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

NASA Astrophysics Data System (ADS)

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

2012-03-01

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

Maximum Entropy Approach in Dynamic Contrast-Enhanced Magnetic Resonance Imaging.

PubMed

Farsani, Zahra Amini; Schmid, Volker J

2017-01-01

In the estimation of physiological kinetic parameters from Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) data, the determination of the arterial input function (AIF) plays a key role. This paper proposes a Bayesian method to estimate the physiological parameters of DCE-MRI along with the AIF in situations, where no measurement of the AIF is available. In the proposed algorithm, the maximum entropy method (MEM) is combined with the maximum a posterior approach (MAP). To this end, MEM is used to specify a prior probability distribution of the unknown AIF. The ability of this method to estimate the AIF is validated using the Kullback-Leibler divergence. Subsequently, the kinetic parameters can be estimated with MAP. The proposed algorithm is evaluated with a data set from a breast cancer MRI study. The application shows that the AIF can reliably be determined from the DCE-MRI data using MEM. Kinetic parameters can be estimated subsequently. The maximum entropy method is a powerful tool to reconstructing images from many types of data. This method is useful for generating the probability distribution based on given information. The proposed method gives an alternative way to assess the input function from the existing data. The proposed method allows a good fit of the data and therefore a better estimation of the kinetic parameters. In the end, this allows for a more reliable use of DCE-MRI. Schattauer GmbH.

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

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

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.

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.

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

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

On the modeling of breath-by-breath oxygen uptake kinetics at the onset of high-intensity exercises: simulated annealing vs. GRG2 method.

PubMed

Bernard, Olivier; Alata, Olivier; Francaux, Marc

2006-03-01

Modeling in the time domain, the non-steady-state O2 uptake on-kinetics of high-intensity exercises with empirical models is commonly performed with gradient-descent-based methods. However, these procedures may impair the confidence of the parameter estimation when the modeling functions are not continuously differentiable and when the estimation corresponds to an ill-posed problem. To cope with these problems, an implementation of simulated annealing (SA) methods was compared with the GRG2 algorithm (a gradient-descent method known for its robustness). Forty simulated Vo2 on-responses were generated to mimic the real time course for transitions from light- to high-intensity exercises, with a signal-to-noise ratio equal to 20 dB. They were modeled twice with a discontinuous double-exponential function using both estimation methods. GRG2 significantly biased two estimated kinetic parameters of the first exponential (the time delay td1 and the time constant tau1) and impaired the precision (i.e., standard deviation) of the baseline A0, td1, and tau1 compared with SA. SA significantly improved the precision of the three parameters of the second exponential (the asymptotic increment A2, the time delay td2, and the time constant tau2). Nevertheless, td2 was significantly biased by both procedures, and the large confidence intervals of the whole second component parameters limit their interpretation. To compare both algorithms on experimental data, 26 subjects each performed two transitions from 80 W to 80% maximal O2 uptake on a cycle ergometer and O2 uptake was measured breath by breath. More than 88% of the kinetic parameter estimations done with the SA algorithm produced the lowest residual sum of squares between the experimental data points and the model. Repeatability coefficients were better with GRG2 for A1 although better with SA for A2 and tau2. Our results demonstrate that the implementation of SA improves significantly the estimation of most of these kinetic parameters, but a large inaccuracy remains in estimating the parameter values of the second exponential.

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.

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.

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.

Optimization of the lithium/thionyl chloride battery

NASA Technical Reports Server (NTRS)

White, Ralph E.

1989-01-01

A 1-D math model for the lithium/thionyl chloride primary cell is used in conjunction with a parameter estimation technique in order to estimate the electro-kinetic parameters of this electrochemical system. The electro-kinetic parameters include the anodic transfer coefficient and exchange current density of the lithium oxidation, alpha sub a,1 and i sub o,i,ref, the cathodic transfer coefficient and the effective exchange current density of the thionyl chloride reduction, alpha sub c,2 and a sup o i sub o,2,ref, and a morphology parameter, Xi. The parameter estimation is performed on simulated data first in order to gain confidence in the method. Data, reported in the literature, for a high rate discharge of an experimental lithium/thionyl chloride cell is used for an analysis.

Compartmental analysis of [11C]flumazenil kinetics for the estimation of ligand transport rate and receptor distribution using positron emission tomography.

PubMed

Koeppe, R A; Holthoff, V A; Frey, K A; Kilbourn, M R; Kuhl, D E

1991-09-01

The in vivo kinetic behavior of [11C]flumazenil ([11C]FMZ), a non-subtype-specific central benzodiazepine antagonist, is characterized using compartmental analysis with the aim of producing an optimized data acquisition protocol and tracer kinetic model configuration for the assessment of [11C]FMZ binding to benzodiazepine receptors (BZRs) in human brain. The approach presented is simple, requiring only a single radioligand injection. Dynamic positron emission tomography data were acquired on 18 normal volunteers using a 60- to 90-min sequence of scans and were analyzed with model configurations that included a three-compartment, four-parameter model, a three-compartment, three-parameter model, with a fixed value for free plus nonspecific binding; and a two-compartment, two-parameter model. Statistical analysis indicated that a four-parameter model did not yield significantly better fits than a three-parameter model. Goodness of fit was improved for three- versus two-parameter configurations in regions with low receptor density, but not in regions with moderate to high receptor density. Thus, a two-compartment, two-parameter configuration was found to adequately describe the kinetic behavior of [11C]FMZ in human brain, with stable estimates of the model parameters obtainable from as little as 20-30 min of data. Pixel-by-pixel analysis yields functional images of transport rate (K1) and ligand distribution volume (DV"), and thus provides independent estimates of ligand delivery and BZR binding.

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 and choice of PSF modelling in the reconstruction can significantly impact model parameters. PMID:24052021

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.

Anhydrous Weight Loss Prediction of Meranti Sawdust during Torrefaction using Rousset Model

NASA Astrophysics Data System (ADS)

Harun, Nur Hazirah Huda Mohd; Samad, Noor Asma Fazli Abdul; Saleh, Suriyati

2018-03-01

In torrefaction, the mass loss distribution is evaluated in terms of anhydrous weight loss (AWL). Since temperature gives significant effects on AWL and the behaviour of biomass is highly associated with the AWL, therefore a suitable model for estimating the reaction kinetics is necessary for describing the thermal degradation and predicting the AWL in order to improve its process. In this study, the kinetic parameters of Meranti sawdust are estimated by applying three-parallel reaction models namely the Rousset Model for torrefaction of Meranti sawdust at temperatures of 240°C, 270°C and 300°C. All kinetic parameters are estimated according to the degradation of biomass constituents which are lignin, cellulose and hemicellulose by following the Arrhenius Law. The result shows that AWL estimation using the kinetic parameters predicted from the Rousset model is in good agreement with the experimental result as the R2 value obtained is 0.99. It shows that the Rousset Model successfully described the degradation of lignin, cellulose and hemicellulose as well as the formation of char, volatile, tar and intermediate compound. Therefore it can be concluded that the Rousset Model is applicable to represent the torrefaction behaviour.

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.

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.

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 small scale systems. In addition, the results of this study can be used to estimate kinetic parameter values in the stage of model selection for different experimental conditions. Copyright © 2017 Elsevier B.V. All rights reserved.

Monochloramine Cometabolism by Mixed-Culture Nitrifiers ...

EPA Pesticide Factsheets

The current research investigated monochloramine cometabolism by nitrifying mixed cultures grown under drinking water relevant conditions and harvested from sand-packed reactors before conducting suspended growth batch kinetic experiments. Three batch reactors were used in each experiment: (1) a positive control to estimate ammonia kinetic parameters, (2) a negative control to account for abiotic reactions, and (3) a cometabolism reactor to estimate cometabolism kinetic constants. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to all experimental data. Cometabolism kinetics were best described by a first order model. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (30% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems. The results demonstrated that monochloramine cometabolism occurred in mixed cultures similar to those found in drinking water distribution systems; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in drinking water distribution systems.

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

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…

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models

PubMed Central

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization. PMID:27243005

Customized Steady-State Constraints for Parameter Estimation in Non-Linear Ordinary Differential Equation Models.

PubMed

Rosenblatt, Marcus; Timmer, Jens; Kaschek, Daniel

2016-01-01

Ordinary differential equation models have become a wide-spread approach to analyze dynamical systems and understand underlying mechanisms. Model parameters are often unknown and have to be estimated from experimental data, e.g., by maximum-likelihood estimation. In particular, models of biological systems contain a large number of parameters. To reduce the dimensionality of the parameter space, steady-state information is incorporated in the parameter estimation process. For non-linear models, analytical steady-state calculation typically leads to higher-order polynomial equations for which no closed-form solutions can be obtained. This can be circumvented by solving the steady-state equations for kinetic parameters, which results in a linear equation system with comparatively simple solutions. At the same time multiplicity of steady-state solutions is avoided, which otherwise is problematic for optimization. When solved for kinetic parameters, however, steady-state constraints tend to become negative for particular model specifications, thus, generating new types of optimization problems. Here, we present an algorithm based on graph theory that derives non-negative, analytical steady-state expressions by stepwise removal of cyclic dependencies between dynamical variables. The algorithm avoids multiple steady-state solutions by construction. We show that our method is applicable to most common classes of biochemical reaction networks containing inhibition terms, mass-action and Hill-type kinetic equations. Comparing the performance of parameter estimation for different analytical and numerical methods of incorporating steady-state information, we show that our approach is especially well-tailored to guarantee a high success rate of optimization.

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.

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.

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

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 cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

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 most cases compared to the other PVC methods. The results indicate that the PVC implementation and choice of PSF modelling in the reconstruction can significantly impact model parameters.

Joint reconstruction of dynamic PET activity and kinetic parametric images using total variation constrained dictionary sparse coding

NASA Astrophysics Data System (ADS)

Yu, Haiqing; Chen, Shuhang; Chen, Yunmei; Liu, Huafeng

2017-05-01

Dynamic positron emission tomography (PET) is capable of providing both spatial and temporal information of radio tracers in vivo. In this paper, we present a novel joint estimation framework to reconstruct temporal sequences of dynamic PET images and the coefficients characterizing the system impulse response function, from which the associated parametric images of the system macro parameters for tracer kinetics can be estimated. The proposed algorithm, which combines statistical data measurement and tracer kinetic models, integrates a dictionary sparse coding (DSC) into a total variational minimization based algorithm for simultaneous reconstruction of the activity distribution and parametric map from measured emission sinograms. DSC, based on the compartmental theory, provides biologically meaningful regularization, and total variation regularization is incorporated to provide edge-preserving guidance. We rely on techniques from minimization algorithms (the alternating direction method of multipliers) to first generate the estimated activity distributions with sub-optimal kinetic parameter estimates, and then recover the parametric maps given these activity estimates. These coupled iterative steps are repeated as necessary until convergence. Experiments with synthetic, Monte Carlo generated data, and real patient data have been conducted, and the results are very promising.

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.

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

Monochloramine Disinfection Kinetics of Nitrosomonas europaea by Propidium Monoazide Quantitative PCR and Live/Dead BacLight Methods▿

PubMed Central

Wahman, David G.; Wulfeck-Kleier, Karen A.; Pressman, Jonathan G.

