such a system must be to exhibit MHD traits at large scales while kinetic behavior is accurately represented at small scales. Here we study this implied transition from kinetic to MHD-like behavior using particle-in-cell (PIC) simulations, initialized using an Orszag–Tang Vortex. The PIC code treats protons, as well as electrons, kinetically, and we address the questionmore » of interest by examining several different indicators of MHD-like behavior.« less

  7. Kinetics of hydrogen peroxide decomposition by catalase: hydroxylic solvent effects.

    PubMed

    Raducan, Adina; Cantemir, Anca Ruxandra; Puiu, Mihaela; Oancea, Dumitru

    2012-11-01

    The effect of water-alcohol (methanol, ethanol, propan-1-ol, propan-2-ol, ethane-1,2-diol and propane-1,2,3-triol) binary mixtures on the kinetics of hydrogen peroxide decomposition in the presence of bovine liver catalase is investigated. In all solvents, the activity of catalase is smaller than in water. The results are discussed on the basis of a simple kinetic model. The kinetic constants for product formation through enzyme-substrate complex decomposition and for inactivation of catalase are estimated. The organic solvents are characterized by several physical properties: dielectric constant (D), hydrophobicity (log P), concentration of hydroxyl groups ([OH]), polarizability (α), Kamlet-Taft parameter (β) and Kosower parameter (Z). The relationships between the initial rate, kinetic constants and medium properties are analyzed by linear and multiple linear regression.

  8. Influence of Prolonged Spaceflight on Heart Rate and Oxygen Uptake Kinetics

    NASA Astrophysics Data System (ADS)

    Hoffmann, U.; Moore, A.; Drescher, U.

    2013-02-01

    During prolonged spaceflight, physical training is used to minimize cardiovascular deconditioning. Measurement of the kinetics of cardiorespiratory parameters, in particular the kinetic analysis of heart rate, respiratory and muscular oxygen uptake, provides useful information with regard to the efficiency and regulation of the cardiorespiratory system. Practically, oxygen uptake kinetics can only be measured at the lung site (V’O2 resp). The dynamics of V’O2 resp, however, is not identical with the dynamics at the site of interest: skeletal muscle. Eight Astronauts were tested pre- and post-flight using pseudo random binary workload changes between 30 and 80 W. Their kinetic responses of heart rate, respiratory as well as muscular V’O2 kinetics were estimated by using time-series analysis. Statistical analysis revealed that the kinetic responses of respiratory as well as muscular V’O2 kinetics are slowed post-flight than pre-flight. Heart rate seems not to be influenced following flight. The influence of other factors (e. g. astronauts’ exercise training) may impact these parameters and is an area for future studies.

  9. Malonic acid concentration as a control parameter in the kinetic analysis of the Belousov-Zhabotinsky reaction under batch conditions.

    PubMed

    Blagojević, Slavica M; Anić, Slobodan R; Cupić, Zeljko D; Pejić, Natasa D; Kolar-Anić, Ljiljana Z

    2008-11-28

    The influence of the initial malonic acid concentration [MA]0 (8.00 x 10(-3) < or = [MA]0 < or = 4.30 x 10(-2) mol dm(-3)) in the presence of bromate (6.20 x 10(-2) mol dm(-3)), bromide (1.50 x 10(-5) mol dm(-3)), sulfuric acid (1.00 mol dm(-3)) and cerium sulfate (2.50 x 10(-3) mol dm(-3)) on the dynamics and the kinetics of the Belousov-Zhabotinsky (BZ) reactions was examined under batch conditions at 30.0 degrees C. The kinetics of the BZ reaction was analyzed by the earlier proposed method convenient for the examinations of the oscillatory reactions. In the defined region of parameters where oscillograms with only large-amplitude relaxation oscillations appeared, the pseudo-first order of the overall malonic acid decomposition with a corresponding rate constant of 2.14 x 10(-2) min(-1) was established. The numerical results on the dynamics and kinetics of the BZ reaction, carried out by the known skeleton model including the Br2O species, were in good agreement with the experimental ones. The already found saddle node infinite period (SNIPER) bifurcation point in transition from a stable quasi-steady state to periodic orbits and vice versa is confirmed by both experimental and numerical investigations of the system under consideration. Namely, the large-amplitude relaxation oscillations with increasing periods between oscillations in approaching the bifurcation points at the beginning and the end of the oscillatory domain, together with excitability of the stable quasi-steady states in their vicinity are obtained.

  10. Effect of soil parameters on the kinetics of the displacement of Fe from FeEDDHA chelates by Cu.

    PubMed

    Schenkeveld, Walter D C; Reichwein, Arjen M; Temminghoff, Erwin J M; van Riemsdijk, Willem H

    2012-06-28

    In soil application, o,o-FeEDDHA (iron (3+) ethylene diamine-N,N'-bis(2-hydroxy phenyl acetic acid) complex) is the active ingredient of FeEDDHA chelate-based Fe fertilizers. The effectiveness of o,o-FeEDDHA is potentially compromised by the displacement of Fe from FeEDDHA by Cu. The actual impact of Cu competition is codetermined by the kinetics of the displacement reaction. In this study, the influence of soil parameters on the displacement kinetics has been examined in goethite suspensions. The displacement reaction predominantly takes place on the reactive surface rather than in solution. The rate at which the o,o-FeEDDHA concentration declined depended on the available reactive surface area, the Cu loading, and the FeEDDHA loading. Soil factors reducing FeEDDHA adsorption (high ionic strength, humic acid adsorption onto the goethite surface, and monovalent instead of divalent cations in the electrolyte) decreased the displacement rate. For meso o,o-FeEDDHA, the displacement rate equation was derived, which is first order in FeEDDHA loading and half order in Cu loading. For soil conditions, the equation can be simplified to an exponential decay function in meso o,o-FeEDDHA solution concentration.

  11. A Parameter-Free Semilocal Exchange Energy Functional for Two-Dimensional Quantum Systems.

    PubMed

    Patra, Abhilash; Jana, Subrata; Samal, Prasanjit

    2018-04-05

    The method of constructing semilocal density functional for exchange in two dimensions using one of the premier approaches, i.e., density matrix expansion, is revisited, and an accurate functional is constructed. The form of the functional is quite simple and includes no adjustable semiempirical parameters. In it, the kinetic energy dependent momentum is used to compensate nonlocal effects of the system. The functional is then examined by considering the very well-known semiconductor quantum dot systems. And despite its very simple form, the results obtained for quantum dots containing a higher number of electrons agrees pretty well with that of the standard exact exchange theory. Some of the desired properties relevant for the two-dimensional exchange functional and the lower bound associated with it are also discussed. It is observed that the above parameter-free semilocal exchange functional satisfies most of the discussed conditions.

  12. Kinetic Model of Growth of Arthropoda Populations

    NASA Astrophysics Data System (ADS)

    Ershov, Yu. A.; Kuznetsov, M. A.

    2018-05-01

    Kinetic equations were derived for calculating the growth of crustacean populations ( Crustacea) based on the biological growth model suggested earlier using shrimp ( Caridea) populations as an example. The development cycle of successive stages for populations can be represented in the form of quasi-chemical equations. The kinetic equations that describe the development cycle of crustaceans allow quantitative prediction of the development of populations depending on conditions. In contrast to extrapolation-simulation models, in the developed kinetic model of biological growth the kinetic parameters are the experimental characteristics of population growth. Verification and parametric identification of the developed model on the basis of the experimental data showed agreement with experiment within the error of the measurement technique.

  13. A model for the kinetics of homotypic cellular aggregation under static conditions

    NASA Technical Reports Server (NTRS)

    Neelamegham, S.; Munn, L. L.; Zygourakis, K.; McIntire, L. V. (Principal Investigator)

    1997-01-01

    We present the formulation and testing of a mathematical model for the kinetics of homotypic cellular aggregation. The model considers cellular aggregation under no-flow conditions as a two-step process. Individual cells and cell aggregates 1) move on the tissue culture surface and 2) collide with other cells (or aggregates). These collisions lead to the formation of intercellular bonds. The aggregation kinetics are described by a system of coupled, nonlinear ordinary differential equations, and the collision frequency kernel is derived by extending Smoluchowski's colloidal flocculation theory to cell migration and aggregation on a two-dimensional surface. Our results indicate that aggregation rates strongly depend upon the motility of cells and cell aggregates, the frequency of cell-cell collisions, and the strength of intercellular bonds. Model predictions agree well with data from homotypic lymphocyte aggregation experiments using Jurkat cells activated by 33B6, an antibody to the beta 1 integrin. Since cell migration speeds and all the other model parameters can be independently measured, the aggregation model provides a quantitative methodology by which we can accurately evaluate the adhesivity and aggregation behavior of cells.

  14. Direct Estimation of Kinetic Parametric Images for Dynamic PET

    PubMed Central

    Wang, Guobao; Qi, Jinyi

    2013-01-01

    Dynamic positron emission tomography (PET) can monitor spatiotemporal distribution of radiotracer in vivo. The spatiotemporal information can be used to estimate parametric images of radiotracer kinetics that are of physiological and biochemical interests. Direct estimation of parametric images from raw projection data allows accurate noise modeling and has been shown to offer better image quality than conventional indirect methods, which reconstruct a sequence of PET images first and then perform tracer kinetic modeling pixel-by-pixel. Direct reconstruction of parametric images has gained increasing interests with the advances in computing hardware. Many direct reconstruction algorithms have been developed for different kinetic models. In this paper we review the recent progress in the development of direct reconstruction algorithms for parametric image estimation. Algorithms for linear and nonlinear kinetic models are described and their properties are discussed. PMID:24396500

  15. Drug-Target Kinetics in Drug Discovery.

    PubMed

    Tonge, Peter J

    2018-01-17

    The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood-brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure-kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug-target kinetics to time-dependent drug activity in the disease state. This Review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The Review concludes with a description of a mechanistic PK/PD model that integrates drug-target kinetics into predictions of drug activity.

  16. Drug–Target Kinetics in Drug Discovery

    PubMed Central

    2017-01-01

    The development of therapies for the treatment of neurological cancer faces a number of major challenges including the synthesis of small molecule agents that can penetrate the blood-brain barrier (BBB). Given the likelihood that in many cases drug exposure will be lower in the CNS than in systemic circulation, it follows that strategies should be employed that can sustain target engagement at low drug concentration. Time dependent target occupancy is a function of both the drug and target concentration as well as the thermodynamic and kinetic parameters that describe the binding reaction coordinate, and sustained target occupancy can be achieved through structural modifications that increase target (re)binding and/or that decrease the rate of drug dissociation. The discovery and deployment of compounds with optimized kinetic effects requires information on the structure–kinetic relationships that modulate the kinetics of binding, and the molecular factors that control the translation of drug–target kinetics to time-dependent drug activity in the disease state. This Review first introduces the potential benefits of drug-target kinetics, such as the ability to delineate both thermodynamic and kinetic selectivity, and then describes factors, such as target vulnerability, that impact the utility of kinetic selectivity. The Review concludes with a description of a mechanistic PK/PD model that integrates drug–target kinetics into predictions of drug activity. PMID:28640596

  17. Optimal acquisition and modeling parameters for accurate assessment of low Ktrans blood-brain barrier permeability using dynamic contrast-enhanced MRI.

    PubMed

    Barnes, Samuel R; Ng, Thomas S C; Montagne, Axel; Law, Meng; Zlokovic, Berislav V; Jacobs, Russell E

    2016-05-01

    To determine optimal parameters for acquisition and processing of dynamic contrast-enhanced MRI (DCE-MRI) to detect small changes in near normal low blood-brain barrier (BBB) permeability. Using a contrast-to-noise ratio metric (K-CNR) for Ktrans precision and accuracy, the effects of kinetic model selection, scan duration, temporal resolution, signal drift, and length of baseline on the estimation of low permeability values was evaluated with simulations. The Patlak model was shown to give the highest K-CNR at low Ktrans . The Ktrans transition point, above which other models yielded superior results, was highly dependent on scan duration and tissue extravascular extracellular volume fraction (ve ). The highest K-CNR for low Ktrans was obtained when Patlak model analysis was combined with long scan times (10-30 min), modest temporal resolution (<60 s/image), and long baseline scans (1-4 min). Signal drift as low as 3% was shown to affect the accuracy of Ktrans estimation with Patlak analysis. DCE acquisition and modeling parameters are interdependent and should be optimized together for the tissue being imaged. Appropriately optimized protocols can detect even the subtlest changes in BBB integrity and may be used to probe the earliest changes in neurodegenerative diseases such as Alzheimer's disease and multiple sclerosis. © 2015 Wiley Periodicals, Inc.

  18. Exact solutions for kinetic models of macromolecular dynamics.

    PubMed

    Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

    2008-05-15

    Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

  19. Kinetic parameters for nutrient enhanced crude oil biodegradation in intertidal marine sediments

    PubMed Central

    Singh, Arvind K.; Sherry, Angela; Gray, Neil D.; Jones, D. Martin; Bowler, Bernard F. J.; Head, Ian M.

    2014-01-01

    Availability of inorganic nutrients, particularly nitrogen and phosphorous, is often a primary control on crude oil hydrocarbon degradation in marine systems. Many studies have empirically determined optimum levels of inorganic N and P for stimulation of hydrocarbon degradation. Nevertheless, there is a paucity of information on fundamental kinetic parameters for nutrient enhanced crude oil biodegradation that can be used to model the fate of crude oil in bioremediation programmes that use inorganic nutrient addition to stimulate oil biodegradation. Here we report fundamental kinetic parameters (Ks and qmax) for nitrate- and phosphate-stimulated crude oil biodegradation under nutrient limited conditions and with respect to crude oil, under conditions where N and P are not limiting. In the marine sediments studied, crude oil degradation was limited by both N and P availability. In sediments treated with 12.5 mg/g of oil but with no addition of N and P, hydrocarbon degradation rates, assessed on the basis of CO2 production, were 1.10 ± 0.03 μmol CO2/g wet sediment/day which were comparable to rates of CO2 production in sediments to which no oil was added (1.05 ± 0.27 μmol CO2/g wet sediment/day). When inorganic nitrogen was added alone maximum rates of CO2 production measured were 4.25 ± 0.91 μmol CO2/g wet sediment/day. However, when the same levels of inorganic nitrogen were added in the presence of 0.5% P w/w of oil (1.6 μmol P/g wet sediment) maximum rates of measured CO2 production increased more than four-fold to 18.40 ± 1.04 μmol CO2/g wet sediment/day. Ks and qmax estimates for inorganic N (in the form of sodium nitrate) when P was not limiting were 1.99 ± 0.86 μmol/g wet sediment and 16.16 ± 1.28 μmol CO2/g wet sediment/day respectively. The corresponding values for P were 63 ± 95 nmol/g wet sediment and 12.05 ± 1.31 μmol CO2/g wet sediment/day. The qmax values with respect to N and P were not significantly different (P < 0.05). When N and P

  20. Kinetic Monte Carlo simulations of water ice porosity: extrapolations of deposition parameters from the laboratory to interstellar space.

    PubMed

    Clements, Aspen R; Berk, Brandon; Cooke, Ilsa R; Garrod, Robin T

    2018-02-21

    Dust grains in cold, dense interstellar clouds build up appreciable ice mantles through the accretion and subsequent surface chemistry of atoms and molecules from the gas. These mantles, of thicknesses on the order of 100 monolayers, are primarily composed of H 2 O, CO, and CO 2 . Laboratory experiments using interstellar ice analogues have shown that porosity could be present and can facilitate diffusion of molecules along the inner pore surfaces. However, the movement of molecules within and upon the ice is poorly described by current chemical kinetics models, making it difficult either to reproduce the formation of experimental porous ice structures or to extrapolate generalized laboratory results to interstellar conditions. Here we use the off-lattice Monte Carlo kinetics model MIMICK to investigate the effects that various deposition parameters have on laboratory ice structures. The model treats molecules as isotropic spheres of a uniform size, using a Lennard-Jones potential. We reproduce experimental trends in the density of amorphous solid water (ASW) for varied deposition angle, rate and surface temperature; ice density decreases when the incident angle or deposition rate is increased, while increasing temperature results in a more-compact water ice. The models indicate that the density behaviour at higher temperatures (≥80 K) is dependent on molecular rearrangement resulting from thermal diffusion. To reproduce trends at lower temperatures, it is necessary to take account of non-thermal diffusion by newly-adsorbed molecules, which bring kinetic energy both from the gas phase and from their acceleration into a surface binding site. Extrapolation of the model to conditions appropriate to protoplanetary disks, in which direct accretion of water from the gas-phase may be the dominant ice formation mechanism, indicate that these ices may be less porous than laboratory ices.

  1. Assessment of methane biodegradation kinetics in two-phase partitioning bioreactors by pulse respirometry.

    PubMed

    Ordaz, Alberto; López, Juan C; Figueroa-González, Ivonne; Muñoz, Raúl; Quijano, Guillermo

    2014-12-15

    Biological methane biodegradation is a promising treatment alternative when the methane produced in waste management facilities cannot be used for energy generation. Two-phase partitioning bioreactors (TPPBs), provided with a non-aqueous phase (NAP) with high affinity for the target pollutant, are particularly suitable for the treatment of poorly water-soluble compounds such as methane. Nevertheless, little is known about the influence of the presence of the NAP on the resulting biodegradation kinetics in TPPBs. In this study, an experimental framework based on the in situ pulse respirometry technique was developed to assess the impact of NAP addition on the methane biodegradation kinetics using Methylosinus sporium as a model methane-degrading microorganism. A comprehensive mass transfer characterization was performed in order to avoid mass transfer limiting scenarios and ensure a correct kinetic parameter characterization. The presence of the NAP mediated significant changes in the apparent kinetic parameters of M. sporium during methane biodegradation, with variations of 60, 120, and 150% in the maximum oxygen uptake rate, half-saturation constant and maximum specific growth rate, respectively, compared with the intrinsic kinetic parameters retrieved from a control without NAP. These significant changes in the kinetic parameters mediated by the NAP must be considered for the design, operation and modeling of TPPBs devoted to air pollution control. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Accurate monoenergetic electron parameters of laser wakefield in a bubble model

    NASA Astrophysics Data System (ADS)

    Raheli, A.; Rahmatallahpur, S. H.

    2012-11-01

    A reliable analytical expression for the potential of plasma waves with phase velocities near the speed of light is derived. The presented spheroid cavity model is more consistent than the previous spherical and ellipsoidal model and it explains the mono-energetic electron trajectory more accurately, especially at the relativistic region. As a result, the quasi-mono-energetic electrons output beam interacting with the laser plasma can be more appropriately described with this model.

  3. Antioxidant pool in beer and kinetics of EPR spin-trapping.

    PubMed

    Kocherginsky, Nikolai M; Kostetski, Yuri Yu; Smirnov, Alex I

    2005-08-24

    The kinetics of spin-trap adduct formation in beer oxidation exhibits an induction period if the reaction is carried out at elevated temperatures and in the presence of air. This lag period lasts until the endogenous antioxidants are almost completely depleted, and its duration is used as an indicator of the flavor stability and shelf life of beer. This paper demonstrates that the total kinetics of the process can be characterized by three parameters-the lag period, the rate of spin-trap adduct formation, and, finally, the steady-state spin-adduct concentration. A steady-state chain reaction mechanism is described, and quantitative estimates of the main kinetic parameters such as the initiation rate, antioxidant pool, effective content of organic molecules participating in the chain reactions, and the rate constant of the 1-hydroxyethyl radical EtOH(*) spin-adduct disappearance are given. An additional new dimensionless parameter is suggested to characterize the antioxidant pool-the product of the lag time and the rate of spin-trap radical formation immediately after the lag time, normalized by the steady-state concentration of the adducts. The results of spin-tapping EPR experiments are compared with the nitroxide reduction kinetics measured in the same beer samples. It is shown that although the kinetics of nitroxide reduction in beer can be used to evaluate the reducing power of beer, the latter parameter does not correlate with the antioxidant pool. The relationship of free radical processes, antioxidant pool, reducing power, and beer staling is discussed.

  4. Gas Dynamics and Kinetics in the Cometary Coma: Theory and Observations

    NASA Technical Reports Server (NTRS)

    Combi, Michael R.; Harris, Walter M.; Smyth, William H.

    2005-01-01

    Our ability to describe the physical state of the expanding coma affects fundamental areas of cometary study both directly and indirectly. In order to convert measured abundances of gas species in the coma to gas production rates, models for the distribution and kinematics of gas species in the coma are required. Conversely, many different types of observations, together with laboratory data and theory, are still required to determine coma model attributes and parameters. Accurate relative and absolute gas production rates and their variations with time and from comet to comet are crucial to our basic understanding of the composition and structure of cometary nuclei and their place in the solar system. We review the gas dynamics and kinetics of cometary comae from both theoretical and observational perspectives, which are important for understanding the wide variety of physical conditions that are encountered.

  5. EAST kinetic equilibrium reconstruction combining with Polarimeter-Interferometer internal measurement constraints

    NASA Astrophysics Data System (ADS)

    Lian, H.; Liu, H. Q.; Li, K.; Zou, Z. Y.; Qian, J. P.; Wu, M. Q.; Li, G. Q.; Zeng, L.; Zang, Q.; Lv, B.; Jie, Y. X.; EAST Team

    2017-12-01

    Plasma equilibrium reconstruction plays an important role in the tokamak plasma research. With a high temporal and spatial resolution, the POlarimeter-INTerferometer (POINT) system on EAST has provided effective measurements for 102s H-mode operation. Based on internal Faraday rotation measurements provided by the POINT system, the equilibrium reconstruction with a more accurate core current profile constraint has been demonstrated successfully on EAST. Combining other experimental diagnostics and external magnetic fields measurement, the kinetic equilibrium has also been reconstructed on EAST. Take the pressure and edge current information from kinetic EFIT into the equilibrium reconstruction with Faraday rotation constraint, the new equilibrium reconstruction not only provides a more accurate internal current profile but also contains edge current and pressure information. One time slice result using new kinetic equilibrium reconstruction with POINT data constraints is demonstrated in this paper and the result shows there is a reversed shear of q profile and the pressure profile is also contained. The new improved equilibrium reconstruction is greatly helpful to the future theoretical analysis.

  6. Construction and Setup of a Bench-scale Algal Photosynthetic Bioreactor with Temperature, Light, and pH Monitoring for Kinetic Growth Tests.

    PubMed

    Karam, Amanda L; McMillan, Catherine C; Lai, Yi-Chun; de Los Reyes, Francis L; Sederoff, Heike W; Grunden, Amy M; Ranjithan, Ranji S; Levis, James W; Ducoste, Joel J

    2017-06-14

    The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software.

  7. Construction and Setup of a Bench-scale Algal Photosynthetic Bioreactor with Temperature, Light, and pH Monitoring for Kinetic Growth Tests

    PubMed Central

    Karam, Amanda L.; McMillan, Catherine C.; Lai, Yi-Chun; de los Reyes, Francis L.; Sederoff, Heike W.; Grunden, Amy M.; Ranjithan, Ranji S.; Levis, James W.; Ducoste, Joel J.

    2017-01-01

    The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software. PMID:28654054

  8. Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

    NASA Astrophysics Data System (ADS)

    Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

    2013-10-01

    Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose (18F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in most

  9. Influence of the partial volume correction method on (18)F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM.

    PubMed

    Bowen, Spencer L; Byars, Larry G; Michel, Christian J; Chonde, Daniel B; Catana, Ciprian

    2013-10-21

    Kinetic parameters estimated from dynamic (18)F-fluorodeoxyglucose ((18)F-FDG) PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For ordered subsets expectation maximization (OSEM), image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting (18)F-FDG dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation geometric transfer matrix PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in cerebral metabolic rate of glucose estimates, although by less than 5% in

  10. Influence of the partial volume correction method on 18F-fluorodeoxyglucose brain kinetic modelling from dynamic PET images reconstructed with resolution model based OSEM

    PubMed Central

    Bowen, Spencer L.; Byars, Larry G.; Michel, Christian J.; Chonde, Daniel B.; Catana, Ciprian

    2014-01-01

    Kinetic parameters estimated from dynamic 18F-fluorodeoxyglucose PET acquisitions have been used frequently to assess brain function in humans. Neglecting partial volume correction (PVC) for a dynamic series has been shown to produce significant bias in model estimates. Accurate PVC requires a space-variant model describing the reconstructed image spatial point spread function (PSF) that accounts for resolution limitations, including non-uniformities across the field of view due to the parallax effect. For OSEM, image resolution convergence is local and influenced significantly by the number of iterations, the count density, and background-to-target ratio. As both count density and background-to-target values for a brain structure can change during a dynamic scan, the local image resolution may also concurrently vary. When PVC is applied post-reconstruction the kinetic parameter estimates may be biased when neglecting the frame-dependent resolution. We explored the influence of the PVC method and implementation on kinetic parameters estimated by fitting 18F-fluorodeoxyglucose dynamic data acquired on a dedicated brain PET scanner and reconstructed with and without PSF modelling in the OSEM algorithm. The performance of several PVC algorithms was quantified with a phantom experiment, an anthropomorphic Monte Carlo simulation, and a patient scan. Using the last frame reconstructed image only for regional spread function (RSF) generation, as opposed to computing RSFs for each frame independently, and applying perturbation GTM PVC with PSF based OSEM produced the lowest magnitude bias kinetic parameter estimates in most instances, although at the cost of increased noise compared to the PVC methods utilizing conventional OSEM. Use of the last frame RSFs for PVC with no PSF modelling in the OSEM algorithm produced the lowest bias in CMRGlc estimates, although by less than 5% in most cases compared to the other PVC methods. The results indicate that the PVC implementation

  11. Co-pyrolysis of biomass and plastic wastes: investigation of apparent kinetic parameters and stability of pyrolysis oils

    NASA Astrophysics Data System (ADS)

    Fekhar, B.; Miskolczi, N.; Bhaskar, T.; Kumar, J.; Dhyani, V.

    2018-05-01

    This work is dedicated to the co-pyrolysis of real waste high density polyethylene (HDPE) and biomass (rice straw) obtained from agriculture. Mixtures of raw materials were pyrolyzed in their 0%/100%, 30%/70%, 50%/50%, 70%/30%, 100%/0% ratios using a thermograph. The atmosphere was nitrogen, and a constant heating rate was used. Based on weight loss and DTG curves, the apparent reaction kinetic parameters (e.g., activation energy) were calculated using first-order kinetic approach and Arrhenius equation. It was found that decomposition of pure plastic has approximately 280 kJ/mol activation energy, while that of was considerably less in case of biomass. Furthermore, HDPE decomposition takes by one stage, while that of biomass was three stages. The larger amount of raw materials (100 g) were also pyrolyzed in the batch rig at 550°C to obtain products for analysis focussing to their long-term application. Pyrolysis oils were investigated by Fourier transformed infrared spectroscopy and standardized methods, such as density, viscosity, boiling range determination. It was concluded, that higher plastic ratio in raw material had the advantageous effect to the pyrolysis oil long-term application. E.g., the concentration of oxygenated compounds, such as aldehydes, ketones, carboxylic acids or even phenol and its derivate could be significantly decreased, which had an advantageous effect to their corrosion property. Lower average molecular weight, viscosity, and density were measured as a function of plastic content.

  12. Development and Application of a High Throughput Protein Unfolding Kinetic Assay

    PubMed Central

    Wang, Qiang; Waterhouse, Nicklas; Feyijinmi, Olusegun; Dominguez, Matthew J.; Martinez, Lisa M.; Sharp, Zoey; Service, Rachel; Bothe, Jameson R.; Stollar, Elliott J.

    2016-01-01

    The kinetics of folding and unfolding underlie protein stability and quantification of these rates provides important insights into the folding process. Here, we present a simple high throughput protein unfolding kinetic assay using a plate reader that is applicable to the studies of the majority of 2-state folding proteins. We validate the assay by measuring kinetic unfolding data for the SH3 (Src Homology 3) domain from Actin Binding Protein 1 (AbpSH3) and its stabilized mutants. The results of our approach are in excellent agreement with published values. We further combine our kinetic assay with a plate reader equilibrium assay, to obtain indirect estimates of folding rates and use these approaches to characterize an AbpSH3-peptide hybrid. Our high throughput protein unfolding kinetic assays allow accurate screening of libraries of mutants by providing both kinetic and equilibrium measurements and provide a means for in-depth ϕ-value analyses. PMID:26745729

  13. Evaluation of the cure kinetics of the wood/pMDI bondline

    Treesearch

    David P. Harper; Michael P. Wolcott; Timothy G. Rials

    2001-01-01

    Micro-dielectric analysis (µDEA) and differentia1 scanning calorimetry (DSC) were used to monitor cure of polymeric diphenyl-methane diisocyanate (pMDI) resin with wood strands in a saturated steam environment. A first-order autocatalyzed kinetic model was employed to determine kinetic parameters. The kinetics were found to follow an Arrhenius relation. A single ramp...

  14. Frequency adaptive metadynamics for the calculation of rare-event kinetics

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele; Lindorff-Larsen, Kresten

    2018-08-01

    The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in contrast to free energies, depend on the route taken. For this reason, specific enhanced sampling methods are needed to calculate long-time scale kinetics. It has recently been demonstrated that it is possible to recover kinetics through the so-called "infrequent metadynamics" simulations, where the simulations are biased in a way that minimally corrupts the dynamics of moving between metastable states. This method, however, requires the bias to be added slowly, thus hampering applications to processes with only modest separations of time scales. Here we present a frequency-adaptive strategy which bridges normal and infrequent metadynamics. We show that this strategy can improve the precision and accuracy of rate calculations at fixed computational cost and should be able to extend rate calculations for much slower kinetic processes.

  15. Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes

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

    García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh

    2015-01-15

    Highlights: • Fractionation of solid wastes into readily and slowly biodegradable fractions. • Kinetic coefficients estimation from mono-digestion batch assays. • Validation of kinetic coefficients with a co-digestion continuous experiment. • Simulation of batch and continuous experiments with an ADM1-based model. - Abstract: A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowlymore » biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 g VS/L d. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes.« less

  16. Covalent bonding: the fundamental role of the kinetic energy.

    PubMed

    Bacskay, George B; Nordholm, Sture

    2013-08-22

    This work addresses the continuing disagreement between two prevalent schools of thought concerning the mechanism of covalent bonding. According to Hellmann, Ruedenberg, and Kutzelnigg, a lowering of the kinetic energy associated with electron delocalization is the key stabilization mechanism. The opposing view of Slater, Feynman, and Bader has maintained that the source of stabilization is electrostatic potential energy lowering due to electron density redistribution to binding regions between nuclei. Despite the large body of accurate quantum chemical work on a range of molecules, the debate concerning the origin of bonding continues unabated, even for H2(+), the simplest of covalently bound molecules. We therefore present here a detailed study of H2(+), including its formation, that uses a sequence of computational methods designed to reveal the relevant contributing mechanisms as well as the spatial density distributions of the kinetic and potential energy contributions. We find that the electrostatic mechanism fails to provide real insight or explanation of bonding, while the kinetic energy mechanism is sound and accurate but complex or even paradoxical to those preferring the apparent simplicity of the electrostatic model. We further argue that the underlying mechanism of bonding is in fact of dynamical character, and analyses that focus on energy do not reveal the origin of covalent bonding in full clarity.

  17. Perfusion kinetics in human brain tumor with DCE-MRI derived model and CFD analysis.

    PubMed

    Bhandari, A; Bansal, A; Singh, A; Sinha, N

    2017-07-05

    Cancer is one of the leading causes of death all over the world. Among the strategies that are used for cancer treatment, the effectiveness of chemotherapy is often hindered by factors such as irregular and non-uniform uptake of drugs inside tumor. Thus, accurate prediction of drug transport and deposition inside tumor is crucial for increasing the effectiveness of chemotherapeutic treatment. In this study, a computational model of human brain tumor is developed that incorporates dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI) data into a voxelized porous media model. The model takes into account realistic transport and perfusion kinetics parameters together with realistic heterogeneous tumor vasculature and accurate arterial input function (AIF), which makes it patient specific. The computational results for interstitial fluid pressure (IFP), interstitial fluid velocity (IFV) and tracer concentration show good agreement with the experimental results. The computational model can be extended further for predicting the deposition of chemotherapeutic drugs in tumor environment as well as selection of the best chemotherapeutic drug for a specific patient. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Toxicity and kinetic parameters of the aerobic biodegradation of the phenol and alkylphenols by a mixed culture.

    PubMed

    Acuña-Argüelles, M E; Olguin-Lora, P; Razo-Flores, E

    2003-04-01

    A mixed culture aerobically metabolized phenol, cresol isomers (o-,m-,p-), 2-ethylphenol and xylenol isomers (2,5-DMP and 3,4-DMP) as the sole carbon and energy source. This culture had a high tolerance towards phenol with values of maximum degradation rate (Vmax) of 47 microM phenol mg-1 protein h-1 and inhibition substrate constant (Ki) of 10 mM. These kinetic parameters were considerably diminished and the toxicity increased with the alkylphenols. For example with 2,5-xylenol, Vmax and Ki values of 0.8 microM 2,5-xylenol mg-1 protein h-1 and 1.3 mM, respectively, were obtained. The cresols were 5-fold more toxic than phenol, whereas 2-ethylphenol and 3,4-xylenol were 11-fold more toxic, and 2,5-xylenol was 34-fold more toxic than phenol.