2009-01-01

Monochloramine disinfection kinetics were determined for the pure-culture ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) by two culture-independent methods, namely, Live/Dead BacLight (LD) and propidium monoazide quantitative PCR (PMA-qPCR). Both methods were first verified with mixtures of heat-killed (nonviable) and non-heat-killed (viable) cells before a series of batch disinfection experiments with stationary-phase cultures (batch grown for 7 days) at pH 8.0, 25°C, and 5, 10, and 20 mg Cl2/liter monochloramine. Two data sets were generated based on the viability method used, either (i) LD or (ii) PMA-qPCR. These two data sets were used to estimate kinetic parameters for the delayed Chick-Watson disinfection model through a Bayesian analysis implemented in WinBUGS. This analysis provided parameter estimates of 490 mg Cl2-min/liter for the lag coefficient (b) and 1.6 × 10−3 to 4.0 × 10−3 liter/mg Cl2-min for the Chick-Watson disinfection rate constant (k). While estimates of b were similar for both data sets, the LD data set resulted in a greater k estimate than that obtained with the PMA-qPCR data set, implying that the PMA-qPCR viability measure was more conservative than LD. For N. europaea, the lag phase was not previously reported for culture-independent methods and may have implications for nitrification in drinking water distribution systems. This is the first published application of a PMA-qPCR method for disinfection kinetic model parameter estimation as well as its application to N. europaea or monochloramine. Ultimately, this PMA-qPCR method will allow evaluation of monochloramine disinfection kinetics for mixed-culture bacteria in drinking water distribution systems. PMID:19561179

Probabilistic parameter estimation of activated sludge processes using Markov Chain Monte Carlo.

PubMed

Sharifi, Soroosh; Murthy, Sudhir; Takács, Imre; Massoudieh, Arash

2014-03-01

One of the most important challenges in making activated sludge models (ASMs) applicable to design problems is identifying the values of its many stoichiometric and kinetic parameters. When wastewater characteristics data from full-scale biological treatment systems are used for parameter estimation, several sources of uncertainty, including uncertainty in measured data, external forcing (e.g. influent characteristics), and model structural errors influence the value of the estimated parameters. This paper presents a Bayesian hierarchical modeling framework for the probabilistic estimation of activated sludge process parameters. The method provides the joint probability density functions (JPDFs) of stoichiometric and kinetic parameters by updating prior information regarding the parameters obtained from expert knowledge and literature. The method also provides the posterior correlations between the parameters, as well as a measure of sensitivity of the different constituents with respect to the parameters. This information can be used to design experiments to provide higher information content regarding certain parameters. The method is illustrated using the ASM1 model to describe synthetically generated data from a hypothetical biological treatment system. The results indicate that data from full-scale systems can narrow down the ranges of some parameters substantially whereas the amount of information they provide regarding other parameters is small, due to either large correlations between some of the parameters or a lack of sensitivity with respect to the parameters. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Direct Parametric Image Reconstruction in Reduced Parameter Space for Rapid Multi-Tracer PET Imaging.

PubMed

Cheng, Xiaoyin; Li, Zhoulei; Liu, Zhen; Navab, Nassir; Huang, Sung-Cheng; Keller, Ulrich; Ziegler, Sibylle; Shi, Kuangyu

2015-02-12

The separation of multiple PET tracers within an overlapping scan based on intrinsic differences of tracer pharmacokinetics is challenging, due to limited signal-to-noise ratio (SNR) of PET measurements and high complexity of fitting models. In this study, we developed a direct parametric image reconstruction (DPIR) method for estimating kinetic parameters and recovering single tracer information from rapid multi-tracer PET measurements. This is achieved by integrating a multi-tracer model in a reduced parameter space (RPS) into dynamic image reconstruction. This new RPS model is reformulated from an existing multi-tracer model and contains fewer parameters for kinetic fitting. Ordered-subsets expectation-maximization (OSEM) was employed to approximate log-likelihood function with respect to kinetic parameters. To incorporate the multi-tracer model, an iterative weighted nonlinear least square (WNLS) method was employed. The proposed multi-tracer DPIR (MTDPIR) algorithm was evaluated on dual-tracer PET simulations ([18F]FDG and [11C]MET) as well as on preclinical PET measurements ([18F]FLT and [18F]FDG). The performance of the proposed algorithm was compared to the indirect parameter estimation method with the original dual-tracer model. The respective contributions of the RPS technique and the DPIR method to the performance of the new algorithm were analyzed in detail. For the preclinical evaluation, the tracer separation results were compared with single [18F]FDG scans of the same subjects measured 2 days before the dual-tracer scan. The results of the simulation and preclinical studies demonstrate that the proposed MT-DPIR method can improve the separation of multiple tracers for PET image quantification and kinetic parameter estimations.

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.

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks.

PubMed

Rumschinski, Philipp; Borchers, Steffen; Bosio, Sandro; Weismantel, Robert; Findeisen, Rolf

2010-05-25

Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates.

Set-base dynamical parameter estimation and model invalidation for biochemical reaction networks

PubMed Central

2010-01-01

Background Mathematical modeling and analysis have become, for the study of biological and cellular processes, an important complement to experimental research. However, the structural and quantitative knowledge available for such processes is frequently limited, and measurements are often subject to inherent and possibly large uncertainties. This results in competing model hypotheses, whose kinetic parameters may not be experimentally determinable. Discriminating among these alternatives and estimating their kinetic parameters is crucial to improve the understanding of the considered process, and to benefit from the analytical tools at hand. Results In this work we present a set-based framework that allows to discriminate between competing model hypotheses and to provide guaranteed outer estimates on the model parameters that are consistent with the (possibly sparse and uncertain) experimental measurements. This is obtained by means of exact proofs of model invalidity that exploit the polynomial/rational structure of biochemical reaction networks, and by making use of an efficient strategy to balance solution accuracy and computational effort. Conclusions The practicability of our approach is illustrated with two case studies. The first study shows that our approach allows to conclusively rule out wrong model hypotheses. The second study focuses on parameter estimation, and shows that the proposed method allows to evaluate the global influence of measurement sparsity, uncertainty, and prior knowledge on the parameter estimates. This can help in designing further experiments leading to improved parameter estimates. PMID:20500862

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.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

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.

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.

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.

Monochloramine cometabolism by Nitrosomonas europaea under drinking water conditions.

PubMed

Maestre, Juan P; Wahman, David G; Speitel, Gerald E

2013-09-01

Chloramine is widely used in United States drinking water systems as a secondary disinfectant, which may promote the growth of nitrifying bacteria because ammonia is present. At the onset of nitrification, both nitrifying bacteria and their products exert a monochloramine demand, decreasing the residual disinfectant concentration in water distribution systems. This work investigated another potentially significant mechanism for residual disinfectant loss: monochloramine cometabolism by ammonia-oxidizing bacteria (AOB). Monochloramine cometabolism was studied with the pure culture AOB Nitrosomonas europaea (ATCC 19718) in batch kinetic experiments under drinking water conditions. Three batch reactors were used in each experiment: a positive control to estimate the ammonia kinetic parameters, a negative control to account for abiotic reactions, and a cometabolism reactor to estimate the cometabolism kinetic constants. Kinetic parameters were estimated in AQUASIM with a simultaneous fit to all experimental data. The cometabolism reactors showed a more rapid monochloramine decay than in the negative controls, demonstrating that cometabolism occurs. Cometabolism kinetics were best described by a pseudo first order model with a reductant term to account for ammonia availability. Monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (30-60% of the observed monochloramine decay). These results suggest that monochloramine cometabolism should occur in practice and may be a significant contribution to monochloramine decay during nitrification episodes in drinking water distribution systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

IPMP Global Fit - A one-step direct data analysis tool for predictive microbiology.

PubMed

Huang, Lihan

2017-12-04

The objective of this work is to develop and validate a unified optimization algorithm for performing one-step global regression analysis of isothermal growth and survival curves for determination of kinetic parameters in predictive microbiology. The algorithm is incorporated with user-friendly graphical interfaces (GUIs) to develop a data analysis tool, the USDA IPMP-Global Fit. The GUIs are designed to guide the users to easily navigate through the data analysis process and properly select the initial parameters for different combinations of mathematical models. The software is developed for one-step kinetic analysis to directly construct tertiary models by minimizing the global error between the experimental observations and mathematical models. The current version of the software is specifically designed for constructing tertiary models with time and temperature as the independent model parameters in the package. The software is tested with a total of 9 different combinations of primary and secondary models for growth and survival of various microorganisms. The results of data analysis show that this software provides accurate estimates of kinetic parameters. In addition, it can be used to improve the experimental design and data collection for more accurate estimation of kinetic parameters. IPMP-Global Fit can be used in combination with the regular USDA-IPMP for solving the inverse problems and developing tertiary models in predictive microbiology. Published by Elsevier B.V.

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.

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.

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.

Maximum likelihood-based analysis of single-molecule photon arrival trajectories

NASA Astrophysics Data System (ADS)

Hajdziona, Marta; Molski, Andrzej

2011-02-01

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 103 photons. When the intensity levels are well-separated and 104 photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

PubMed Central

Rhodes, Samhita S; Camara, Amadou KS; Ropella, Kristina M; Audi, Said H; Riess, Matthias L; Pagel, Paul S; Stowe, David F

2006-01-01

Background The phase-space relationship between simultaneously measured myoplasmic [Ca2+] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca2+] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca2+ sensitivity responsible for alterations in Ca2+-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury. Methods We used a four state computational model to predict LVP using experimentally measured, averaged myoplasmic [Ca2+] transients from unpaced, isolated guinea pig hearts as the model input. Values of model parameters were estimated by minimizing the error between experimentally measured LVP and model-predicted LVP. Results We found that IR injury resulted in reduced myofilament Ca2+ sensitivity, and decreased cross-bridge association and dissociation rates. Dopamine (8 μM) reduced myofilament Ca2+ sensitivity before, but enhanced it after ischemia while improving cross-bridge kinetics before and after IR injury. Dobutamine (4 μM) reduced myofilament Ca2+ sensitivity while improving cross-bridge kinetics before and after ischemia. Digoxin (1 μM) increased myofilament Ca2+ sensitivity and cross-bridge kinetics after but not before ischemia. Levosimendan (1 μM) enhanced myofilament Ca2+ affinity and cross-bridge kinetics only after ischemia. Conclusion Estimated model parameters reveal mechanistic changes in Ca2+-contraction coupling due to IR injury, specifically the inefficient utilization of Ca2+ for contractile function with diastolic contracture (increase in resting diastolic LVP). The model parameters also reveal drug-induced improvements in Ca2+-contraction coupling before and after IR injury. PMID:16512898

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.

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.

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.

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.

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

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

Use of spectral analysis with iterative filter for voxelwise determination of regional rates of cerebral protein synthesis with L-[1-11C]leucine PET.

PubMed

Veronese, Mattia; Schmidt, Kathleen C; Smith, Carolyn Beebe; Bertoldo, Alessandra

2012-06-01

A spectral analysis approach was used to estimate kinetic parameters of the L-[1-(11)C]leucine positron emission tomography (PET) method and regional rates of cerebral protein synthesis (rCPS) on a voxel-by-voxel basis. Spectral analysis applies to both heterogeneous and homogeneous tissues; it does not require prior assumptions concerning number of tissue compartments. Parameters estimated with spectral analysis can be strongly affected by noise, but numerical filters improve estimation performance. Spectral analysis with iterative filter (SAIF) was originally developed to improve estimation of leucine kinetic parameters and rCPS in region-of-interest (ROI) data analyses. In the present study, we optimized SAIF for application at the voxel level. In measured L-[1-(11)C]leucine PET data, voxel-level SAIF parameter estimates averaged over all voxels within a ROI (mean voxel-SAIF) generally agreed well with corresponding estimates derived by applying the originally developed SAIF to ROI time-activity curves (ROI-SAIF). Region-of-interest-SAIF and mean voxel-SAIF estimates of rCPS were highly correlated. Simulations showed that mean voxel-SAIF rCPS estimates were less biased and less variable than ROI-SAIF estimates in the whole brain and cortex; biases were similar in white matter. We conclude that estimation of rCPS with SAIF is improved when the method is applied at voxel level than in ROI analysis.

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.

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, there are no scale relationships to be found that link the laboratory and the field scale, accurately incorporating the additional processes, phenomena and characteristics, such as a) advective and dispersive transport of one or more contaminants, b) advective and dispersive transport and availability of electron acceptors, c) mass transfer limitations and d) spatial heterogeneities, at the larger scale and applying well defined lab scale parameters should accurately describe field scale processes.

A Model for the Estimation of Hepatic Insulin Extraction After a Meal.

PubMed

Piccinini, Francesca; Dalla Man, Chiara; Vella, Adrian; Cobelli, Claudio

2016-09-01

Quantitative assessment of hepatic insulin extraction (HE) after an oral glucose challenge, e.g., a meal, is important to understand the regulation of carbohydrate metabolism. The aim of the current study is to develop a model of system for estimating HE. Nine different models, of increasing complexity, were tested on data of 204 normal subjects, who underwent a mixed meal tolerance test, with frequent measurement of plasma glucose, insulin, and C-peptide concentrations. All these models included a two-compartment model of C-peptide kinetics, an insulin secretion model, a compartmental model of insulin kinetics (with number of compartments ranging from one to three), and different HE descriptions, depending on plasma glucose and insulin. Model performances were compared on the basis of data fit, precision of parameter estimates, and parsimony criteria. The three-compartment model of insulin kinetics, coupled with HE depending on glucose concentration, showed the best fit and a good ability to precisely estimate the parameters. In addition, the model calculates basal and total indices of HE ( HE b and HE tot , respectively), and provides an index of HE sensitivity to glucose ( S G HE ). A new physiologically based HE model has been developed, which allows an improved quantitative description of glucose regulation. The use of the new model provides an in-depth description of insulin kinetics, thus enabling a better understanding of a given subject's metabolic state.

Maximum likelihood-based analysis of single-molecule photon arrival trajectories.

PubMed

Hajdziona, Marta; Molski, Andrzej

2011-02-07

In this work we explore the statistical properties of the maximum likelihood-based analysis of one-color photon arrival trajectories. This approach does not involve binning and, therefore, all of the information contained in an observed photon strajectory is used. We study the accuracy and precision of parameter estimates and the efficiency of the Akaike information criterion and the Bayesian information criterion (BIC) in selecting the true kinetic model. We focus on the low excitation regime where photon trajectories can be modeled as realizations of Markov modulated Poisson processes. The number of observed photons is the key parameter in determining model selection and parameter estimation. For example, the BIC can select the true three-state model from competing two-, three-, and four-state kinetic models even for relatively short trajectories made up of 2 × 10(3) photons. When the intensity levels are well-separated and 10(4) photons are observed, the two-state model parameters can be estimated with about 10% precision and those for a three-state model with about 20% precision.

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.

Kinetic modeling of the photocatalytic degradation of clofibric acid in a slurry reactor.

PubMed

Manassero, Agustina; Satuf, María Lucila; Alfano, Orlando Mario

2015-01-01

A kinetic study of the photocatalytic degradation of the pharmaceutical clofibric acid is presented. Experiments were carried out under UV radiation employing titanium dioxide in water suspension. The main reaction intermediates were identified and quantified. Intrinsic expressions to represent the kinetics of clofibric acid and the main intermediates were derived. The modeling of the radiation field in the reactor was carried out by Monte Carlo simulation. Experimental runs were performed by varying the catalyst concentration and the incident radiation. Kinetic parameters were estimated from the experiments by applying a non-linear regression procedure. Good agreement was obtained between model predictions and experimental data, with an error of 5.9 % in the estimations of the primary pollutant concentration.

Automated region selection for analysis of dynamic cardiac SPECT data

NASA Astrophysics Data System (ADS)

Di Bella, E. V. R.; Gullberg, G. T.; Barclay, A. B.; Eisner, R. L.

1997-06-01

Dynamic cardiac SPECT using Tc-99m labeled teboroxime can provide kinetic parameters (washin, washout) indicative of myocardial blood flow. A time-consuming and subjective step of the data analysis is drawing regions of interest to delineate blood pool and myocardial tissue regions. The time-activity curves of the regions are then used to estimate local kinetic parameters. In this work, the appropriate regions are found automatically, in a manner similar to that used for calculating maximum count circumferential profiles in conventional static cardiac studies. The drawbacks to applying standard static circumferential profile methods are the high noise level and high liver uptake common in dynamic teboroxime studies. Searching along each ray for maxima to locate the myocardium does not typically provide useful information. Here we propose an iterative scheme in which constraints are imposed on the radii searched along each ray. The constraints are based on the shape of the time-activity curves of the circumferential profile members and on an assumption that the short axis slices are approximately circular. The constraints eliminate outliers and help to reduce the effects of noise and liver activity. Kinetic parameter estimates from the automatically generated regions were comparable to estimates from manually selected regions in dynamic canine teboroxime studies.

Optimal experimental design for assessment of enzyme kinetics in a drug discovery screening environment.

PubMed

Sjögren, Erik; Nyberg, Joakim; Magnusson, Mats O; Lennernäs, Hans; Hooker, Andrew; Bredberg, Ulf

2011-05-01

A penalized expectation of determinant (ED)-optimal design with a discrete parameter distribution was used to find an optimal experimental design for assessment of enzyme kinetics in a screening environment. A data set for enzyme kinetic data (V(max) and K(m)) was collected from previously reported studies, and every V(max)/K(m) pair (n = 76) was taken to represent a unique drug compound. The design was restricted to 15 samples, an incubation time of up to 40 min, and starting concentrations (C(0)) for the incubation between 0.01 and 100 μM. The optimization was performed by finding the sample times and C(0) returning the lowest uncertainty (S.E.) of the model parameter estimates. Individual optimal designs, one general optimal design and one, for laboratory practice suitable, pragmatic optimal design (OD) were obtained. In addition, a standard design (STD-D), representing a commonly applied approach for metabolic stability investigations, was constructed. Simulations were performed for OD and STD-D by using the Michaelis-Menten (MM) equation, and enzyme kinetic parameters were estimated with both MM and a monoexponential decay. OD generated a better result (relative standard error) for 99% of the compounds and an equal or better result [(root mean square error (RMSE)] for 78% of the compounds in estimation of metabolic intrinsic clearance. Furthermore, high-quality estimates (RMSE < 30%) of both V(max) and K(m) could be obtained for a considerable number (26%) of the investigated compounds by using the suggested OD. The results presented in this study demonstrate that the output could generally be improved compared with that obtained from the standard approaches used today.

Application of the distributed activation energy model to the kinetic study of pyrolysis of the fresh water algae Chlorococcum humicola.

PubMed

Kirtania, Kawnish; Bhattacharya, Sankar

2012-03-01

Apart from capturing carbon dioxide, fresh water algae can be used to produce biofuel. To assess the energy potential of Chlorococcum humicola, the alga's pyrolytic behavior was studied at heating rates of 5-20K/min in a thermobalance. To model the weight loss characteristics, an algorithm was developed based on the distributed activation energy model and applied to experimental data to extract the kinetics of the decomposition process. When the kinetic parameters estimated by this method were applied to another set of experimental data which were not used to estimate the parameters, the model was capable of predicting the pyrolysis behavior, in the new set of data with a R(2) value of 0.999479. The slow weight loss, that took place at the end of the pyrolysis process, was also accounted for by the proposed algorithm which is capable of predicting the pyrolysis kinetics of C. humicola at different heating rates. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

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.

Estimation of Ordinary Differential Equation Parameters Using Constrained Local Polynomial Regression.

PubMed

Ding, A Adam; Wu, Hulin

2014-10-01

We propose a new method to use a constrained local polynomial regression to estimate the unknown parameters in ordinary differential equation models with a goal of improving the smoothing-based two-stage pseudo-least squares estimate. The equation constraints are derived from the differential equation model and are incorporated into the local polynomial regression in order to estimate the unknown parameters in the differential equation model. We also derive the asymptotic bias and variance of the proposed estimator. Our simulation studies show that our new estimator is clearly better than the pseudo-least squares estimator in estimation accuracy with a small price of computational cost. An application example on immune cell kinetics and trafficking for influenza infection further illustrates the benefits of the proposed new method.

Estimation of Ordinary Differential Equation Parameters Using Constrained Local Polynomial Regression

PubMed Central

Ding, A. Adam; Wu, Hulin

2015-01-01

We propose a new method to use a constrained local polynomial regression to estimate the unknown parameters in ordinary differential equation models with a goal of improving the smoothing-based two-stage pseudo-least squares estimate. The equation constraints are derived from the differential equation model and are incorporated into the local polynomial regression in order to estimate the unknown parameters in the differential equation model. We also derive the asymptotic bias and variance of the proposed estimator. Our simulation studies show that our new estimator is clearly better than the pseudo-least squares estimator in estimation accuracy with a small price of computational cost. An application example on immune cell kinetics and trafficking for influenza infection further illustrates the benefits of the proposed new method. PMID:26401093

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

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.

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.

The kinetics for ammonium and nitrite oxidation under the effect of hydroxylamine.

PubMed

Wan, Xinyu; Xiao, Pengying; Zhang, Daijun; Lu, Peili; Yao, Zongbao; He, Qiang

2016-01-01

The kinetics for ammonium (NH4(+)) oxidation and nitrite (NO2(-)) oxidation under the effect of hydroxylamine (NH2OH) were studied by respirometry using the nitrifying sludge from a laboratory-scale sequencing batch reactor. Modified models were used to estimate kinetics parameters of ammonia and nitrite oxidation under the effect of hydroxylamine. An inhibition effect of hydroxylamine on the ammonia oxidation was observed under different hydroxylamine concentration levels. The self-inhibition coefficient of hydroxylamine oxidation and noncompetitive inhibition coefficient of hydroxylamine for nitrite oxidation was estimated by simulating exogenous oxygen-uptake rate profiles, respectively. The inhibitive effect of NH2OH on nitrite-oxidizing bacteria was stronger than on ammonia-oxidizing bacteria. This work could provide fundamental data for the kinetic investigation of the nitrification process.