  19. Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures.

    PubMed

    Kurata, Hiroyuki; Sugimoto, Yurie

    2018-02-01

    Many kinetic models of Escherichia coli central metabolism have been built, but few models accurately reproduced the dynamic behaviors of wild type and multiple genetic mutants. In 2016, our latest kinetic model improved problems of existing models to reproduce the cell growth and glucose uptake of wild type, ΔpykA:pykF and Δpgi in a batch culture, while it overestimated the glucose uptake and cell growth rates of Δppc and hardly captured the typical characteristics of the glyoxylate and TCA cycle fluxes for Δpgi and Δppc. Such discrepancies between the simulated and experimental data suggested biological complexity. In this study, we overcame these problems by assuming critical mechanisms regarding the OAA-regulated isocitrate dehydrogenase activity, aceBAK gene regulation and growth suppression. The present model accurately predicts the extracellular and intracellular dynamics of wild type and many gene knockout mutants in batch and continuous cultures. It is now the most accurate, detailed kinetic model of E. coli central carbon metabolism and will contribute to advances in mathematical modeling of cell factories. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  20. Mechanistic study of manganese-substituted glycerol dehydrogenase using a kinetic and thermodynamic analysis.

    PubMed

    Fang, Baishan; Niu, Jin; Ren, Hong; Guo, Yingxia; Wang, Shizhen

    2014-01-01

    Mechanistic insights regarding the activity enhancement of dehydrogenase by metal ion substitution were investigated by a simple method using a kinetic and thermodynamic analysis. By profiling the binding energy of both the substrate and product, the metal ion's role in catalysis enhancement was revealed. Glycerol dehydrogenase (GDH) from Klebsiella pneumoniae sp., which demonstrated an improvement in activity by the substitution of a zinc ion with a manganese ion, was used as a model for the mechanistic study of metal ion substitution. A kinetic model based on an ordered Bi-Bi mechanism was proposed considering the noncompetitive product inhibition of dihydroxyacetone (DHA) and the competitive product inhibition of NADH. By obtaining preliminary kinetic parameters of substrate and product inhibition, the number of estimated parameters was reduced from 10 to 4 for a nonlinear regression-based kinetic parameter estimation. The simulated values of time-concentration curves fit the experimental values well, with an average relative error of 11.5% and 12.7% for Mn-GDH and GDH, respectively. A comparison of the binding energy of enzyme ternary complex for Mn-GDH and GDH derived from kinetic parameters indicated that metal ion substitution accelerated the release of dioxyacetone. The metal ion's role in catalysis enhancement was explicated.

  1. Kinetic sensitivity of a receptor-binding radiopharmaceutical: Technetium-99m galactosyl-neoglycoalbumin

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

    Vera, D.R.; Woodle, E.S.; Stadalnik, R.C.

    1989-09-01

    Kinetic sensitivity is the ability of a physiochemical parameter to alter the time-activity curve of a radiotracer. The kinetic sensitivity of liver and blood time-activity data resulting from a single bolus injection of ({sup 99m}Tc)galactosyl-neoglycoalbumin (( Tc)NGA) into healthy pigs was examined. Three parameters, hepatic plasma flow scaled as flow per plasma volume, ligand-receptor affinity, and total receptor concentration, were tested using (Tc)NGA injections of various molar doses and affinities. Simultaneous measurements of plasma volume (iodine-125 human serum albumin dilution), and hepatic plasma flow (indocyanine green extraction) were performed during 12 (Tc)NGA studies. Paired data sets demonstrated differences (P(chi v2)more » less than 0.01) in liver and blood time-activity curves in response to changes in each of the tested parameters. We conclude that the (Tc)NGA radiopharmacokinetic system is therefore sensitive to hepatic plasma flow, ligand-receptor affinity, and receptor concentration. In vivo demonstration of kinetic sensitivity permits delineation of the physiologic parameters that determine the biodistribution of a radiopharmaceutical. This delineation is a prerequisite to a valid analytic assessment of receptor biochemistry via kinetic modeling.« less

  2. A Sequential Fluid-mechanic Chemical-kinetic Model of Propane HCCI Combustion

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

    Aceves, S M; Flowers, D L; Martinez-Frias, J

    2000-11-29

    We have developed a methodology for predicting combustion and emissions in a Homogeneous Charge Compression Ignition (HCCI) Engine. This methodology combines a detailed fluid mechanics code with a detailed chemical kinetics code. Instead of directly linking the two codes, which would require an extremely long computational time, the methodology consists of first running the fluid mechanics code to obtain temperature profiles as a function of time. These temperature profiles are then used as input to a multi-zone chemical kinetics code. The advantage of this procedure is that a small number of zones (10) is enough to obtain accurate results. Thismore » procedure achieves the benefits of linking the fluid mechanics and the chemical kinetics codes with a great reduction in the computational effort, to a level that can be handled with current computers. The success of this procedure is in large part a consequence of the fact that for much of the compression stroke the chemistry is inactive and thus has little influence on fluid mechanics and heat transfer. Then, when chemistry is active, combustion is rather sudden, leaving little time for interaction between chemistry and fluid mixing and heat transfer. This sequential methodology has been capable of explaining the main characteristics of HCCI combustion that have been observed in experiments. In this paper, we use our model to explore an HCCI engine running on propane. The paper compares experimental and numerical pressure traces, heat release rates, and hydrocarbon and carbon monoxide emissions. The results show an excellent agreement, even in parameters that are difficult to predict, such as chemical heat release rates. Carbon monoxide emissions are reasonably well predicted, even though it is intrinsically difficult to make good predictions of CO emissions in HCCI engines. The paper includes a sensitivity study on the effect of the heat transfer correlation on the results of the analysis. Importantly, the paper

  3. An accurate computational method for the diffusion regime verification

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Strizhak, Peter E.

    2018-04-01

    The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

  4. Chemiomics: network reconstruction and kinetics of port wine aging.

    PubMed

    Monforte, Ana Rita; Jacobson, Dan; Silva Ferreira, A C

    2015-03-11

    Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this study was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the use of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. The approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.

  5. Chemiomics: Network Reconstruction and Kinetics of Port Wine Aging

    DOE PAGES

    Monforte, Ana Rita; Jacobson, Dan; Silva Ferreira, A. C.

    2015-02-11

    Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this paper was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the usemore » of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. Finally, the approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.« less

  6. New insights on timing of oil and gas generation in the central Gulf Coast interior zone based on hydrous-pyrolysis kinetic parameters

    USGS Publications Warehouse

    Lewan, Michael D.; Dutton, Shirley P.; Ruppel, Stephen C.; Hentz, Tucker F.

    2002-01-01

    Timing of oil and gas generation from Turonian and Smackover source rocks in the central Gulf CoastInterior Zone was determined in one-dimensional burial-history curves (BHCs) using hydrous-pyrolysis kinetic parameters. The results predict that basal Smackover source-rock intervals with Type-IIS kerogen completed oil generation between 121 and 99 Ma, and Turonian source-rocks with Type-II kerogen remain immature over most of the same area. The only exception to the latter occurs in the northwestern part of the Mississippi salt basin, where initial stages of oil generation have started as a result of higher thermal gradients. This maturity difference between Turonian and Smackover source rocks is predicted with present-day thermal gradients. Predicted oil generation prior to the Sabine and Monroe uplifts suggests that a significant amount of the oil emplaced in Cretaceous reservoirs of these uplifts would have been lost during periods of erosion. Hydrous-pyrolysis kineticparameters predict that cracking of Smackover oil to gas started 52 Ma, which postdates major uplift and erosional events of the Sabine and Monroe uplifts. This generated gas would accumulate and persist in these uplift areas as currently observed. The predicted timing of oil and gas generation with hydrous-pyrolysis kinetic parameters is in accordance with the observed scarcity of oil from Turonian source rocks, predominance of gas accumulations on the Sabine and Monroe uplifts, and predominance of oil accumulations along the northern rim of the Interior Zone.

  7. Combined heat transfer and kinetic models to predict cooking loss during heat treatment of beef meat.

    PubMed

    Kondjoyan, Alain; Oillic, Samuel; Portanguen, Stéphane; Gros, Jean-Bernard

    2013-10-01

    A heat transfer model was used to simulate the temperature in 3 dimensions inside the meat. This model was combined with a first-order kinetic models to predict cooking losses. Identification of the parameters of the kinetic models and first validations were performed in a water bath. Afterwards, the performance of the combined model was determined in a fan-assisted oven under different air/steam conditions. Accurate knowledge of the heat transfer coefficient values and consideration of the retraction of the meat pieces are needed for the prediction of meat temperature. This is important since the temperature at the center of the product is often used to determine the cooking time. The combined model was also able to predict cooking losses from meat pieces of different sizes and subjected to different air/steam conditions. It was found that under the studied conditions, most of the water loss comes from the juice expelled by protein denaturation and contraction and not from evaporation. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Kinetic Folding Mechanism of Erythropoietin

    PubMed Central

    Banks, Douglas D.; Scavezze, Joanna L.; Siska, Christine C.

    2009-01-01

    This report describes what to our knowledge is the first kinetic folding studies of erythropoietin, a glycosylated four-helical bundle cytokine responsible for the regulation of red blood cell production. Kinetic responses for folding and unfolding reactions initiated by manual mixing were monitored by far-ultraviolet circular dichroism and fluorescence spectroscopy, and folding reactions initiated by stopped-flow mixing were monitored by fluorescence. The urea concentration dependence of the observed kinetics were best described by a three-state model with a transiently populated intermediate species that is on-pathway and obligatory. This folding scheme was further supported by the excellent agreement between the free energy of unfolding and m-value calculated from the microscopic rate constants derived from this model and these parameters determined from separate equilibrium unfolding experiments. Compared to the kinetics of other members of the four-helical bundle cytokine family, erythropoietin folding and unfolding reactions were slower and less susceptible to aggregation. We tentatively attribute these slower rates and protection from association events to the large amount of carbohydrate attached to erythropoietin at four sites. PMID:19450492

  9. Identifying and Characterizing Kinetic Instabilities using Solar Wind Observations of Non-Maxwellian Plasmas

    NASA Astrophysics Data System (ADS)

    Klein, K. G.

    2016-12-01

    Weakly collisional plasmas, of the type typically observed in the solar wind, are commonly in a state other than local thermodynamic equilibrium. This deviation from a Maxwellian velocity distribution can be characterized by pressure anisotropies, disjoint beams streaming at differing speeds, leptokurtic distributions at large energies, and other non-thermal features. As these features may be artifacts of dynamic processes, including the the acceleration and expansion of the solar wind, and as the free energy contained in these features can drive kinetic micro-instabilities, accurate measurement and modeling of these features is essential for characterizing the solar wind. After a review of these features, a technique is presented for the efficient calculation of kinetic instabilities associated with a general, non-Maxwellian plasma. As a proof of principle, this technique is applied to bi-Maxwellian systems for which kinetic instability thresholds are known, focusing on parameter scans including beams and drifting heavy minor ions. The application of this technique to fits of velocity distribution functions from current, forthcoming, and proposed missions including WIND, DSCOVR, Solar Probe Plus, and THOR, as well as the underlying measured distribution functions, is discussed. Particular attention is paid to the effects of instrument pointing and integration time, as well as potential deviation between instabilities associated with the Maxwellian fits and those associated with the observed, potentially non-Maxwellian, velocity distribution. Such application may further illuminate the role instabilities play in the evolution of the solar wind.

  10. Significance of Xenobiotic Metabolism for Bioaccumulation Kinetics of Organic Chemicals in Gammarus pulex

    PubMed Central

    2012-01-01

    Bioaccumulation and biotransformation are key toxicokinetic processes that modify toxicity of chemicals and sensitivity of organisms. Bioaccumulation kinetics vary greatly among organisms and chemicals; thus, we investigated the influence of biotransformation kinetics on bioaccumulation in a model aquatic invertebrate using fifteen 14C-labeled organic xenobiotics from diverse chemical classes and physicochemical properties (1,2,3-trichlorobenzene, imidacloprid, 4,6-dinitro-o-cresol, ethylacrylate, malathion, chlorpyrifos, aldicarb, carbofuran, carbaryl, 2,4-dichlorophenol, 2,4,5-trichlorophenol, pentachlorophenol, 4-nitrobenzyl-chloride, 2,4-dichloroaniline, and sea-nine (4,5-dichloro-2-octyl-3-isothiazolone)). We detected and identified metabolites using HPLC with UV and radio-detection as well as high resolution mass spectrometry (LTQ-Orbitrap). Kinetics of uptake, biotransformation, and elimination of parent compounds and metabolites were modeled with a first-order one-compartment model. Bioaccumulation factors were calculated for parent compounds and metabolite enrichment factors for metabolites. Out of 19 detected metabolites, we identified seven by standards or accurate mass measurements and two via pathway analysis and analogies to other compounds. 1,2,3-Trichlorobenzene, imidacloprid, and 4,6-dinitro-o-cresol were not biotransformed. Dietary uptake contributed little to overall uptake. Differentiation between parent and metabolites increased accuracy of bioaccumulation parameters compared to total 14C measurements. Biotransformation dominated toxicokinetics and strongly affected internal concentrations of parent compounds and metabolites. Many metabolites reached higher internal concentrations than their parents, characterized by large metabolite enrichment factors. PMID:22321051

  11. Kinetic energy budgets in areas of intense convection

    NASA Technical Reports Server (NTRS)

    Fuelberg, H. E.; Berecek, E. M.; Ebel, D. M.; Jedlovec, G. J.

    1980-01-01

    A kinetic energy budget analysis of the AVE-SESAME 1 period which coincided with the deadly Red River Valley tornado outbreak is presented. Horizontal flux convergence was found to be the major kinetic energy source to the region, while cross contour destruction was the major sink. Kinetic energy transformations were dominated by processes related to strong jet intrusion into the severe storm area. A kinetic energy budget of the AVE 6 period also is presented. The effects of inherent rawinsonde data errors on widely used basic kinematic parameters, including velocity divergence, vorticity advection, and kinematic vertical motion are described. In addition, an error analysis was performed in terms of the kinetic energy budget equation. Results obtained from downward integration of the continuity equation to obtain kinematic values of vertical motion are described. This alternate procedure shows promising results in severe storm situations.

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

    PubMed

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

    2014-03-15

    Ex situ solid phase extraction with granular activated carbon (GAC) is a promising technique to remediate contaminated sediments. The methods' efficiency depends on the rate by which contaminants are transferred from the sediment to the surface of GAC. Here, we derive kinetic parameters for extraction of polycyclic aromatic hydrocarbons (PAH) from sediment by GAC, using a first-order multi-compartment kinetic model. The parameters were obtained by modeling sediment-GAC exchange kinetic data following a tiered model calibration approach. First, parameters for PAH desorption from sediment were calibrated using data from systems with 50% (by weight) GAC acting as an infinite sink. Second, the estimated parameters were used as fixed input to obtain GAC uptake kinetic parameters in sediment slurries with 4% GAC, representing the ex situ remediation scenario. PAH uptake rate constants (kGAC) by GAC ranged from 0.44 to 0.0005 d(-1), whereas GAC sorption coefficients (KGAC) ranged from 10(5.57) to 10(8.57) L kg(-1). These values are the first provided for GAC in the presence of sediment and show that ex situ extraction with GAC is sufficiently fast and effective to reduce the risks of the most available PAHs among those studied, such as fluorene, phenanthrene and anthracene. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Characterization of 12 GnRH peptide agonists - a kinetic perspective.

    PubMed

    Nederpelt, Indira; Georgi, Victoria; Schiele, Felix; Nowak-Reppel, Katrin; Fernández-Montalván, Amaury E; IJzerman, Adriaan P; Heitman, Laura H

    2016-01-01

    Drug-target residence time is an important, yet often overlooked, parameter in drug discovery. Multiple studies have proposed an increased residence time to be beneficial for improved drug efficacy and/or longer duration of action. Currently, there are many drugs on the market targeting the gonadotropin-releasing hormone (GnRH) receptor for the treatment of hormone-dependent diseases. Surprisingly, the kinetic receptor-binding parameters of these analogues have not yet been reported. Therefore, this project focused on determining the receptor-binding kinetics of 12 GnRH peptide agonists, including many marketed drugs. A novel radioligand-binding competition association assay was developed and optimized for the human GnRH receptor with the use of a radiolabelled peptide agonist, [(125) I]-triptorelin. In addition to radioligand-binding studies, a homogeneous time-resolved FRET Tag-lite™ method was developed as an alternative assay for the same purpose. Two novel competition association assays were successfully developed and applied to determine the kinetic receptor-binding characteristics of 12 high-affinity GnRH peptide agonists. Results obtained from both methods were highly correlated. Interestingly, the binding kinetics of the peptide agonists were more divergent than their affinities with residence times ranging from 5.6 min (goserelin) to 125 min (deslorelin). Our research provides new insights by incorporating kinetic, next to equilibrium, binding parameters in current research and development that can potentially improve future drug discovery targeting the GnRH receptor. © 2015 The British Pharmacological Society.

  14. Kinetic rate laws as derived from order parameter theory I: Theoretical concepts

    NASA Astrophysics Data System (ADS)

    Salje, Ekhard

    1988-03-01

    A theoretical concept is outlined, which links the kinetics of structural transformations with thermodynamic theories of structural phase transitions. Starting from Landau theory and Markovian processes, the general rate laws for crystals with long correlation lengths are derived. The rate laws in Ginzburg-Landau theory are 269_2004_Article_BF00311038_TeX2GIFE1.gif 1{text{n }}Δ Q - 1{text{n }}fleft( Q right) ∝ - t/tau {text{ for }}T ≪ T_c {text{ and }}T ≫ T_c and Q 2∝ for T ≈ T c . The physical meaning of the time constant τ and the correction term f( Q) are explained. Fluctuations of the order parameter lead to damping behaviour with explicit dependence on the wavelength of the fluctuation wave and modulation-dependent variations of the lattice strain. Lattice relaxations and activation processes are discussed. Typical rate laws are found to follow 269_2004_Article_BF00311038_TeX2GIFE2.gif begin{gathered} ln Δ Q = rlnΔ t, \\ lnQ/Q + {1\\varepsilon }/{2k_B T}left( {Q^2 - Q_0^2 } right) = {Δ t}/{tau *} \\ which leads for short time intervals to a linear rate law 269_2004_Article_BF00311038_TeX2GIFE3.gif Δ Q ∝ Δ t It is shown that linear terms in the Landau potential are equivalent to a logarithmic decay of the excess entropy Δ S ∝ ln Δ t which is also expected to be the dominant rate law in field-induced pseudo-spin glasses: 269_2004_Article_BF00311038_TeX2GIFE4.gif Δ Q ∝ 1{text{n }}Δ t{text{ and }}1{text{n}}left( {Δ {text{Q}} \\cdot Δ {text{t}}} right) = A{text{ }}Δ t + B Fluctuations lead to spatially heterogeneous distributions of the order parameter. A two phase field is found in this case where the nucleation energy is overcome by fluctuation processes. Random fields, arising, for example, from lattice imperfections, lead also to spacially inhomogeneous material. The dominant microstructure is the lattice modulation mostly in the form of a cross hatched pattern (tweed) but also in the form of incommensurate modulations.

  15. Accurate reconstruction of the optical parameter distribution in participating medium based on the frequency-domain radiative transfer equation

    NASA Astrophysics Data System (ADS)

    Qiao, Yao-Bin; Qi, Hong; Zhao, Fang-Zhou; Ruan, Li-Ming

    2016-12-01

    Reconstructing the distribution of optical parameters in the participating medium based on the frequency-domain radiative transfer equation (FD-RTE) to probe the internal structure of the medium is investigated in the present work. The forward model of FD-RTE is solved via the finite volume method (FVM). The regularization term formatted by the generalized Gaussian Markov random field model is used in the objective function to overcome the ill-posed nature of the inverse problem. The multi-start conjugate gradient (MCG) method is employed to search the minimum of the objective function and increase the efficiency of convergence. A modified adjoint differentiation technique using the collimated radiative intensity is developed to calculate the gradient of the objective function with respect to the optical parameters. All simulation results show that the proposed reconstruction algorithm based on FD-RTE can obtain the accurate distributions of absorption and scattering coefficients. The reconstructed images of the scattering coefficient have less errors than those of the absorption coefficient, which indicates the former are more suitable to probing the inner structure. Project supported by the National Natural Science Foundation of China (Grant No. 51476043), the Major National Scientific Instruments and Equipment Development Special Foundation of China (Grant No. 51327803), and the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (Grant No. 51121004).

  16. A mixed fluid-kinetic solver for the Vlasov-Poisson equations

    NASA Astrophysics Data System (ADS)

    Cheng, Yongtao

    Plasmas are ionized gases that appear in a wide range of applications including astrophysics and space physics, as well as in laboratory settings such as in magnetically confined fusion. There are two prevailing types of modeling strategies to describe a plasma system: kinetic models and fluid models. Kinetic models evolve particle probability density distributions (PDFs) in phase space, which are accurate but computationally expensive. Fluid models evolve a small number of moments of the distribution function and reduce the dimension of the solution. However, some approximation is necessary to close the system, and finding an accurate moment closure that correctly captures the dynamics away from thermodynamic equilibrium is a difficult and still open problem. The main contributions of the present work can be divided into two main parts: (1) a new class of moment closures, based on a modification of existing quadrature-based moment-closure methods, is developed using bi-B-spline and bi-bubble representations; and (2) a novel mixed solver that combines a fluid and a kinetic solver is proposed, which uses the new class of moment-closure methods described in the first part. For the newly developed quadrature-based moment-closure based on bi-B-spline and bi-bubble representation, the explicit form of flux terms and the moment-realizability conditions are given. It is shown that while the bi-delta system is weakly hyperbolic, the newly proposed fluid models are strongly hyperbolic. Using a high-order Runge-Kutta discontinuous Galerkin method together with Strang operator splitting, the resulting models are applied to the Vlasov-Poisson-Fokker-Planck system in the high field limit. In the second part of this work, results from kinetic solver are used to provide a corrected closure to the fluid model. This correction keeps the fluid model hyperbolic and gives fluid results that match the moments as computed from the kinetic solution. Furthermore, a prolongation operation

  17. A study of the kinetics of isothermal nicotine desorption from silicon dioxide

    NASA Astrophysics Data System (ADS)

    Adnadjevic, Borivoj; Lazarevic, Natasa; Jovanovic, Jelena

    2010-12-01

    The isothermal kinetics of nicotine desorption from silicon dioxide (SiO 2) was investigated. The isothermal thermogravimetric curves of nicotine at temperatures of 115 °C, 130 °C and 152 °C were recorded. The kinetic parameters ( Ea, ln A) of desorption of nicotine were calculated using various methods (stationary point, model constants and differential isoconversion method). By applying the "model-fitting" method, it was found that the kinetic model of nicotine desorption from silicon dioxide was a phase boundary controlled reaction (contracting volume). The values of the kinetic parameters, Ea,α and ln Aα, complexly change with changing degree of desorption and a compensation effect exists. A new mechanism of activation for the desorption of the absorbed molecules of nicotine was suggested in agreement with model of selective energy transfer.

  18. Numerical solutions of the semiclassical Boltzmann ellipsoidal-statistical kinetic model equation

    PubMed Central

    Yang, Jaw-Yen; Yan, Chin-Yuan; Huang, Juan-Chen; Li, Zhihui

    2014-01-01

    Computations of rarefied gas dynamical flows governed by the semiclassical Boltzmann ellipsoidal-statistical (ES) kinetic model equation using an accurate numerical method are presented. The semiclassical ES model was derived through the maximum entropy principle and conserves not only the mass, momentum and energy, but also contains additional higher order moments that differ from the standard quantum distributions. A different decoding procedure to obtain the necessary parameters for determining the ES distribution is also devised. The numerical method in phase space combines the discrete-ordinate method in momentum space and the high-resolution shock capturing method in physical space. Numerical solutions of two-dimensional Riemann problems for two configurations covering various degrees of rarefaction are presented and various contours of the quantities unique to this new model are illustrated. When the relaxation time becomes very small, the main flow features a display similar to that of ideal quantum gas dynamics, and the present solutions are found to be consistent with existing calculations for classical gas. The effect of a parameter that permits an adjustable Prandtl number in the flow is also studied. PMID:25104904

  19. Estimation of Free Radical Ionization Energies by the Kinetic Method and the Relationship between the Kinetic Method and the Hammett Equation.

    PubMed

    Chen, G; Wong, P; Cooks, R G

    1997-09-01

    Substituted 1,2-diphenylethanes undergo competitive dissociations upon electron ionization (EI) to generate substituted benzyl cation and benzyl radical pairs. Application of the kinetic method to the previous reported EI mass spectra of these covalently bound precursor ions (data are taken from McLafferty et al. J. Am. Chem. Soc. 1970, 92, 6867)) is used to estimate the ionization energies of substituted benzyl free radicals. A correlation is observed between the Hammett σ constant of the substituents and the kinetic method parameter, ln(k(x)/k(H)), where k(x) is the rate of fragmentation to give the substituted product ion and k(H) is the rate to give the benzyl ion itself. Systems involving weakly bound cluster ions, including proton-bound dimers of meta- and para-substituted pyridines and meta- and para-substituted anilines, and electron-bound dimers of meta- and para-substituted nitrobenzenes, also show good correlations between the kinetic method parameter and the Hammett σ constant.

  20. LSENS: A General Chemical Kinetics and Sensitivity Analysis Code for homogeneous gas-phase reactions. Part 3: Illustrative test problems

    NASA Technical Reports Server (NTRS)

    Bittker, David A.; Radhakrishnan, Krishnan

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 3 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 3 explains the kinetics and kinetics-plus-sensitivity analysis problems supplied with LSENS and presents sample results. These problems illustrate the various capabilities of, and reaction models that can be solved by, the code and may provide a convenient starting point for the user to construct the problem data file required to execute LSENS. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions.

  1. The Use of Artificial Neural Network for Prediction of Dissolution Kinetics

    PubMed Central

    Elçiçek, H.; Akdoğan, E.; Karagöz, S.

    2014-01-01

    Colemanite is a preferred boron mineral in industry, such as boric acid production, fabrication of heat resistant glass, and cleaning agents. Dissolution of the mineral is one of the most important processes for these industries. In this study, dissolution of colemanite was examined in water saturated with carbon dioxide solutions. Also, prediction of dissolution rate was determined using artificial neural networks (ANNs) which are based on the multilayered perceptron. Reaction temperature, total pressure, stirring speed, solid/liquid ratio, particle size, and reaction time were selected as input parameters to predict the dissolution rate. Experimental dataset was used to train multilayer perceptron (MLP) networks to allow for prediction of dissolution kinetics. Developing ANNs has provided highly accurate predictions in comparison with an obtained mathematical model used through regression method. We conclude that ANNs may be a preferred alternative approach instead of conventional statistical methods for prediction of boron minerals. PMID:25028674

  2. Kinetic synergistic transitions in the Ostwald ripening processes

    NASA Astrophysics Data System (ADS)

    Sachkov, I. N.; Turygina, V. F.; Dolganov, A. N.

    2018-01-01

    There is proposed approach to mathematical description of the kinetic transitions in Ostwald ripening processes of volatile substance in nonuniformly heated porous materials. It is based upon the finite element method. There are implemented computer software. The main feature of the software is to calculate evaporation and condensation fluxes on the walls of a nonuniformly heated cylindrical capillary. Kinetic transitions are detected for three modes of volatile substances migration which are different by condensation zones location. There are controlling dimensionless parameters of the kinetic transition which are revealed during research. There is phase diagram of the Ostwald ripening process modes realization.

  3. Kinetics of Mixed Microbial Assemblages Enhance Removal of Highly Dilute Organic Substrates

    PubMed Central

    Lewis, David L.; Hodson, Robert E.; Hwang, Huey-Min

    1988-01-01

    Our experiments with selected organic substrates reveal that the rate-limiting process governing microbial degradation rates changes with substrate concentration, S, in such a manner that substrate removal is enhanced at lower values of S. This enhancement is the result of the dominance of very efficient systems for substrate removal at low substrate concentrations. The variability of dominant kinetic parameters over a range of S causes the kinetics of complex assemblages to be profoundly dissimilar to those of systems possessing a single set of kinetic parameters; these findings necessitate taking a new approach to predicting substrate removal rates over wide ranges of S. PMID:16347715

  4. Kinetic parameters of cholinesterase interactions with organophosphates: retrieval and comparison tools available through ESTHER database: ESTerases, alpha/beta Hydrolase Enzymes and Relatives.

    PubMed

    Chatonnet, A; Hotelier, T; Cousin, X

    1999-05-14

    Cholinesterases are targets for organophosphorus compounds which are used as insecticides, chemical warfare agents and drugs for the treatment of disease such as glaucoma, or parasitic infections. The widespread use of these chemicals explains the growing of this area of research and the ever increasing number of sequences, structures, or biochemical data available. Future advances will depend upon effective management of existing information as well as upon creation of new knowledge. The ESTHER database goal is to facilitate retrieval and comparison of data about structure and function of proteins presenting the alpha/beta hydrolase fold. Protein engineering and in vitro production of enzymes allow direct comparison of biochemical parameters. Kinetic parameters of enzymatic reactions are now included in the database. These parameters can be searched and compared with a table construction tool. ESTHER can be reached through internet (http://www.ensam.inra.fr/cholinesterase). The full database or the specialised X-window Client-server system can be downloaded from our ftp server (ftp://ftp.toulouse.inra.fr./pub/esther). Forms can be used to send updates or corrections directly from the web.

  5. A rapid and accurate method, ventilated chamber C-history method, of measuring the emission characteristic parameters of formaldehyde/VOCs in building materials.

    PubMed

    Huang, Shaodan; Xiong, Jianyin; Zhang, Yinping

    2013-10-15

    The indoor pollution caused by formaldehyde and volatile organic compounds (VOCs) emitted from building materials poses an adverse effect on people's health. It is necessary to understand and control the behaviors of the emission sources. Based on detailed mass transfer analysis on the emission process in a ventilated chamber, this paper proposes a novel method of measuring the three emission characteristic parameters, i.e., the initial emittable concentration, the diffusion coefficient and the partition coefficient. A linear correlation between the logarithm of dimensionless concentration and time is derived. The three parameters can then be calculated from the intercept and slope of the correlation. Compared with the closed chamber C-history method, the test is performed under ventilated condition thus some commonly-used measurement instruments (e.g., GC/MS, HPLC) can be applied. While compared with other methods, the present method can rapidly and accurately measure the three parameters, with experimental time less than 12h and R(2) ranging from 0.96 to 0.99 for the cases studied. Independent experiment was carried out to validate the developed method, and good agreement was observed between the simulations based on the determined parameters and experiments. The present method should prove useful for quick characterization of formaldehyde/VOC emissions from indoor materials. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Communication: An accurate global potential energy surface for the ground electronic state of ozone

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

    Dawes, Richard, E-mail: dawesr@mst.edu, E-mail: hguo@unm.edu; Lolur, Phalgun; Li, Anyang

    We report a new full-dimensional and global potential energy surface (PES) for the O + O{sub 2} → O{sub 3} ozone forming reaction based on explicitly correlated multireference configuration interaction (MRCI-F12) data. It extends our previous [R. Dawes, P. Lolur, J. Ma, and H. Guo, J. Chem. Phys. 135, 081102 (2011)] dynamically weighted multistate MRCI calculations of the asymptotic region which showed the widely found submerged reef along the minimum energy path to be the spurious result of an avoided crossing with an excited state. A spin-orbit correction was added and the PES tends asymptotically to the recently developed long-rangemore » electrostatic model of Lepers et al. [J. Chem. Phys. 137, 234305 (2012)]. This PES features: (1) excellent equilibrium structural parameters, (2) good agreement with experimental vibrational levels, (3) accurate dissociation energy, and (4) most-notably, a transition region without a spurious reef. The new PES is expected to allow insight into the still unresolved issues surrounding the kinetics, dynamics, and isotope signature of ozone.« less

  7. Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production with Chlamydomonas reinhardtii: Part I. Model development and parameter identification.

    PubMed

    Fouchard, Swanny; Pruvost, Jérémy; Degrenne, Benoit; Titica, Mariana; Legrand, Jack

    2009-01-01

    Chlamydomonas reinhardtii is a green microalga capable of turning its metabolism towards H2 production under specific conditions. However this H2 production, narrowly linked to the photosynthetic process, results from complex metabolic reactions highly dependent on the environmental conditions of the cells. A kinetic model has been developed to relate culture evolution from standard photosynthetic growth to H2 producing cells. It represents transition in sulfur-deprived conditions, known to lead to H2 production in Chlamydomonas reinhardtii, and the two main processes then induced which are an over-accumulation of intracellular starch and a progressive reduction of PSII activity for anoxia achievement. Because these phenomena are directly linked to the photosynthetic growth, two kinetic models were associated, the first (one) introducing light dependency (Haldane type model associated to a radiative light transfer model), the second (one) making growth a function of available sulfur amount under extracellular and intracellular forms (Droop formulation). The model parameters identification was realized from experimental data obtained with especially designed experiments and a sensitivity analysis of the model to its parameters was also conducted. Model behavior was finally studied showing interdependency between light transfer conditions, photosynthetic growth, sulfate uptake, photosynthetic activity and O2 release, during transition from oxygenic growth to anoxic H2 production conditions.