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.

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.

Tracking of cell nuclei for assessment of in vitro uptake kinetics in ultrasound-mediated drug delivery using fibered confocal fluorescence microscopy.

PubMed

Derieppe, Marc; de Senneville, Baudouin Denis; Kuijf, Hugo; Moonen, Chrit; Bos, Clemens

2014-10-01

Previously, we demonstrated the feasibility to monitor ultrasound-mediated uptake of a cell-impermeable model drug in real time with fibered confocal fluorescence microscopy. Here, we present a complete post-processing methodology, which corrects for cell displacements, to improve the accuracy of pharmacokinetic parameter estimation. Nucleus detection was performed based on the radial symmetry transform algorithm. Cell tracking used an iterative closest point approach. Pharmacokinetic parameters were calculated by fitting a two-compartment model to the time-intensity curves of individual cells. Cells were tracked successfully, improving time-intensity curve accuracy and pharmacokinetic parameter estimation. With tracking, 93 % of the 370 nuclei showed a fluorescence signal variation that was well-described by a two-compartment model. In addition, parameter distributions were narrower, thus increasing precision. Dedicated image analysis was implemented and enabled studying ultrasound-mediated model drug uptake kinetics in hundreds of cells per experiment, using fiber-based confocal fluorescence microscopy.

Estimation of foot joint kinetics in three and four segment foot models using an existing proportionality scheme: Application in paediatric barefoot walking.

PubMed

Deschamps, Kevin; Eerdekens, Maarten; Desmet, Dirk; Matricali, Giovanni Arnoldo; Wuite, Sander; Staes, Filip

2017-08-16

Recent studies which estimated foot segment kinetic patterns were found to have inconclusive data on one hand, and did not dissociate the kinetics of the chopart and lisfranc joint. The current study aimed therefore at reproducing independent, recently published three-segment foot kinetic data (Study 1) and in a second stage expand the estimation towards a four-segment model (Study 2). Concerning the reproducibility study, two recently published three segment foot models (Bruening et al., 2014; Saraswat et al., 2014) were reproduced and kinetic parameters were incorporated in order to calculate joint moments and powers of paediatric cohorts during gait. Ground reaction forces were measured with an integrated force/pressure plate measurement set-up and a recently published proportionality scheme was applied to determine subarea total ground reaction forces. Regarding Study 2, moments and powers were estimated with respect to the Instituto Ortopedico Rizzoli four-segment model. The proportionality scheme was expanded in this study and the impact of joint centre location on kinetic data was evaluated. Findings related to Study 1 showed in general good agreement with the kinetic data published by Bruening et al. (2014). Contrarily, the peak ankle, midfoot and hallux powers published by Saraswat et al. (2014) are disputed. Findings of Study 2 revealed that the chopart joint encompasses both power absorption and generation, whereas the Lisfranc joint mainly contributes to power generation. The results highlights the necessity for further studies in the field of foot kinetic models and provides a first estimation of the kinetic behaviour of the Lisfranc joint. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

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.

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.

Isotherm, kinetic, and thermodynamic study of ciprofloxacin sorption on sediments.

PubMed

Mutavdžić Pavlović, Dragana; Ćurković, Lidija; Grčić, Ivana; Šimić, Iva; Župan, Josip

2017-04-01

In this study, equilibrium isotherms, kinetics and thermodynamics of ciprofloxacin on seven sediments in a batch sorption process were examined. The effects of contact time, initial ciprofloxacin concentration, temperature and ionic strength on the sorption process were studied. The K d parameter from linear sorption model was determined by linear regression analysis, while the Freundlich and Dubinin-Radushkevich (D-R) sorption models were applied to describe the equilibrium isotherms by linear and nonlinear methods. The estimated K d values varied from 171 to 37,347 mL/g. The obtained values of E (free energy estimated from D-R isotherm model) were between 3.51 and 8.64 kJ/mol, which indicated a physical nature of ciprofloxacin sorption on studied sediments. According to obtained n values as measure of intensity of sorption estimate from Freundlich isotherm model (from 0.69 to 1.442), ciprofloxacin sorption on sediments can be categorized from poor to moderately difficult sorption characteristics. Kinetics data were best fitted by the pseudo-second-order model (R 2  > 0.999). Thermodynamic parameters including the Gibbs free energy (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) were calculated to estimate the nature of ciprofloxacin sorption. Results suggested that sorption on sediments was a spontaneous exothermic process.

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.

Estimation of parameters in rational reaction rates of molecular biological systems via weighted least squares

NASA Astrophysics Data System (ADS)

Wu, Fang-Xiang; Mu, Lei; Shi, Zhong-Ke

2010-01-01

The models of gene regulatory networks are often derived from statistical thermodynamics principle or Michaelis-Menten kinetics equation. As a result, the models contain rational reaction rates which are nonlinear in both parameters and states. It is challenging to estimate parameters nonlinear in a model although there have been many traditional nonlinear parameter estimation methods such as Gauss-Newton iteration method and its variants. In this article, we develop a two-step method to estimate the parameters in rational reaction rates of gene regulatory networks via weighted linear least squares. This method takes the special structure of rational reaction rates into consideration. That is, in the rational reaction rates, the numerator and the denominator are linear in parameters. By designing a special weight matrix for the linear least squares, parameters in the numerator and the denominator can be estimated by solving two linear least squares problems. The main advantage of the developed method is that it can produce the analytical solutions to the estimation of parameters in rational reaction rates which originally is nonlinear parameter estimation problem. The developed method is applied to a couple of gene regulatory networks. The simulation results show the superior performance over Gauss-Newton method.

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.

Chloramine demand estimation using surrogate chemical and microbiological parameters.

PubMed

Moradi, Sina; Liu, Sanly; Chow, Christopher W K; van Leeuwen, John; Cook, David; Drikas, Mary; Amal, Rose

2017-07-01

A model is developed to enable estimation of chloramine demand in full scale drinking water supplies based on chemical and microbiological factors that affect chloramine decay rate via nonlinear regression analysis method. The model is based on organic character (specific ultraviolet absorbance (SUVA)) of the water samples and a laboratory measure of the microbiological (F m ) decay of chloramine. The applicability of the model for estimation of chloramine residual (and hence chloramine demand) was tested on several waters from different water treatment plants in Australia through statistical test analysis between the experimental and predicted data. Results showed that the model was able to simulate and estimate chloramine demand at various times in real drinking water systems. To elucidate the loss of chloramine over the wide variation of water quality used in this study, the model incorporates both the fast and slow chloramine decay pathways. The significance of estimated fast and slow decay rate constants as the kinetic parameters of the model for three water sources in Australia was discussed. It was found that with the same water source, the kinetic parameters remain the same. This modelling approach has the potential to be used by water treatment operators as a decision support tool in order to manage chloramine disinfection. Copyright © 2017. Published by Elsevier B.V.

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

PubMed Central

Dräger, Andreas; Kronfeld, Marcel; Ziller, Michael J; Supper, Jochen; Planatscher, Hannes; Magnus, Jørgen B; Oldiges, Marco; Kohlbacher, Oliver; Zell, Andreas

2009-01-01

Background To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1) experimental measurement of participating molecules, (2) assignment of rate laws to each reaction, and (3) parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e. g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem. Results We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in C. glutamicum. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1) coarse-grained comparison of the algorithms on all models and (2) fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis. Conclusion A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics model. A Langevin model is advisable to take stochastic effects into account. To estimate the model parameters, three algorithms are particularly useful: For first attempts the settings-free Tribes algorithm yields valuable results. Particle swarm optimization and differential evolution provide significantly better results with appropriate settings. PMID:19144170

Bioaccumulation of polycyclic aromatic compounds: 2. Modeling bioaccumulation in marine organisms chronically exposed to dispersed oil.

PubMed

Baussant, T; Sanni, S; Skadsheim, A; Jonsson, G; Børseth, J F; Gaudebert, B

2001-06-01

Within the frame of a large environmental study, we report on a research program that investigated the potential for bioaccumulation and subsequent effect responses in several marine organisms exposed to chronic levels of dispersed crude oil. Body burden can be estimated from kinetic parameters (rate constants for uptake and elimination), and appropriate body burden-effect relationships may improve assessments of environmental risks or the potential for such outcomes following chronic discharges at sea. We conducted a series of experiments in a flow-through system to describe the bioaccumulation kinetics of polycyclic aromatic hydrocarbons (PAH) at low concentrations of dispersed crude oils. Mussels (Mytilus edulis) and juvenile turbot (Scophthalmus maximus) were exposed for periods ranging from 8 to 21 d. Postexposure, the organisms were kept for a period of 9 to 10 d in running seawater to study elimination processes. Rate constants of uptake (k1) and elimination (k2) of the PAHs during and following exposure were calculated using a first-order kinetic model that assumed a decrease of the substances in the environment over time. The estimated bioconcentration factor was calculated from the ratio of k1/k2. The kinetic parameters of two-, three-, and four-ring PAHs in mussel and fish are compared with estimates based on hydrophobicity alone, expressed by the octanol-water partition coefficient, Kow (partitioning theory). A combination of reduced bioavailability of PAHs from oil droplets and degradation processes of PAHs in body tissues seems to explain discrepancies between kinetic rates based on Kow and actual kinetic rates measured in fish. Mussels showed a pattern more in compliance with the partitioning theory.

Growth modeling of Listeria monocytogenes in pasteurized liquid egg.

PubMed

Ohkochi, Miho; Koseki, Shigenobu; Kunou, Masaaki; Sugiura, Katsuaki; Tsubone, Hirokazu

2013-09-01

The growth kinetics of Listeria monocytogenes and natural flora in commercially produced pasteurized liquid egg was examined at 4.1 to 19.4°C, and a growth simulation model that can estimate the range of the number of L. monocytogenes bacteria was developed. The experimental kinetic data were fitted to the Baranyi model, and growth parameters, such as maximum specific growth rate (μ(max)), maximum population density (N(max)), and lag time (λ), were estimated. As a result of estimating these parameters, we found that L. monocytogenes can grow without spoilage below 12.2°C, and we then focused on storage temperatures below 12.2°C in developing our secondary models. The temperature dependency of the μ(max) was described by Ratkowsky's square root model. The N(max) of L. monocytogenes was modeled as a function of temperature, because the N(max) of L. monocytogenes decreased as storage temperature increased. A tertiary model of L. monocytogenes was developed using the Baranyi model and μ(max) and N(max) secondary models. The ranges of the numbers of L. monocytogenes bacteria were simulated using Monte Carlo simulations with an assumption that these parameters have variations that follow a normal distribution. Predictive simulations under both constant and fluctuating temperature conditions demonstrated a high accuracy, represented by root mean square errors of 0.44 and 0.34, respectively. The predicted ranges also seemed to show a reasonably good estimation, with 55.8 and 51.5% of observed values falling into the prediction range of the 25th to 75th percentile, respectively. These results suggest that the model developed here can be used to estimate the kinetics and range of L. monocytogenes growth in pasteurized liquid egg under refrigerated temperature.