  8. Parameter Estimation and Model Selection in Computational Biology

    PubMed Central

    Lillacci, Gabriele; Khammash, Mustafa

    2010-01-01

    A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection. PMID:20221262

  9. Water-Exchange-Modified Kinetic Parameters from Dynamic Contrast-Enhanced MRI as Prognostic Biomarkers of Survival in Advanced Hepatocellular Carcinoma Treated with Antiangiogenic Monotherapy

    PubMed Central

    Lee, Sang Ho; Hayano, Koichi; Zhu, Andrew X.; Sahani, Dushyant V.; Yoshida, Hiroyuki

    2015-01-01

    Background To find prognostic biomarkers in pretreatment dynamic contrast-enhanced MRI (DCE-MRI) water-exchange-modified (WX) kinetic parameters for advanced hepatocellular carcinoma (HCC) treated with antiangiogenic monotherapy. Methods Twenty patients with advanced HCC underwent DCE-MRI and were subsequently treated with sunitinib. Pretreatment DCE-MRI data on advanced HCC were analyzed using five different WX kinetic models: the Tofts-Kety (WX-TK), extended TK (WX-ETK), two compartment exchange, adiabatic approximation to tissue homogeneity (WX-AATH), and distributed parameter (WX-DP) models. The total hepatic blood flow, arterial flow fraction (γ), arterial blood flow (BF A), portal blood flow, blood volume, mean transit time, permeability-surface area product, fractional interstitial volume (v I), extraction fraction, mean intracellular water molecule lifetime (τ C), and fractional intracellular volume (v C) were calculated. After receiver operating characteristic analysis with leave-one-out cross-validation, individual parameters for each model were assessed in terms of 1-year-survival (1YS) discrimination using Kaplan-Meier analysis, and association with overall survival (OS) using univariate Cox regression analysis with permutation testing. Results The WX-TK-model-derived γ (P = 0.022) and v I (P = 0.010), and WX-ETK-model-derived τ C (P = 0.023) and v C (P = 0.042) were statistically significant prognostic biomarkers for 1YS. Increase in the WX-DP-model-derived BF A (P = 0.025) and decrease in the WX-TK, WX-ETK, WX-AATH, and WX-DP-model-derived v C (P = 0.034, P = 0.038, P = 0.028, P = 0.041, respectively) were significantly associated with an increase in OS. Conclusions The WX-ETK-model-derived v C was an effective prognostic biomarker for advanced HCC treated with sunitinib. PMID:26366997

  10. Thermogravimetric kinetic study of agricultural residue biomass pyrolysis based on combined kinetics.

    PubMed

    Wang, Xun; Hu, Mian; Hu, Wanyong; Chen, Zhihua; Liu, Shiming; Hu, Zhiquan; Xiao, Bo

    2016-11-01

    Pyrolytic kinetic of an agricultural residue (AR) feedstock, a mixture of plants (cotton, wheat, rich, corn) stems, was investigated based on combined kinetics. The most suitable mechanism for AR one-step pyrolysis was f(α)=(1-α)(1.1816)α(-1.8428) with kinetic parameters of: apparent activation energy 221.7kJ/mol, pre-exponential factor 4.17E16s(-1). Pyrolysis of AR feedstock could not be described by one-step reaction attributes to heterogeneous features of pyrolysis processes. Combined kinetics three-parallel-reaction (CK-TPR) model fitted the pyrolysis experimental data very well. Reaction mechanisms for pseudo hemicelluloses, cellulose, lignin in CK-TPR model was f(α)=(1-α)(1.6244)α(-0.3371)[-ln(1-α)](-0.0515), f(α)=(1-α)(1.0597)α(-0.6909)[-ln(1-α)](0.9026) and f(α)=(1-α)(2.9577)α(-4.7719), respectively. Apparent activation energy of three pseudo components followed the order of Elignin(197.3kJ/mol)>Ecellulose(176.3kJ/mol)>Ehemicelluloses (151.1kJ/mol). Mechanism of hemicelluloses pyrolysis could be further expressed as f(α)=(1-α)(1.4). The pyrolytic mechanism of cellulose met the Nucleation well. However, mechanism of lignin pyrolysis was complex, which possibly was the combined effects of Nucleation, Diffusion, Geometrical contraction, and Power law. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Theory of bi-molecular association dynamics in 2D for accurate model and experimental parameterization of binding rates

    PubMed Central

    Yogurtcu, Osman N.; Johnson, Margaret E.

    2015-01-01

    The dynamics of association between diffusing and reacting molecular species are routinely quantified using simple rate-equation kinetics that assume both well-mixed concentrations of species and a single rate constant for parameterizing the binding rate. In two-dimensions (2D), however, even when systems are well-mixed, the assumption of a single characteristic rate constant for describing association is not generally accurate, due to the properties of diffusional searching in dimensions d ≤ 2. Establishing rigorous bounds for discriminating between 2D reactive systems that will be accurately described by rate equations with a single rate constant, and those that will not, is critical for both modeling and experimentally parameterizing binding reactions restricted to surfaces such as cellular membranes. We show here that in regimes of intrinsic reaction rate (ka) and diffusion (D) parameters ka/D > 0.05, a single rate constant cannot be fit to the dynamics of concentrations of associating species independently of the initial conditions. Instead, a more sophisticated multi-parametric description than rate-equations is necessary to robustly characterize bimolecular reactions from experiment. Our quantitative bounds derive from our new analysis of 2D rate-behavior predicted from Smoluchowski theory. Using a recently developed single particle reaction-diffusion algorithm we extend here to 2D, we are able to test and validate the predictions of Smoluchowski theory and several other theories of reversible reaction dynamics in 2D for the first time. Finally, our results also mean that simulations of reactive systems in 2D using rate equations must be undertaken with caution when reactions have ka/D > 0.05, regardless of the simulation volume. We introduce here a simple formula for an adaptive concentration dependent rate constant for these chemical kinetics simulations which improves on existing formulas to better capture non-equilibrium reaction dynamics from dilute

  12. An investigation into the crystallization tendency/kinetics of amorphous active pharmaceutical ingredients: A case study with dipyridamole and cinnarizine.

    PubMed

    Baghel, Shrawan; Cathcart, Helen; Redington, Wynette; O'Reilly, Niall J

    2016-07-01

    Amorphous drug formulations have great potential to enhance solubility and thus bioavailability of BCS class II drugs. However, the higher free energy and molecular mobility of the amorphous form drive them towards the crystalline state which makes them unstable. Accurate determination of the crystallization tendency/kinetics is the key to the successful design and development of such systems. In this study, dipyridamole (DPM) and cinnarizine (CNZ) have been selected as model compounds. Thermodynamic fragility (mT) was measured from the heat capacity change at the glass transition temperature (Tg) whereas dynamic fragility (mD) was evaluated using methods based on extrapolation of configurational entropy to zero [Formula: see text] , and heating rate dependence of Tg [Formula: see text] . The mean relaxation time of amorphous drugs was calculated from the Vogel-Tammann-Fulcher (VTF) equation. Furthermore, the correlation between fragility and glass forming ability (GFA) of the model drugs has been established and the relevance of these parameters to crystallization of amorphous drugs is also assessed. Moreover, the crystallization kinetics of model drugs under isothermal conditions has been studied using Johnson-Mehl-Avrami (JMA) approach to determine the Avrami constant 'n' which provides an insight into the mechanism of crystallization. To further probe into the crystallization mechanism, the non-isothermal crystallization kinetics of model systems were also analysed by statistically fitting the crystallization data to 15 different kinetic models and the relevance of model-free kinetic approach has been established. The crystallization mechanism for DPM and CNZ at each extent of transformation has been predicted. The calculated fragility, glass forming ability (GFA) and crystallization kinetics are found to be in good correlation with the stability prediction of amorphous solid dispersions. Thus, this research work involves a multidisciplinary approach to

  13. Parameter Estimates in Differential Equation Models for Chemical Kinetics

    ERIC Educational Resources Information Center

    Winkel, Brian

    2011-01-01

    We discuss the need for devoting time in differential equations courses to modelling and the completion of the modelling process with efforts to estimate the parameters in the models using data. We estimate the parameters present in several differential equation models of chemical reactions of order n, where n = 0, 1, 2, and apply more general…

  14. Accurate prediction of vaccine stability under real storage conditions and during temperature excursions.

    PubMed

    Clénet, Didier

    2018-04-01

    Due to their thermosensitivity, most vaccines must be kept refrigerated from production to use. To successfully carry out global immunization programs, ensuring the stability of vaccines is crucial. In this context, two important issues are critical, namely: (i) predicting vaccine stability and (ii) preventing product damage due to excessive temperature excursions outside of the recommended storage conditions (cold chain break). We applied a combination of advanced kinetics and statistical analyses on vaccine forced degradation data to accurately describe the loss of antigenicity for a multivalent freeze-dried inactivated virus vaccine containing three variants. The screening of large amounts of kinetic models combined with a statistical model selection approach resulted in the identification of two-step kinetic models. Predictions based on kinetic analysis and experimental stability data were in agreement, with approximately five percentage points difference from real values for long-term stability storage conditions, after excursions of temperature and during experimental shipments of freeze-dried products. Results showed that modeling a few months of forced degradation can be used to predict various time and temperature profiles endured by vaccines, i.e. long-term stability, short time excursions outside the labeled storage conditions or shipments at ambient temperature, with high accuracy. Pharmaceutical applications of the presented kinetics-based approach are discussed. Copyright © 2018 The Author. Published by Elsevier B.V. All rights reserved.

  15. Validation of Non-Invasive Tracer Kinetic Analysis of 18F-Florbetaben PET Using a Dual Time-Window Acquisition Protocol.

    PubMed

    Bullich, Santiago; Barthel, Henryk; Koglin, Norman; Becker, Georg A; De Santi, Susan; Jovalekic, Aleksandar; Stephens, Andrew W; Sabri, Osama

    2017-11-24

    Accurate amyloid PET quantification is necessary for monitoring amyloid-beta accumulation and response to therapy. Currently, most of the studies are analyzed using the static standardized uptake value ratio (SUVR) approach because of its simplicity. However, this approach may be influenced by changes in cerebral blood flow (CBF) or radiotracer clearance. Full tracer kinetic models require arterial blood sampling and dynamic image acquisition. The objectives of this work were: (1) to validate a non-invasive kinetic modeling approach for 18 F-florbetaben PET using an acquisition protocol with the best compromise between quantification accuracy and simplicity and (2) to assess the impact of CBF changes and radiotracer clearance on SUVRs and non-invasive kinetic modeling data in 18 F-florbetaben PET. Methods: Data from twenty subjects (10 patients with probable Alzheimer's dementia/ 10 healthy volunteers) were used to compare the binding potential (BP ND ) obtained from the full kinetic analysis to the SUVR and to non-invasive tracer kinetic methods (simplified reference tissue model (SRTM), and multilinear reference tissue model 2 (MRTM2)). Different approaches using shortened or interrupted acquisitions were compared to the results of the full acquisition (0-140 min). Simulations were carried out to assess the effect of CBF and radiotracer clearance changes on SUVRs and non-invasive kinetic modeling outputs. Results: A 0-30 and 120-140 min dual time-window acquisition protocol using appropriate interpolation of the missing time points provided the best compromise between patient comfort and quantification accuracy. Excellent agreement was found between BP ND obtained using full and dual time-window (2TW) acquisition protocols (BP ND,2TW =0.01+ 1.00 BP ND,FULL , R2=0.97 (MRTM2); BP ND,2TW = 0.05+ 0.92·BP ND,FULL , R2=0.93 (SRTM)). Simulations showed a limited impact of CBF and radiotracer clearance changes on MRTM parameters and SUVRs. Conclusion: This study

  16. Sorption kinetics of diuron on volcanic ash derived soils.

    PubMed

    Cáceres-Jensen, Lizethly; Rodríguez-Becerra, Jorge; Parra-Rivero, Joselyn; Escudey, Mauricio; Barrientos, Lorena; Castro-Castillo, Vicente

    2013-10-15

    Diuron sorption kinetic was studied in Andisols, Inceptisol and Ultisols soils in view of their distinctive physical and chemical properties: acidic pH and variable surface charge. Two types of kinetic models were used to fit the experimental dates: those that allow to establish principal kinetic parameters and modeling of sorption process (pseudo-first-order, pseudo-second-order), and some ones frequently used to describe solute transport mechanisms of organic compounds on different sorbents intended for remediation purposes (Elovich equation, intraparticle diffusion, Boyd, and two-site nonequilibrium models). The best fit was obtained with the pseudo-second-order model. The rate constant and the initial rate constant values obtained through this model demonstrated the behavior of Diuron in each soil, in Andisols were observed the highest values for both parameters. The application of the models to describe solute transport mechanisms allowed establishing that in all soils the mass transfer controls the sorption kinetic across the boundary layer and intraparticle diffusion into macropores and micropores. The slowest sorption rate was observed on Ultisols, behavior which must be taken into account when the leaching potential of Diuron is considered. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

    PubMed

    Ralph, Duncan K; Matsen, Frederick A

    2016-01-01

    VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.

  18. Kinetic study of olive oil degradation monitored by fourier transform infrared spectrometry. Application to oil characterization.

    PubMed

    Román Falcó, Iván P; Grané Teruel, Nuria; Prats Moya, Soledad; Martín Carratalá, M Luisa

    2012-11-28

    A new approach for the determination of kinetic parameters of the cis/trans isomerization during the oxidation process of 24 virgin olive oils belonging to 8 different varieties is presented. The accelerated process of degradation at 100 °C was monitored by recording the Fourier transform infrared spectra. The parameters obtained confirm pseudo-first-order kinetics for the degradation of cis and the appearance of trans double bonds. The kinetic approach affords the induction time and the rate coefficient; these parameters are related to the fatty acid profile of the fresh olive oils. The data obtained were used to compare the oil stability of the samples with the help of multivariate statistical techniques. Fatty acid allowed a classification of the samples in five groups, one of them constituted by the cultivars with higher stability. Meanwhile, the kinetic parameters showed greater ability for the characterization of olive oils, allowing the classification in seven groups.

  19. Port wine oxidation management: a multiparametric kinetic approach.

    PubMed

    Martins, Rui Costa; Monforte, Ana Rita; Silva Ferreira, António

    2013-06-05

    Port wine is a flagship fortified wine of Portugal, which undergoes a particularly long aging period, developing a dynamic sensory profile over time, responsible for several wine categories, which is dependent upon the type of aging (bottle or barrel). Therefore, the quality of the product is dependent upon the chemical mechanisms occurring during the aging process, such as oxidation or Maillard reactions. To attain the desired quality management, it is necessary to understand how technological parameters, such as temperature or oxygen exposure, affect the kinetics of the formation of key odorants, such as sotolon. There is a lack of information about the impact of the storage conditions (oxygen and temperature) on Port wine quality. In this study, the effect of these two parameters were investigated to increase the knowledge database concerning aging management of Port wines. It was found that sotolon formation is highly dependent upon oxygen and temperature. There is however a synergistic effect between these two parameters that could significantly increase the concentration. The kinetic parameters of oxygen, sotolon, and other compounds related to Port aging (cis- and trans-5-hydroxy-2-methyl-1,3-dioxan, 2-furfural, 5-hydroxy-methyl-furfural, and 5-methyl-furfural) are also reported. Kinetic models with Monte Carlo simulations, where the oxygen permeability dispersion and temperature are the parameters under evaluation, were applied. On the basis of the modeling predictions, it would seem that the temperature of a cellar would have a more significant impact on the Port wines stored in containers where the oxygen intake is higher (barrels) when compared to containers with low oxygen permeability (bottles using cork stoppers).

  20. Joint estimation of subject motion and tracer kinetic parameters of dynamic PET data in an EM framework

    NASA Astrophysics Data System (ADS)

    Jiao, Jieqing; Salinas, Cristian A.; Searle, Graham E.; Gunn, Roger N.; Schnabel, Julia A.

    2012-02-01

    Dynamic Positron Emission Tomography is a powerful tool for quantitative imaging of in vivo biological processes. The long scan durations necessitate motion correction, to maintain the validity of the dynamic measurements, which can be particularly challenging due to the low signal-to-noise ratio (SNR) and spatial resolution, as well as the complex tracer behaviour in the dynamic PET data. In this paper we develop a novel automated expectation-maximisation image registration framework that incorporates temporal tracer kinetic information to correct for inter-frame subject motion during dynamic PET scans. We employ the Zubal human brain phantom to simulate dynamic PET data using SORTEO (a Monte Carlo-based simulator), in order to validate the proposed method for its ability to recover imposed rigid motion. We have conducted a range of simulations using different noise levels, and corrupted the data with a range of rigid motion artefacts. The performance of our motion correction method is compared with pairwise registration using normalised mutual information as a voxel similarity measure (an approach conventionally used to correct for dynamic PET inter-frame motion based solely on intensity information). To quantify registration accuracy, we calculate the target registration error across the images. The results show that our new dynamic image registration method based on tracer kinetics yields better realignment of the simulated datasets, halving the target registration error when compared to the conventional method at small motion levels, as well as yielding smaller residuals in translation and rotation parameters. We also show that our new method is less affected by the low signal in the first few frames, which the conventional method based on normalised mutual information fails to realign.

  1. A robust and accurate center-frequency estimation (RACE) algorithm for improving motion estimation performance of SinMod on tagged cardiac MR images without known tagging parameters.

    PubMed

    Liu, Hong; Wang, Jie; Xu, Xiangyang; Song, Enmin; Wang, Qian; Jin, Renchao; Hung, Chih-Cheng; Fei, Baowei

    2014-11-01

    A robust and accurate center-frequency (CF) estimation (RACE) algorithm for improving the performance of the local sine-wave modeling (SinMod) method, which is a good motion estimation method for tagged cardiac magnetic resonance (MR) images, is proposed in this study. The RACE algorithm can automatically, effectively and efficiently produce a very appropriate CF estimate for the SinMod method, under the circumstance that the specified tagging parameters are unknown, on account of the following two key techniques: (1) the well-known mean-shift algorithm, which can provide accurate and rapid CF estimation; and (2) an original two-direction-combination strategy, which can further enhance the accuracy and robustness of CF estimation. Some other available CF estimation algorithms are brought out for comparison. Several validation approaches that can work on the real data without ground truths are specially designed. Experimental results on human body in vivo cardiac data demonstrate the significance of accurate CF estimation for SinMod, and validate the effectiveness of RACE in facilitating the motion estimation performance of SinMod. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Kinetic study on ferulic acid production from banana stem waste via mechanical extraction

    NASA Astrophysics Data System (ADS)

    Zainol, Norazwina; Masngut, Nasratun; Khairi Jusup, Muhamad

    2018-04-01

    Banana is the tropical plants associated with lots of medicinal properties. It has been reported to be a potential source of phenolic compounds such as ferulic acid (FA). FA has excellent antioxidant properties higher than vitamin C and E. FA also have a wide range of biological activities, such as antioxidant activities and anti-microbial activities. This paper presents an experimental and kinetic study on ferulic acid (FA) production from banana stem waste (BSW) via mechanical extraction. The objective of this research is to determine the kinetic parameters in the ferulic acid production. The banana stem waste was randomly collected from the local banana plantation in Felda Lepar Hilir, Pahang. The banana stem juice was mechanically extracted by using sugarcane press machine (KR3176) and further analyzed in high performance liquid chromatography. The differential and integral method was applied to determine the kinetic parameter of the extraction process and the data obtained were fitted into the 0th, 1st and 2nd order of extraction process. Based on the results, the kinetic parameter and R2 value from were 0.05 and 0.93, respectively. It was determined that the 0th kinetic order fitted the reaction processes to best represent the mechanical extraction.

  3. Kinetics and mechanism of soot formation in hydrocarbon combustion

    NASA Technical Reports Server (NTRS)

    Frenklach, Michael

    1990-01-01

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

  4. Oxidative desulfurization: kinetic modelling.

    PubMed

    Dhir, S; Uppaluri, R; Purkait, M K

    2009-01-30

    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

  5. Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

    PubMed

    Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

    2012-07-03

    Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

  6. Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

    PubMed Central

    Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

    2012-01-01

    Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

  7. Explosive sport training and torque kinetics in children.

    PubMed

    Dotan, Raffy; Mitchell, Cameron J; Cohen, Rotem; Gabriel, David; Klentrou, Panagiota; Falk, Bareket

    2013-07-01

    A high rate of force development (RFD) is often more important than maximal force in daily and sports activities. In children, resistance training has been shown to increase maximal force. It is unclear whether, or to what extent, can children improve RFD and force kinetics. For this study, we compared strength and force kinetics of boy gymnasts with those of untrained boys and untrained men. Eight boy gymnasts (age, 9.5 ± 1.2 y), 20 untrained boys (age, 10.1 ± 1.3 y), and 20 untrained men (age, 22.9 ± 4.4 y) performed maximal, explosive, isometric elbow flexions (EF) and knee flexions (KF). Peak torque (maximal voluntary contraction (MVC)), elapsed times to 10%-100% MVC, peak rate of torque development (RTDpk), and other kinetics parameters were determined. When gymnasts were compared with untrained boys, size-normalized EF MVC was 11%-20% higher, RTDpk was 32% higher, and times to 30% and 80% MVC were 16% and 55% shorter, respectively (p < 0.05). No corresponding differences were observed in KF. Furthermore, although the normalized EF MVC was 28% lower in gymnasts than in men (p < 0.001), their torque kinetics parameters were similar. These findings highlight the specificity of gymnastics training, which markedly elevated the torque kinetics of young, prepubertal boys to adult levels, but only moderately affected peak torque. It is suggested that neurologic adaptations, such as enhanced firing and activation rates or increased type II motor-unit recruitment, as well as changes in musculotendinous stiffness, could explain these findings.

  8. Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

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

    Li, Yulan; Hu, Shenyang Y.; Sun, Xin

    2011-06-15

    Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux

  9. Study on the effectiveness of the kinetic method in patients with rheumatic diseases and temporomandibular joint dysfunction.

    PubMed

    Havriş, Maria Daniela; Ancuţa, Codrina; Iordache, Cristina; Chirieac, Rodica Marieta

    2012-01-01

    Selecting the appropriate treatment decision is essential for achieving optimal results in the management of algo-dysfunctional syndrome of the temporo-mandibular joint (TMJD). The study aims to decide on the most effective (symptomatic control, preserved motility) kinetic program in patients with TMJ involvement. prospective observational study on 83 consecutive patients with rheumatic diseases and TMJ dysfunction. Clinical assessment (pain, noises, muscle spasm, range of motion, ROM) was performed at baseline and after 3 months of specific kinetic rehabilitation program. Change in clinical parameters and TM3 index was reported, p<0.05. over 45% TMJ involvement at baseline as defined by TMJ index (mean value of 13.56) and only 36.66% at 3 months (p<0.05). Significant improvement in pain (presence, severity) was demonstrated at 3 moths (p<0.05): 18.05% spontaneous pain, 75.9% provoked pain, with 12.11% respectively 2.41% decreased in nocturnal respectively diurnal pain. Significant decrease (p<0.05) in joint noises at movements: 27.71% when opening and 12.04% when closing the mouth, 8.43 at protrusion and 3.61% at retraction, while 18% at the side movements. Complex accurate kinetic reeducation is mandatory for achieving correct posture (head, neck and trunk), normal mastication, swallowing and respiration, as well as correction of neuromuscular imbalances in patients with TMJD secondary to rheumatic disorders.

  10. Accurate estimation of seismic source parameters of induced seismicity by a combined approach of generalized inversion and genetic algorithm: Application to The Geysers geothermal area, California

    NASA Astrophysics Data System (ADS)

    Picozzi, M.; Oth, A.; Parolai, S.; Bindi, D.; De Landro, G.; Amoroso, O.

    2017-05-01

    The accurate determination of stress drop, seismic efficiency, and how source parameters scale with earthquake size is an important issue for seismic hazard assessment of induced seismicity. We propose an improved nonparametric, data-driven strategy suitable for monitoring induced seismicity, which combines the generalized inversion technique together with genetic algorithms. In the first step of the analysis the generalized inversion technique allows for an effective correction of waveforms for attenuation and site contributions. Then, the retrieved source spectra are inverted by a nonlinear sensitivity-driven inversion scheme that allows accurate estimation of source parameters. We therefore investigate the earthquake source characteristics of 633 induced earthquakes (Mw 2-3.8) recorded at The Geysers geothermal field (California) by a dense seismic network (i.e., 32 stations, more than 17.000 velocity records). We find a nonself-similar behavior, empirical source spectra that require an ωγ source model with γ > 2 to be well fit and small radiation efficiency ηSW. All these findings suggest different dynamic rupture processes for smaller and larger earthquakes and that the proportion of high-frequency energy radiation and the amount of energy required to overcome the friction or for the creation of new fractures surface changes with earthquake size. Furthermore, we observe also two distinct families of events with peculiar source parameters that in one case suggests the reactivation of deep structures linked to the regional tectonics, while in the other supports the idea of an important role of steeply dipping faults in the fluid pressure diffusion.

  11. Controlling Release Kinetics of PLG Microspheres Using a Manufacturing Technique

    NASA Astrophysics Data System (ADS)

    Berchane, Nader

    2005-11-01

    Controlled drug delivery offers numerous advantages compared with conventional free dosage forms, in particular: improved efficacy and patient compliance. Emulsification is a widely used technique to entrap drugs in biodegradable microspheres for controlled drug delivery. The size of the formed microspheres has a significant influence on drug release kinetics. Despite the advantages of controlled drug delivery, previous attempts to achieve predetermined release rates have seen limited success. This study develops a tool to tailor desired release kinetics by combining microsphere batches of specified mean diameter and size distribution. A fluid mechanics based correlation that predicts the average size of Poly(Lactide-co-Glycolide) [PLG] microspheres from the manufacturing technique, is constructed and validated by comparison with experimental results. The microspheres produced are accurately represented by the Rosin-Rammler mathematical distribution function. A mathematical model is formulated that incorporates the microsphere distribution function to predict the release kinetics from mono-dispersed and poly-dispersed populations. Through this mathematical model, different release kinetics can be achieved by combining different sized populations in different ratios. The resulting design tool should prove useful for the pharmaceutical industry to achieve designer release kinetics.

  12. On the Nonequilibrium Interface Kinetics of Rapid Coupled Eutectic Growth

    NASA Astrophysics Data System (ADS)

    Dong, H.; Chen, Y. Z.; Shan, G. B.; Zhang, Z. R.; Liu, F.

    2017-08-01

    Nonequilibrium interface kinetics (NEIK) is expected to play an important role in coupled growth of eutectic alloys, when solidification velocity is high and intermetallic compound or topologically complex phases form in the crystallized product. In order to quantitatively evaluate the effect of NEIK on the rapid coupled eutectic growth, in this work, two nonequilibrium interface kinetic effects, i.e., atom attachment and solute trapping at the solid-liquid interface, were incorporated into the analyses of the coupled eutectic growth under the rapid solidification condition. First, a coupled growth model incorporating the preceding two nonequilibrium kinetic effects was derived. On this basis, an expression of kinetic undercooling (Δ T k), which is used to characterize the NEIK, was defined. The calculations based on the as-derived couple growth model show good agreement with the reported experimental results achieved in rapidly solidified eutectic Al-Sm alloys consisting of a solid solution phase ( α-Al) and an intermetallic compound phase (Al11Sm3). In terms of the definition of Δ T k defined in this work, the role of NEIK in the coupled growth of the Al-Sm eutectic system was analyzed. The results show that with increasing the coupled growth velocity, Δ T k increases continuously, and its ratio to the total undercooling reaches 0.32 at the maximum growth velocity for coupled eutectic growth. Parametric analyses on two key alloy parameters that influence Δ T k, i.e., interface kinetic parameter ( μ i ) and solute distribution coefficient ( k e ), indicate that both μ i and k e influence the NEIK significantly and the decrease of either these two parameters enhances the NEIK effect.

  13. Distributed activation energy model parameters of some Turkish coals

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

    Gunes, M.; Gunes, S.K.

    2008-07-01

    A multi-reaction model based on distributed activation energy has been applied to some Turkish coals. The kinetic parameters of distributed activation energy model were calculated via computer program developed for this purpose. It was observed that the values of mean of activation energy distribution vary between 218 and 248 kJ/mol, and the values of standard deviation of activation energy distribution vary between 32 and 70 kJ/mol. The correlations between kinetic parameters of the distributed activation energy model and certain properties of coal have been investigated.

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

    PubMed Central

    2013-01-01

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

  15. On a Fast and Accurate In Situ Measuring Strategy for Recrystallization Kinetics and Its Application to an Al-Fe-Si Alloy

    NASA Astrophysics Data System (ADS)

    Kühbach, Markus; Brüggemann, Thiemo; Molodov, Konstantin D.; Gottstein, Günter

    2015-03-01

    In the current study, we detail a novel in situ X-ray diffraction-based bulk measurement technique, which allows for the continuous tracking of primary recrystallization kinetics. The approach is based on measuring the diffracted intensity that is correlated with the evolution of the volume fraction of particular texture components during annealing of a sample within a texture goniometer. The method is applied in an experimental study on a cold-rolled industrial Al-Fe-Si alloy. For comparison purposes, the macrotexture and the hardness evolution were monitored ex situ along isothermal and nonisothermal annealing. These measurements were then contrasted to the in situ obtained growth kinetics of recrystallizing grains in beta-fiber deformation and cube orientation. The results showed clearly that this method can be reliably utilized for the characterization of recrystallization kinetics in an industrial context.

  16. Receptor binding kinetics equations: Derivation using the Laplace transform method.

    PubMed

    Hoare, Sam R J

    Measuring unlabeled ligand receptor binding kinetics is valuable in optimizing and understanding drug action. Unfortunately, deriving equations for estimating kinetic parameters is challenging because it involves calculus; integration can be a frustrating barrier to the pharmacologist seeking to measure simple rate parameters. Here, a well-known tool for simplifying the derivation, the Laplace transform, is applied to models of receptor-ligand interaction. The method transforms differential equations to a form in which simple algebra can be applied to solve for the variable of interest, for example the concentration of ligand-bound receptor. The goal is to provide instruction using familiar examples, to enable investigators familiar with handling equilibrium binding equations to derive kinetic equations for receptor-ligand interaction. First, the Laplace transform is used to derive the equations for association and dissociation of labeled ligand binding. Next, its use for unlabeled ligand kinetic equations is exemplified by a full derivation of the kinetics of competitive binding equation. Finally, new unlabeled ligand equations are derived using the Laplace transform. These equations incorporate a pre-incubation step with unlabeled or labeled ligand. Four equations for measuring unlabeled ligand kinetics were compared and the two new equations verified by comparison with numerical solution. Importantly, the equations have not been verified with experimental data because no such experiments are evident in the literature. Equations were formatted for use in the curve-fitting program GraphPad Prism 6.0 and fitted to simulated data. This description of the Laplace transform method will enable pharmacologists to derive kinetic equations for their model or experimental paradigm under study. Application of the transform will expand the set of equations available for the pharmacologist to measure unlabeled ligand binding kinetics, and for other time

  17. Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes.

    PubMed

    García-Gen, Santiago; Sousbie, Philippe; Rangaraj, Ganesh; Lema, Juan M; Rodríguez, Jorge; Steyer, Jean-Philippe; Torrijos, Michel

    2015-01-01

    A methodology to estimate disintegration and hydrolysis kinetic parameters of solid wastes and validate an ADM1-based anaerobic co-digestion model is presented. Kinetic parameters of the model were calibrated from batch reactor experiments treating individually fruit and vegetable wastes (among other residues) following a new protocol for batch tests. In addition, decoupled disintegration kinetics for readily and slowly biodegradable fractions of solid wastes was considered. Calibrated parameters from batch assays of individual substrates were used to validate the model for a semi-continuous co-digestion operation treating simultaneously 5 fruit and vegetable wastes. The semi-continuous experiment was carried out in a lab-scale CSTR reactor for 15 weeks at organic loading rate ranging between 2.0 and 4.7 gVS/Ld. The model (built in Matlab/Simulink) fit to a large extent the experimental results in both batch and semi-continuous mode and served as a powerful tool to simulate the digestion or co-digestion of solid wastes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  18. Kinetics of shear-induced gel deswelling/solvent release.

    PubMed

    Zeo, Undina; Tarabukina, Elena; Budtova, Tatiana

    2005-11-02

    The kinetics of shear-induced deswelling of gel particles based on synthetic (sodium polyacrylate) and natural (alginate) polymers was studied by rheo-optical technique. A swollen spherical gel particle of 100+/-50 microm diameter was placed in silicone oil and the evolution of the gel size as a function of time and shear rate was monitored. Different aqueous polymer solutions were used as synthetic gel solvent: polyvinylpyrrolidone, hydroxypropyl cellulose and glucose-based polymer. The interfacial tension (gel solvent)/(silicone oil), gel degree of swelling, solvent quality and viscosity are the main parameters influencing the kinetics of shear-induced gel deswelling. The kinetics of gel volume loss was approximated by a modified Weibull equation.

  19. Cluster kinetics model for mixtures of glassformers

    NASA Astrophysics Data System (ADS)

    Brenskelle, Lisa A.; McCoy, Benjamin J.

    2007-10-01

    For glassformers we propose a binary mixture relation for parameters in a cluster kinetics model previously shown to represent pure compound data for viscosity and dielectric relaxation as functions of either temperature or pressure. The model parameters are based on activation energies and activation volumes for cluster association-dissociation processes. With the mixture parameters, we calculated dielectric relaxation times and compared the results to experimental values for binary mixtures. Mixtures of sorbitol and glycerol (seven compositions), sorbitol and xylitol (three compositions), and polychloroepihydrin and polyvinylmethylether (three compositions) were studied.

  20. Kinetics of enzymatic trans-esterification of glycerides for biodiesel production.

    PubMed

    Calabrò, Vincenza; Ricca, Emanuele; De Paola, Maria Gabriela; Curcio, Stefano; Iorio, Gabriele

    2010-08-01

    In this paper, the reaction of enzymatic trans-esterification of glycerides with ethanol in a reaction medium containing hexane at a temperature of 37 degrees C has been studied. The enzyme was Lipase from Mucor miehei, immobilized on ionic exchange resin, aimed at achieving high catalytic specific surface and recovering, regenerating and reusing the biocatalyst. A kinetic analysis has been carried out to identify the reaction path; the rate equation and kinetic parameters have been also calculated. The kinetic model has been validated by comparison between predicted and experimental results. Mass transport resistances estimation was undertaken in order to verify that the kinetics found was intrinsic. Model potentialities in terms of reactors design and optimization are also shown.

  1. Characterization of 12 GnRH peptide agonists – a kinetic perspective

    PubMed Central

    Nederpelt, Indira; Georgi, Victoria; Schiele, Felix; Nowak‐Reppel, Katrin; Fernández‐Montalván, Amaury E.; IJzerman, Adriaan P.

    2015-01-01

    Background and Purpose Drug‐target residence time is an important, yet often overlooked, parameter in drug discovery. Multiple studies have proposed an increased residence time to be beneficial for improved drug efficacy and/or longer duration of action. Currently, there are many drugs on the market targeting the gonadotropin‐releasing hormone (GnRH) receptor for the treatment of hormone‐dependent diseases. Surprisingly, the kinetic receptor‐binding parameters of these analogues have not yet been reported. Therefore, this project focused on determining the receptor‐binding kinetics of 12 GnRH peptide agonists, including many marketed drugs. Experimental Approach A novel radioligand‐binding competition association assay was developed and optimized for the human GnRH receptor with the use of a radiolabelled peptide agonist, [125I]‐triptorelin. In addition to radioligand‐binding studies, a homogeneous time‐resolved FRET Tag‐lite™ method was developed as an alternative assay for the same purpose. Key Results Two novel competition association assays were successfully developed and applied to determine the kinetic receptor‐binding characteristics of 12 high‐affinity GnRH peptide agonists. Results obtained from both methods were highly correlated. Interestingly, the binding kinetics of the peptide agonists were more divergent than their affinities with residence times ranging from 5.6 min (goserelin) to 125 min (deslorelin). Conclusions and Implications Our research provides new insights by incorporating kinetic, next to equilibrium, binding parameters in current research and development that can potentially improve future drug discovery targeting the GnRH receptor. PMID:26398856

  2. Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach.

    PubMed

    Koutinas, Michalis; Kiparissides, Alexandros; Silva-Rocha, Rafael; Lam, Ming-Chi; Martins Dos Santos, Vitor A P; de Lorenzo, Victor; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

    2011-07-01

    The majority of models describing the kinetic properties of a microorganism for a given substrate are unstructured and empirical. They are formulated in this manner so that the complex mechanism of cell growth is simplified. Herein, a novel approach for modelling microbial growth kinetics is proposed, linking biomass growth and substrate consumption rates to the gene regulatory programmes that control these processes. A dynamic model of the TOL (pWW0) plasmid of Pseudomonas putida mt-2 has been developed, describing the molecular interactions that lead to the transcription of the upper and meta operons, known to produce the enzymes for the oxidative catabolism of m-xylene. The genetic circuit model was combined with a growth kinetic model decoupling biomass growth and substrate consumption rates, which are expressed as independent functions of the rate-limiting enzymes produced by the operons. Estimation of model parameters and validation of the model's predictive capability were successfully performed in batch cultures of mt-2 fed with different concentrations of m-xylene, as confirmed by relative mRNA concentration measurements of the promoters encoded in TOL. The growth formation and substrate utilisation patterns could not be accurately described by traditional Monod-type models for a wide range of conditions, demonstrating the critical importance of gene regulation for the development of advanced models closely predicting complex bioprocesses. In contrast, the proposed strategy, which utilises quantitative information pertaining to upstream molecular events that control the production of rate-limiting enzymes, predicts the catabolism of a substrate and biomass formation and could be of central importance for the design of optimal bioprocesses. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Kinetic compensation effect in logistic distributed activation energy model for lignocellulosic biomass pyrolysis.

    PubMed

    Xu, Di; Chai, Meiyun; Dong, Zhujun; Rahman, Md Maksudur; Yu, Xi; Cai, Junmeng

    2018-06-04

    The kinetic compensation effect in the logistic distributed activation energy model (DAEM) for lignocellulosic biomass pyrolysis was investigated. The sum of square error (SSE) surface tool was used to analyze two theoretically simulated logistic DAEM processes for cellulose and xylan pyrolysis. The logistic DAEM coupled with the pattern search method for parameter estimation was used to analyze the experimental data of cellulose pyrolysis. The results showed that many parameter sets of the logistic DAEM could fit the data at different heating rates very well for both simulated and experimental processes, and a perfect linear relationship between the logarithm of the frequency factor and the mean value of the activation energy distribution was found. The parameters of the logistic DAEM can be estimated by coupling the optimization method and isoconversional kinetic methods. The results would be helpful for chemical kinetic analysis using DAEM. Copyright © 2018 Elsevier Ltd. All rights reserved.

  4. Polynomial Fitting of DT-MRI Fiber Tracts Allows Accurate Estimation of Muscle Architectural Parameters

    PubMed Central

    Damon, Bruce M.; Heemskerk, Anneriet M.; Ding, Zhaohua

    2012-01-01

    Fiber curvature is a functionally significant muscle structural property, but its estimation from diffusion-tensor MRI fiber tracking data may be confounded by noise. The purpose of this study was to investigate the use of polynomial fitting of fiber tracts for improving the accuracy and precision of fiber curvature (κ) measurements. Simulated image datasets were created in order to provide data with known values for κ and pennation angle (θ). Simulations were designed to test the effects of increasing inherent fiber curvature (3.8, 7.9, 11.8, and 15.3 m−1), signal-to-noise ratio (50, 75, 100, and 150), and voxel geometry (13.8 and 27.0 mm3 voxel volume with isotropic resolution; 13.5 mm3 volume with an aspect ratio of 4.0) on κ and θ measurements. In the originally reconstructed tracts, θ was estimated accurately under most curvature and all imaging conditions studied; however, the estimates of κ were imprecise and inaccurate. Fitting the tracts to 2nd order polynomial functions provided accurate and precise estimates of κ for all conditions except very high curvature (κ=15.3 m−1), while preserving the accuracy of the θ estimates. Similarly, polynomial fitting of in vivo fiber tracking data reduced the κ values of fitted tracts from those of unfitted tracts and did not change the θ values. Polynomial fitting of fiber tracts allows accurate estimation of physiologically reasonable values of κ, while preserving the accuracy of θ estimation. PMID:22503094

  5. Accurate Ray-tracing of Realistic Neutron Star Atmospheres for Constraining Their Parameters

    NASA Astrophysics Data System (ADS)

    Vincent, Frederic H.; Bejger, Michał; Różańska, Agata; Straub, Odele; Paumard, Thibaut; Fortin, Morgane; Madej, Jerzy; Majczyna, Agnieszka; Gourgoulhon, Eric; Haensel, Paweł; Zdunik, Leszek; Beldycki, Bartosz

    2018-03-01

    Thermal-dominated X-ray spectra of neutron stars in quiescent, transient X-ray binaries and neutron stars that undergo thermonuclear bursts are sensitive to mass and radius. The mass–radius relation of neutron stars depends on the equation of state (EoS) that governs their interior. Constraining this relation accurately is therefore of fundamental importance to understand the nature of dense matter. In this context, we introduce a pipeline to calculate realistic model spectra of rotating neutron stars with hydrogen and helium atmospheres. An arbitrarily fast-rotating neutron star with a given EoS generates the spacetime in which the atmosphere emits radiation. We use the LORENE/NROTSTAR code to compute the spacetime numerically and the ATM24 code to solve the radiative transfer equations self-consistently. Emerging specific intensity spectra are then ray-traced through the neutron star’s spacetime from the atmosphere to a distant observer with the GYOTO code. Here, we present and test our fully relativistic numerical pipeline. To discuss and illustrate the importance of realistic atmosphere models, we compare our model spectra to simpler models like the commonly used isotropic color-corrected blackbody emission. We highlight the importance of considering realistic model-atmosphere spectra together with relativistic ray-tracing to obtain accurate predictions. We also insist upon the crucial impact of the star’s rotation on the observables. Finally, we close a controversy that has been ongoing in the literature in the recent years, regarding the validity of the ATM24 code.

  6. Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

    PubMed

    Du, Bin; Zielinski, Daniel C; Kavvas, Erol S; Dräger, Andreas; Tan, Justin; Zhang, Zhen; Ruggiero, Kayla E; Arzumanyan, Garri A; Palsson, Bernhard O

    2016-06-06

    The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations. Overall, our work generally supports the use of approximate rate laws when

  7. Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

    PubMed

    Nagy, Péter

    2013-05-01

    Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. This review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

  8. Water sorption equilibria and kinetics of henna leaves

    NASA Astrophysics Data System (ADS)

    Sghaier, Khamsa; Peczalski, Roman; Bagane, Mohamed

    2018-05-01

    In this work, firstly the sorption isotherms of henna leaves were determined using a dynamic vapor sorption ( DVS) device at 3 temperatures (30, 40, 50 °C). The equilibrium data were well fitted by the GAB model. Secondly, drying kinetics were measured using a pilot convective dryer for 3 air temperatures (same as above), 3 velocities (0.5, 1, 1.42 m/s) and 4 relative humidities (20, 30, 35, 40%). The drying kinetic coefficients were identified by fitting the DVS and pilot dryer data by Lewis semi-empirical model. In order to compare the obtained kinetic parameters with literature, the water diffusivities were also identified by fitting the data by the simplified solution of fickian diffusion equation. The identified kinetic coefficient was mainly dependent on air temperature and velocity what proved that it represented rather the external transfer and not the internal one.

  9. Polarization and Compressibility of Oblique Kinetic Alfven Waves

    NASA Technical Reports Server (NTRS)

    Hunana, Peter; Goldstein, M. L.; Passot, T.; Sulem, P. L.; Laveder, D.; Zank, G. P.

    2012-01-01

    Even though solar wind, as a collisionless plasma, is properly described by the kineticMaxwell-Vlasov description, it can be argued that much of our understanding of solar wind observational data comes from an interpretation and numerical modeling which is based on a fluid description of magnetohydrodynamics. In recent years, there has been a significant interest in better understanding the importance of kinetic effects, i.e. the differences between the kinetic and usual fluid descriptions. Here we concentrate on physical properties of oblique kinetic Alfvn waves (KAWs), which are often recognized as one of the key ingredients in the solar wind turbulence cascade. We use three different fluid models with various degrees of complexity and calculate polarization and magnetic compressibility of oblique KAWs (propagation angle q = 88), which we compare to solutions derived from linear kinetic theory. We explore a wide range of possible proton plasma b = [0.1,10.0] and a wide range of length scales krL = [0.001,10.0]. It is shown that the classical isotropic two-fluid model is very compressible in comparison with kinetic theory and that the largest discrepancy occurs at scales larger than the proton gyroscale. We also show that the two-fluid model contains a large error in the polarization of electric field, even at scales krL 1. Furthermore, to understand these discrepancies between the two-fluid model and the kinetic theory, we employ two versions of the Landau fluid model that incorporate linear low-frequency kinetic effects such as Landau damping and finite Larmor radius (FLR) corrections into the fluid description. It is shown that Landau damping significantly reduces the magnetic compressibility and that FLR corrections (i.e. nongyrotropic contributions) are required to correctly capture the polarization.We also show that, in addition to Landau damping, FLR corrections are necessary to accurately describe the damping rate of KAWs. We conclude that kinetic effects

  10. 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.

  11. Linear and non-linear regression analysis for the sorption kinetics of methylene blue onto activated carbon.

    PubMed

    Kumar, K Vasanth

    2006-10-11

    Batch kinetic experiments were carried out for the sorption of methylene blue onto activated carbon. The experimental kinetics were fitted to the pseudo first-order and pseudo second-order kinetics by linear and a non-linear method. The five different types of Ho pseudo second-order expression have been discussed. A comparison of linear least-squares method and a trial and error non-linear method of estimating the pseudo second-order rate kinetic parameters were examined. The sorption process was found to follow a both pseudo first-order kinetic and pseudo second-order kinetic model. Present investigation showed that it is inappropriate to use a type 1 and type pseudo second-order expressions as proposed by Ho and Blanachard et al. respectively for predicting the kinetic rate constants and the initial sorption rate for the studied system. Three correct possible alternate linear expressions (type 2 to type 4) to better predict the initial sorption rate and kinetic rate constants for the studied system (methylene blue/activated carbon) was proposed. Linear method was found to check only the hypothesis instead of verifying the kinetic model. Non-linear regression method was found to be the more appropriate method to determine the rate kinetic parameters.

  12. Kinetics of particle deposition at heterogeneous surfaces

    NASA Astrophysics Data System (ADS)

    Stojiljković, D. Lj.; Vrhovac, S. B.

    2017-12-01

    The random sequential adsorption (RSA) approach is used to analyze adsorption of spherical particles of fixed diameter d0 on nonuniform surfaces covered by square cells arranged in a square lattice pattern. To characterize such pattern two dimensionless parameters are used: the cell size α and the cell-cell separation β, measured in terms of the particle diameter d0. Adsorption is assumed to occur if the particle (projected) center lies within a cell area. We focus on the kinetics of deposition process in the case when no more than a single disk can be placed onto any square cell (α < 1 /√{ 2 } ≈ 0 . 707). We find that the asymptotic approach of the coverage fraction θ(t) to the jamming limit θJ is algebraic if the parameters α and β satisfy the simple condition, β + α / 2 < 1. If this condition is not satisfied, the late time kinetics of deposition process is not consistent with the power law behavior. However, if the geometry of the pattern approaches towards ;noninteracting conditions; (β > 1), when adsorption on each cell can be decoupled, approach of the coverage fraction θ(t) to θJ becomes closer to the exponential law. Consequently, changing the pattern parameters in the present model allows to interpolate the deposition kinetics between the continuum limit and the lattice-like behavior. Structural properties of the jammed-state coverings are studied in terms of the radial distribution function g(r) and spatial distribution of particles inside the cell. Various, non-trivial spatial distributions are observed depending on the geometry of the pattern.

  13. SigrafW: An easy-to-use program for fitting enzyme kinetic data.

    PubMed

    Leone, Francisco Assis; Baranauskas, José Augusto; Furriel, Rosa Prazeres Melo; Borin, Ivana Aparecida

    2005-11-01

    SigrafW is Windows-compatible software developed using the Microsoft® Visual Basic Studio program that uses the simplified Hill equation for fitting kinetic data from allosteric and Michaelian enzymes. SigrafW uses a modified Fibonacci search to calculate maximal velocity (V), the Hill coefficient (n), and the enzyme-substrate apparent dissociation constant (K). The estimation of V, K, and the sum of the squares of residuals is performed using a Wilkinson nonlinear regression at any Hill coefficient (n). In contrast to many currently available kinetic analysis programs, SigrafW shows several advantages for the determination of kinetic parameters of both hyperbolic and nonhyperbolic saturation curves. No initial estimates of the kinetic parameters are required, a measure of the goodness-of-the-fit for each calculation performed is provided, the nonlinear regression used for calculations eliminates the statistical bias inherent in linear transformations, and the software can be used for enzyme kinetic simulations either for educational or research purposes. Persons interested in receiving a free copy of the software should contact Dr. F. A. Leone. Copyright © 2005 International Union of Biochemistry and Molecular Biology, Inc.

  14. Usefulness of CA125 and their kinetic parameters and positron emission tomography/computed tomography (PET/CT) with fluorodeoxyglucose ([18F] FDG) in the detection of recurrent ovarian cancer levels.

    PubMed

    Palomar Muñoz, Azahara; Cordero García, José Manuel; Talavera Rubio, Prado; García Vicente, Ana M; González García, Beatriz; Bellón Guardia, María Emiliana; Soriano Castrejón, Ángel; Aranda Aguilar, Enrique

    2017-12-21

    To assess the usefulness of cancer antigen 125 (CA125) serum levels and kinetic values, velocity (CA125vel) and doubling time (CA125dt), as well as fluorodeoxyglucose ([ 18 F]FDG) positron emission tomography/computed tomography (PET/CT), in the detection of ovarian cancer recurrence. To assess the optimal cut-off for CA125, CA125vel and CA125dt to detect relapse with [ 18 F]FDG-PET/CT. A retrospective analysis was performed of 59 [ 18 F]FDG-PET/CT (48 patients) for suspected recurrence of ovarian cancer. Receiver operating characteristic (ROC) curves were plotted and area-under-the curve (AUC) statistics were computed for CA125, CA125vel and CA125dt. The results obtained in the group with normal and high (>35U/ml) CA125 levels were compared. Forty-four cases of recurrence were diagnosed (7 had CA125 ≤35U/ml), whereas 15 showed no disease. All of them were correctly catalogued by PET/CT. In ROC analysis, the discriminatory power of CA125 was relatively high (AUC 0.835) and the optimal cut-off point to reflect active disease was 23.9U/ml. The ROC analyses for the CA125vel and CA125dt showed an AUC of 0.849 and 0.728, respectively, with an optimal cut-off point of 1.96U/ml/month and 0.76 months, respectively. In patients with normal CA125 and recurrence of ovarian cancer, the CA125vel was significantly higher than in patients without recurrence (p=0.029). [ 18 F]FDG-PET/CT is more accurate than CA125 parameters in the detection of ovarian cancer recurrence. CA125 serum levels are essential; nevertheless, CA125 kinetic values must be considered to detect relapse. Particularly in patients with CA125 within normal values, in which a higher CA125vel is indicative of recurrence. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

  15. Nonisothermal Carbothermal Reduction Kinetics of Titanium-Bearing Blast Furnace Slag

    NASA Astrophysics Data System (ADS)

    Hu, Mengjun; Wei, Ruirui; Hu, Meilong; Wen, Liangying; Ying, Fangqing

    2018-05-01

    The kinetics of carbothermal reduction of titanium-bearing blast furnace (BF) slag has been studied by thermogravimetric analysis and quadrupole mass spectrometry. The kinetic parameters (activation energy, preexponential factor, and reaction model function) were determined using the Flynn-Wall-Ozawa and Šatava-Šesták methods. The results indicated that reduction of titanium-bearing BF slag can be divided into two stages, namely reduction of phases containing iron and gasification of carbon (< 1095°C), followed by reduction of phases containing titanium (> 1095°C). CO2 was the main off-gas in the temperature range of 530-700°C, whereas CO became the main off-gas when the temperature was greater than 900°C. The activation energy calculated using the Flynn-Wall-Ozawa method was 221.2 kJ/mol. D4 is the mechanism function for carbothermal reduction of titanium-bearing BF slag. Meanwhile, a nonisothermal reduction model is proposed based on the obtained kinetic parameters.

  16. Characterizing the kinetics of suspended cylindrical particles by polarization measurements

    NASA Astrophysics Data System (ADS)

    Liao, Ran; Ou, Xueheng; Ma, Hui

    2015-09-01

    Polarization has promising potential to retrieve the information of the steady samples, such as tissues. However, for the fast changing sample such as the suspended algae in the water, the kinetics of the particles also influence the scattered polarization. The present paper will show our recent results to extract the information about the kinetics of the suspended cylindrical particles by polarization measurements. The sample is the aqueous suspension of the glass fibers stirred by a magnetic stirrer. We measure the scattered polarization of the fibers by use of a simultaneous polarization measurement system and obtain the time series of two orthogonal polarization components. By use of correlation analysis, we obtain the time parameters from the auto-correlation functions of the polarization components, and observe the changes with the stirring speeds. Results show that these time parameters indicate the immigration of the fibers. After discussion, we find that they may further characterize the kinetics, including the translation and rotation, of the glass fibers in the fluid field.

  17. Second-order kinetic model for the sorption of cadmium onto tree fern: a comparison of linear and non-linear methods.

    PubMed

    Ho, Yuh-Shan

    2006-01-01

    A comparison was made of the linear least-squares method and a trial-and-error non-linear method of the widely used pseudo-second-order kinetic model for the sorption of cadmium onto ground-up tree fern. Four pseudo-second-order kinetic linear equations are discussed. Kinetic parameters obtained from the four kinetic linear equations using the linear method differed but they were the same when using the non-linear method. A type 1 pseudo-second-order linear kinetic model has the highest coefficient of determination. Results show that the non-linear method may be a better way to obtain the desired parameters.

  18. Optimization of physiological parameter for macroscopic modeling of reacted singlet oxygen concentration in an in-vivo model

    NASA Astrophysics Data System (ADS)

    Wang, Ken Kang-Hsin; Busch, Theresa M.; Finlay, Jarod C.; Zhu, Timothy C.

    2009-02-01

    Singlet oxygen (1O2) is generally believed to be the major cytotoxic agent during photodynamic therapy (PDT), and the reaction between 1O2 and tumor cells define the treatment efficacy. From a complete set of the macroscopic kinetic equations which describe the photochemical processes of PDT, we can express the reacted 1O2 concentration, [1O2]rx, in a form related to time integration of the product of 1O2 quantum yield and the PDT dose rate. The production of [1O2]rx involves physiological and photophysical parameters which need to be determined explicitly for the photosensitizer of interest. Once these parameters are determined, we expect the computed [1O2]rx to be an explicit dosimetric indicator for clinical PDT. Incorporating the diffusion equation governing the light transport in turbid medium, the spatially and temporally-resolved [1O2]rx described by the macroscopic kinetic equations can be numerically calculated. A sudden drop of the calculated [1O2]rx along with the distance following the decrease of light fluence rate is observed. This suggests that a possible correlation between [1O2]rx and necrosis boundary may occur in the tumor subject to PDT irradiation. In this study, we have theoretically examined the sensitivity of the physiological parameter from two clinical related conditions: (1) collimated light source on semi-infinite turbid medium and (2) linear light source in turbid medium. In order to accurately determine the parameter in a clinical relevant environment, the results of the computed [1O2]rx are expected to be used to fit the experimentally-measured necrosis data obtained from an in vivo animal model.

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

    PubMed Central

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

    1998-01-01

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

  20. Continuum theory of phase separation kinetics for active Brownian particles.

    PubMed

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

    2013-10-04

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

  1. Parameter estimation for lithium ion batteries

    NASA Astrophysics Data System (ADS)

    Santhanagopalan, Shriram

    With an increase in the demand for lithium based batteries at the rate of about 7% per year, the amount of effort put into improving the performance of these batteries from both experimental and theoretical perspectives is increasing. There exist a number of mathematical models ranging from simple empirical models to complicated physics-based models to describe the processes leading to failure of these cells. The literature is also rife with experimental studies that characterize the various properties of the system in an attempt to improve the performance of lithium ion cells. However, very little has been done to quantify the experimental observations and relate these results to the existing mathematical models. In fact, the best of the physics based models in the literature show as much as 20% discrepancy when compared to experimental data. The reasons for such a big difference include, but are not limited to, numerical complexities involved in extracting parameters from experimental data and inconsistencies in interpreting directly measured values for the parameters. In this work, an attempt has been made to implement simplified models to extract parameter values that accurately characterize the performance of lithium ion cells. The validity of these models under a variety of experimental conditions is verified using a model discrimination procedure. Transport and kinetic properties are estimated using a non-linear estimation procedure. The initial state of charge inside each electrode is also maintained as an unknown parameter, since this value plays a significant role in accurately matching experimental charge/discharge curves with model predictions and is not readily known from experimental data. The second part of the dissertation focuses on parameters that change rapidly with time. For example, in the case of lithium ion batteries used in Hybrid Electric Vehicle (HEV) applications, the prediction of the State of Charge (SOC) of the cell under a variety of

  2. Thermal contact through a two-temperature kinetic Ising chain

    NASA Astrophysics Data System (ADS)

    Bauer, M.; Cornu, F.

    2018-05-01

    We consider a model for thermal contact through a diathermal interface between two macroscopic bodies at different temperatures: an Ising spin chain with nearest neighbor interactions is endowed with a Glauber dynamics with different temperatures and kinetic parameters on alternating sites. The inhomogeneity of the kinetic parameter is a novelty with respect to the model of Racz and Zia (1994 Phys. Rev. E 49 139), and we exhibit its influence upon the stationary non equilibrium values of the two-spin correlations at any distance. By mapping to the dynamics of spin domain walls and using free fermion techniques, we determine the scaled generating function for the cumulants of the exchanged heat amounts per unit of time in the long time limit.

  3. Analysis of a kinetic multi-segment foot model part II: kinetics and clinical implications.

    PubMed

    Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

    2012-04-01

    Kinematic multi-segment foot models have seen increased use in clinical and research settings, but the addition of kinetics has been limited and hampered by measurement limitations and modeling assumptions. In this second of two companion papers, we complete the presentation and analysis of a three segment kinetic foot model by incorporating kinetic parameters and calculating joint moments and powers. The model was tested on 17 pediatric subjects (ages 7-18 years) during normal gait. Ground reaction forces were measured using two adjacent force platforms, requiring targeted walking and the creation of two sub-models to analyze ankle, midtarsal, and 1st metatarsophalangeal joints. Targeted walking resulted in only minimal kinematic and kinetic differences compared with walking at self selected speeds. Joint moments and powers were calculated and ensemble averages are presented as a normative database for comparison purposes. Ankle joint powers are shown to be overestimated when using a traditional single-segment foot model, as substantial angular velocities are attributed to the mid-tarsal joint. Power transfer is apparent between the 1st metatarsophalangeal and mid-tarsal joints in terminal stance/pre-swing. While the measurement approach presented here is limited to clinical populations with only minimal impairments, some elements of the model can also be incorporated into routine clinical gait analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Ion kinetic scale in the solar wind observed.

    PubMed

    Śafránková, Jana; Němeček, Zdeněk; Přech, Lubomír; Zastenker, Georgy N

    2013-01-11

    This Letter shows the first results from the solar wind monitor onboard the Spektr-R spacecraft which measures plasma moments with a time resolution of 31 ms. This high-time resolution allows us to make direct observations of solar wind turbulence below ion kinetic length scales. We present examples of the frequency spectra of the density, velocity, and thermal velocity. Our study reveals that although these parameters exhibit the same behavior at the magnetohydrodynamic scale, their spectra are remarkably different at the kinetic scale.

  5. Supercritical water oxidation of quinazoline: Reaction kinetics and modeling.

    PubMed

    Gong, Yanmeng; Guo, Yang; Wang, Shuzhong; Song, Wenhan; Xu, Donghai

    2017-03-01

    This paper presents a first quantitative kinetic model for supercritical water oxidation (SCWO) of quinazoline that describes the formation and interconversion of intermediates and final products at 673-873 K. The set of 11 reaction pathways for phenol, pyrimidine, naphthalene, NH 3 , etc, involved in the simplified reaction network proved sufficient for fitting the experimental results satisfactorily. We validated the model prediction ability on CO 2 yields at initial quinazoline loading not used in the parameter estimation. Reaction rate analysis and sensitivity analysis indicate that nearly all reactions reach their thermodynamic equilibrium within 300 s. The pyrimidine yielding from quinazoline is the dominant ring-opening pathway and provides a significant contribution to CO 2 formation. Low sensitivity of NH 3 decomposition rate to concentration confirms its refractory nature in SCWO. Nitrogen content in liquid products decreases whereas that in gaseous phase increases as reaction time prolonged. The nitrogen predicted by the model in gaseous phase combined with the experimental nitrogen in liquid products gives an accurate nitrogen balance of conversion process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. A gas-kinetic BGK scheme for the compressible Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Xu, Kun

    2000-01-01

    This paper presents an improved gas-kinetic scheme based on the Bhatnagar-Gross-Krook (BGK) model for the compressible Navier-Stokes equations. The current method extends the previous gas-kinetic Navier-Stokes solver developed by Xu and Prendergast by implementing a general nonequilibrium state to represent the gas distribution function at the beginning of each time step. As a result, the requirement in the previous scheme, such as the particle collision time being less than the time step for the validity of the BGK Navier-Stokes solution, is removed. Therefore, the applicable regime of the current method is much enlarged and the Navier-Stokes solution can be obtained accurately regardless of the ratio between the collision time and the time step. The gas-kinetic Navier-Stokes solver developed by Chou and Baganoff is the limiting case of the current method, and it is valid only under such a limiting condition. Also, in this paper, the appropriate implementation of boundary condition for the kinetic scheme, different kinetic limiting cases, and the Prandtl number fix are presented. The connection among artificial dissipative central schemes, Godunov-type schemes, and the gas-kinetic BGK method is discussed. Many numerical tests are included to validate the current method.

  7. Global investigation of potential energy surfaces for the pyrolysis of C(1)-C(3) hydrocarbons: toward the development of detailed kinetic models from first principles.

    PubMed

    Ryazantsev, Mikhail N; Jamal, Adeel; Maeda, Satoshi; Morokuma, Keiji

    2015-11-07

    Detailed kinetic models (DKMs) are the most fundamental "bottom-up" approaches to computational investigation of the pyrolysis and oxidation of fuels. The weakest points of existing DKMs are incomplete information about the reaction types that can be involved in the potential energy surfaces (PESs) in pyrolysis and oxidation processes. Also, the computational thermodynamic parameters available in the literature vary widely with the level of theory employed. More sophisticated models require improvement both in our knowledge of the type of the reactions involved and the consistency of thermodynamic and kinetic parameters. In this paper, we aim to address these issues by developing ab initio models that can be used to describe early stages of pyrolysis of C1-C3 hydrocarbons. We applied a recently developed global reaction route mapping (GRRM) strategy to systematically investigate the PES of the pyrolysis of C1-C3 hydrocarbons at a consistent level of theory. The reactions are classified into 14 reaction types. The critical points on the PES for all reactions in the network are calculated at the highly accurate UCCSD(T)-F12b/cc-pVTZ//UM06-2X/cc-pVTZ level of theory. The data reported in this paper can be used for first principle calculations of kinetic constants and for a subsequent study on modeling the evolution of the species from the reaction network of the pyrolysis and oxidation of C1-C3 hydrocarbons.

  8. Determining the Kinetic Parameters Characteristic of Microalgal Growth.

    ERIC Educational Resources Information Center

    Martinez Sancho, Maria Eugenie; And Others

    1991-01-01

    An activity in which students obtain a growth curve for algae, identify the exponential and linear growth phases, and calculate the parameters which characterize both phases is described. The procedure, a list of required materials, experimental conditions, analytical technique, and a discussion of the interpretations of individual results are…

  9. Kinetic modeling of ethane pyrolysis at high conversion.

    PubMed

    Xu, Chen; Al Shoaibi, Ahmed Sultan; Wang, Chenguang; Carstensen, Hans-Heinrich; Dean, Anthony M

    2011-09-29

    The primary objective of this study is to develop an improved first-principle-based mechanism that describes the molecular weight growth kinetics observed during ethane pyrolysis. A proper characterization of the kinetics of ethane pyrolysis is a prerequisite for any analysis of hydrocarbon pyrolysis and oxidation. Flow reactor experiments were performed with ~50/50 ethane/nitrogen mixtures with temperatures ranging from 550 to 850 °C at an absolute pressure of ~0.8 atm and a residence time of ~5 s. These conditions result in ethane conversions ranging from virtually no reaction to ~90%. Comparisons of predictions using our original mechanism to these data yielded very satisfactory results in terms of the temperature dependence of ethane conversion and prediction of the major products ethylene and hydrogen. However, there were discrepancies in some of the minor species concentrations that are involved in the molecular weight growth kinetics. We performed a series of CBS-QB3 analyses for the C(3)H(7), C(4)H(7), and C(4)H(9) potential energy surfaces to better characterize the radical addition reactions that lead to molecular weight growth. We also extended a published C(6)H(9) PES to include addition of vinyl to butadiene. The results were then used to calculate pressure-dependent rate constants for the multiple reaction pathways of these addition reactions. Inclusion of the unadjusted rate constants resulting from these analyses in the mechanism significantly improved the description of several of the species involved in molecular weight growth kinetics. We compare the predictions of this improved model to those obtained with a consensus model recently published as well as to ethane steam cracking data. We find that a particularly important reaction is that of vinyl addition to butadiene. Another important observation is that several radical addition reactions are partially equilibrated. Not only does this mean that reliable thermodynamic parameters are essential

  10. Highly resolved fluid flows: "liquid plasmas" at the kinetic level.

    PubMed

    Morfill, Gregor E; Rubin-Zuzic, Milenko; Rothermel, Hermann; Ivlev, Alexei V; Klumov, Boris A; Thomas, Hubertus M; Konopka, Uwe; Steinberg, Victor

    2004-04-30

    Fluid flow around an obstacle was observed at the kinetic (individual particle) level using "complex (dusty) plasmas" in their liquid state. These "liquid plasmas" have bulk properties similar to water (e.g., viscosity), and a comparison in terms of similarity parameters suggests that they can provide a unique tool to model classical fluids. This allows us to study "nanofluidics" at the most elementary-the particle-level, including the transition from fluid behavior to purely kinetic transport. In this (first) experimental investigation we describe the kinetic flow topology, discuss our observations in terms of fluid theories, and follow this up with numerical simulations.