SPECIFYING PHYSIOLOGICAL PARAMETERS FOR THE KINETICS OF INHALED TOLUENE IN RATS PERFORMING THE VISUAL SIGNAL DETECTION TASK (SDT).

EPA Science Inventory

A physiologically-based pharmacokinetic (PBPK) model is being developed to estimate the dosimetry of toluene in rats inhaling the VOC under various experimental conditions. The effects of physical activity are currently being estimated utilizing a three-step process. First, we d...

[Evaluation of the influence of humidity and temperature on the drug stability by initial average rate experiment].

PubMed

He, Ning; Sun, Hechun; Dai, Miaomiao

2014-05-01

To evaluate the influence of temperature and humidity on the drug stability by initial average rate experiment, and to obtained the kinetic parameters. The effect of concentration error, drug degradation extent, humidity and temperature numbers, humidity and temperature range, and average humidity and temperature on the accuracy and precision of kinetic parameters in the initial average rate experiment was explored. The stability of vitamin C, as a solid state model, was investigated by an initial average rate experiment. Under the same experimental conditions, the kinetic parameters obtained from this proposed method were comparable to those from classical isothermal experiment at constant humidity. The estimates were more accurate and precise by controlling the extent of drug degradation, changing humidity and temperature range, or by setting the average temperature closer to room temperature. Compared with isothermal experiments at constant humidity, our proposed method saves time, labor, and materials.

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.

Simulated maximum likelihood method for estimating kinetic rates in gene expression.

PubMed

Tian, Tianhai; Xu, Songlin; Gao, Junbin; Burrage, Kevin

2007-01-01

Kinetic rate in gene expression is a key measurement of the stability of gene products and gives important information for the reconstruction of genetic regulatory networks. Recent developments in experimental technologies have made it possible to measure the numbers of transcripts and protein molecules in single cells. Although estimation methods based on deterministic models have been proposed aimed at evaluating kinetic rates from experimental observations, these methods cannot tackle noise in gene expression that may arise from discrete processes of gene expression, small numbers of mRNA transcript, fluctuations in the activity of transcriptional factors and variability in the experimental environment. In this paper, we develop effective methods for estimating kinetic rates in genetic regulatory networks. The simulated maximum likelihood method is used to evaluate parameters in stochastic models described by either stochastic differential equations or discrete biochemical reactions. Different types of non-parametric density functions are used to measure the transitional probability of experimental observations. For stochastic models described by biochemical reactions, we propose to use the simulated frequency distribution to evaluate the transitional density based on the discrete nature of stochastic simulations. The genetic optimization algorithm is used as an efficient tool to search for optimal reaction rates. Numerical results indicate that the proposed methods can give robust estimations of kinetic rates with good accuracy.

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.

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.

Migration of antioxidants from polylactic acid films, a parameter estimation approach: Part I - A model including convective mass transfer coefficient.

PubMed

Samsudin, Hayati; Auras, Rafael; Burgess, Gary; Dolan, Kirk; Soto-Valdez, Herlinda

2018-03-01

A two-step solution based on the boundary conditions of Crank's equations for mass transfer in a film was developed. Three driving factors, the diffusion (D), partition (K p,f ) and convective mass transfer coefficients (h), govern the sorption and/or desorption kinetics of migrants from polymer films. These three parameters were simultaneously estimated. They provide in-depth insight into the physics of a migration process. The first step was used to find the combination of D, K p,f and h that minimized the sums of squared errors (SSE) between the predicted and actual results. In step 2, an ordinary least square (OLS) estimation was performed by using the proposed analytical solution containing D, K p,f and h. Three selected migration studies of PLA/antioxidant-based films were used to demonstrate the use of this two-step solution. Additional parameter estimation approaches such as sequential and bootstrap were also performed to acquire a better knowledge about the kinetics of migration. The proposed model successfully provided the initial guesses for D, K p,f and h. The h value was determined without performing a specific experiment for it. By determining h together with D, under or overestimation issues pertaining to a migration process can be avoided since these two parameters are correlated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the information content of long-term wastewater characteristics data in relation to activated sludge model parameters.

PubMed

Alikhani, Jamal; Takacs, Imre; Al-Omari, Ahmed; Murthy, Sudhir; Massoudieh, Arash

2017-03-01

A parameter estimation framework was used to evaluate the ability of observed data from a full-scale nitrification-denitrification bioreactor to reduce the uncertainty associated with the bio-kinetic and stoichiometric parameters of an activated sludge model (ASM). Samples collected over a period of 150 days from the effluent as well as from the reactor tanks were used. A hybrid genetic algorithm and Bayesian inference were used to perform deterministic and parameter estimations, respectively. The main goal was to assess the ability of the data to obtain reliable parameter estimates for a modified version of the ASM. The modified ASM model includes methylotrophic processes which play the main role in methanol-fed denitrification. Sensitivity analysis was also used to explain the ability of the data to provide information about each of the parameters. The results showed that the uncertainty in the estimates of the most sensitive parameters (including growth rate, decay rate, and yield coefficients) decreased with respect to the prior information.

Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

DTIC Science & Technology

2015-03-03

whether we could simultaneously estimate kinetic parameters and regulatory connectivity, in the absence of specific mechanistic knowledge , from synthetic...that manage metabolism. Of course, these issues are not independent; any description of enzyme activity regulation will be a function of system state...the absence of specific mechanistic knowledge , from synthetic experimental data. Toward these questions, we explored five hypothetical cell-free

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.

Actin dynamics at the living cell submembrane imaged by total internal reflection fluorescence photobleaching.

PubMed Central

Sund, S E; Axelrod, D

2000-01-01

Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about relevant chemical kinetic rates in vivo. Total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP), an established technique previously demonstrated to measure reversible biomolecular kinetic rates at surfaces in vitro, is extended here to measure reversible biomolecular kinetic rates of actin at the cytofacial (subplasma membrane) surface of living cells. For the first time, spatial imaging (with a charge-coupled device camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging produces both spatial maps of kinetic parameters (off-rates and mobile fractions) and estimates of kinetic correlation distances, cell-wide kinetic gradients, and dependences of kinetic parameters on initial fluorescence intensity. For microinjected rhodamine actin in living cultured smooth muscle (BC3H1) cells, the unbinding rate at or near the cytofacial surface of the plasma membrane (averaged over the entire cell) is measured at 0.032 +/- 0.007 s(-1). The corresponding rate for actin marked by microinjected rhodamine phalloidin is very similar, 0.033 +/- 0.013 s(-1), suggesting that TIR/FRAP is reporting the dynamics of entire filaments or protofilaments. For submembrane fluorescence-marked actin, the intensity, off-rate, and mobile fraction show a positive correlation over a characteristic distance of 1-3 microm and a negative correlation over larger distances greater than approximately 7-14 microm. Furthermore, the kinetic parameters display a statistically significant cell-wide gradient, with the cell having a "fast" and "slow" end with respect to actin kinetics. PMID:10969025

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 provide dimensionality reduction, better estimation performance, and lower computational complexity, and can help to alleviate the problem of data overfitting. PMID:21548948

Biodegradation modelling of a dissolved gasoline plume applying independent laboratory and field parameters

NASA Astrophysics Data System (ADS)

Schirmer, Mario; Molson, John W.; Frind, Emil O.; Barker, James F.

2000-12-01

Biodegradation of organic contaminants in groundwater is a microscale process which is often observed on scales of 100s of metres or larger. Unfortunately, there are no known equivalent parameters for characterizing the biodegradation process at the macroscale as there are, for example, in the case of hydrodynamic dispersion. Zero- and first-order degradation rates estimated at the laboratory scale by model fitting generally overpredict the rate of biodegradation when applied to the field scale because limited electron acceptor availability and microbial growth are not considered. On the other hand, field-estimated zero- and first-order rates are often not suitable for predicting plume development because they may oversimplify or neglect several key field scale processes, phenomena and characteristics. This study uses the numerical model BIO3D to link the laboratory and field scales by applying laboratory-derived Monod kinetic degradation parameters to simulate a dissolved gasoline field experiment at the Canadian Forces Base (CFB) Borden. All input parameters were derived from independent laboratory and field measurements or taken from the literature a priori to the simulations. The simulated results match the experimental results reasonably well without model calibration. A sensitivity analysis on the most uncertain input parameters showed 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. It is concluded that laboratory-derived Monod kinetic parameters can adequately describe field scale degradation, provided all controlling factors are incorporated in the field scale model. These factors include advective-dispersive transport of multiple contaminants and electron acceptors and large-scale spatial heterogeneities.

Mathematical model for Trametes versicolor growth in submerged cultivation.

PubMed

Tisma, Marina; Sudar, Martina; Vasić-Racki, Durda; Zelić, Bruno

2010-08-01

Trametes versicolor is a white-rot fungus known as a producer of extracellular enzymes such as laccase, manganese-peroxidase, and lignin-peroxidase. The production of these enzymes requires detailed knowledge of the growth characteristics and physiology of the fungus. Submerged cultivations of T. versicolor on glucose, fructose, and sucrose as sole carbon sources were performed in shake flasks. Sucrose hydrolysis catalyzed by the whole cells of T. versicolor was considered as one-step enzymatic reaction described with Michaelis-Menten kinetics. Kinetic parameters of invertase-catalyzed sucrose hydrolysis were estimated (K (m) = 7.99 g dm(-3) and V (m) = 0.304 h(-1)). Monod model was used for description of kinetics of T. versicolor growth on glucose and fructose as sole carbon sources. Growth associated model parameters were estimated from the experimental results obtained by independent experiments (mu(G)(max) = 0.14 h(-1), K(G)(S) = 8.06 g dm(-3), mu(F)(max) = 0.37 h(-1) and K(F)(S) = 54.8 g dm(-3)). Developed mathematical model is in good agreement with the experimental results.

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.

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

Application of Hill's equation for estimating area under the concentration-time curve (AUC) and use of time to AUC 90% for expressing kinetics of drug disposition.

PubMed

Cheng, Hsien C

2009-01-01

Half life and its derived pharmacokinetic parameters are calculated on an assumption that the terminal phase of drug disposition follows a constant rate of disposition. In reality, this assumption may not necessarily be the case. A new method is needed for analyzing PK parameters if the disposition does not follow a first order PK kinetic. Cumulative area under the concentration-time curve (AUC) is plotted against time to yield a hyperbolic (or sigmoidal) AUC-time relationship curve which is then analyzed by Hill's equation to yield AUC(inf), time to achieving AUC50% (T(AUC50%)) or AUC90% (T(AUC90%)), and the Hill's slope. From these parameters, an AUC-time relationship curve can be reconstructed. Projected plasma concentration can be calculated for any time point. Time at which cumulative AUC reaches 90% (T(AUC90%)) can be used as an indicator for expressing how fast a drug is cleared. Clearance is calculated in a traditional manner (i.v. dose/AUC(inf)), and the volume of distribution is proposed to be calculated at T(AUC50%) (0.5 i.v. dose/plasma concentration at T(AUC50%)). This method of estimating AUC is applicable for both i.v. and oral data. It is concluded that the Hill's equation can be used as an alternative method for estimating AUC and analysis of PK parameters if the disposition does not follow a first order kinetic. T(AUC90%) is proposed to be used as an indicator for expressing how fast a drug is cleared from the system.

Modeling Dynamic Contrast-Enhanced MRI Data with a Constrained Local AIF.

PubMed

Duan, Chong; Kallehauge, Jesper F; Pérez-Torres, Carlos J; Bretthorst, G Larry; Beeman, Scott C; Tanderup, Kari; Ackerman, Joseph J H; Garbow, Joel R

2018-02-01

This study aims to develop a constrained local arterial input function (cL-AIF) to improve quantitative analysis of dynamic contrast-enhanced (DCE)-magnetic resonance imaging (MRI) data by accounting for the contrast-agent bolus amplitude error in the voxel-specific AIF. Bayesian probability theory-based parameter estimation and model selection were used to compare tracer kinetic modeling employing either the measured remote-AIF (R-AIF, i.e., the traditional approach) or an inferred cL-AIF against both in silico DCE-MRI data and clinical, cervical cancer DCE-MRI data. When the data model included the cL-AIF, tracer kinetic parameters were correctly estimated from in silico data under contrast-to-noise conditions typical of clinical DCE-MRI experiments. Considering the clinical cervical cancer data, Bayesian model selection was performed for all tumor voxels of the 16 patients (35,602 voxels in total). Among those voxels, a tracer kinetic model that employed the voxel-specific cL-AIF was preferred (i.e., had a higher posterior probability) in 80 % of the voxels compared to the direct use of a single R-AIF. Maps of spatial variation in voxel-specific AIF bolus amplitude and arrival time for heterogeneous tissues, such as cervical cancer, are accessible with the cL-AIF approach. The cL-AIF method, which estimates unique local-AIF amplitude and arrival time for each voxel within the tissue of interest, provides better modeling of DCE-MRI data than the use of a single, measured R-AIF. The Bayesian-based data analysis described herein affords estimates of uncertainties for each model parameter, via posterior probability density functions, and voxel-wise comparison across methods/models, via model selection in data modeling.

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

PubMed

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

2013-03-14

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

Fundamental properties of Fanaroff-Riley type II radio galaxies investigated via Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Kapińska, A. D.; Uttley, P.; Kaiser, C. R.

2012-08-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large-scale structure. We explore the intrinsic and extrinsic properties of the population of Fanaroff-Riley type II (FR II) objects, i.e. their kinetic luminosities, lifetimes and the central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux-limited radio catalogues of the Third Cambridge Revised Revised Catalogue (3CRR) and Best et al. We construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, we compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The new Monte Carlo method we present here allows us to (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, as has not been done before, we allow the source physical properties (kinetic luminosities, lifetimes and central densities) to co-evolve with redshift, and we find that all the investigated parameters most likely undergo cosmological evolution. Strikingly, we find that the break in the kinetic luminosity function must undergo redshift evolution of at least (1 + z)3. The fundamental parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. We use the estimated kinetic luminosity functions to set constraints on the duty cycles of these powerful radio sources. A comparison of the duty cycles of powerful FR IIs with those determined from radiative luminosities of active galactic nuclei of comparable black hole mass suggests a transition in behaviour from high to low redshifts, corresponding to either a drop in the typical black hole mass of powerful FR IIs at low redshifts, or a transition to a kinetically dominated, radiatively inefficient FR II population.

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.

Integral Design Methodology of Photocatalytic Reactors for Air Pollution Remediation.

PubMed

Passalía, Claudio; Alfano, Orlando M; Brandi, Rodolfo J

2017-06-07

An integral reactor design methodology was developed to address the optimal design of photocatalytic wall reactors to be used in air pollution control. For a target pollutant to be eliminated from an air stream, the proposed methodology is initiated with a mechanistic derived reaction rate. The determination of intrinsic kinetic parameters is associated with the use of a simple geometry laboratory scale reactor, operation under kinetic control and a uniform incident radiation flux, which allows computing the local superficial rate of photon absorption. Thus, a simple model can describe the mass balance and a solution may be obtained. The kinetic parameters may be estimated by the combination of the mathematical model and the experimental results. The validated intrinsic kinetics obtained may be directly used in the scaling-up of any reactor configuration and size. The bench scale reactor may require the use of complex computational software to obtain the fields of velocity, radiation absorption and species concentration. The complete methodology was successfully applied to the elimination of airborne formaldehyde. The kinetic parameters were determined in a flat plate reactor, whilst a bench scale corrugated wall reactor was used to illustrate the scaling-up methodology. In addition, an optimal folding angle of the corrugated reactor was found using computational fluid dynamics tools.

Gaussian process inference for estimating pharmacokinetic parameters of dynamic contrast-enhanced MR images.

PubMed

Wang, Shijun; Liu, Peter; Turkbey, Baris; Choyke, Peter; Pinto, Peter; Summers, Ronald M

2012-01-01

In this paper, we propose a new pharmacokinetic model for parameter estimation of dynamic contrast-enhanced (DCE) MRI by using Gaussian process inference. Our model is based on the Tofts dual-compartment model for the description of tracer kinetics and the observed time series from DCE-MRI is treated as a Gaussian stochastic process. The parameter estimation is done through a maximum likelihood approach and we propose a variant of the coordinate descent method to solve this likelihood maximization problem. The new model was shown to outperform a baseline method on simulated data. Parametric maps generated on prostate DCE data with the new model also provided better enhancement of tumors, lower intensity on false positives, and better boundary delineation when compared with the baseline method. New statistical parameter maps from the process model were also found to be informative, particularly when paired with the PK parameter maps.

Under-sampling trajectory design for compressed sensing based DCE-MRI.

PubMed

Liu, Duan-duan; Liang, Dong; Zhang, Na; Liu, Xin; Zhang, Yuan-ting

2013-01-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) needs high temporal and spatial resolution to accurately estimate quantitative parameters and characterize tumor vasculature. Compressed Sensing (CS) has the potential to accomplish this mutual importance. However, the randomness in CS under-sampling trajectory designed using the traditional variable density (VD) scheme may translate to uncertainty in kinetic parameter estimation when high reduction factors are used. Therefore, accurate parameter estimation using VD scheme usually needs multiple adjustments on parameters of Probability Density Function (PDF), and multiple reconstructions even with fixed PDF, which is inapplicable for DCE-MRI. In this paper, an under-sampling trajectory design which is robust to the change on PDF parameters and randomness with fixed PDF is studied. The strategy is to adaptively segment k-space into low-and high frequency domain, and only apply VD scheme in high-frequency domain. Simulation results demonstrate high accuracy and robustness comparing to VD design.

Solidification kinetics of a near eutectic Al-Si alloy, unmodified and modified with Sr

NASA Astrophysics Data System (ADS)

Aparicio, R.; Barrera, G.; Trapaga, G.; Ramirez-Argaez, M.; Gonzalez-Rivera, C.

2013-07-01

The purpose of this work was to explore the differences in solidification kinetics between unmodified and Sr modified eutectic Al-Si alloy as revealed by Fourier Thermal Analysis (FTA) and grain-growth kinetics characterization. Thermal analysis were performed in cylindrical stainless steel cups coated with a thin layer of boron nitride, using two type-K thermocouples connected to a data acquisition system. Grain growth kinetics characterization was carried out using solid fraction evolution and grain density data. FTA results for the non modified and modified alloys suggest that there are changes in the solidification rate during eutectic nucleation followed, during growth, by similar solidification rate evolutions, suggesting that this parameter is governed principally by the heat extraction conditions. On the other hand the change of the grain growth parameters estimated for the experimental probes suggest that the presence of Sr may modify the relationship between grain growth rate and undercooling in eutectic Al-Si.

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 with decreased kinetics and ball speed. Although increased time within specific phases correlates with decreases in the magnitude of upper extremity kinetics linked to overuse injuries, it also correlates with decreased ball speed. Based on these findings, it may appear that minimizing the risk of injury (ie, decreased kinetics) and maximizing performance quality (ie, increased ball speed) are incompatible with one another. However, there may be an optimal balance in timing that is effective for satisfying both outcomes.

Mathematical Methods for Studying DNA and Protein Interactions

NASA Astrophysics Data System (ADS)

LeGresley, Sarah

Deoxyribnucleic Acid (DNA) damage can lead to health related issues such as developmental disorders, aging, and cancer. It has been estimated that damage rates may be as high as 100,000 per cell per day. Because of the devastating effects that DNA damage can have, DNA repair mechanisms are of great interest yet are not completely understood. To gain a better understanding of possible DNA repair mechanisms, my dissertation focused on mathematical methods for understanding the interactions between DNA and proteins. I developed a damaged DNA model to estimate the probabilities of damaged DNA being located at specific positions. Experiments were then performed that suggested that the damaged DNA may be repositioned. These experimental results were consistent with the model's prediction that damaged DNA has preferred locations. To study how proteins might be moving along the DNA, I studied the use of the uniform motion "n-step" model. The n-step model has been used to determine the kinetics parameters (e.g. rates at which a protein moves along the DNA, how much energy is required to move a protein along a specified amount of DNA, etc.) of proteins moving along the DNA. Monte Carlo methods were used to simulate proteins moving with different types of non-uniform motion (e.g. backward, jumping, etc.) along the DNA. Estimates for the kinetics parameters in the n-step model were found by fitting of the Monte Carlo simulation data. Analysis indicated that non-uniform motion of the protein may lead to over or underestimation of the kinetic parameters of this n-step model.

Ocean mixing beneath Pine Island Glacier ice shelf, West Antarctica

NASA Astrophysics Data System (ADS)

Kimura, Satoshi; Jenkins, Adrian; Dutrieux, Pierre; Forryan, Alexander; Naveira Garabato, Alberto C.; Firing, Yvonne

2016-12-01

Ice shelves around Antarctica are vulnerable to an increase in ocean-driven melting, with the melt rate depending on ocean temperature and the strength of flow inside the ice-shelf cavities. We present measurements of velocity, temperature, salinity, turbulent kinetic energy dissipation rate, and thermal variance dissipation rate beneath Pine Island Glacier ice shelf, West Antarctica. These measurements were obtained by CTD, ADCP, and turbulence sensors mounted on an Autonomous Underwater Vehicle (AUV). The highest turbulent kinetic energy dissipation rate is found near the grounding line. The thermal variance dissipation rate increases closer to the ice-shelf base, with a maximum value found ˜0.5 m away from the ice. The measurements of turbulent kinetic energy dissipation rate near the ice are used to estimate basal melting of the ice shelf. The dissipation-rate-based melt rate estimates is sensitive to the stability correction parameter in the linear approximation of universal function of the Monin-Obukhov similarity theory for stratified boundary layers. We argue that our estimates of basal melting from dissipation rates are within a range of previous estimates of basal melting.

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.

Precipitation-Induced Changes in Microstrain and Its Relation with Hardness and Tempering Parameter in 17-4 PH Stainless Steel

NASA Astrophysics Data System (ADS)

Mahadevan, S.; Manojkumar, R.; Jayakumar, T.; Das, C. R.; Rao, B. P. C.