  11. First-order kinetic gas generation model parameters for wet landfills.

    PubMed

    Faour, Ayman A; Reinhart, Debra R; You, Huaxin

    2007-01-01

    Landfill gas collection data from wet landfill cells were analyzed and first-order gas generation model parameters were estimated for the US EPA landfill gas emissions model (LandGEM). Parameters were determined through statistical comparison of predicted and actual gas collection. The US EPA LandGEM model appeared to fit the data well, provided it is preceded by a lag phase, which on average was 1.5 years. The first-order reaction rate constant, k, and the methane generation potential, L(o), were estimated for a set of landfills with short-term waste placement and long-term gas collection data. Mean and 95% confidence parameter estimates for these data sets were found using mixed-effects model regression followed by bootstrap analysis. The mean values for the specific methane volume produced during the lag phase (V(sto)), L(o), and k were 33 m(3)/Megagrams (Mg), 76 m(3)/Mg, and 0.28 year(-1), respectively. Parameters were also estimated for three full scale wet landfills where waste was placed over many years. The k and L(o) estimated for these landfills were 0.21 year(-1), 115 m(3)/Mg, 0.11 year(-1), 95 m(3)/Mg, and 0.12 year(-1) and 87 m(3)/Mg, respectively. A group of data points from wet landfills cells with short-term data were also analyzed. A conservative set of parameter estimates was suggested based on the upper 95% confidence interval parameters as a k of 0.3 year(-1) and a L(o) of 100 m(3)/Mg if design is optimized and the lag is minimized.

  12. Relationships between PEMFC Cathode Kinetic Losses and Contaminants’ Dipole Moment and Adsorption Energy on Pt

    DOE PAGES

    St-Pierre, Jean; Zhai, Yunfeng; Ge, Junjie

    2016-01-05

    A database summarizing the effects of 21 contaminants on the performance of proton exchange membrane fuel cells (PEMFCs) was used to examine relationships between cathode kinetic losses and contaminant physicochemical parameters. Impedance spectroscopy data were employed to obtain oxygen reduction kinetic resistances by fitting data in the 10-158 Hz range to a simplified equivalent circuit. The contaminant dipole moment and the adsorption energy of the contaminant on a Pt surface were chosen as parameters. Dipole moments did not correlate with dimensionless cathode kinetic resistances. In contrast, adsorption energies were quantitatively and linearly correlated with minimum dimensionless cathode kinetic resistances. Contaminantsmore » influence the oxygen reduction for contaminant adsorption energies smaller than -24.5 kJ mol -1, a value near the high limit of the adsorption energy of O 2 on Pt. Dimensionless cathode kinetic resistances linearly increase with decreasing O 2 adsorption energies below -24.5 kJ mol -1. Measured total cell voltage losses are mostly larger than the cathode kinetic losses calculated from kinetic resistance changes, which indicates the existence of other sources of performance degradation. Modifications to the experimental procedure are proposed to ensure that data are comparable on a similar basis and improve the correlation between contaminant adsorption energy and kinetic cell voltage losses.« less

  13. Relationships between PEMFC Cathode Kinetic Losses and Contaminants’ Dipole Moment and Adsorption Energy on Pt

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

    St-Pierre, Jean; Zhai, Yunfeng; Ge, Junjie

    A database summarizing the effects of 21 contaminants on the performance of proton exchange membrane fuel cells (PEMFCs) was used to examine relationships between cathode kinetic losses and contaminant physicochemical parameters. Impedance spectroscopy data were employed to obtain oxygen reduction kinetic resistances by fitting data in the 10-158 Hz range to a simplified equivalent circuit. The contaminant dipole moment and the adsorption energy of the contaminant on a Pt surface were chosen as parameters. Dipole moments did not correlate with dimensionless cathode kinetic resistances. In contrast, adsorption energies were quantitatively and linearly correlated with minimum dimensionless cathode kinetic resistances. Contaminantsmore » influence the oxygen reduction for contaminant adsorption energies smaller than -24.5 kJ mol -1, a value near the high limit of the adsorption energy of O 2 on Pt. Dimensionless cathode kinetic resistances linearly increase with decreasing O 2 adsorption energies below -24.5 kJ mol -1. Measured total cell voltage losses are mostly larger than the cathode kinetic losses calculated from kinetic resistance changes, which indicates the existence of other sources of performance degradation. Modifications to the experimental procedure are proposed to ensure that data are comparable on a similar basis and improve the correlation between contaminant adsorption energy and kinetic cell voltage losses.« less

  14. Rethinking wave-kinetic theory applied to zonal flows

    NASA Astrophysics Data System (ADS)

    Parker, Jeffrey

    2017-10-01

    Over the past two decades, a number of studies have employed a wave-kinetic theory to describe fluctuations interacting with zonal flows. Recent work has uncovered a defect in this wave-kinetic formulation: the system is dominated by the growth of (arbitrarily) small-scale zonal structures. Theoretical calculations of linear growth rates suggest, and nonlinear simulations confirm, that this system leads to the concentration of zonal flow energy in the smallest resolved scales, irrespective of the numerical resolution. This behavior results from the assumption that zonal flows are extremely long wavelength, leading to the neglect of key terms responsible for conservation of enstrophy. A corrected theory, CE2-GO, is presented; it is free of these errors yet preserves the intuitive phase-space mathematical structure. CE2-GO properly conserves enstrophy as well as energy, and yields accurate growth rates of zonal flow. Numerical simulations are shown to be well-behaved and not dependent on box size. The steady-state limit simplifies into an exact wave-kinetic form which offers the promise of deeper insight into the behavior of wavepackets. The CE2-GO theory takes its place in a hierarchy of models as the geometrical-optics reduction of the more complete cumulant-expansion statistical theory CE2. The new theory represents the minimal statistical description, enabling an intuitive phase-space formulation and an accurate description of turbulence-zonal flow dynamics. This work was supported by an NSF Graduate Research Fellowship, a US DOE Fusion Energy Sciences Fellowship, and US DOE Contract Nos. DE-AC52-07NA27344 and DE-AC02-09CH11466.

  15. Characterization, kinetic, and thermodynamic studies of marine pectinase from Bacillus subtilis.

    PubMed

    Joshi, Manasi; Nerurkar, Madhura; Adivarekar, Ravindra

    2015-01-01

    Characterization, kinetic and thermodynamic parameters of purified pectinase from Bacillus subtilis, isolated from a marine sediment sample collected from Chinchani beach at Tarapore, India, were studied. Marine pectinase produced under submerged growth conditions was purified by ammonium sulfate precipitation followed by gel filtration chromatography using DEAE cellulose. Partial characterization of the marine pectinase was carried out in terms of effect of pH, temperature, substrate concentration, and metal ions. It was found that pectinase from marine B. subtilis showed maximal activity in alkaline buffer at pH 9.0 and at 40°C. It was also found that metal ions, namely, Mn(2+) and Fe(2+), stimulate pectinase activity. Marine pectinase followed Michaelis-Menten kinetics. The kinetics and thermodynamic parameters of the purified marine pectinase from B. subtilis were studied as the characterization of the enzyme is vital for its use in industrial processes.

  16. Accurate acceleration of kinetic Monte Carlo simulations through the modification of rate constants.

    PubMed

    Chatterjee, Abhijit; Voter, Arthur F

    2010-05-21

    We present a novel computational algorithm called the accelerated superbasin kinetic Monte Carlo (AS-KMC) method that enables a more efficient study of rare-event dynamics than the standard KMC method while maintaining control over the error. In AS-KMC, the rate constants for processes that are observed many times are lowered during the course of a simulation. As a result, rare processes are observed more frequently than in KMC and the time progresses faster. We first derive error estimates for AS-KMC when the rate constants are modified. These error estimates are next employed to develop a procedure for lowering process rates with control over the maximum error. Finally, numerical calculations are performed to demonstrate that the AS-KMC method captures the correct dynamics, while providing significant CPU savings over KMC in most cases. We show that the AS-KMC method can be employed with any KMC model, even when no time scale separation is present (although in such cases no computational speed-up is observed), without requiring the knowledge of various time scales present in the system.

  17. Kinetics and mechanism of olefin catalytic hydroalumination by organoaluminum compounds

    NASA Astrophysics Data System (ADS)

    Koledina, K. F.; Gubaidullin, I. M.

    2016-05-01

    The complex reaction mechanism of α-olefin catalytic hydroalumination by alkylalanes is investigated via mathematical modeling that involves plotting the kinetic models for the individual reactions that make up a complex system and a separate study of their principles. Kinetic parameters of olefin catalytic hydroalumination are estimated. Activation energies of the possible steps of the schemes of complex reaction mechanisms are compared and possible reaction pathways are determined.

  18. Comparison of kinetic and extended magnetohydrodynamics computational models for the linear ion temperature gradient instability in slab geometry

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

    Schnack, D. D.; Department of Physics, University of Wisconsin-Madison, Madison, Wisconsin 53706; Cheng, J.

    We perform linear stability studies of the ion temperature gradient (ITG) instability in unsheared slab geometry using kinetic and extended magnetohydrodynamics (MHD) models, in the regime k{sub ∥}/k{sub ⊥}≪1. The ITG is a parallel (to B) sound wave that may be destabilized by finite ion Larmor radius (FLR) effects in the presence of a gradient in the equilibrium ion temperature. The ITG is stable in both ideal and resistive MHD; for a given temperature scale length L{sub Ti0}, instability requires that either k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} be sufficiently large. Kinetic models capture FLR effects to all ordersmore » in either parameter. In the extended MHD model, these effects are captured only to lowest order by means of the Braginskii ion gyro-viscous stress tensor and the ion diamagnetic heat flux. We present the linear electrostatic dispersion relations for the ITG for both kinetic Vlasov and extended MHD (two-fluid) models in the local approximation. In the low frequency fluid regime, these reduce to the same cubic equation for the complex eigenvalue ω=ω{sub r}+iγ. An explicit solution is derived for the growth rate and real frequency in this regime. These are found to depend on a single non-dimensional parameter. We also compute the eigenvalues and the eigenfunctions with the extended MHD code NIMROD, and a hybrid kinetic δf code that assumes six-dimensional Vlasov ions and isothermal fluid electrons, as functions of k{sub ⊥}ρ{sub i} and ρ{sub i}/L{sub Ti0} using a spatially dependent equilibrium. These solutions are compared with each other, and with the predictions of the local kinetic and fluid dispersion relations. Kinetic and fluid calculations agree well at and near the marginal stability point, but diverge as k{sub ⊥}ρ{sub i} or ρ{sub i}/L{sub Ti0} increases. There is good qualitative agreement between the models for the shape of the unstable global eigenfunction for L{sub Ti0}/ρ{sub i}=30 and 20. The results quantify

  19. Isotherm Modelling, Kinetic Study and Optimization of Batch Parameters Using Response Surface Methodology for Effective Removal of Cr(VI) Using Fungal Biomass

    PubMed Central

    Chidambaram, Ramalingam

    2015-01-01

    Biosorption is a promising alternative method to replace the existing conventional technique for Cr(VI) removal from the industrial effluent. In the present experimental design, the removal of Cr(VI) from the aqueous solution was studied by Aspergillus niger MSR4 under different environmental conditions in the batch systems. The optimum conditions of biosorption were determined by investigating pH (2.0) and temperature (27°C). The effects of parameters such as biomass dosage (g/L), initial Cr(VI) concentration (mg/L) and contact time (min) on Cr(VI) biosorption were analyzed using a three parameter Box–Behnken design (BBD). The experimental data well fitted to the Langmuir isotherm, in comparison to the other isotherm models tested. The results of the D-R isotherm model suggested that a chemical ion-exchange mechanism was involved in the biosorption process. The biosorption process followed the pseudo-second-order kinetic model, which indicates that the rate limiting step is chemisorption process. Fourier transform infrared (FT-IR) spectroscopic studies revealed the possible involvement of functional groups, such as hydroxyl, carboxyl, amino and carbonyl group in the biosorption process. The thermodynamic parameters for Cr(VI) biosorption were also calculated, and the negative ∆Gº values indicated the spontaneous nature of biosorption process. PMID:25786227

  20. Accurate Modeling Method for Cu Interconnect

    NASA Astrophysics Data System (ADS)

    Yamada, Kenta; Kitahara, Hiroshi; Asai, Yoshihiko; Sakamoto, Hideo; Okada, Norio; Yasuda, Makoto; Oda, Noriaki; Sakurai, Michio; Hiroi, Masayuki; Takewaki, Toshiyuki; Ohnishi, Sadayuki; Iguchi, Manabu; Minda, Hiroyasu; Suzuki, Mieko

    This paper proposes an accurate modeling method of the copper interconnect cross-section in which the width and thickness dependence on layout patterns and density caused by processes (CMP, etching, sputtering, lithography, and so on) are fully, incorporated and universally expressed. In addition, we have developed specific test patterns for the model parameters extraction, and an efficient extraction flow. We have extracted the model parameters for 0.15μm CMOS using this method and confirmed that 10%τpd error normally observed with conventional LPE (Layout Parameters Extraction) was completely dissolved. Moreover, it is verified that the model can be applied to more advanced technologies (90nm, 65nm and 55nm CMOS). Since the interconnect delay variations due to the processes constitute a significant part of what have conventionally been treated as random variations, use of the proposed model could enable one to greatly narrow the guardbands required to guarantee a desired yield, thereby facilitating design closure.

  1. On the relationships between Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, Equilibrium Chemistry Approximation kinetics and quadratic kinetics

    DOE PAGES

    Tang, J. Y.

    2015-09-03

    The Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use which of the two are often ambiguous. Here I show that these two kinetics are special approximations to the Equilibrium Chemistry Approximation kinetics, which is the first order approximation to the quadratic kinetics that solves the equation of enzyme-substrate complex exactly for a single enzyme single substrate biogeochemical reaction with the law of mass action and the assumption of quasi-steady-state formore » the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates and enzymes. In particular, I showed that the derivation of the Michaelis–Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis–Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in the Equilibrium Chemistry Approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis–Menten kinetics was found to persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln k 2 + of the reaction velocity v with respect to the maximum product genesis rate k 2 +, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln k 1 + of v with respect to the intrinsic substrate affinity k 1 +, persistently over-predict the normalized sensitivity ∂ ln v / ∂ ln [ E ] T of v with respect the total enzyme concentration [ E ] T and persistently under-predict the normalized sensitivity ∂ ln v / ∂ ln [ S ] T of v with respect to the total substrate concentration [ S ] T

  2. Rock Cutting Depth Model Based on Kinetic Energy of Abrasive Waterjet

    NASA Astrophysics Data System (ADS)

    Oh, Tae-Min; Cho, Gye-Chun

    2016-03-01

    Abrasive waterjets are widely used in the fields of civil and mechanical engineering for cutting a great variety of hard materials including rocks, metals, and other materials. Cutting depth is an important index to estimate operating time and cost, but it is very difficult to predict because there are a number of influential variables (e.g., energy, geometry, material, and nozzle system parameters). In this study, the cutting depth is correlated to the maximum kinetic energy expressed in terms of energy (i.e., water pressure, water flow rate, abrasive feed rate, and traverse speed), geometry (i.e., standoff distance), material (i.e., α and β), and nozzle system parameters (i.e., nozzle size, shape, and jet diffusion level). The maximum kinetic energy cutting depth model is verified with experimental test data that are obtained using one type of hard granite specimen for various parameters. The results show a unique curve for a specific rock type in a power function between cutting depth and maximum kinetic energy. The cutting depth model developed here can be very useful for estimating the process time when cutting rock using an abrasive waterjet.

  3. Modelling dimercaptosuccinic acid (DMSA) plasma kinetics in humans.

    PubMed

    van Eijkeren, Jan C H; Olie, J Daniël N; Bradberry, Sally M; Vale, J Allister; de Vries, Irma; Meulenbelt, Jan; Hunault, Claudine C

    2016-11-01

    No kinetic models presently exist which simulate the effect of chelation therapy on lead blood concentrations in lead poisoning. Our aim was to develop a kinetic model that describes the kinetics of dimercaptosuccinic acid (DMSA; succimer), a commonly used chelating agent, that could be used in developing a lead chelating model. This was a kinetic modelling study. We used a two-compartment model, with a non-systemic gastrointestinal compartment (gut lumen) and the whole body as one systemic compartment. The only data available from the literature were used to calibrate the unknown model parameters. The calibrated model was then validated by comparing its predictions with measured data from three different experimental human studies. The model predicted total DMSA plasma and urine concentrations measured in three healthy volunteers after ingestion of DMSA 10 mg/kg. The model was then validated by using data from three other published studies; it predicted concentrations within a factor of two, representing inter-human variability. A simple kinetic model simulating the kinetics of DMSA in humans has been developed and validated. The interest of this model lies in the future potential to use it to predict blood lead concentrations in lead-poisoned patients treated with DMSA.

  4. Stepwise kinetic equilibrium models of quantitative polymerase chain reaction.

    PubMed

    Cobbs, Gary

    2012-08-16

    Numerous models for use in interpreting quantitative PCR (qPCR) data are present in recent literature. The most commonly used models assume the amplification in qPCR is exponential and fit an exponential model with a constant rate of increase to a select part of the curve. Kinetic theory may be used to model the annealing phase and does not assume constant efficiency of amplification. Mechanistic models describing the annealing phase with kinetic theory offer the most potential for accurate interpretation of qPCR data. Even so, they have not been thoroughly investigated and are rarely used for interpretation of qPCR data. New results for kinetic modeling of qPCR are presented. Two models are presented in which the efficiency of amplification is based on equilibrium solutions for the annealing phase of the qPCR process. Model 1 assumes annealing of complementary targets strands and annealing of target and primers are both reversible reactions and reach a dynamic equilibrium. Model 2 assumes all annealing reactions are nonreversible and equilibrium is static. Both models include the effect of primer concentration during the annealing phase. Analytic formulae are given for the equilibrium values of all single and double stranded molecules at the end of the annealing step. The equilibrium values are then used in a stepwise method to describe the whole qPCR process. Rate constants of kinetic models are the same for solutions that are identical except for possibly having different initial target concentrations. Analysis of qPCR curves from such solutions are thus analyzed by simultaneous non-linear curve fitting with the same rate constant values applying to all curves and each curve having a unique value for initial target concentration. The models were fit to two data sets for which the true initial target concentrations are known. Both models give better fit to observed qPCR data than other kinetic models present in the literature. They also give better estimates of

  5. Thermodynamically Feasible Kinetic Models of Reaction Networks

    PubMed Central

    Ederer, Michael; Gilles, Ernst Dieter

    2007-01-01

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

  6. Positron kinetics in an idealized PET environment

    PubMed Central

    Robson, R. E.; Brunger, M. J.; Buckman, S. J.; Garcia, G.; Petrović, Z. Lj.; White, R. D.

    2015-01-01

    The kinetic theory of non-relativistic positrons in an idealized positron emission tomography PET environment is developed by solving the Boltzmann equation, allowing for coherent and incoherent elastic, inelastic, ionizing and annihilating collisions through positronium formation. An analytic expression is obtained for the positronium formation rate, as a function of distance from a spherical source, in terms of the solutions of the general kinetic eigenvalue problem. Numerical estimates of the positron range - a fundamental limitation on the accuracy of PET, are given for positrons in a model of liquid water, a surrogate for human tissue. Comparisons are made with the ‘gas-phase’ assumption used in current models in which coherent scattering is suppressed. Our results show that this assumption leads to an error of the order of a factor of approximately 2, emphasizing the need to accurately account for the structure of the medium in PET simulations. PMID:26246002

  7. Oil-generation kinetics for organic facies with Type-II and -IIS kerogen in the Menilite Shales of the Polish Carpathians

    USGS Publications Warehouse

    Lewan, M.D.; Kotarba, M.J.; Curtis, John B.; Wieclaw, D.; Kosakowski, P.

    2006-01-01

    The Menilite Shales (Oligocene) of the Polish Carpathians are the source of low-sulfur oils in the thrust belt and some high-sulfur oils in the Carpathian Foredeep. These oil occurrences indicate that the high-sulfur oils in the Foredeep were generated and expelled before major thrusting and the low-sulfur oils in the thrust belt were generated and expelled during or after major thrusting. Two distinct organic facies have been observed in the Menilite Shales. One organic facies has a high clastic sediment input and contains Type-II kerogen. The other organic facies has a lower clastic sediment input and contains Type-IIS kerogen. Representative samples of both organic facies were used to determine kinetic parameters for immiscible oil generation by isothermal hydrous pyrolysis and S2 generation by non-isothermal open-system pyrolysis. The derived kinetic parameters showed that timing of S2 generation was not as different between the Type-IIS and -II kerogen based on open-system pyrolysis as compared with immiscible oil generation based on hydrous pyrolysis. Applying these kinetic parameters to a burial history in the Skole unit showed that some expelled oil would have been generated from the organic facies with Type-IIS kerogen before major thrusting with the hydrous-pyrolysis kinetic parameters but not with the open-system pyrolysis kinetic parameters. The inability of open-system pyrolysis to determine earlier petroleum generation from Type-IIS kerogen is attributed to the large polar-rich bitumen component in S2 generation, rapid loss of sulfur free-radical initiators in the open system, and diminished radical selectivity and rate constant differences at higher temperatures. Hydrous-pyrolysis kinetic parameters are determined in the presence of water at lower temperatures in a closed system, which allows differentiation of bitumen and oil generation, interaction of free-radical initiators, greater radical selectivity, and more distinguishable rate constants as

  8. LSENS, a general chemical kinetics and sensitivity analysis code for homogeneous gas-phase reactions. 2: Code description and usage

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Bittker, David A.

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part 2 of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part 2 describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part 1 (NASA RP-1328) derives the governing equations describes the numerical solution procedures for the types of problems that can be solved by lSENS. Part 3 (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

  9. Parameter estimation in tree graph metabolic networks.

    PubMed

    Astola, Laura; Stigter, Hans; Gomez Roldan, Maria Victoria; van Eeuwijk, Fred; Hall, Robert D; Groenenboom, Marian; Molenaar, Jaap J

    2016-01-01

    We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree-like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

  10. Performance of a kinetic model for intracellular ice formation based on the extent of supercooling.

    PubMed

    Pitt, R E; Chandrasekaran, M; Parks, J E

    1992-06-01

    Cryomicroscopy was used to study the incidence of intracellular ice formation (IIF) in protoplasts isolated from rye (Secale cereale) leaves during subfreezing isothermal periods and in in vitro mature bovine oocytes during cooling at constant rates. IIF in protoplasts occurred at random times during isothermal periods, and the kinetics of IIF were faster as isothermal temperature decreased. Mean IIF times decreased from approximately 1700 s at -4.0 degrees C to less than 1 s at -18.5 degrees C. Total incidence of IIF after 200 s increased from 4% at -4.0 degrees C to near 100% at -15.5 degrees C. IIF behavior in protoplasts was qualitatively similar to that for Drosophila melanogaster embryos over the same temperature ranges (Myers et al., Cryobiology 26, 472-484, 1989), but the kinetics of IIF were about five times faster in protoplasts. IIF observations in linear cooling of bovine oocytes indicated a median IIF temperature of -11 degrees C at 16 degrees C/min and total incidences of 97%, 50%, and 19% at 16, 8, and 4 degrees C/min, respectively. A stochastic model of IIF was developed which preserved certain features of an earlier model (Pitt et al. Cryobiology 28, 72-86, 1991), namely Weibull behavior in IIF temperatures during rapid linear cooling, but with a departure from the concept of a supercooling tolerance. Instead, the new model uses the osmotic state of the cell, represented by the extent of supercooling, as the independent variable governing the kinetics of IIF. Two kinetic parameters are needed for the model: a scale factor tau 0 dictating the sensitivity to supercooling, and an exponent rho dictating the strength of time dependency. The model was fit to the data presented in this study as well as those from Myers et al. and Pitt et al. for D. melanogaster embryos with and without cryoprotectant, and from Toner et al. (Cryobiology 28, 55-71, 1991) for mouse oocytes. In protoplasts, D. melanogaster embryos, and mouse oocytes, the parameters were

  11. Being Careful with PASCO's Kinetic Friction Experiment: Uncovering Pre-Sliding Displacement?

    ERIC Educational Resources Information Center

    Lawlor, T. M.

    2008-01-01

    The widely used PASCO laboratory equipment is an excellent way to introduce students to many topics in physics. In one case, PASCO's equipment may be too good! Various experiments exist for calculating the kinetic coefficient of friction by measuring the acceleration of a sliding object under some constant force. With ever more accurate equipment,…

  12. Kinetics of thermophilic anaerobes in fixed-bed reactors.

    PubMed

    Perez, M; Romero, L I; Sales, D

    2001-08-01

    The main objective of this study is to estimate growth kinetic constants and the concentration of "active" attached biomass in two anaerobic thermophilic reactors which contain different initial sizes of immobilized anaerobic mixed cultures and decompose distillery wastewater. This paper studies the substrate decomposition in two lab-scale fixed-bed reactors operating at batch conditions with corrugated tubes as support media. It can be demonstrated that high micro-organisms-substrate ratios favor the degradation activity of the different anaerobic cultures, allowing the stable operation without lag-phases and giving better quality in effluent. The kinetic parameters obtained--maximum specific growth rates (mu(max)), non-biodegradable substrate (S(NB)) and "active or viable biomass" concentrations (X(V0))--were obtained by applying the Romero kinetic model [L.I. Romero, 1991. Desarrollo de un modelo matemático general para los procesos fermentativos, Cinética de la degradación anaerobia, Ph.D. Thesis, University of Cádiz (Spain), Serv. Pub. Univ. Cádiz], with COD as substrate and methane (CH4) as the main product of the anaerobic process. This method is suitable to calculate and to differentiate the main kinetic parameters of both the total anaerobic mixed culture and the methanogenic population. Comparison of experimental measured concentration of volatile attached solids (VS(att)) in both reactors with the estimated "active" biomass concentrations obtained by applying Romero kinetic model [L.I. Romero, 1991. Desarrollo de un modelo matemático general para los procesos fermentativos, Cinética de la degradación anaerobia, Ph.D. Thesis, University of Cádiz (Spain), Serv. Pub. Univ. Cádiz] shows that a large amount of inert matter is present in the fixed-bed reactor.

  13. A Study of the Optimal Model of the Flotation Kinetics of Copper Slag from Copper Mine BOR

    NASA Astrophysics Data System (ADS)

    Stanojlović, Rodoljub D.; Sokolović, Jovica M.

    2014-10-01

    In this study the effect of mixtures of copper slag and flotation tailings from copper mine Bor, Serbia on the flotation results of copper recovery and flotation kinetics parameters in a batch flotation cell has been investigated. By simultaneous adding old flotation tailings in the ball mill at the rate of 9%, it is possible to increase copper recovery for about 20%. These results are compared with obtained copper recovery of pure copper slag. The results of batch flotation test were fitted by MatLab software for modeling the first-order flotation kinetics in order to determine kinetics parameters and define an optimal model of the flotation kinetics. Six kinetic models are tested on the batch flotation copper recovery against flotation time. All models showed good correlation, however the modified Kelsall model provided the best fit.

  14. Contribution of counterions and degree of ionization for birefringence creation and relaxation kinetics parameters of PAH/PAZO films

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

    Raposo, Maria, E-mail: mfr@fct.unl.pt; Monteiro Timóteo, Ana Rita; Ribeiro, Paulo A.

    2015-09-21

    Photo induced birefringent materials can be used to develop optical and conversion energy devices, and consequently, the study of the variables that influences the creation and relaxation of birefringence should be carefully analyzed. In this work, the parameters of birefringence creation and relaxation kinetics curves obtained on layer-by-layer (LBL) films, prepared from azo-polyectrolyte poly[1-[4-(3-carboxy-4 hydroxyphenylazo) benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) and poly(allylamine hydrochloride)(PAH), are related with the presence of counterions and the degree of ionization of the polyelectrolytes. Those kinetics curves obtained on PAH/PAZO LBL films, prepared from PAH solutions with different pHs and maintaining the pH of PAZO solutionmore » constant at pH = 9, were analyzed taking into account the films composition which was characterized by X-ray photoelectron spectroscopy. The creation and relaxation birefringence curves are justified by two processes: one associated to local mobility of the azobenzene with a characteristic time 30 s and intensity constant and other associated with polymeric chains mobility with the characteristic time and intensity decreasing with pH. These results allow us to conclude that the birefringence creation process, associated to local mobility of azobenzenes is independent of the degree of ionization and of number of counterions or co-ions present while the birefringence creation process associated to mobility of chains have its characteristic time and intensity dependent of both degree of ionization and number of counterions. The birefringence relaxation processes are dependent of the degree of ionization. The analysis of the films composition revealed, in addition, the presence of a protonated secondary or tertiary amine revealing that PAZO may have positive charges and consequently a zwitterionic behavior.« less

  15. Programmable energy landscapes for kinetic control of DNA strand displacement.

    PubMed

    Machinek, Robert R F; Ouldridge, Thomas E; Haley, Natalie E C; Bath, Jonathan; Turberfield, Andrew J

    2014-11-10

    DNA is used to construct synthetic systems that sense, actuate, move and compute. The operation of many dynamic DNA devices depends on toehold-mediated strand displacement, by which one DNA strand displaces another from a duplex. Kinetic control of strand displacement is particularly important in autonomous molecular machinery and molecular computation, in which non-equilibrium systems are controlled through rates of competing processes. Here, we introduce a new method based on the creation of mismatched base pairs as kinetic barriers to strand displacement. Reaction rate constants can be tuned across three orders of magnitude by altering the position of such a defect without significantly changing the stabilities of reactants or products. By modelling reaction free-energy landscapes, we explore the mechanistic basis of this control mechanism. We also demonstrate that oxDNA, a coarse-grained model of DNA, is capable of accurately predicting and explaining the impact of mismatches on displacement kinetics.

  16. Estimation of turbulent kinetic energy using 4D phase-contrast MRI: Effect of scan parameters and target vessel size.

    PubMed

    Ha, Hojin; Hwang, Dongha; Kim, Guk Bae; Kweon, Jihoon; Lee, Sang Joon; Baek, Jehyun; Kim, Young-Hak; Kim, Namkug; Yang, Dong Hyun

    2016-07-01

    Quantifying turbulence velocity fluctuation is important because it indicates the fluid energy dissipation of the blood flow, which is closely related to the pressure drop along the blood vessel. This study aims to evaluate the effects of scan parameters and the target vessel size of 4D phase-contrast (PC)-MRI on quantification of turbulent kinetic energy (TKE). Comprehensive 4D PC-MRI measurements with various velocity-encoding (VENC), echo time (TE), and voxel size values were carried out to estimate TKE distribution in stenotic flow. The total TKE (TKEsum), maximum TKE (TKEmax), and background noise level (TKEnoise) were compared for each scan parameter. The feasibility of TKE estimation in small vessels was also investigated. Results show that the optimum VENC for stenotic flow with a peak velocity of 125cm/s was 70cm/s. Higher VENC values overestimated the TKEsum by up to six-fold due to increased TKEnoise, whereas lower VENC values (30cm/s) underestimated it by 57.1%. TE and voxel size did not significantly influence the TKEsum and TKEnoise, although the TKEmax significantly increased as the voxel size increased. TKE quantification in small-sized vessels (3-5-mm diameter) was feasible unless high-velocity turbulence caused severe phase dispersion in the reference image. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Extracting surface diffusion coefficients from batch adsorption measurement data: application of the classic Langmuir kinetics model.

    PubMed

    Chu, Khim Hoong

    2017-11-09

    Surface diffusion coefficients may be estimated by fitting solutions of a diffusion model to batch kinetic data. For non-linear systems, a numerical solution of the diffusion model's governing equations is generally required. We report here the application of the classic Langmuir kinetics model to extract surface diffusion coefficients from batch kinetic data. The use of the Langmuir kinetics model in lieu of the conventional surface diffusion model allows derivation of an analytical expression. The parameter estimation procedure requires determining the Langmuir rate coefficient from which the pertinent surface diffusion coefficient is calculated. Surface diffusion coefficients within the 10 -9 to 10 -6  cm 2 /s range obtained by fitting the Langmuir kinetics model to experimental kinetic data taken from the literature are found to be consistent with the corresponding values obtained from the traditional surface diffusion model. The virtue of this simplified parameter estimation method is that it reduces the computational complexity as the analytical expression involves only an algebraic equation in closed form which is easily evaluated by spreadsheet computation.

  18. The effect of heart motion on parameter bias in dynamic cardiac SPECT

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

    Ross, S.G.; Gullberg, G.T.; Huesman, R.H.