2016-06-01

17-4 PH (precipitation hardening) stainless steel is a soft martensitic stainless steel strengthened by aging at appropriate temperature for sufficient duration. Precipitation of copper particles in the martensitic matrix during aging causes coherency strains which improves the mechanical properties, namely hardness and strength of the matrix. The contributions to X-ray diffraction (XRD) profile broadening due to coherency strains caused by precipitation and crystallite size changes due to aging are separated and quantified using the modified Williamson-Hall approach. The estimated normalized mean square strain and crystallite size are used to explain the observed changes in hardness. Microstructural changes observed in secondary electron images are in qualitative agreement with crystallite size changes estimated from XRD profile analysis. The precipitation kinetics in the age-hardening regime and overaged regime are studied from hardness changes and they follow the Avrami kinetics and Wilson's model, respectively. In overaged condition, the hardness changes are linearly correlated to the tempering parameter (also known as Larson-Miller parameter). Similar linear variation is observed between the normalized mean square strain (determined from XRD line profile analysis) and the tempering parameter, in the incoherent regime which is beyond peak microstrain conditions.

Estimation of the nucleation kinetics for the anti-solvent crystallisation of paracetamol in methanol/water solutions

NASA Astrophysics Data System (ADS)

Ó'Ciardhá, Clifford T.; Frawley, Patrick J.; Mitchell, Niall A.

2011-08-01

In this work the primary nucleation kinetics have been estimated for the anti-solvent crystallisation of paracetamol in methanol-water solutions from metastable zone widths (MSZW) and induction times at 25 °C. Laser back-scattering via a focused beam reflectance Measurement (FBRM ®) is utilised to detect the onset of nucleation. The theoretical approach of Kubota was employed to estimate the nucleation kinetics, which accounts for the sensitivity of the nucleation detection technique. This approach is expanded in this work to analyse the induction time for an anti-solvent crystallisation process. Solvent composition is known to have a significant impact on the measured induction times and MSZW. The induction time in this paper was measured from 40% to 70% mass water and the MSZW is measured from 40% to 60% mass water. The primary focus of the paper was to gauge the extent of how solvent composition affects nucleation kinetics so that this effect may be incorporated into a population balance model. Furthermore, the effects of solvent composition on the estimated nucleation rates are investigated. The primary nucleation rates were found to decrease with dynamic solvent composition, with the extent of their reduction linked to the gradient of the solubility curve. Finally, both MSZW and induction time methods have been found to produce similar estimates for the nucleation parameters.

Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

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

Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca; Haider, Masoom A.; Jaffray, David A.

Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarselymore » sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.« less

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.

Dynamic single photon emission computed tomography—basic principles and cardiac applications

PubMed Central

Gullberg, Grant T; Reutter, Bryan W; Sitek, Arkadiusz; Maltz, Jonathan S; Budinger, Thomas F

2011-01-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time–activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time–activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements. PMID:20858925

TOPICAL REVIEW: Dynamic single photon emission computed tomography—basic principles and cardiac applications

NASA Astrophysics Data System (ADS)

Gullberg, Grant T.; Reutter, Bryan W.; Sitek, Arkadiusz; Maltz, Jonathan S.; Budinger, Thomas F.

2010-10-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time-activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time-activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements.

Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

DTIC Science & Technology

2015-03-16

sensitivity value was the maximum uncertainty in that value estimated by the Sobol method. 2.4. Global Sensitivity Analysis of the Reduced Order Coagulation...sensitivity analysis, using the variance-based method of Sobol , to estimate which parameters controlled the performance of the reduced order model [69]. We...Environment. Comput. Sci. Eng. 2007, 9, 90–95. 69. Sobol , I. Global sensitivity indices for nonlinear mathematical models and their Monte Carlo estimates

Kinetic modelling of a diesel-polluted clayey soil bioremediation process.

PubMed

Fernández, Engracia Lacasa; Merlo, Elena Moliterni; Mayor, Lourdes Rodríguez; Camacho, José Villaseñor

2016-07-01

A mathematical model is proposed to describe a diesel-polluted clayey soil bioremediation process. The reaction system under study was considered a completely mixed closed batch reactor, which initially contacted a soil matrix polluted with diesel hydrocarbons, an aqueous liquid-specific culture medium and a microbial inoculation. The model coupled the mass transfer phenomena and the distribution of hydrocarbons among four phases (solid, S; water, A; non-aqueous liquid, NAPL; and air, V) with Monod kinetics. In the first step, the model simulating abiotic conditions was used to estimate only the mass transfer coefficients. In the second step, the model including both mass transfer and biodegradation phenomena was used to estimate the biological kinetic and stoichiometric parameters. In both situations, the model predictions were validated with experimental data that corresponded to previous research by the same authors. A correct fit between the model predictions and the experimental data was observed because the modelling curves captured the major trends for the diesel distribution in each phase. The model parameters were compared to different previously reported values found in the literature. Pearson correlation coefficients were used to show the reproducibility level of the model. Copyright © 2016. Published by Elsevier B.V.

Estimations of ABL fluxes and other turbulence parameters from Doppler lidar data

NASA Technical Reports Server (NTRS)

Tzvi, Gal-Chen; Mei, XU; Eberhard, Wynn

1990-01-01

Techniques for extracting boundary layer parameters from measurements of a short pulse CO2 Doppler Lidar are described. The radial velocity measurements have a range resolution of 150 m. With a pulse repetition rate of 20 Hz, it is possible to perform scannings in two perpendicular vertical planes in approx. 72 s. By continuously operating the Lidar for about an hour, one can extract stable statistics of the radial velocities. Assuming that the turbulence is horizontally homogeneous, the mean wind, its standard deviations, and the momentum fluxes were estimated. From the vertically pointing beam, the first, second, and third moments of the vertical velocity were also estimated. Spectral analysis of the radial velocities is also performed from which, by examining the amplitude of the power spectrum at the inertial range, the kinetic energy dissipation was deduced. Finally, using the statistical form of the Navier-Stokes equations, the surface heat flux is derived as the residual balance between the vertical gradient of the third moment of the vertical velocity and the kinetic energy dissipation.

Cumulated Activity Comparison of 64Cu-/177Lu-Labeled Anti-Epidermal Growth Factor Receptor Antibody in Esophageal Squamous Cell Carcinoma Model.

PubMed

Laffon, Eric; Thumerel, Matthieu; Jougon, Jacques; Marthan, Roger

2017-06-01

This work aimed at estimating the kinetic parameters, and hence cumulated activity (A C ), of a diagnostic/therapeutic convergence radiopharmaceutical, namely 64 Cu-/ 177 Lu-labeled antibody ( 64 Cu-/ 177 Lu-cetuximab), that acts as anti-epidermal growth factor receptor. Methods: In mice bearing esophageal squamous cell carcinoma tumors, to estimate uptake (K), release rate constant (k R ), and hence A C , a kinetic model analysis was applied to recently published biodistribution data of immuno-PET imaging with 64 Cu-cetuximab and of small-animal SPECT/CT imaging with 177 Lu-cetuximab, including blood and TE-8 tumor. Results: K, k R , and A C were estimated to be 0.0566/0.0593 g⋅h -1 ⋅g -1 , 0.0150/0.0030 h -1 , and 2.3 × 10 10 /4.1 × 10 12 disintegrations (per gram of TE-8 tumor), with an injected activity of 3.70/12.95 MBq, for 64 Cu-/ 177 Lu-cetuximab, respectively. Conclusion: A model is available for comparing kinetic parameters and A C of the companion diagnostic/therapeutic 64 Cu-/ 177 Lu-cetuximab that may be considered as a step for determining whether one can really use the former to predict dosimetry of the latter. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

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

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.

Estimation of homogeneous nucleation flux via a kinetic model

NASA Technical Reports Server (NTRS)

Wilcox, C. F.; Bauer, S. H.

1991-01-01

The proposed kinetic model for condensation under homogeneous conditions, and the onset of unidirectional cluster growth in supersaturated gases, does not suffer from the conceptual flaws that characterize classical nucleation theory. When a full set of simultaneous rate equation is solved, a characteristic time emerges, for each cluster size, at which the production rate, and its rate of conversion to the next size (n + 1) are equal. Procedures for estimating the essential parameters are proposed; condensation fluxes J(kin) exp ss are evaluated. Since there are practical limits to the cluster size that can be incorporated in the set of simultaneous first-order differential equations, a code was developed for computing an approximate J(th) exp ss based on estimates of a 'constrained equilibrium' distribution, and identification of its minimum.

Statistical Ring Opening Metathesis Copolymerization of Norbornene and Cyclopentene by Grubbs' 1st-Generation Catalyst.

PubMed

Nikovia, Christiana; Maroudas, Andreas-Philippos; Goulis, Panagiotis; Tzimis, Dionysios; Paraskevopoulou, Patrina; Pitsikalis, Marinos

2015-08-27

Statistical copolymers of norbornene (NBE) with cyclopentene (CP) were prepared by ring-opening metathesis polymerization, employing the 1st-generation Grubbs' catalyst, in the presence or absence of triphenylphosphine, PPh₃. The reactivity ratios were estimated using the Finemann-Ross, inverted Finemann-Ross, and Kelen-Tüdos graphical methods, along with the computer program COPOINT, which evaluates the parameters of binary copolymerizations from comonomer/copolymer composition data by integrating a given copolymerization equation in its differential form. Structural parameters of the copolymers were obtained by calculating the dyad sequence fractions and the mean sequence length, which were derived using the monomer reactivity ratios. The kinetics of thermal decomposition of the copolymers along with the respective homopolymers was studied by thermogravimetric analysis within the framework of the Ozawa-Flynn-Wall and Kissinger methodologies. Finally, the effect of triphenylphosphine on the kinetics of copolymerization, the reactivity ratios, and the kinetics of thermal decomposition were examined.

Optimization and adsorption kinetic studies of aqueous manganese ion removal using chitin extracted from shells of edible Philippine crabs

NASA Astrophysics Data System (ADS)

Quimque, Mark Tristan J.; Jimenez, Marvin C.; Acas, Meg Ina S.; Indoc, Danrelle Keth L.; Gomez, Enjelyn C.; Tabuñag, Jenny Syl D.

2017-01-01

Manganese is a common contaminant in drinking water along with other metal pollutants. This paper investigates the use of chitin, extracted from crab shells obtained as restaurant throwaway, as an adsorbent in removing manganese ions from aqueous medium. In particular, this aims to optimize the adsorption parameters and look into the kinetics of the process. The adsorption experiments done in this study employed the batch equilibration method. In the optimization, the following parameters were considered: pH and concentration of Mn (II) sorbate solution, particle size and dosage of adsorbent chitin, and adsorbent-adsorbate contact time. At the optimal condition, the order of the adsorption reaction was estimated using kinetic models which describes the process best. It was found out that the adsorption of aqueous Mn (II) ions onto chitin obeys the pseudo-second order model. This model assumes that the adsorption occurred via chemisorption

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.