    1996-12-31

    Dynamic cardiac SPECT can be used to estimate kinetic rate parameters which describe the wash-in and wash-out of tracer activity between the blood and the myocardial tissue. These kinetic parameters can in turn be correlated to myocardial perfusion. There are, however, many physical aspects associated with dynamic SPECT which can introduce errors into the estimates. This paper describes a study which investigates the effect of heart motion on kinetic parameter estimates. Dynamic SPECT simulations are performed using a beating version of the MCAT phantom. The results demonstrate that cardiac motion has a significant effect on the blood, tissue, and backgroundmore » content of regions of interest. This in turn affects estimates of wash-in, while it has very little effect on estimates of wash-out. The effect of cardiac motion on parameter estimates appears not to be as great as effects introduced by photon noise and geometric collimator response. It is also shown that cardiac motion results in little extravascular contamination of the left ventricle blood region of interest.« less

  19. On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics

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

    Tang, J. Y.

    The Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme–substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steadymore » state for the enzyme–substrate complex and that the product genesis from enzyme–substrate complex is much slower than the equilibration between enzyme–substrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis–Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis–Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis–Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln k 2 + of the reaction velocity v with respect to the maximum product genesis rate k 2 +, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln k 1 + of v with respect to the intrinsic substrate affinity k 1 +, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln [ E] T of v with respect the total enzyme concentration [ E] T, and persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln [ S] T of v with respect to the total substrate

  20. On the relationships between the Michaelis–Menten kinetics, reverse Michaelis–Menten kinetics, equilibrium chemistry approximation kinetics, and quadratic kinetics

    DOE PAGES

    Tang, J. Y.

    2015-12-01

    The Michaelis–Menten kinetics and the reverse Michaelis–Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme–substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steadymore » state for the enzyme–substrate complex and that the product genesis from enzyme–substrate complex is much slower than the equilibration between enzyme–substrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis–Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis–Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis–Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln k 2 + of the reaction velocity v with respect to the maximum product genesis rate k 2 +, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln k 1 + of v with respect to the intrinsic substrate affinity k 1 +, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln [ E] T of v with respect the total enzyme concentration [ E] T, and persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln [ S] T of v with respect to the total substrate

  1. TH-E-BRF-06: Kinetic Modeling of Tumor Response to Fractionated Radiotherapy

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

    Zhong, H; Gordon, J; Chetty, I

    2014-06-15

    Purpose: Accurate calibration of radiobiological parameters is crucial to predicting radiation treatment response. Modeling differences may have a significant impact on calibrated parameters. In this study, we have integrated two existing models with kinetic differential equations to formulate a new tumor regression model for calibrating radiobiological parameters for individual patients. Methods: A system of differential equations that characterizes the birth-and-death process of tumor cells in radiation treatment was analytically solved. The solution of this system was used to construct an iterative model (Z-model). The model consists of three parameters: tumor doubling time Td, half-life of dying cells Tr and cellmore » survival fraction SFD under dose D. The Jacobian determinant of this model was proposed as a constraint to optimize the three parameters for six head and neck cancer patients. The derived parameters were compared with those generated from the two existing models, Chvetsov model (C-model) and Lim model (L-model). The C-model and L-model were optimized with the parameter Td fixed. Results: With the Jacobian-constrained Z-model, the mean of the optimized cell survival fractions is 0.43±0.08, and the half-life of dying cells averaged over the six patients is 17.5±3.2 days. The parameters Tr and SFD optimized with the Z-model differ by 1.2% and 20.3% from those optimized with the Td-fixed C-model, and by 32.1% and 112.3% from those optimized with the Td-fixed L-model, respectively. Conclusion: The Z-model was analytically constructed from the cellpopulation differential equations to describe changes in the number of different tumor cells during the course of fractionated radiation treatment. The Jacobian constraints were proposed to optimize the three radiobiological parameters. The developed modeling and optimization methods may help develop high-quality treatment regimens for individual patients.« less

  2. Accurate parameters of the oldest known rocky-exoplanet hosting system: Kepler-10 revisited

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

    Fogtmann-Schulz, Alexandra; Hinrup, Brian; Van Eylen, Vincent

    2014-02-01

    Since the discovery of Kepler-10, the system has received considerable interest because it contains a small, rocky planet which orbits the star in less than a day. The system's parameters, announced by the Kepler team and subsequently used in further research, were based on only five months of data. We have reanalyzed this system using the full span of 29 months of Kepler photometric data, and obtained improved information about its star and the planets. A detailed asteroseismic analysis of the extended time series provides a significant improvement on the stellar parameters: not only can we state that Kepler-10 ismore » the oldest known rocky-planet-harboring system at 10.41 ± 1.36 Gyr, but these parameters combined with improved planetary parameters from new transit fits gives us the radius of Kepler-10b to within just 125 km. A new analysis of the full planetary phase curve leads to new estimates on the planetary temperature and albedo, which remain degenerate in the Kepler band. Our modeling suggests that the flux level during the occultation is slightly lower than at the transit wings, which would imply that the nightside of this planet has a non-negligible temperature.« less

  3. Thermodynamically consistent model calibration in chemical kinetics

    PubMed Central

    2011-01-01

    Background The dynamics of biochemical reaction systems are constrained by the fundamental laws of thermodynamics, which impose well-defined relationships among the reaction rate constants characterizing these systems. Constructing biochemical reaction systems from experimental observations often leads to parameter values that do not satisfy the necessary thermodynamic constraints. This can result in models that are not physically realizable and may lead to inaccurate, or even erroneous, descriptions of cellular function. Results We introduce a thermodynamically consistent model calibration (TCMC) method that can be effectively used to provide thermodynamically feasible values for the parameters of an open biochemical reaction system. The proposed method formulates the model calibration problem as a constrained optimization problem that takes thermodynamic constraints (and, if desired, additional non-thermodynamic constraints) into account. By calculating thermodynamically feasible values for the kinetic parameters of a well-known model of the EGF/ERK signaling cascade, we demonstrate the qualitative and quantitative significance of imposing thermodynamic constraints on these parameters and the effectiveness of our method for accomplishing this important task. MATLAB software, using the Systems Biology Toolbox 2.1, can be accessed from http://www.cis.jhu.edu/~goutsias/CSS lab/software.html. An SBML file containing the thermodynamically feasible EGF/ERK signaling cascade model can be found in the BioModels database. Conclusions TCMC is a simple and flexible method for obtaining physically plausible values for the kinetic parameters of open biochemical reaction systems. It can be effectively used to recalculate a thermodynamically consistent set of parameter values for existing thermodynamically infeasible biochemical reaction models of cellular function as well as to estimate thermodynamically feasible values for the parameters of new models. Furthermore, TCMC can

  4. Budgets of divergent and rotational kinetic energy during two periods of intense convection

    NASA Technical Reports Server (NTRS)

    Buechler, D. E.; Fuelberg, H. E.

    1986-01-01

    The derivations of the energy budget equations for divergent and rotational components of kinetic energy are provided. The intense convection periods studied are: (1) synoptic scale data of 3 or 6 hour intervals and (2) mesoalphascale data every 3 hours. Composite energies and averaged budgets for the periods are presented; the effects of random data errors on derived energy parameters is investigated. The divergent kinetic energy and rotational kinetic energy budgets are compared; good correlation of the data is observed. The kinetic energies and budget terms increase with convective development; however, the conversion of the divergent and rotational energies are opposite.

  5. Kinetics of MDR Transport in Tumor-Initiating Cells

    PubMed Central

    Koshkin, Vasilij; Yang, Burton B.; Krylov, Sergey N.

    2013-01-01

    Multidrug resistance (MDR) driven by ABC (ATP binding cassette) membrane transporters is one of the major causes of treatment failure in human malignancy. MDR capacity is thought to be unevenly distributed among tumor cells, with higher capacity residing in tumor-initiating cells (TIC) (though opposite finding are occasionally reported). Functional evidence for enhanced MDR of TICs was previously provided using a “side population” assay. This assay estimates MDR capacity by a single parameter - cell’s ability to retain fluorescent MDR substrate, so that cells with high MDR capacity (“side population”) demonstrate low substrate retention. In the present work MDR in TICs was investigated in greater detail using a kinetic approach, which monitors MDR efflux from single cells. Analysis of kinetic traces obtained allowed for the estimation of both the velocity (V max) and affinity (K M) of MDR transport in single cells. In this way it was shown that activation of MDR in TICs occurs in two ways: through the increase of V max in one fraction of cells, and through decrease of K M in another fraction. In addition, kinetic data showed that heterogeneity of MDR parameters in TICs significantly exceeds that of bulk cells. Potential consequences of these findings for chemotherapy are discussed. PMID:24223908

  6. Determination of well flat band condition in thin film FDSOI transistors using C-V measurement for accurate parameter extraction

    NASA Astrophysics Data System (ADS)

    Mohamad, B.; Leroux, C.; Reimbold, G.; Ghibaudo, G.

    2018-01-01

    For advanced gate stacks, effective work function (WFeff) and equivalent oxide thickness (EOT) are fundamental parameters for technology optimization. On FDSOI transistors, and contrary to the bulk technologies, while EOT can still be extracted at strong inversion from the typical gate-to-channel capacitance (Cgc), it is no longer the case for WFeff due to the disappearance of an observable flat band condition on capacitance characteristics. In this work, a new experimental method, the Cbg(VBG) characteristic, is proposed in order to extract the well flat band condition (VFB, W). This characteristic enables an accurate and direct evaluation of WFeff. Moreover, using the previous extraction of the gate oxide (tfox), and buried oxide (tbox) from typical capacitance characteristics (Cgc and Cbc), it allows the extraction of the channel thickness (tch). Furthermore, the measurement of the well flat band condition on Cbg(VBG) characteristics for two different Si and SiGe channel also proves the existence of a dipole at the SiGe/SiO2 interface.

  7. Kinetic modeling of active plasma resonance spectroscopy

    NASA Astrophysics Data System (ADS)

    Oberrath, Jens

    2016-09-01

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

  8. Lamtoro charcoal (l. leucocephala) as bioreductor in nickel laterite reduction: performance and kinetics study

    NASA Astrophysics Data System (ADS)

    Petrus, H. T. B. M.; Diga, A.; Rhamdani, A. R.; Warmada, I. W.; Yuliansyah, A. T.; Perdana, I.

    2017-04-01

    The performance and kinetic of nickel laterite reduction were studied. In this work, the reduction of nickel laterite ores by anthracite coal, representing the high-grade carbon content matter, and lamtoro charcoal, representing the bioreductor, were conducted in air and CO2 atmosphere, within the temperature ranged from 800°C and 1000°C. XRD analysis was applied to observe the performance of anthracite and lamtoro as a reductor. Two models were applied, sphere particle geometry model and Ginstling-Brounhstein diffusion model, to study the kinetic parameters. The results indicated that the type of reductant and the reduction atmosphere used greatly influence the kinetic parameters. The obtained values of activation energy vary in the range of 13.42-18.12 kcal/mol.

  9. Accurate modelling of unsteady flows in collapsible tubes.

    PubMed

    Marchandise, Emilie; Flaud, Patrice

    2010-01-01

    The context of this paper is the development of a general and efficient numerical haemodynamic tool to help clinicians and researchers in understanding of physiological flow phenomena. We propose an accurate one-dimensional Runge-Kutta discontinuous Galerkin (RK-DG) method coupled with lumped parameter models for the boundary conditions. The suggested model has already been successfully applied to haemodynamics in arteries and is now extended for the flow in collapsible tubes such as veins. The main difference with cardiovascular simulations is that the flow may become supercritical and elastic jumps may appear with the numerical consequence that scheme may not remain monotone if no limiting procedure is introduced. We show that our second-order RK-DG method equipped with an approximate Roe's Riemann solver and a slope-limiting procedure allows us to capture elastic jumps accurately. Moreover, this paper demonstrates that the complex physics associated with such flows is more accurately modelled than with traditional methods such as finite difference methods or finite volumes. We present various benchmark problems that show the flexibility and applicability of the numerical method. Our solutions are compared with analytical solutions when they are available and with solutions obtained using other numerical methods. Finally, to illustrate the clinical interest, we study the emptying process in a calf vein squeezed by contracting skeletal muscle in a normal and pathological subject. We compare our results with experimental simulations and discuss the sensitivity to parameters of our model.

  10. Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

    NASA Astrophysics Data System (ADS)

    Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

    2012-12-01

    Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

  11. Effects of Different PER Translational Kinetics on the Dynamics of a Core Circadian Clock Model

    PubMed Central

    Nieto, Paula S.; Revelli, Jorge A.; Garbarino-Pico, Eduardo; Condat, Carlos A.; Guido, Mario E.; Tamarit, Francisco A.

    2015-01-01

    Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis. PMID:25607544

  12. Effects of different per translational kinetics on the dynamics of a core circadian clock model.

    PubMed

    Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

    2015-01-01

    Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

  13. Kinetics and Mechanisms of Thiol–Disulfide Exchange Covering Direct Substitution and Thiol Oxidation-Mediated Pathways

    PubMed Central

    2013-01-01

    Abstract Significance: Disulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol–disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters. Critical Issues: This review is focused on the kinetics and mechanisms of thiol–disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail. Recent Advances and Future Directions: Kinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery. Antioxid. Redox Signal. 18, 1623–1641. PMID:23075118

  14. [Comparison of kinematic and kinetic parameters between the locomotion patterns in nordic walking, walking and running].

    PubMed

    Kleindienst, F I; Michel, K J; Schwarz, J; Krabbe, B

    2006-03-01

    Based on a higher cardio-pulmonary and cardio-vascular benefit and a promised reduction of mechanical load of the musculoskeletal system Nordic Walking (NW) shows an increased market potential. The present study should investigate whether there are biomechanical differences between the locomotion patterns NW, walking and running. Moreover possible resultant load differences should be determined. Eleven subjects, who were already experienced with the NW-technique, participated in this experiment. The kinematic data were collected using two high-speed camera systems from posterior and from lateral at the same time. Simultaneously the ground reaction forces were recorded. The kinematic and the kinetic data reveal differences between the three analyzed locomotion patterns. For NW as well as walking the mechanical load of the lower extremity is lower compared to running. None of the kinematic parameters suggest a "physiological benefit" of NW compared to walking. Moreover NW shows higher vertical and horizontal forces during landing. Exclusively the lower vertical force peak during push off indicates a lower mechanical load for NW in comparison to walking. Consequently it is questionable is NW -- based on its promised "biomechanical benefits" compared to walking -- should be still recommended for overweight people and for people with existing musculoskeletal problems of the lower limb.

  15. Methane oxidation in a landfill cover soil reactor: Changing of kinetic parameters and microorganism community structure.

    PubMed

    Xing, Zhi L; Zhao, Tian T; Gao, Yan H; Yang, Xu; Liu, Shuai; Peng, Xu Y

    2017-02-23

    Changing of CH 4 oxidation potential and biological characteristics with CH 4 concentration was studied in a landfill cover soil reactor (LCSR). The maximum rate of CH 4 oxidation reached 32.40 mol d -1 m -2 by providing sufficient O 2 in the LCSR. The kinetic parameters of methane oxidation in landfill cover soil were obtained by fitting substrate diffusion and consumption model based on the concentration profile of CH 4 and O 2 . The values of [Formula: see text] (0.93-2.29%) and [Formula: see text] (140-524 nmol kg soil-DW -1 ·s -1 ) increased with CH 4 concentration (9.25-20.30%), while the values of [Formula: see text] (312.9-2.6%) and [Formula: see text] (1.3 × 10 -5 to 9.0 × 10 -3 nmol mL -1 h -1 ) were just the opposite. MiSeq pyrosequencing data revealed that Methylobacter (the relative abundance was decreased with height of LCSR) and Methylococcales_unclassified (the relative abundance was increased expect in H 80) became the key players after incubation with increasing CH 4 concentration. These findings provide information for assessing CH 4 oxidation potential and changing of biological characteristics in landfill cover soil.

  16. The nonlocal electron kinetics for a low-pressure glow discharge dusty plasma

    NASA Astrophysics Data System (ADS)

    Liang, Yonggan; Wang, Ying; Li, Hui; Tian, Ruihuan; Yuan, Chengxun; Kudryavtsev, A. A.; Rabadanov, K. M.; Wu, Jian; Zhou, Zhongxiang; Tian, Hao

    2018-05-01

    The nonlocal electron kinetic model based on the Boltzmann equation is developed in low-pressure argon glow discharge dusty plasmas. The additional electron-dust elastic and inelastic collision processes are considered when solving the kinetic equation numerically. The orbital motion limited theory and collision enhanced collection approximation are employed to calculate the dust surface potential. The electron energy distribution function (EEDF), effective electron temperature Teff, and dust surface potential are investigated under different plasma and dust conditions by solving the Boltzmann and the dust charging current balance equations self-consistently. A comparison of the calculation results obtained from nonlocal and local kinetic models is made. It is shown that the appearance of dust particles leads to a deviation of the EEDF from its original profile for both nonlocal and local kinetic models. With the increase in dust density and size, the effective electron temperature and dust surface potential decrease due to the high-energy electron loss on the dust surface. Meanwhile, the nonlocal and local results differ much from each other under the same calculation condition. It is concluded that, for low-pressure (PR ≤ 1 cm*Torr) glow discharge dusty plasmas, the existence of dust particles will amplify the difference of local and nonlocal EEDFs, which makes the local kinetic model more improper to determine the main parameters of the positive column. The nonlocal kinetic model should be used for the calculation of the EEDFs and dusty plasma parameters.

  17. Accurate motion parameter estimation for colonoscopy tracking using a regression method

    NASA Astrophysics Data System (ADS)

    Liu, Jianfei; Subramanian, Kalpathi R.; Yoo, Terry S.

    2010-03-01

    Co-located optical and virtual colonoscopy images have the potential to provide important clinical information during routine colonoscopy procedures. In our earlier work, we presented an optical flow based algorithm to compute egomotion from live colonoscopy video, permitting navigation and visualization of the corresponding patient anatomy. In the original algorithm, motion parameters were estimated using the traditional Least Sum of squares(LS) procedure which can be unstable in the context of optical flow vectors with large errors. In the improved algorithm, we use the Least Median of Squares (LMS) method, a robust regression method for motion parameter estimation. Using the LMS method, we iteratively analyze and converge toward the main distribution of the flow vectors, while disregarding outliers. We show through three experiments the improvement in tracking results obtained using the LMS method, in comparison to the LS estimator. The first experiment demonstrates better spatial accuracy in positioning the virtual camera in the sigmoid colon. The second and third experiments demonstrate the robustness of this estimator, resulting in longer tracked sequences: from 300 to 1310 in the ascending colon, and 410 to 1316 in the transverse colon.

  18. Dynamic contrast-enhanced CT of head and neck tumors: perfusion measurements using a distributed-parameter tracer kinetic model. Initial results and comparison with deconvolution-based analysis

    NASA Astrophysics Data System (ADS)

    Bisdas, Sotirios; Konstantinou, George N.; Sherng Lee, Puor; Thng, Choon Hua; Wagenblast, Jens; Baghi, Mehran; San Koh, Tong

    2007-10-01

    The objective of this work was to evaluate the feasibility of a two-compartment distributed-parameter (DP) tracer kinetic model to generate functional images of several physiologic parameters from dynamic contrast-enhanced CT data obtained of patients with extracranial head and neck tumors and to compare the DP functional images to those obtained by deconvolution-based DCE-CT data analysis. We performed post-processing of DCE-CT studies, obtained from 15 patients with benign and malignant head and neck cancer. We introduced a DP model of the impulse residue function for a capillary-tissue exchange unit, which accounts for the processes of convective transport and capillary-tissue exchange. The calculated parametric maps represented blood flow (F), intravascular blood volume (v1), extravascular extracellular blood volume (v2), vascular transit time (t1), permeability-surface area product (PS), transfer ratios k12 and k21, and the fraction of extracted tracer (E). Based on the same regions of interest (ROI) analysis, we calculated the tumor blood flow (BF), blood volume (BV) and mean transit time (MTT) by using a modified deconvolution-based analysis taking into account the extravasation of the contrast agent for PS imaging. We compared the corresponding values by using Bland-Altman plot analysis. We outlined 73 ROIs including tumor sites, lymph nodes and normal tissue. The Bland-Altman plot analysis revealed that the two methods showed an accepted degree of agreement for blood flow, and, thus, can be used interchangeably for measuring this parameter. Slightly worse agreement was observed between v1 in the DP model and BV but even here the two tracer kinetic analyses can be used interchangeably. Under consideration of whether both techniques may be used interchangeably was the case of t1 and MTT, as well as for measurements of the PS values. The application of the proposed DP model is feasible in the clinical routine and it can be used interchangeably for measuring

  19. Revealing kinetics and state-dependent binding properties of IKur-targeting drugs that maximize atrial fibrillation selectivity

    NASA Astrophysics Data System (ADS)

    Ellinwood, Nicholas; Dobrev, Dobromir; Morotti, Stefano; Grandi, Eleonora

    2017-09-01

    The KV1.5 potassium channel, which underlies the ultra-rapid delayed-rectifier current (IKur) and is predominantly expressed in atria vs. ventricles, has emerged as a promising target to treat atrial fibrillation (AF). However, while numerous KV1.5-selective compounds have been screened, characterized, and tested in various animal models of AF, evidence of antiarrhythmic efficacy in humans is still lacking. Moreover, current guidelines for pre-clinical assessment of candidate drugs heavily rely on steady-state concentration-response curves or IC50 values, which can overlook adverse cardiotoxic effects. We sought to investigate the effects of kinetics and state-dependent binding of IKur-targeting drugs on atrial electrophysiology in silico and reveal the ideal properties of IKur blockers that maximize anti-AF efficacy and minimize pro-arrhythmic risk. To this aim, we developed a new Markov model of IKur that describes KV1.5 gating based on experimental voltage-clamp data in atrial myocytes from patient right-atrial samples in normal sinus rhythm. We extended the IKur formulation to account for state-specificity and kinetics of KV1.5-drug interactions and incorporated it into our human atrial cell model. We simulated 1- and 3-Hz pacing protocols in drug-free conditions and with a [drug] equal to the IC50 value. The effects of binding and unbinding kinetics were determined by examining permutations of the forward (kon) and reverse (koff) binding rates to the closed, open, and inactivated states of the KV1.5 channel. We identified a subset of ideal drugs exhibiting anti-AF electrophysiological parameter changes at fast pacing rates (effective refractory period prolongation), while having little effect on normal sinus rhythm (limited action potential prolongation). Our results highlight that accurately accounting for channel interactions with drugs, including kinetics and state-dependent binding, is critical for developing safer and more effective pharmacological anti

  20. Critical Evaluation of Kinetic Method Measurements: Possible Origins of Nonlinear Effects

    NASA Astrophysics Data System (ADS)

    Bourgoin-Voillard, Sandrine; Afonso, Carlos; Lesage, Denis; Zins, Emilie-Laure; Tabet, Jean-Claude; Armentrout, P. B.

    2013-03-01

    The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities ( ΔH° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.

  1. Kinetics of mercuric chloride retention by soils

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

    Amacher, M.C.; Selim, H.M.; Iskandar, I.K.

    A nonlinear multireaction model was used to describe kinetic data for HgCl{sub 2} retention by five soils. A three-parameter version of the model consisting of a reversible nonlinear (nth order, n < 1) reaction and an irreversible first-order reaction was capable of describing HgCl{sub 2} retention data for Cecil (clayey, kaolinitic, thermic Typic Kanhapludult) and Windsor (mixed, mesic Typic Udipsamment) soils at all initial solution Hg concentrations, and data for Norwood, (fine-silty, mixed (calcareous), thermic, Typic Udifluvent), Olivier (fine-silty, mixed, thermic Aquic Fragiudalt), and Sharkey (very-fine, montmorillonitic, nonacid, thermic Vertic Haplaquept) soils at initial solution Hg concentrations below 5 mg/L.more » A five-parameter version of the model, with an added reversible nonlinear reaction, provided a more accurate description of the retention data for the Norwood, Olivier, and Sharkey soils at initial solution Hg concentrations above 5 mg/L. The second reaction needed to describe the data at higher Hg concentrations suggests the presence of a second type of sorption sites, or a precipitation or coprecipitation reaction not encountered at lower Hg concentrations. Release of Hg from the soils was induced by serial dilution of the soil solution, but not all the soil Hg was reversibly retained. This was also indicated by the model. Release of soil Hg depended on the concentration of retained Hg with significant Hg release occurring only at high concentrations of retained Hg. A multireaction model is needed to describe Hg retention in soils because of the many solid phases that can remove Hg from solution.« less

  2. LSENS, A General Chemical Kinetics and Sensitivity Analysis Code for Homogeneous Gas-Phase Reactions. Part 2; Code Description and Usage

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Bittker, David A.

    1994-01-01

    LSENS, the Lewis General Chemical Kinetics and Sensitivity Analysis Code, has been developed for solving complex, homogeneous, gas-phase chemical kinetics problems and contains sensitivity analysis for a variety of problems, including nonisothermal situations. This report is part II of a series of three reference publications that describe LSENS, provide a detailed guide to its usage, and present many example problems. Part II describes the code, how to modify it, and its usage, including preparation of the problem data file required to execute LSENS. Code usage is illustrated by several example problems, which further explain preparation of the problem data file and show how to obtain desired accuracy in the computed results. LSENS is a flexible, convenient, accurate, and efficient solver for chemical reaction problems such as static system; steady, one-dimensional, inviscid flow; reaction behind incident shock wave, including boundary layer correction; and perfectly stirred (highly backmixed) reactor. In addition, the chemical equilibrium state can be computed for the following assigned states: temperature and pressure, enthalpy and pressure, temperature and volume, and internal energy and volume. For static problems the code computes the sensitivity coefficients of the dependent variables and their temporal derivatives with respect to the initial values of the dependent variables and/or the three rate coefficient parameters of the chemical reactions. Part I (NASA RP-1328) derives the governing equations and describes the numerical solution procedures for the types of problems that can be solved by LSENS. Part III (NASA RP-1330) explains the kinetics and kinetics-plus-sensitivity-analysis problems supplied with LSENS and presents sample results.

  3. Kinetics modelling of color deterioration during thermal processing of tomato paste with the use of response surface methodology

    NASA Astrophysics Data System (ADS)

    Ganje, Mohammad; Jafari, Seid Mahdi; Farzaneh, Vahid; Malekjani, Narges

    2018-06-01

    To study the kinetics of color degradation, the tomato paste was designed to be processed at three different temperatures including 60, 70 and 80 °C for 25, 50, 75 and 100 min. a/b ratio, total color difference, saturation index and hue angle were calculated with the use of three main color parameters including L (lightness), a (redness-greenness) and b (yellowness-blueness) values. Kinetics of color degradation was developed by Arrhenius equation and the alterations were modelled with the use of response surface methodology (RSM). It was detected that all of the studied responses followed a first order reaction kinetics with an exception in TCD parameter (zeroth order). TCD and a/b respectively with the highest and lowest activation energy presented the highest sensitivity to the temperature alterations. The maximum and minimum rates of alterations were observed by TCD and b parameters, respectively. It was obviously determined that all of the studied parameters (responses) were affected by the selected independent parameters.

  4. Kafirin adsorption on ion-exchange resins: isotherm and kinetic studies.

    PubMed

    Kumar, Prashant; Lau, Pei Wen; Kale, Sandeep; Johnson, Stuart; Pareek, Vishnu; Utikar, Ranjeet; Lali, Arvind

    2014-08-22

    Kafirin is a natural, hydrophobic and celiac safe prolamin protein obtained from sorghum seeds. Today kafirin is found to be useful in designing delayed delivery systems and coatings of pharmaceuticals and nutraceuticals where its purity is important and this can be obtained by adsorptive chromatography. This study is the first scientific insight into the isotherm and kinetic studies of kafirin adsorption on anion- and cation-exchange resins for practical applications in preparative scale chromatography. Adsorption isotherms of kafirin were determined for five anion- and two cation-exchange resins in batch systems. Isotherm parameters such as maximum binding capacity and dissociation constant were determined from Langmuir isotherm, and adsorptive capacity and affinity constant from Freundlich isotherm. Langmuir isotherm was found to fit the adsorption equilibrium data well. Batch uptake kinetics for kafirin adsorption on these resins was also carried out and critical parameters including the diffusion coefficient, film mass transfer coefficient, and Biot number for film-pore diffusion model were calculated. Both the isotherm and the kinetic parameters were considered for selection of appropriate resin for kafirin purification. UNOsphere Q (78.26 mg/ml) and Toyopearl SP-650M (57.4 mg/ml) were found to offer better kafirin binding capacities and interaction strength with excellent uptake kinetics under moderate operating conditions. With these adsorbents, film diffusion resistance was found to be major governing factor for adsorption (Bi<10 and δ<1). Based on designer objective function, UNOsphere Q was found be best adsorbent for binding of kafirin. The data presented is valuable for designing large scale preparative adsorptive chromatographic kafirin purification systems. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism - case study of Faecalibacterium prausnitzii

    NASA Astrophysics Data System (ADS)

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B. A.; Lannebère, Sylvain; van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 104 to 5 × 107 cells.mL-1). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM kcat = 5.3×105 s-1, at 37 °C) and glucose (KM = 6 μM kcat = 2.4 × 105 s-1). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  6. Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii.

    PubMed

    Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B A; Lannebère, Sylvain; Van de Wiele, Tom; Rabaey, Korneel

    2015-07-01

    Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

  7. Decay and Spatial Diffusion of Turbulent Kinetic Energy In The Presence of a Linear Kinetic Energy Gradient

    NASA Astrophysics Data System (ADS)

    Meneveau, Charles

    2015-11-01

    A topic that elicited the interest of John Lumley is pressure transport in turbulence. In 1978 (JL, in Advances in Applied Mechanics, pages 123-176) he showed that pressure transport likely acts in the opposite direction to the spatial flux of kinetic energy due to triple velocity correlations. Here we examine a flow in which the interplay of turbulent decay and spatial transport is particularly relevant. Specifically, using a specially designed active grid and screens placed in the Corrsin wind tunnel, such a flow is realized. Data are acquired using X-wire thermal anemometry at different spanwise and downstream locations. In order to resolve the dissipation rate accurately, measurements are also acquired using the NSTAP probe developed and manufactured by Princeton researchers and kindly provided to us (M. Hultmark, Y. Fan, L. Smits). The results show power-law decay with downstream distance, with a decay exponent that becomes larger in the high kinetic energy side of the flow. Measurements of the dissipation enable us to obtain the spanwise gradient of the spatial flux. One possible explanation for the observations is upgrading transport of kinetic energy due to pressure-velocity correlations, although its magnitude required to close the budget appears very large. Absence of simultaneous pressure velocity measurement preclude us to fully elucidate the observed trends. In collaboration with Adrien Thormann, Johns Hopkins University. Financial support: National Science Foundation.

  8. On the biophysics and kinetics of toehold-mediated DNA strand displacement

    PubMed Central

    Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

    2013-01-01

    Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

  9. On the biophysics and kinetics of toehold-mediated DNA strand displacement.

    PubMed

    Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

    2013-12-01

    Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

  10. Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.

    PubMed

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

    2016-05-26

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

  11. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

    PubMed

    Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda

    2014-01-01

    Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms. © 2013 FEBS.

  12. Development of associations and kinetic models for microbiological data to be used in comprehensive food safety prediction software.

    PubMed

    Halder, Amit; Black, D Glenn; Davidson, P Michael; Datta, Ashim

    2010-08-01

    The objective of this study was to use an existing database of food products and their associated processes, link it with a list of the foodborne pathogenic microorganisms associated with those products and finally identify growth and inactivation kinetic parameters associated with those pathogens. The database was to be used as a part of the development of comprehensive software which could predict food safety and quality for any food product. The main issues in building such a predictive system included selection of predictive models, associations of different food types with pathogens (as determined from outbreak histories), and variability in data from different experiments. More than 1000 data sets from published literature were analyzed and grouped according to microorganisms and food types. Final grouping of data consisted of the 8 most prevalent pathogens for 14 different food groups, covering all of the foods (>7000) listed in the USDA Natl. Nutrient Database. Data for each group were analyzed in terms of 1st-order inactivation, 1st-order growth, and sigmoidal growth models, and their kinetic response for growth and inactivation as a function of temperature were reported. Means and 95% confidence intervals were calculated for prediction equations. The primary advantage in obtaining group-specific kinetic data is the ability to extend microbiological growth and death simulation to a large array of product and process possibilities, while still being reasonably accurate. Such simulation capability could provide vital ''what if'' scenarios for industry, Extension, and academia in food safety.

  13. Calcite Dissolution Kinetics

    NASA Astrophysics Data System (ADS)

    Berelson, W.; Subhas, A.; Dong, S.; Naviaux, J.; Adkins, J. F.

    2016-12-01

    does not adequately describe the kinetics of dissolution. The interplay of mineral composition and surface area, solution carbonate chemistry, temperature and pressure are factors the impact carbonate dissolution rates in natural settings. We suggest that these parameters be considered in CO2 mitigation strategies.

  14. Kinetics of cross-slope running.

    PubMed

    Willwacher, Steffen; Fischer, Katina Mira; Benker, Rita; Dill, Stephan; Brüggemann, Gert-Peter

    2013-11-15

    The purpose of the present study was to identify kinetic responses to running on mediolaterally elevated (cross-sloped) running surfaces. Ground reaction forces (GRFs), GRF lever arms and joint moment characteristics of 19 male runners were analyzed when running at 3.5m/s on a custom-made, tiltable runway. Tilt angles of 3° and 6° for medial and lateral elevation were analyzed using a 10 camera Vicon Nexus system and a force platform. The point of force application of the GRF showed a systematic shift in the order of 1-1.5cm to either the lateral or medial aspect of the foot for lateral or medial inclinations, respectively. Consequently, the strongest significant effects of tilt orientation and level on joint kinetics and ground reaction force lever arms were identified at the ankle, knee and hip joint in the frontal plane of movement. External eversion moments at the ankle were significantly increased by 35% for 6° of lateral elevation and decreased by 16% for 6° of medial elevation. Altering the cross-slope of the running surface changed the pattern of ankle joint moments in the transversal plane. Effect sizes were on average larger for laterally elevated conditions, indicating a higher sensitivity of kinetic parameters to this kind of surface tilt. These alterations in joint kinetics should be considered in the choice of the running environment, especially for specific risk groups, like runners in rehabilitation processes. © 2013 Elsevier Ltd. All rights reserved.

  15. Kinetic modeling of kraft delignification of Eucalyptus globulus

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

    Santos, A.; Rodriguez, F.; Gilarranz, M.A.

    1997-10-01

    A kinetic model for the kraft pulping delignification of Eucalyptus globulus is proposed. This model is discriminated among some kinetic expressions often used in the literature, and the kinetic parameters are determined by fitting of experimental results. A total of 25 isothermal experiments at liquor-to-wood ratios of 50 and 5 L/kg have been carried out. Initial, bulk, and residual delignification stages have been observed during the lignin removal, the transitions being, referring to the lignin initial content, about 82 and 3%. Carbohydrate removal and effective alkali-metal and hydrosulfide consumption have been related with the lignin removal by means of effectivemore » stoichiometric coefficients for each stage, coefficients also being calculated by fitting of the experimental data. The kinetic model chosen has been used to simulate typical kraft pulping experiments carried out at nonisothermal conditions, using a temperature ramp. The model yields simulated values close to those obtained experimentally for the wood studied and also ably reproduces the trends of the literature data.« less

  16. The role of impulse parameters in force variability

    NASA Technical Reports Server (NTRS)

    Carlton, L. G.; Newell, K. M.

    1986-01-01

    One of the principle limitations of the human motor system is the ability to produce consistent motor responses. When asked to repeatedly make the same movement, performance outcomes are characterized by a considerable amount of variability. This occurs whether variability is expressed in terms of kinetics or kinematics. Variability in performance is of considerable importance because for tasks requiring accuracy it is a critical variable in determining the skill of the performer. What has long been sought is a description of the parameter or parameters that determine the degree of variability. Two general experimental protocals were used. One protocal is to use dynamic actions and record variability in kinematic parameters such as spatial or temporal error. A second strategy was to use isometric actions and record kinetic variables such as peak force produced. What might be the important force related factors affecting variability is examined and an experimental approach to examine the influence of each of these variables is provided.

  17. Accurate Nanoscale Crystallography in Real-Space Using Scanning Transmission Electron Microscopy.

    PubMed

    Dycus, J Houston; Harris, Joshua S; Sang, Xiahan; Fancher, Chris M; Findlay, Scott D; Oni, Adedapo A; Chan, Tsung-Ta E; Koch, Carl C; Jones, Jacob L; Allen, Leslie J; Irving, Douglas L; LeBeau, James M

    2015-08-01

    Here, we report reproducible and accurate measurement of crystallographic parameters using scanning transmission electron microscopy. This is made possible by removing drift and residual scan distortion. We demonstrate real-space lattice parameter measurements with <0.1% error for complex-layered chalcogenides Bi2Te3, Bi2Se3, and a Bi2Te2.7Se0.3 nanostructured alloy. Pairing the technique with atomic resolution spectroscopy, we connect local structure with chemistry and bonding. Combining these results with density functional theory, we show that the incorporation of Se into Bi2Te3 causes charge redistribution that anomalously increases the van der Waals gap between building blocks of the layered structure. The results show that atomic resolution imaging with electrons can accurately and robustly quantify crystallography at the nanoscale.

  18. Kinetics of heterotrophic biomass and storage mechanism in wetland cores measured by respirometry.

    PubMed

    Ortigara, A R C; Foladori, P; Andreottola, G

    2011-01-01

    Although oxygen uptake rate has been widely used in activated sludge for measuring kinetic and stoichiometric parameters or for wastewater characterization, its application in constructed wetlands (CWs) cores has been recently proposed. The aim of this research is to estimate the kinetic and stoichiometric parameters of the heterotrophic biomass in CW cores. Respirometric tests were carried out with pure carbonaceous substrate and real wastewater. Endogenous respiration was about 2 gO2 m(-3) h(-1) (per unit of bed volume), while the kinetic parameters obtained for COD oxidation were very high (maximum rate per unit of bed volume of 10.7-26.8 gCOD m(-3) h(-1)) which indicates high biodegradation potential in fully aerobic environment. Regarding to stoichiometric parameter, the maximum growth yield, Y(H), was 0.56-0.59 mgCOD/mgCOD, while the storage yield, Y(STO), was 0.75-0.77 mgCOD/mgCOD. The storage mechanism was observed in CW cores during COD oxidation, which leads to the transformation of the external soluble substrate in internal storage products, probably as response to intermittent loads applied in CW systems, transient concentrations of readily biodegradable substrate and alternance of feast/famine periods.

  19. Kinetic study on anaerobic oxidation of methane coupled to denitrification.

    PubMed

    Yu, Hou; Kashima, Hiroyuki; Regan, John M; Hussain, Abid; Elbeshbishy, Elsayed; Lee, Hyung-Sool

    2017-09-01

    Monod kinetic parameters provide information required for kinetic analysis of anaerobic oxidation of methane coupled to denitrification (AOM-D). This information is critical for engineering AOM-D processes in wastewater treatment facilities. We first experimentally determined Monod kinetic parameters for an AOM-D enriched culture and obtained the following values: maximum specific growth rate (μ max ) 0.121/d, maximum substrate-utilization rate (q max ) 28.8mmol CH 4 /g cells-d, half maximum-rate substrate concentration (K s ) 83μΜ CH 4 , growth yield (Y) 4.76gcells/mol CH 4 , decay coefficient (b) 0.031/d, and threshold substrate concentration (S min ) 28.8μM CH 4 . Clone library analysis of 16S rRNA and mcrA gene fragments suggested that AOM-D reactions might have occurred via the syntrophic interaction between denitrifying bacteria (e.g., Ignavibacterium, Acidovorax, and Pseudomonas spp.) and hydrogenotrophic methanogens (Methanobacterium spp.), supporting reverse methanogenesis-dependent AOM-D in our culture. High μ max and q max , and low K s for the AOM-D enrichment imply that AOM-D could play a significant role in mitigating atmospheric methane efflux. In addition, these high kinetic features suggest that engineered AOM-D systems may provide a sustainable alternative to nitrogen removal in wastewater treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, Scott A.; Killeen, Kevin P.; Lear, Kevin L.

    1995-01-01

    We report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, we can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%.

  1. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, S.A.; Killeen, K.P.; Lear, K.L.

    1995-03-14

    The authors report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, they can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%. 4 figs.

  2. Direct Measurements of Quantum Kinetic Energy Tensor in Stable and Metastable Water near the Triple Point: An Experimental Benchmark.

    PubMed

    Andreani, Carla; Romanelli, Giovanni; Senesi, Roberto

    2016-06-16

    This study presents the first direct and quantitative measurement of the nuclear momentum distribution anisotropy and the quantum kinetic energy tensor in stable and metastable (supercooled) water near its triple point, using deep inelastic neutron scattering (DINS). From the experimental spectra, accurate line shapes of the hydrogen momentum distributions are derived using an anisotropic Gaussian and a model-independent framework. The experimental results, benchmarked with those obtained for the solid phase, provide the state of the art directional values of the hydrogen mean kinetic energy in metastable water. The determinations of the direction kinetic energies in the supercooled phase, provide accurate and quantitative measurements of these dynamical observables in metastable and stable phases, that is, key insight in the physical mechanisms of the hydrogen quantum state in both disordered and polycrystalline systems. The remarkable findings of this study establish novel insight into further expand the capacity and accuracy of DINS investigations of the nuclear quantum effects in water and represent reference experimental values for theoretical investigations.

  3. Parameter extraction using global particle swarm optimization approach and the influence of polymer processing temperature on the solar cell parameters

    NASA Astrophysics Data System (ADS)

    Kumar, S.; Singh, A.; Dhar, A.

    2017-08-01

    The accurate estimation of the photovoltaic parameters is fundamental to gain an insight of the physical processes occurring inside a photovoltaic device and thereby to optimize its design, fabrication processes, and quality. A simulative approach of accurately determining the device parameters is crucial for cell array and module simulation when applied in practical on-field applications. In this work, we have developed a global particle swarm optimization (GPSO) approach to estimate the different solar cell parameters viz., ideality factor (η), short circuit current (Isc), open circuit voltage (Voc), shunt resistant (Rsh), and series resistance (Rs) with wide a search range of over ±100 % for each model parameter. After validating the accurateness and global search power of the proposed approach with synthetic and noisy data, we applied the technique to the extract the PV parameters of ZnO/PCDTBT based hybrid solar cells (HSCs) prepared under different annealing conditions. Further, we examine the variation of extracted model parameters to unveil the physical processes occurring when different annealing temperatures are employed during the device fabrication and establish the role of improved charge transport in polymer films from independent FET measurements. The evolution of surface morphology, optical absorption, and chemical compositional behaviour of PCDTBT co-polymer films as a function of processing temperature has also been captured in the study and correlated with the findings from the PV parameters extracted using GPSO approach.

  4. Parameterization of annealing kinetics in pharmaceutical glasses.

    PubMed

    Hodge, Ian M

    2013-07-01

    Numerical simulations indicate that neglecting the canonical nonlinearity of glassy-state annealing kinetics in pharmaceutical (and other) glasses leads to good KWW fits to the dependence of enthalpy on annealing time, but with spurious KWW parameters that are affected by nonlinearity. A simplified treatment of nonlinearity that uses the Struik shift factor is found to be a useful approximation for these analyses, and can account for previously reported differences between linear and nonlinear KWW parameters (Kawakami K, Pikal MJ. 2005. J Pharm Sci 94:948-965). Copyright © 2013 Wiley Periodicals, Inc.

  5. The solution of the point kinetics equations via converged accelerated Taylor series (CATS)

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

    Ganapol, B.; Picca, P.; Previti, A.

    This paper deals with finding accurate solutions of the point kinetics equations including non-linear feedback, in a fast, efficient and straightforward way. A truncated Taylor series is coupled to continuous analytical continuation to provide the recurrence relations to solve the ordinary differential equations of point kinetics. Non-linear (Wynn-epsilon) and linear (Romberg) convergence accelerations are employed to provide highly accurate results for the evaluation of Taylor series expansions and extrapolated values of neutron and precursor densities at desired edits. The proposed Converged Accelerated Taylor Series, or CATS, algorithm automatically performs successive mesh refinements until the desired accuracy is obtained, making usemore » of the intermediate results for converged initial values at each interval. Numerical performance is evaluated using case studies available from the literature. Nearly perfect agreement is found with the literature results generally considered most accurate. Benchmark quality results are reported for several cases of interest including step, ramp, zigzag and sinusoidal prescribed insertions and insertions with adiabatic Doppler feedback. A larger than usual (9) number of digits is included to encourage honest benchmarking. The benchmark is then applied to the enhanced piecewise constant algorithm (EPCA) currently being developed by the second author. (authors)« less

  6. Photochemical parameters of atmospheric source gases: accurate determination of OH reaction rate constants over atmospheric temperatures, UV and IR absorption spectra

    NASA Astrophysics Data System (ADS)

    Orkin, V. L.; Khamaganov, V. G.; Martynova, L. E.; Kurylo, M. J.

    2012-12-01

    The emissions of halogenated (Cl, Br containing) organics of both natural and anthropogenic origin contribute to the balance of and changes in the stratospheric ozone concentration. The associated chemical cycles are initiated by the photochemical decomposition of the portion of source gases that reaches the stratosphere. Reactions with hydroxyl radicals and photolysis are the main processes dictating the compound lifetime in the troposphere and release of active halogen in the stratosphere for a majority of halogen source gases. Therefore, the accuracy of photochemical data is of primary importance for the purpose of comprehensive atmospheric modeling and for simplified kinetic estimations of global impacts on the atmosphere, such as in ozone depletion (i.e., the Ozone Depletion Potential, ODP) and climate change (i.e., the Global Warming Potential, GWP). The sources of critically evaluated photochemical data for atmospheric modeling, NASA/JPL Publications and IUPAC Publications, recommend uncertainties within 10%-60% for the majority of OH reaction rate constants with only a few cases where uncertainties lie at the low end of this range. These uncertainties can be somewhat conservative because evaluations are based on the data from various laboratories obtained during the last few decades. Nevertheless, even the authors of the original experimental works rarely estimate the total combined uncertainties of the published OH reaction rate constants to be less than ca. 10%. Thus, uncertainties in the photochemical properties of potential and current atmospheric trace gases obtained under controlled laboratory conditions still may constitute a major source of uncertainty in estimating the compound's environmental impact. One of the purposes of the presentation is to illustrate the potential for obtaining accurate laboratory measurements of the OH reaction rate constant over the temperature range of atmospheric interest. A detailed inventory of accountable sources of

  7. An accurate metric for the spacetime around rotating neutron stars

    NASA Astrophysics Data System (ADS)

    Pappas, George

    2017-04-01

    The problem of having an accurate description of the spacetime around rotating neutron stars is of great astrophysical interest. For astrophysical applications, one needs to have a metric that captures all the properties of the spacetime around a rotating neutron star. Furthermore, an accurate appropriately parametrized metric, I.e. a metric that is given in terms of parameters that are directly related to the physical structure of the neutron star, could be used to solve the inverse problem, which is to infer the properties of the structure of a neutron star from astrophysical observations. In this work, we present such an approximate stationary and axisymmetric metric for the exterior of rotating neutron stars, which is constructed using the Ernst formalism and is parametrized by the relativistic multipole moments of the central object. This metric is given in terms of an expansion on the Weyl-Papapetrou coordinates with the multipole moments as free parameters and is shown to be extremely accurate in capturing the physical properties of a neutron star spacetime as they are calculated numerically in general relativity. Because the metric is given in terms of an expansion, the expressions are much simpler and easier to implement, in contrast to previous approaches. For the parametrization of the metric in general relativity, the recently discovered universal 3-hair relations are used to produce a three-parameter metric. Finally, a straightforward extension of this metric is given for scalar-tensor theories with a massless scalar field, which also admit a formulation in terms of an Ernst potential.

  8. Kinetic Parameters of Efflux of Penicillins by the Multidrug Efflux Transporter AcrAB-TolC of Escherichia coli▿

    PubMed Central

    Lim, Siew Ping; Nikaido, Hiroshi

    2010-01-01

    The multidrug efflux transporter AcrAB-TolC is known to pump out a diverse range of antibiotics, including β-lactams. However, the kinetic constants of the efflux process, needed for the quantitative understanding of resistance, were not available until those accompanying the efflux of some cephalosporins were recently determined by combining efflux with the hydrolysis of drugs by the periplasmic β-lactamase. In the present study we extended this approach to the study of a wide range of penicillins, from ampicillin and penicillin V to ureidopenicillins and isoxazolylpenicillins, by combining efflux with hydrolysis with the OXA-7 penicillinase. We found that the penicillins had a much stronger apparent affinity to AcrB and higher maximum rates of efflux than the cephalosporins. All penicillins showed strong positive cooperativity kinetics for export. The kinetic constants obtained were validated, as the MICs theoretically predicted on the basis of efflux and hydrolysis kinetics were remarkably similar to the observed MICs (except for the isoxazolylpenicillins). Surprisingly, however, the efflux kinetics of cloxacillin, for example, whose MIC decreased 512-fold in Escherichia coli upon the genetic deletion of the acrB gene, were quite similar to those of ampicillin, whose MIC decreased only 2-fold with the same treatment. Analysis of this phenomenon showed that the extensive decrease in the MIC for the acrB mutant is primarily due to the low permeation of the drug and that comparison of the MICs between the parent and the acrB strains is a very poor measure of the ability of AcrB to pump a drug out. PMID:20160052

  9. Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

    NASA Astrophysics Data System (ADS)

    Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

    2018-03-01

    The oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deeper oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.

  10. Density variation effect on multi-ions with kinetic Alfven wave around cusp region—a kinetic approach

    NASA Astrophysics Data System (ADS)

    Tamrakar, Radha; Varma, P.; Tiwari, M. S.

    2018-01-01

    The kinetic Alfven waves in the presence of homogeneous magnetic field plasma with multi-ions effect are investigated. The dispersion relation and normalised damping rate are derived for low-β plasma using kinetic theory. The effect of density variation of H+, He+ and O+ ions is observed on frequency and damping rate of the wave. The variation of frequency (ω) and normalised damping rate (γ / Ω_{H^{ +}} ) of the wave are studied with respect to k_{ \\bot} ρj, where k_{ \\bot} is the perpendicular wave number, ρj is the ion gyroradius and j denotes H+, He+ and O+ ions. The variation with k_{ \\bot} ρj is considered over wide range. The parameters appropriate to cusp region are used for the explanation of results. It is found that with hydrogen and helium ions gyration, the frequency of wave is influenced by the density variation of H+ and He+ ions but remains insensitive to the change in density of O+ ions. For oxygen ion gyration, the frequency of wave varies over a short range only for O+ ion density variation. The wave shows damping at lower altitude due to variation in density of lighter H+ and He+ ions whereas at higher altitude only heavy O+ ions contribute in wave damping. The damping of wave may be due to landau damping or energy transfer from wave to particles. The present study signifies that the both lighter and heavier ions dominate differently to change the characteristics of kinetic Alfven wave and density variation is also an important parameter to understand wave phenomena in cusp region.

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

    PubMed Central

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

    2012-01-01

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

  12. Rotation and kinetic modifications of the tokamak ideal-wall pressure limit.

    PubMed

    Menard, J E; Wang, Z; Liu, Y; Bell, R E; Kaye, S M; Park, J-K; Tritz, K

    2014-12-19

    The impact of toroidal rotation, energetic ions, and drift-kinetic effects on the tokamak ideal wall mode stability limit is considered theoretically and compared to experiment for the first time. It is shown that high toroidal rotation can be an important destabilizing mechanism primarily through the angular velocity shear; non-Maxwellian fast ions can also be destabilizing, and drift-kinetic damping can potentially offset these destabilization mechanisms. These results are obtained using the unique parameter regime accessible in the spherical torus NSTX of high toroidal rotation speed relative to the thermal and Alfvén speeds and high kinetic pressure relative to the magnetic pressure. Inclusion of rotation and kinetic effects significantly improves agreement between measured and predicted ideal stability characteristics and may provide new insight into tearing mode triggering.

  13. Solvolysis kinetics of three components of biomass using polyhydric alcohols as solvents.

    PubMed

    Shi, Yan; Xia, Xueying; Li, Jingdan; Wang, Jing; Zhao, Tiantian; Yang, Hongmin; Jiang, Jianchun; Jiang, Xiaoxiang

    2016-12-01

    The solvolysis behavior and reaction kinetics of the three components of biomass (cellulose, hemicelluloses and lignin) liquefied in polyhydric alcohols (PEG 400 or glycerol) were investigated in this paper. Three stages were observed during the solvolysis process and the main degradation stage could be further divided into two zones. The influences of solvents on the liquefaction process of three main components were compared. Based on Starink and Malek methods, kinetic parameters and mechanism functions were obtained. The derived average activation energy of cellulose, hemicellulose and lignin were 108.73, 95.66 and 94.13kJmol -1 in PEG 400, while the values were 102.16, 77.43 and 89.10kJmol -1 in glycerol, respectively. Higher efficiency was observed when using glycerol as solvent, which could be ascribed to the higher polarity value of glycerol. The conversion curves calculated with obtained mechanism models and kinetic parameters were in good agreement with the experimental data. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Charge transfer kinetics at the solid-solid interface in porous electrodes

    NASA Astrophysics Data System (ADS)

    Bai, Peng; Bazant, Martin Z.

    2014-04-01

    Interfacial charge transfer is widely assumed to obey the Butler-Volmer kinetics. For certain liquid-solid interfaces, the Marcus-Hush-Chidsey theory is more accurate and predictive, but it has not been applied to porous electrodes. Here we report a simple method to extract the charge transfer rates in carbon-coated LiFePO4 porous electrodes from chronoamperometry experiments, obtaining curved Tafel plots that contradict the Butler-Volmer equation but fit the Marcus-Hush-Chidsey prediction over a range of temperatures. The fitted reorganization energy matches the Born solvation energy for electron transfer from carbon to the iron redox site. The kinetics are thus limited by electron transfer at the solid-solid (carbon-LixFePO4) interface rather than by ion transfer at the liquid-solid interface, as previously assumed. The proposed experimental method generalizes Chidsey’s method for phase-transforming particles and porous electrodes, and the results show the need to incorporate Marcus kinetics in modelling batteries and other electrochemical systems.

  15. Sample Handling and Chemical Kinetics in an Acoustically Levitated Drop Microreactor

    PubMed Central

    2009-01-01

    Accurate measurement of enzyme kinetics is an essential part of understanding the mechanisms of biochemical reactions. The typical means of studying such systems use stirred cuvettes, stopped-flow apparatus, microfluidic systems, or other small sample containers. These methods may prove to be problematic if reactants or products adsorb to or react with the container’s surface. As an alternative approach, we have developed an acoustically-levitated drop reactor eventually intended to study enzyme-catalyzed reaction kinetics related to free radical and oxidative stress chemistry. Microliter-scale droplet generation, reactant introduction, maintenance, and fluid removal are all important aspects in conducting reactions in a levitated drop. A three capillary bundle system has been developed to address these needs. We report kinetic measurements for both luminol chemiluminescence and the reaction of pyruvate with nicotinamide adenine dinucleotide, catalyzed by lactate dehydrogenase, to demonstrate the feasibility of using a levitated drop in conjunction with the developed capillary sample handling system as a microreactor. PMID:19769373

  16. Removal of ibuprofen, naproxen and carbamazepine in aqueous solution onto natural clay: equilibrium, kinetics, and thermodynamic study

    NASA Astrophysics Data System (ADS)

    Khazri, Hassen; Ghorbel-Abid, Ibtissem; Kalfat, Rafik; Trabelsi-Ayadi, Malika

    2017-10-01

    This study aimed to describe the adsorption of three pharmaceuticals compounds (ibuprofen, naproxen and carbamazepine) onto natural clay on the basis of equilibrium parameters such as a function of time, effect of pH, varying of the concentration and the temperature. Adsorption kinetic data were modeled using the Lagergren's first-order and the pseudo-second-order kinetic equations. The kinetic results of adsorption are described better using the pseudo-second order model. The isotherm results were tested in the Langmuir, Freundlich and Dubinin-Radushkevich models. The thermodynamic parameters obtained indicate that the adsorption of pharmaceuticals on the clay is a spontaneous and endothermic process.

  17. Online quench-flow electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for elucidating kinetic and chemical enzymatic reaction mechanisms.

    PubMed

    Clarke, David J; Stokes, Adam A; Langridge-Smith, Pat; Mackay, C Logan

    2010-03-01

    We have developed an automated quench-flow microreactor which interfaces directly to an electrospray ionization (ESI) mass spectrometer. We have used this device in conjunction with ESI Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) to demonstrate the potential of this approach for studying the mechanistic details of enzyme reactions. For the model system chosen to test this device, namely, the pre-steady-state hydrolysis of p-nitrophenyl acetate by the enzyme chymotrypsin, the kinetic parameters obtained are in good agreement with those in the literature. To our knowledge, this is the first reported use of online quench-flow coupled with FTICR MS. Furthermore, we have exploited the power of FTICR MS to interrogate the quenched covalently bound enzyme intermediate using top-down fragmentation. The accurate mass capabilities of FTICR MS permitted the nature of the intermediate to be assigned with high confidence. Electron capture dissociation (ECD) fragmentation allowed us to locate the intermediate to a five amino acid section of the protein--which includes the known catalytic residue, Ser(195). This experimental approach, which uniquely can provide both kinetic and chemical details of enzyme mechanisms, is a potentially powerful tool for studies of enzyme catalysis.

  18. Extraction kinetics and properties of proanthocyanidins from pomegranate peel

    USDA-ARS?s Scientific Manuscript database

    With an objective of developing a safe and efficient method to extract proanthocyanidins products from pomegranate peel for use in nutraceuticals or as food additives, the effects of extraction parameters on the production efficiency, product properties, and extraction kinetics were systematically s...

  19. Identification of the most sensitive parameters in the activated sludge model implemented in BioWin software.

    PubMed

    Liwarska-Bizukojc, Ewa; Biernacki, Rafal

    2010-10-01

    In order to simulate biological wastewater treatment processes, data concerning wastewater and sludge composition, process kinetics and stoichiometry are required. Selection of the most sensitive parameters is an important step of model calibration. The aim of this work is to verify the predictability of the activated sludge model, which is implemented in BioWin software, and select its most influential kinetic and stoichiometric parameters with the help of sensitivity analysis approach. Two different measures of sensitivity are applied: the normalised sensitivity coefficient (S(i,j)) and the mean square sensitivity measure (delta(j)(msqr)). It occurs that 17 kinetic and stoichiometric parameters of the BioWin activated sludge (AS) model can be regarded as influential on the basis of S(i,j) calculations. Half of the influential parameters are associated with growth and decay of phosphorus accumulating organisms (PAOs). The identification of the set of the most sensitive parameters should support the users of this model and initiate the elaboration of determination procedures for the parameters, for which it has not been done yet. Copyright 2010 Elsevier Ltd. All rights reserved.

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

    PubMed Central

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

    1993-01-01

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

  1. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching.

    PubMed

    Huynh, Linh; Tagkopoulos, Ilias

    2015-08-21

    In computer-aided biological design, the trifecta of characterized part libraries, accurate models and optimal design parameters is crucial for producing reliable designs. As the number of parts and model complexity increase, however, it becomes exponentially more difficult for any optimization method to search the solution space, hence creating a trade-off that hampers efficient design. To address this issue, we present a hierarchical computer-aided design architecture that uses a two-step approach for biological design. First, a simple model of low computational complexity is used to predict circuit behavior and assess candidate circuit branches through branch-and-bound methods. Then, a complex, nonlinear circuit model is used for a fine-grained search of the reduced solution space, thus achieving more accurate results. Evaluation with a benchmark of 11 circuits and a library of 102 experimental designs with known characterization parameters demonstrates a speed-up of 3 orders of magnitude when compared to other design methods that provide optimality guarantees.

  2. Convergence in parameters and predictions using computational experimental design.

    PubMed

    Hagen, David R; White, Jacob K; Tidor, Bruce

    2013-08-06

    Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

  3. A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions.

    PubMed

    Chang, Ivan; Baldi, Pierre

    2013-05-15

    Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation-reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus important, current models suffer from limitations to the steady-state domain, lack empirical validation or are too specialized to a single system or set of conditions. To address these limitations, we introduce a novel unifying modeling framework for kinetic descriptions of oxidoreductases. The framework is based on a set of seven elementary reactions that (i) form the basis for 69 pairs of enzyme state transitions for encoding various specific microscopic intra-enzyme reaction networks (micro-models), and (ii) lead to various specific macroscopic steady-state kinetic equations (macro-models) via thermodynamic assumptions. Thus, a synergistic bridge between the micro and macro kinetics can be achieved, enabling us to extract unitary rate constants, simulate reaction variance and validate the micro-models using steady-state empirical data. To help facilitate the application of this framework, we make available RedoxMech: a Mathematica™ software package that automates the generation and customization of micro-models. The Mathematica™ source code for RedoxMech, the documentation and the experimental datasets are all available from: http://www.igb.uci.edu/tools/sb/metabolic-modeling. pfbaldi@ics.uci.edu Supplementary data are available at Bioinformatics online.

  4. Biosorption of As(III) and As(V) on the surface of TW/MnFe2O4 composite from wastewater: kinetics, mechanistic and thermodynamics

    NASA Astrophysics Data System (ADS)

    Podder, M. S.; Majumder, C. B.

    2017-10-01

    In the present study, TW/MnFe2O4 composite (MTW) was synthesized and estimated as an effective biosorbent for removing As (III) and As(V) from wastewater. Physicochemical analysis of composite was performed through SEM-EDX. 86.615 and 83.478% removal efficiency were obtained by composite dosage of 2 g/L at contact time 120 min at temperature 30 °C and pH 7.0 and 4.0 for As(III) and As(V), respectively. Kinetic results study showed that Brouers-Weron-Sotolongo and Ritchie second-order for As(III) and Brouers-Weron-Sotolongo model for As(V) were capable to describe an accurate explanation of adsorption kinetic. Applicability of mechanistic models in the current study exposed that the rate-controlling step in the biosorption of both As(III) and As(V) on the surface of composite was film diffusion rather than intraparticle diffusion. The estimated thermodynamic parameters Δ G 0, Δ H 0 and Δ S 0 revealed that the biosorption of both As(III) and As(V) on the composite was feasible, spontaneous and exothermic.

  5. A kinetic and thermochemical database for organic sulfur and oxygen compounds.

    PubMed

    Class, Caleb A; Aguilera-Iparraguirre, Jorge; Green, William H

    2015-05-28

    Potential energy surfaces and reaction kinetics were calculated for 40 reactions involving sulfur and oxygen. This includes 11 H2O addition, 8 H2S addition, 11 hydrogen abstraction, 7 beta scission, and 3 elementary tautomerization reactions, which are potentially relevant in the combustion and desulfurization of sulfur compounds found in various fuel sources. Geometry optimizations and frequencies were calculated for reactants and transition states using B3LYP/CBSB7, and potential energies were calculated using CBS-QB3 and CCSD(T)-F12a/VTZ-F12. Rate coefficients were calculated using conventional transition state theory, with corrections for internal rotations and tunneling. Additionally, thermochemical parameters were calculated for each of the compounds involved in these reactions. With few exceptions, rate parameters calculated using the two potential energy methods agreed reasonably, with calculated activation energies differing by less than 5 kJ mol(-1). The computed rate coefficients and thermochemical parameters are expected to be useful for kinetic modeling.

  6. Variation Quality and Kinetic Parameter of Commercial n-3 PUFA-Rich Oil during Oxidation via Rancimat

    PubMed Central

    Yang, Kai-Min; Chiang, Po-Yuan

    2017-01-01

    Different biological sources of n-3 polyunsaturated fatty acids (n-3 PUFA) in mainstream commercial products include algae and fish. Lipid oxidation in n-3 PUFA-rich oil is the most important cause of its deterioration. We investigated the kinetic parameters of n-3 PUFA-rich oil during oxidation via Rancimat (at a temperature range of 70~100 °C). This was done on the basis of the Arrhenius equation, which indicates that the activation energies (Ea) for oxidative stability are 82.84–96.98 KJ/mol. The chemical substrates of different oxidative levels resulting from oxidation via Rancimat at 80 °C were evaluated. At the initiation of oxidation, the tocopherols in the oil degraded very quickly, resulting in diminished protection against further oxidation. Then, the degradation of the fatty acids with n-3 PUFA-rich oil was evident because of decreased levels of PUFA along with increased levels of saturated fatty acids (SFA). The quality deterioration from n-3 PUFA-rich oil at the various oxidative levels was analyzed chemometrically. The anisidine value (p-AV, r: 0.92) and total oxidation value (TOTOX, r: 0.91) exhibited a good linear relationship in a principal component analysis (PCA), while oxidative change and a significant quality change to the induction period (IP) were detected through an agglomerative hierarchical cluster (AHC) analysis. PMID:28350348

  7. Variation Quality and Kinetic Parameter of Commercial n-3 PUFA-Rich Oil during Oxidation via Rancimat.

    PubMed

    Yang, Kai-Min; Chiang, Po-Yuan

    2017-03-28

    Different biological sources of n -3 polyunsaturated fatty acids ( n -3 PUFA) in mainstream commercial products include algae and fish. Lipid oxidation in n -3 PUFA-rich oil is the most important cause of its deterioration. We investigated the kinetic parameters of n -3 PUFA-rich oil during oxidation via Rancimat (at a temperature range of 70~100 °C). This was done on the basis of the Arrhenius equation, which indicates that the activation energies ( E a) for oxidative stability are 82.84-96.98 KJ/mol. The chemical substrates of different oxidative levels resulting from oxidation via Rancimat at 80 °C were evaluated. At the initiation of oxidation, the tocopherols in the oil degraded very quickly, resulting in diminished protection against further oxidation. Then, the degradation of the fatty acids with n -3 PUFA-rich oil was evident because of decreased levels of PUFA along with increased levels of saturated fatty acids (SFA). The quality deterioration from n -3 PUFA-rich oil at the various oxidative levels was analyzed chemometrically. The anisidine value (p-AV, r: 0.92) and total oxidation value (TOTOX, r: 0.91) exhibited a good linear relationship in a principal component analysis (PCA), while oxidative change and a significant quality change to the induction period (IP) were detected through an agglomerative hierarchical cluster (AHC) analysis.

  8. A means to estimate thermal and kinetic parameters of coal dust layer from hot surface ignition tests.

    PubMed

    Park, Haejun; Rangwala, Ali S; Dembsey, Nicholas A

    2009-08-30

    A method to estimate thermal and kinetic parameters of Pittsburgh seam coal subject to thermal runaway is presented using the standard ASTM E 2021 hot surface ignition test apparatus. Parameters include thermal conductivity (k), activation energy (E), coupled term (QA) of heat of reaction (Q) and pre-exponential factor (A) which are required, but rarely known input values to determine the thermal runaway propensity of a dust material. Four different dust layer thicknesses: 6.4, 12.7, 19.1 and 25.4mm, are tested, and among them, a single steady state dust layer temperature profile of 12.7 mm thick dust layer is used to estimate k, E and QA. k is calculated by equating heat flux from the hot surface layer and heat loss rate on the boundary assuming negligible heat generation in the coal dust layer at a low hot surface temperature. E and QA are calculated by optimizing a numerically estimated steady state dust layer temperature distribution to the experimentally obtained temperature profile of a 12.7 mm thick dust layer. Two unknowns, E and QA, are reduced to one from the correlation of E and QA obtained at criticality of thermal runaway. The estimated k is 0.1 W/mK matching the previously reported value. E ranges from 61.7 to 83.1 kJ/mol, and the corresponding QA ranges from 1.7 x 10(9) to 4.8 x 10(11)J/kg s. The mean values of E (72.4 kJ/mol) and QA (2.8 x 10(10)J/kg s) are used to predict the critical hot surface temperatures for other thicknesses, and good agreement is observed between measured and experimental values. Also, the estimated E and QA ranges match the corresponding ranges calculated from the multiple tests method and values reported in previous research.

  9. Kinetic Analysis of Rhodamines Efflux Mediated by the Multidrug Resistance Protein (MRP1)

    PubMed Central

    Saengkhae, Chantarawan; Loetchutinat, Chatchanok; Garnier-Suillerot, Arlette

    2003-01-01

    Characterization of rhodamine 123 as functional assay for MDR has been primarily focused on P-glycoprotein-mediated MDR. Several studies have suggested that Rh123 is also a substrate for MRP1. However, no quantitative studies of the MRP1-mediated efflux of rhodamines have, up to now, been performed. Measurement of the kinetic characteristics of substrate transport is a powerful approach to enhancing our understanding of their function and mechanism. In the present study, we have used a continuous fluorescence assay with four rhodamine dyes (rhodamine 6G, tetramethylrosamine, tetramethylrhodamine ethyl ester, and tetramethylrhodamine methyl ester) to quantify drug transport by MRP1 in living GLC4/ADR cells. The formation of a substrate concentration gradient was observed. MRP1-mediated transport of rhodamine was glutathione-dependent. The kinetics parameter, ka = VM/km, was very similar for the four rhodamine analogs but ∼10-fold less than the values of the same parameter determined previously for the MRP1-mediated efflux of anthracycline. The findings presented here are the first to show quantitative information about the kinetics parameters for MRP1-mediated efflux of rhodamine dyes. PMID:12944313

  10. Line shape parameters of the 22-GHz water line for accurate modeling in atmospheric applications

    NASA Astrophysics Data System (ADS)

    Koshelev, M. A.; Golubiatnikov, G. Yu.; Vilkov, I. N.; Tretyakov, M. Yu.

    2018-01-01

    The paper concerns refining parameters of one of the major atmospheric diagnostic lines of water vapor at 22 GHz. Two high resolution microwave spectrometers based on different principles of operation covering together the pressure range from a few milliTorr up to a few Torr were used. Special efforts were made to minimize possible sources of systematic measurement errors. Satisfactory self-consistency of the obtained data was achieved ensuring reliability of the obtained parameters. Collisional broadening and shifting parameters of the line in pure water vapor and in its mixture with air were determined at room temperature. Comparative analysis of the obtained parameters with previous data is given. The speed dependence effect impact on the line shape was evaluated.

  11. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  12. Theoretical and experimental study on the effects of particle size and temperature on the reaction kinetics of cubic nano-Cu2O

    NASA Astrophysics Data System (ADS)

    Tang, Huanfeng; Huang, Zaiyin; Xiao, Ming; Liang, Min; Chen, Liying; Tan, XueCai

    2017-09-01

    The activities, selectivities, and stabilities of nanoparticles in heterogeneous reactions are size-dependent. In order to investigate the influencing laws of particle size and temperature on kinetic parameters in heterogeneous reactions, cubic nano-Cu2O particles of four different sizes in the range of 40-120 nm have been controllably synthesized. In situ microcalorimetry has been used to attain thermodynamic data on the reaction of Cu2O with aqueous HNO3 and, combined with thermodynamic principles and kinetic transition-state theory, the relevant reaction kinetic parameters have been evaluated. The size dependences of the kinetic parameters are discussed in terms of the established kinetic model and the experimental results. It was found that the reaction rate constants increased with decreasing particle size. Accordingly, the apparent activation energy, pre-exponential factor, activation enthalpy, activation entropy, and activation Gibbs energy decreased with decreasing particle size. The reaction rate constants and activation Gibbs energies increased with increasing temperature. Moreover, the logarithms of the apparent activation energies, pre-exponential factors, and rate constants were found to be linearly related to the reciprocal of particle size, consistent with the kinetic models. The influence of particle size on these reaction kinetic parameters may be explained as follows: the apparent activation energy is affected by the partial molar enthalpy, the pre-exponential factor is affected by the partial molar entropy, and the reaction rate constant is affected by the partial molar Gibbs energy. [Figure not available: see fulltext.

  13. Nonlocal kinetic energy functionals by functional integration.

    PubMed

    Mi, Wenhui; Genova, Alessandro; Pavanello, Michele

    2018-05-14

    Since the seminal studies of Thomas and Fermi, researchers in the Density-Functional Theory (DFT) community are searching for accurate electron density functionals. Arguably, the toughest functional to approximate is the noninteracting kinetic energy, T s [ρ], the subject of this work. The typical paradigm is to first approximate the energy functional and then take its functional derivative, δT s [ρ]δρ(r), yielding a potential that can be used in orbital-free DFT or subsystem DFT simulations. Here, this paradigm is challenged by constructing the potential from the second-functional derivative via functional integration. A new nonlocal functional for T s [ρ] is prescribed [which we dub Mi-Genova-Pavanello (MGP)] having a density independent kernel. MGP is constructed to satisfy three exact conditions: (1) a nonzero "Kinetic electron" arising from a nonzero exchange hole; (2) the second functional derivative must reduce to the inverse Lindhard function in the limit of homogenous densities; (3) the potential is derived from functional integration of the second functional derivative. Pilot calculations show that MGP is capable of reproducing accurate equilibrium volumes, bulk moduli, total energy, and electron densities for metallic (body-centered cubic, face-centered cubic) and semiconducting (crystal diamond) phases of silicon as well as of III-V semiconductors. The MGP functional is found to be numerically stable typically reaching self-consistency within 12 iterations of a truncated Newton minimization algorithm. MGP's computational cost and memory requirements are low and comparable to the Wang-Teter nonlocal functional or any generalized gradient approximation functional.

  14. Nonlocal kinetic energy functionals by functional integration

    NASA Astrophysics Data System (ADS)

    Mi, Wenhui; Genova, Alessandro; Pavanello, Michele

    2018-05-01

    Since the seminal studies of Thomas and Fermi, researchers in the Density-Functional Theory (DFT) community are searching for accurate electron density functionals. Arguably, the toughest functional to approximate is the noninteracting kinetic energy, Ts[ρ], the subject of this work. The typical paradigm is to first approximate the energy functional and then take its functional derivative, δ/Ts[ρ ] δ ρ (r ) , yielding a potential that can be used in orbital-free DFT or subsystem DFT simulations. Here, this paradigm is challenged by constructing the potential from the second-functional derivative via functional integration. A new nonlocal functional for Ts[ρ] is prescribed [which we dub Mi-Genova-Pavanello (MGP)] having a density independent kernel. MGP is constructed to satisfy three exact conditions: (1) a nonzero "Kinetic electron" arising from a nonzero exchange hole; (2) the second functional derivative must reduce to the inverse Lindhard function in the limit of homogenous densities; (3) the potential is derived from functional integration of the second functional derivative. Pilot calculations show that MGP is capable of reproducing accurate equilibrium volumes, bulk moduli, total energy, and electron densities for metallic (body-centered cubic, face-centered cubic) and semiconducting (crystal diamond) phases of silicon as well as of III-V semiconductors. The MGP functional is found to be numerically stable typically reaching self-consistency within 12 iterations of a truncated Newton minimization algorithm. MGP's computational cost and memory requirements are low and comparable to the Wang-Teter nonlocal functional or any generalized gradient approximation functional.

  15. Pyrolysis kinetics and thermal behavior of waste sawdust biomass using thermogravimetric analysis.

    PubMed

    Mishra, Ranjeet Kumar; Mohanty, Kaustubha

    2018-03-01

    The present study reports pyrolysis behavior of three waste biomass using thermogravimetric analysis to determine kinetic parameters at five different heating rates. Physiochemical characterization confirmed that these biomass have the potential for fuel and energy production. Pyrolysis experiments were carried out at five different heating rates (5-25 °C min -1 ). Five model-free methods such as Kissinger-Akahira-Sunose (KAS), Ozawa-Flynn-Wall (OFW), Friedman, Coats-Redfern, and distributed activation energy (DAEM) were used to calculate the kinetic parameters. The activation energy was found to be 171.66 kJ mol -1 , 148.44 kJ mol -1 , and 171.24 kJ mol -1 from KAS model; 179.29 kJ mol -1 , 156.58 kJ mol -1 , and 179.47 kJ mol -1 from OFW model; 168.58 kJ mol -1 , 181.53 kJ mol -1 , and 184.61 kJ mol -1 from Friedman model; and 206.62 kJ mol -1 , 171.63 kJ mol -1 , and 160.45 kJ mol -1 from DAEM model for PW, SW, AN biomass respectively. The calculated kinetic parameters are in good agreement with other reported biomass. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. The mathematical origins of the kinetic compensation effect: 2. The effect of systematic errors.

    PubMed

    Barrie, Patrick J

    2012-01-07

    The kinetic compensation effect states that there is a linear relationship between Arrhenius parameters ln A and E for a family of related processes. It is a widely observed phenomenon in many areas of science, notably heterogeneous catalysis. This paper explores mathematical, rather than physicochemical, explanations for the compensation effect in certain situations. Three different topics are covered theoretically and illustrated by examples. Firstly, the effect of systematic errors in experimental kinetic data is explored, and it is shown that these create apparent compensation effects. Secondly, analysis of kinetic data when the Arrhenius parameters depend on another parameter is examined. In the case of temperature programmed desorption (TPD) experiments when the activation energy depends on surface coverage, it is shown that a common analysis method induces a systematic error, causing an apparent compensation effect. Thirdly, the effect of analysing the temperature dependence of an overall rate of reaction, rather than a rate constant, is investigated. It is shown that this can create an apparent compensation effect, but only under some conditions. This result is illustrated by a case study for a unimolecular reaction on a catalyst surface. Overall, the work highlights the fact that, whenever a kinetic compensation effect is observed experimentally, the possibility of it having a mathematical origin should be carefully considered before any physicochemical conclusions are drawn.

  17. Accurate FRET Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation

    PubMed Central

    Lee, Nam Ki; Kapanidis, Achillefs N.; Wang, You; Michalet, Xavier; Mukhopadhyay, Jayanta; Ebright, Richard H.; Weiss, Shimon

    2005-01-01

    Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes. ALEX yields accurate FRET independent of instrumental factors, such as excitation intensity or detector alignment. Using DNA fragments, we showed that ALEX-based distances agree well with predictions from a cylindrical model of DNA; ALEX-based distances fit better to theory than distances obtained at the ensemble level. Distance measurements within transcription complexes agreed well with ensemble-FRET measurements, and with structural models based on ensemble-FRET and x-ray crystallography. ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature. PMID:15653725

  18. Measurement of Enzyme Kinetics by Use of a Blood Glucometer: Hydrolysis of Sucrose and Lactose

    ERIC Educational Resources Information Center

    Heinzerling, Peter; Schrader, Frank; Schanze, Sascha

    2012-01-01

    An alternative analytical method for measuring the kinetic parameters of the enzymes invertase and lactase is described. Invertase hydrolyzes sucrose to glucose and fructose and lactase hydrolyzes lactose to glucose and galactose. In most enzyme kinetics studies, photometric methods or test strips are used to quantify the derivates of the…

  19. A novel AIF tracking method and comparison of DCE-MRI parameters using individual and population-based AIFs in human breast cancer

    NASA Astrophysics Data System (ADS)

    Li, Xia; Welch, E. Brian; Arlinghaus, Lori R.; Bapsi Chakravarthy, A.; Xu, Lei; Farley, Jaime; Loveless, Mary E.; Mayer, Ingrid A.; Kelley, Mark C.; Meszoely, Ingrid M.; Means-Powell, Julie A.; Abramson, Vandana G.; Grau, Ana M.; Gore, John C.; Yankeelov, Thomas E.

    2011-09-01

    Quantitative analysis of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data requires the accurate determination of the arterial input function (AIF). A novel method for obtaining the AIF is presented here and pharmacokinetic parameters derived from individual and population-based AIFs are then compared. A Philips 3.0 T Achieva MR scanner was used to obtain 20 DCE-MRI data sets from ten breast cancer patients prior to and after one cycle of chemotherapy. Using a semi-automated method to estimate the AIF from the axillary artery, we obtain the AIF for each patient, AIFind, and compute a population-averaged AIF, AIFpop. The extended standard model is used to estimate the physiological parameters using the two types of AIFs. The mean concordance correlation coefficient (CCC) for the AIFs segmented manually and by the proposed AIF tracking approach is 0.96, indicating accurate and automatic tracking of an AIF in DCE-MRI data of the breast is possible. Regarding the kinetic parameters, the CCC values for Ktrans, vp and ve as estimated by AIFind and AIFpop are 0.65, 0.74 and 0.31, respectively, based on the region of interest analysis. The average CCC values for the voxel-by-voxel analysis are 0.76, 0.84 and 0.68 for Ktrans, vp and ve, respectively. This work indicates that Ktrans and vp show good agreement between AIFpop and AIFind while there is a weak agreement on ve.

  20. Theoretical study of gas hydrate decomposition kinetics--model development.

    PubMed

    Windmeier, Christoph; Oellrich, Lothar R

    2013-10-10

    In order to provide an estimate of the order of magnitude of intrinsic gas hydrate dissolution and dissociation kinetics, the "Consecutive Desorption and Melting Model" (CDM) is developed by applying only theoretical considerations. The process of gas hydrate decomposition is assumed to comprise two consecutive and repetitive quasi chemical reaction steps. These are desorption of the guest molecule followed by local solid body melting. The individual kinetic steps are modeled according to the "Statistical Rate Theory of Interfacial Transport" and the Wilson-Frenkel approach. All missing required model parameters are directly linked to geometric considerations and a thermodynamic gas hydrate equilibrium model.

  1. An investigation on the modelling of kinetics of thermal decomposition of hazardous mercury wastes.

    PubMed

    Busto, Yailen; M G Tack, Filip; Peralta, Luis M; Cabrera, Xiomara; Arteaga-Pérez, Luis E

    2013-09-15

    The kinetics of mercury removal from solid wastes generated by chlor-alkali plants were studied. The reaction order and model-free method with an isoconversional approach were used to estimate the kinetic parameters and reaction mechanism that apply to the thermal decomposition of hazardous mercury wastes. As a first approach to the understanding of thermal decomposition for this type of systems (poly-disperse and multi-component), a novel scheme of six reactions was proposed to represent the behaviour of mercury compounds in the solid matrix during the treatment. An integration-optimization algorithm was used in the screening of nine mechanistic models to develop kinetic expressions that best describe the process. The kinetic parameters were calculated by fitting each of these models to the experimental data. It was demonstrated that the D₁-diffusion mechanism appeared to govern the process at 250°C and high residence times, whereas at 450°C a combination of the diffusion mechanism (D₁) and the third order reaction mechanism (F3) fitted the kinetics of the conversions. The developed models can be applied in engineering calculations to dimension the installations and determine the optimal conditions to treat a mercury containing sludge. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway.

    PubMed

    Dana, Saswati; Nakakuki, Takashi; Hatakeyama, Mariko; Kimura, Shuhei; Raha, Soumyendu

    2011-01-01

    Mutation and/or dysfunction of signaling proteins in the mitogen activated protein kinase (MAPK) signal transduction pathway are frequently observed in various kinds of human cancer. Consistent with this fact, in the present study, we experimentally observe that the epidermal growth factor (EGF) induced activation profile of MAP kinase signaling is not straightforward dose-dependent in the PC3 prostate cancer cells. To find out what parameters and reactions in the pathway are involved in this departure from the normal dose-dependency, a model-based pathway analysis is performed. The pathway is mathematically modeled with 28 rate equations yielding those many ordinary differential equations (ODE) with kinetic rate constants that have been reported to take random values in the existing literature. This has led to us treating the ODE model of the pathways kinetics as a random differential equations (RDE) system in which the parameters are random variables. We show that our RDE model captures the uncertainty in the kinetic rate constants as seen in the behavior of the experimental data and more importantly, upon simulation, exhibits the abnormal EGF dose-dependency of the activation profile of MAP kinase signaling in PC3 prostate cancer cells. The most likely set of values of the kinetic rate constants obtained from fitting the RDE model into the experimental data is then used in a direct transcription based dynamic optimization method for computing the changes needed in these kinetic rate constant values for the restoration of the normal EGF dose response. The last computation identifies the parameters, i.e., the kinetic rate constants in the RDE model, that are the most sensitive to the change in the EGF dose response behavior in the PC3 prostate cancer cells. The reactions in which these most sensitive parameters participate emerge as candidate drug targets on the signaling pathway. 2011 Elsevier Ireland Ltd. All rights reserved.

  3. Quantitative kinetic theory of active matter

    NASA Astrophysics Data System (ADS)

    Ihle, Thomas; Chou, Yen-Liang

    2014-03-01

    Models of self-driven agents similar to the Vicsek model [Phys. Rev. Lett. 75 (1995) 1226] are studied by means of kinetic theory. In these models, particles try to align their travel directions with the average direction of their neighbours. At strong alignment a globally ordered state of collective motion forms. An Enskog-like kinetic theory is derived from the exact Chapman-Kolmogorov equation in phase space using Boltzmann's mean-field approximation of molecular chaos. The kinetic equation is solved numerically by a nonlocal Lattice-Boltzmann-like algorithm. Steep soliton-like waves are observed that lead to an abrupt jump of the global order parameter if the noise level is changed. The shape of the wave is shown to follow a novel scaling law and to quantitatively agree within 3 % with agent-based simulations at large particle speeds. This provides a mean-field mechanism to change the second-order character of the flocking transition to first order. Diagrammatic techniques are used to investigate small particle speeds, where the mean-field assumption of Molecular Chaos is invalid and where correlation effects need to be included.

  4. 3D nozzle flow simulations including state-to-state kinetics calculation

    NASA Astrophysics Data System (ADS)

    Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

    2014-12-01

    In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

  5. Stress enhanced calcium kinetics in a neuron.

    PubMed

    Kant, Aayush; Bhandakkar, Tanmay K; Medhekar, Nikhil V

    2018-02-01

    Accurate modeling of the mechanobiological response of a Traumatic Brain Injury is beneficial toward its effective clinical examination, treatment and prevention. Here, we present a stress history-dependent non-spatial kinetic model to predict the microscale phenomena of secondary insults due to accumulation of excess calcium ions (Ca[Formula: see text]) induced by the macroscale primary injuries. The model is able to capture the experimentally observed increase and subsequent partial recovery of intracellular Ca[Formula: see text] concentration in response to various types of mechanical impulses. We further establish the accuracy of the model by comparing our predictions with key experimental observations.

  6. "Batch" kinetics in flow: online IR analysis and continuous control.

    PubMed

    Moore, Jason S; Jensen, Klavs F

    2014-01-07

    Currently, kinetic data is either collected under steady-state conditions in flow or by generating time-series data in batch. Batch experiments are generally considered to be more suitable for the generation of kinetic data because of the ability to collect data from many time points in a single experiment. Now, a method that rapidly generates time-series reaction data from flow reactors by continuously manipulating the flow rate and reaction temperature has been developed. This approach makes use of inline IR analysis and an automated microreactor system, which allowed for rapid and tight control of the operating conditions. The conversion/residence time profiles at several temperatures were used to fit parameters to a kinetic model. This method requires significantly less time and a smaller amount of starting material compared to one-at-a-time flow experiments, and thus allows for the rapid generation of kinetic data. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Effect of Optical Defocus on the Kinetic Perimetry in Young Myopic Participants.

    PubMed

    Hirasawa, Kazunori; Shoji, Nobuyuki

    2015-01-01

    The prospective study evaluated the effects of optical defocus on kinetic sensitivity using automated kinetic perimetry. The 17 eyes of 17 healthy young participants were evaluated. All of the participants had myopia (≥ -5.00 D) and mild to no astigmatism (<1.00 D). Automated kinetic perimetry was performed using the Octopus 900 perimeter with Goldmann stimuli III4e, I4e, I3e, I2e, and I1e, with stimuli presented at 14 predetermined meridians, and a velocity of 3°/s. Optical defocus was induced with soft contact lenses, and varied in 1 D increments between 0 and +7 D. Kinetic sensitivity at each defocus was evaluated and compared to sensitivity with no defocus. Although kinetic sensitivity with the III4e and I4e stimuli decreased slightly at the inferior nasal, total kinetic sensitivity measured with the III4e and I4e stimuli was unaffected by optical defocus. Conversely, kinetic sensitivity measured with the I3e, I2e, and I1e stimuli decreased at defocus greater than +6 D (p < 0.05), + 3 D (p < 0.01), and at a defocus greater than +1 D (p < 0.01), respectively. Kinetic sensitivity was unaffected by defocus when measured with III4e and I4e stimuli. However, measurements with I3e, I2e, and I1e stimuli were affected, in particular measurements with I2e and I1e stimuli. Therefore, we conclude that optimal refractive correction with a contact lens or a spectacle lens is required in order to obtain accurate kinetic perimetry results, particularly for lower intensity stimuli.

  8. The Kinetics of Heterogeneous Electron Transfer Reactions in Polar Solvents

    DTIC Science & Technology

    1994-04-20

    focussed on systems for which rate constants and activation parameters are available as a function of the solvent, and as a function of temperature . The... temperature . The role of reactant structure in determining the kinetic parameters is also considered. Double layer effects both at unmodified and...that the Gibbs activation energy to form a monovalent cation from a neutral molecule via electrooxidation is different from that to form a monovalent

  9. On the relationships of gas transfer velocity with turbulent kinetic energy dissipation rate and wind waves

    NASA Astrophysics Data System (ADS)

    Zhao, D.

    2012-12-01

    The exchange of carbon dioxide across the air-sea interface is an important component of the atmospheric CO2 budget. Understanding how future changes in climate will affect oceanic uptake and releaser CO2 requires accurate estimation of air-sea CO2 flux. This flux is typically expressed as the product of gas transfer velocity, CO2 partial pressure difference in seawater and air, and the CO2 solubility. As the key parameter, gas transfer velocity has long been known to be controlled by the near-surface turbulence in water, which is affected by many factors, such as wind forcing, ocean waves, water-side convection and rainfall. Although the wind forcing is believed as the major factor dominating the near-surface turbulence, many studies have shown that the wind waves and their breaking would greatly enhance turbulence compared with the classical solid wall theory. Gas transfer velocity has been parameterized in terms of wind speed, turbulent kinetic energy dissipation rate, and wave parameters on the basis of observational data or theoretical analysis. However, great discrepancies, as large as one order, exist among these formulas. In this study, we will systematically analyze the differences of gas transfer velocity proposed so far, and try to find the reason that leads to their uncertainties. Finally, a new formula for gas transfer velocity will be given in terms of wind speed and wind wave parameter.

  10. Thermodynamic and kinetic studies of As(V) removal from water by zirconium oxide-coated marine sand.

    PubMed

    Khan, Tabrez Alam; Chaudhry, Saif Ali; Ali, Imran

    2013-08-01

    Arsenic contamination of groundwater is a major threat to human beings globally. Among various methods available for arsenic removal, adsorption is fast, inexpensive, selective, accurate, reproducible and eco-friendly in nature. The present paper describes removal of arsenate from water on zirconium oxide-coated sand (novel adsorbent). In the present work, zirconium oxide-coated sand was prepared and characterised by infrared and X-ray diffraction techniques. Batch experiments were performed to optimise different adsorption parameters such as initial arsenate concentration (100-1,000 μg/L), dose (1-8 g/L), pH of the solution (2-14), contact time (15-150 min.), and temperature (20, 30, 35 and 40 °C). The experimental data were analysed by Langmuir, Freundlich, Temkin and Dubinin-Radushkevich isotherm models. Furthermore, thermodynamic and kinetic parameters were evaluated to know the mode of adsorption between ZrOCMS and As(V). The maximum removal of arsenic, 97 %, was achieved at initial arsenic concentration of 200 μg/L, after 75 min at dosage of 5.0 g/L, pH 7.0 and 27 ± 2 °C. For 600 μg/L concentration, the maximum Langmuir monolayer adsorption capacity was found to be 270 μg/g at 35 °C. Kinetic modelling data indicated that adsorption process followed pseudo-second-order kinetics. The mechanism is controlled by liquid film diffusion model. Thermodynamic parameter, ΔH°, was -57.782, while the values of ΔG° were -9.460, -12.183, -13.343 and -13.905 kJ/mol at 20, 30, 35 and 40 °C, respectively, suggesting exothermic and spontaneous nature of the process. The change in entropy, ΔS°= -0.23 kJ/mol indicated that the entropy decreased due to adsorption of arsenate ion onto the solid adsorbent. The results indicated that the reported zirconium oxide-coated marine sand (ZrOCMS) was good adsorbent with 97 % removal capacity at 200 μg/L concentration. It is interesting to note that the permissible limit of arsenic as per World Health Organization is 10

  11. Quantitative production of compound I from a cytochrome P450 enzyme at low temperatures. Kinetics, activation parameters, and kinetic isotope effects for oxidation of benzyl alcohol.

    PubMed

    Wang, Qin; Sheng, Xin; Horner, John H; Newcomb, Martin

    2009-08-05

    Cytochrome P450 enzymes are commonly thought to oxidize substrates via an iron(IV)-oxo porphyrin radical cation transient termed Compound I, but kinetic studies of P450 Compounds I are essentially nonexistent. We report production of Compound I from cytochrome P450 119 (CYP119) in high conversion from the corresponding Compound II species at low temperatures in buffer mixtures containing 50% glycerol by photolysis with 365 nm light from a pulsed lamp. Compound I was studied as a reagent in oxidations of benzyl alcohol and its benzylic mono- and dideuterio isotopomers. Pseudo-first-order rate constants obtained at -50 degrees C with concentrations of substrates between 1.0 and 6.0 mM displayed saturation kinetics that gave binding constants for the substrate in the Compound I species (K(bind)) and first-order rate constants for the oxidation reactions (k(ox)). Representative results are K(bind) = 214 M(-1) and k(ox) = 0.48 s(-1) for oxidation of benzyl alcohol. For the dideuterated substrate C(6)H(5)CD(2)OH, kinetics were studied between -50 and -25 degrees C, and a van't Hoff plot for complexation and an Arrhenius plot for the oxidation reaction were constructed. The H/D kinetic isotope effects (KIEs) at -50 degrees C were resolved into a large primary KIE (P = 11.9) and a small, inverse secondary KIE (S = 0.96). Comparison of values extrapolated to 22 degrees C of both the rate constant for oxidation of C(6)H(5)CD(2)OH and the KIE for the nondeuterated and dideuterated substrates to values obtained previously in laser flash photolysis experiments suggested that tunneling could be a significant component of the total rate constant at -50 degrees C.

  12. Fourth-Order Vibrational Transition State Theory and Chemical Kinetics

    NASA Astrophysics Data System (ADS)

    Stanton, John F.; Matthews, Devin A.; Gong, Justin Z.

    2015-06-01

    Second-order vibrational perturbation theory (VPT2) is an enormously successful and well-established theory for treating anharmonic effects on the vibrational levels of semi-rigid molecules. Partially as a consequence of the fact that the theory is exact for the Morse potential (which provides an appropriate qualitative model for stretching anharmonicity), VPT2 calculations for such systems with appropriate ab initio potential functions tend to give fundamental and overtone levels that fall within a handful of wavenumbers of experimentally measured positions. As a consequence, the next non-vanishing level of perturbation theory -- VPT4 -- offers only slight improvements over VPT2 and is not practical for most calculations since it requires information about force constants up through sextic. However, VPT4 (as well as VPT2) can be used for other applications such as the next vibrational correction to rotational constants (the ``gammas'') and other spectroscopic parameters. In addition, the marriage of VPT with the semi-classical transition state theory of Miller (SCTST) has recently proven to be a powerful and accurate treatment for chemical kinetics. In this talk, VPT4-based SCTST tunneling probabilities and cumulative reaction probabilities are give for the first time for selected low-dimensional model systems. The prospects for VPT4, both practical and intrinsic, will also be discussed.

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

    PubMed

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

    2018-06-13

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

  14. Green-ampt infiltration parameters in riparian buffers

    Treesearch

    L.M. Stahr; D.E. Eisenhauer; M.J. Helmers; Mike G. Dosskey; T.G. Franti

    2004-01-01

    Riparian buffers can improve surface water quality by filtering contaminants from runoff before they enter streams. Infiltration is an important process in riparian buffers. Computer models are often used to assess the performance of riparian buffers. Accurate prediction of infiltration by these models is dependent upon accurate estimates of infiltration parameters....

  15. Characterization of metal adsorption kinetic properties in batch and fixed-bed reactors.

    PubMed

    Chen, J Paul; Wang, Lin

    2004-01-01

    Copper adsorption kinetic properties in batch and fixed-bed reactors were studied in this paper. The isothermal adsorption experiments showed that the copper adsorption capacity of a granular activated carbon (Filtrasorb 200) increased when ionic strength was higher. The presence of EDTA diminished the adsorption. An intraparticle diffusion model and a fixed-bed model were successfully used to describe the batch kinetic and fixed-bed operation behaviors. The kinetics became faster when the solution pH was not controlled, implying that the surface precipitation caused some metal uptake. The external mass transfer coefficient, the diffusivity and the dispersion coefficient were obtained from the modeling. It was found that both external mass transfer and dispersion coefficients increased when the flow rate was higher. Finally effects of kinetic parameters on simulation of fixed-bed operation were conducted.

  16. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    NASA Astrophysics Data System (ADS)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  17. Multi-GPU unsteady 2D flow simulation coupled with a state-to-state chemical kinetics

    NASA Astrophysics Data System (ADS)

    Tuttafesta, Michele; Pascazio, Giuseppe; Colonna, Gianpiero

    2016-10-01

    In this work we are presenting a GPU version of a CFD code for high enthalpy reacting flow, using the state-to-state approach. In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma and state-to-state kinetics is the most accurate approach used for this kind of problems. This model consists in writing a continuity equation for the population of each vibrational level of the molecules in the mixture, determining at the same time the species densities and the distribution of the population in internal levels. An explicit scheme is employed here to integrate the governing equations, so as to exploit the GPU structure and obtain an efficient algorithm. The best performances are obtained for reacting flows in state-to-state approach, reaching speedups of the order of 100, thanks to the use of an operator splitting scheme for the kinetics equations.

  18. FY2014 Parameters for Helions and Gold Ions in Booster, AGS, and RHIC

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

    Gardner, C. J.

    The nominal parameters for helions (helion is the bound state of two protons and one neutron, the nucleus of a helium-3 atom) and gold ions in Booster, AGS, and RHIC are given for the FY2014 running period. The parameters are found using various formulas to derive mass, helion anomalous g-factor, kinetic parameters, RF parameters, ring parameters, etc..

  19. Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

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

    Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

    In this paper, the oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deepermore » oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Finally, kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.« less

  20. Comparison of NBG-18, NBG-17, IG-110 and IG-11 oxidation kinetics in air

    DOE PAGES

    Lee, Jo Jo; Ghosh, Tushar K.; Loyalka, Sudarshan K.

    2017-12-14

    In this paper, the oxidation rates of several nuclear-grade graphites, NBG-18, NBG-17, IG-110 and IG-11, were measured in air using thermogravimetry. Kinetic parameters and oxidation behavior for each grade were compared by coke type, filler grain size and microstructure. The thickness of the oxidized layer for each grade was determined by layer peeling and direct density measurements. The results for NBG-17 and IG-11 were compared with those available in the literature and our recently reported results for NBG-18 and IG-110 oxidation in air. The finer-grained graphites IG-110 and IG-11 were more oxidized than medium-grained NBG-18 and NBG-17 because of deepermore » oxidant penetration, higher porosity and higher probability of available active sites. Variation in experimental conditions also had a marked effect on the reported kinetic parameters by several studies. Finally, kinetic parameters such as activation energy and transition temperature were sensitive to air flow rates as well as sample size and geometry.« less