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

Not Available

An Apple IIe microcomputer is being used to collect data and to control a pyrolysis system. Pyrolysis data for bitumen and kerogen are widely used to estimate source rock maturity. For a detailed analysis of kinetic parameters, however, data must be obtained more precisely than for routine pyrolysis. The authors discuss the program which controls the temperature ramp of the furnace that heats the sample, and collects data from a thermocouple in the furnace and from the flame ionization detector measuring evolved hydrocarbons. These data are stored on disk for later use by programs that display the results of themore » experiment or calculate kinetic parameters. The program is written in Applesoft BASIC with subroutines in Apple assembler for speed and efficiency.« less

Pyrolysis characteristics and kinetics of microalgae via thermogravimetric analysis (TGA): A state-of-the-art review.

PubMed

Bach, Quang-Vu; Chen, Wei-Hsin

2017-12-01

Pyrolysis is a promising route for biofuels production from microalgae at moderate temperatures (400-600°C) in an inert atmosphere. Depending on the operating conditions, pyrolysis can produce biochar and/or bio-oil. In practice, knowledge for thermal decomposition characteristics and kinetics of microalgae during pyrolysis is essential for pyrolyzer design and pyrolysis optimization. Recently, the pyrolysis kinetics of microalgae has become a crucial topic and received increasing interest from researchers. Thermogravimetric analysis (TGA) has been employed as a proven technique for studying microalgae pyrolysis in a kinetic control regime. In addition, a number of kinetic models have been applied to process the TGA data for kinetic evaluation and parameters estimation. This paper aims to provide a state-of-the art review on recent research activities in pyrolysis characteristics and kinetics of various microalgae. Common kinetic models predicting the thermal degradation of microalgae are examined and their pros and cons are illustrated. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estimating Arrhenius parameters using temperature programmed molecular dynamics.

PubMed

Imandi, Venkataramana; Chatterjee, Abhijit

2016-07-21

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight various aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.

libSRES: a C library for stochastic ranking evolution strategy for parameter estimation.

PubMed

Ji, Xinglai; Xu, Ying

2006-01-01

Estimation of kinetic parameters in a biochemical pathway or network represents a common problem in systems studies of biological processes. We have implemented a C library, named libSRES, to facilitate a fast implementation of computer software for study of non-linear biochemical pathways. This library implements a (mu, lambda)-ES evolutionary optimization algorithm that uses stochastic ranking as the constraint handling technique. Considering the amount of computing time it might require to solve a parameter-estimation problem, an MPI version of libSRES is provided for parallel implementation, as well as a simple user interface. libSRES is freely available and could be used directly in any C program as a library function. We have extensively tested the performance of libSRES on various pathway parameter-estimation problems and found its performance to be satisfactory. The source code (in C) is free for academic users at http://csbl.bmb.uga.edu/~jix/science/libSRES/

Modeling of Tracer Transport Delays for Improved Quantification of Regional Pulmonary 18F-FDG Kinetics, Vascular Transit Times, and Perfusion

PubMed Central

Wellman, Tyler J.; Winkler, Tilo; Vidal Melo, Marcos F.

2015-01-01

18F-FDG-PET is increasingly used to assess pulmonary inflammatory cell activity. However, current models of pulmonary 18F-FDG kinetics do not account for delays in 18F-FDG transport between the plasma sampling site and the lungs. We developed a three-compartment model of 18F-FDG kinetics that includes a delay between the right heart and the local capillary blood pool, and used this model to estimate regional pulmonary perfusion. We acquired dynamic 18F-FDG scans in 12 mechanically ventilated sheep divided into control and lung injury groups (n=6 each). The model was fit to tracer kinetics in three isogravitational regions-of-interest to estimate regional lung transport delays and regional perfusion. 13NN bolus infusion scans were acquired during a period of apnea to measure regional perfusion using an established reference method. The delayed input function model improved description of 18F-FDG kinetics (lower Akaike Information Criterion) in 98% of studied regions. Local transport delays ranged from 2.0–13.6s, averaging 6.4±2.9s, and were highest in non-dependent regions. Estimates of regional perfusion derived from model parameters were highly correlated with perfusion measurements based on 13NN-PET (R2=0.92, p<0.001). By incorporating local vascular transports delays, this model of pulmonary 18F-FDG kinetics allows for simultaneous assessment of regional lung perfusion, transit times, and inflammation. PMID:25940652

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

Numerical Problem Solving Using Mathcad in Undergraduate Reaction Engineering

ERIC Educational Resources Information Center

Parulekar, Satish J.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

A Nonlinear, Multiinput, Multioutput Process Control Laboratory Experiment

ERIC Educational Resources Information Center

Young, Brent R.; van der Lee, James H.; Svrcek, William Y.

2006-01-01

Experience in using a user-friendly software, Mathcad, in the undergraduate chemical reaction engineering course is discussed. Example problems considered for illustration deal with simultaneous solution of linear algebraic equations (kinetic parameter estimation), nonlinear algebraic equations (equilibrium calculations for multiple reactions and…

Robust fitting for neuroreceptor mapping.

PubMed

Chang, Chung; Ogden, R Todd

2009-03-15

Among many other uses, positron emission tomography (PET) can be used in studies to estimate the density of a neuroreceptor at each location throughout the brain by measuring the concentration of a radiotracer over time and modeling its kinetics. There are a variety of kinetic models in common usage and these typically rely on nonlinear least-squares (LS) algorithms for parameter estimation. However, PET data often contain artifacts (such as uncorrected head motion) and so the assumptions on which the LS methods are based may be violated. Quantile regression (QR) provides a robust alternative to LS methods and has been used successfully in many applications. We consider fitting various kinetic models to PET data using QR and study the relative performance of the methods via simulation. A data adaptive method for choosing between LS and QR is proposed and the performance of this method is also studied.

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.

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.

Integrated computational model of the bioenergetics of isolated lung mitochondria

PubMed Central

Zhang, Xiao; Jacobs, Elizabeth R.; Camara, Amadou K. S.; Clough, Anne V.

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria. PMID:29889855

Integrated computational model of the bioenergetics of isolated lung mitochondria.

PubMed

Zhang, Xiao; Dash, Ranjan K; Jacobs, Elizabeth R; Camara, Amadou K S; Clough, Anne V; Audi, Said H

2018-01-01

Integrated computational modeling provides a mechanistic and quantitative framework for describing lung mitochondrial bioenergetics. Thus, the objective of this study was to develop and validate a thermodynamically-constrained integrated computational model of the bioenergetics of isolated lung mitochondria. The model incorporates the major biochemical reactions and transport processes in lung mitochondria. A general framework was developed to model those biochemical reactions and transport processes. Intrinsic model parameters such as binding constants were estimated using previously published isolated enzymes and transporters kinetic data. Extrinsic model parameters such as maximal reaction and transport velocities were estimated by fitting the integrated bioenergetics model to published and new tricarboxylic acid cycle and respirometry data measured in isolated rat lung mitochondria. The integrated model was then validated by assessing its ability to predict experimental data not used for the estimation of the extrinsic model parameters. For example, the model was able to predict reasonably well the substrate and temperature dependency of mitochondrial oxygen consumption, kinetics of NADH redox status, and the kinetics of mitochondrial accumulation of the cationic dye rhodamine 123, driven by mitochondrial membrane potential, under different respiratory states. The latter required the coupling of the integrated bioenergetics model to a pharmacokinetic model for the mitochondrial uptake of rhodamine 123 from buffer. The integrated bioenergetics model provides a mechanistic and quantitative framework for 1) integrating experimental data from isolated lung mitochondria under diverse experimental conditions, and 2) assessing the impact of a change in one or more mitochondrial processes on overall lung mitochondrial bioenergetics. In addition, the model provides important insights into the bioenergetics and respiration of lung mitochondria and how they differ from those of mitochondria from other organs. To the best of our knowledge, this model is the first for the bioenergetics of isolated lung mitochondria.

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.

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

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 et al., J. Phys. Chem. C, 2007, 111, 2149]. However, some fundamental understanding of the processes is still missing. Further research in future might help to tackle this problem. The most important questions, which need to be answered to constrain CNT, are raised in this study.

Color changes kinetics during deep fat frying of carrot slice

NASA Astrophysics Data System (ADS)

Salehi, Fakhreddin

2018-05-01

Heat and mass transfer phenomena take place during frying cause physicochemical changes, which affect the colour and surface of the fried products. The effect of frying temperature on the colour changes and heat transfer during deep fat frying of carrot has been investigated. The colour scale parameters redness (a*), yellowness (b*) and lightness (L*), and color change intensity (ΔE) were used to estimate colour changes during frying as a function of oil temperature. L* value of fried carrot decreased during frying. The redness of fried carrot decreased during the early stages of frying, while it increased afterwards (become more red). A first-order kinetic equation was used for each one of the three colour parameters, in which the rate constant is a function of oil temperatures. The results showed that oil temperature has a significant effect on the colour parameters. Different kinetic models were used to fit the experimental data and the results revealed that the quadratic model was the most suitable to describe the color change intensity (ΔE) (R > 0.96). Center temperature of carrot slice increased with increase in oil temperature and time during frying.

Escherichia coli Survival in, and Release from, White-Tailed Deer Feces

PubMed Central

Fry, Jessica; Ives, Rebecca L.; Rose, Joan B.

2014-01-01

White-tailed deer are an important reservoir for pathogens that can contribute a large portion of microbial pollution in fragmented agricultural and forest landscapes. The scarcity of experimental data on survival of microorganisms in and release from deer feces makes prediction of their fate and transport less reliable and development of efficient strategies for environment protection more difficult. The goal of this study was to estimate parameters for modeling Escherichia coli survival in and release from deer (Odocoileus virginianus) feces. Our objectives were as follows: (i) to measure survival of E. coli in deer pellets at different temperatures, (ii) to measure kinetics of E. coli release from deer pellets at different rainfall intensities, and (iii) to estimate parameters of models describing survival and release of microorganisms from deer feces. Laboratory experiments were conducted to study E. coli survival in deer pellets at three temperatures and to estimate parameters of Chick's exponential model with temperature correction based on the Arrhenius equation. Kinetics of E. coli release from deer pellets were measured at two rainfall intensities and used to derive the parameters of Bradford-Schijven model of bacterial release. The results showed that parameters of the survival and release models obtained for E. coli in this study substantially differed from those obtained by using other source materials, e.g., feces of domestic animals and manures. This emphasizes the necessity of comprehensive studies of survival of naturally occurring populations of microorganisms in and release from wildlife animal feces in order to achieve better predictions of microbial fate and transport in fragmented agricultural and forest landscapes. PMID:25480751

Validation of the Predictive Value of Modeled Human Chorionic Gonadotrophin Residual Production in Low-Risk Gestational Trophoblastic Neoplasia Patients Treated in NRG Oncology/Gynecologic Oncology Group-174 Phase III Trial.

PubMed

You, Benoit; Deng, Wei; Hénin, Emilie; Oza, Amit; Osborne, Raymond

2016-01-01

In low-risk gestational trophoblastic neoplasia, chemotherapy effect is monitored and adjusted with serum human chorionic gonadotrophin (hCG) levels. Mathematical modeling of hCG kinetics may allow prediction of methotrexate (MTX) resistance, with production parameter "hCGres." This approach was evaluated using the GOG-174 (NRG Oncology/Gynecologic Oncology Group-174) trial database, in which weekly MTX (arm 1) was compared with dactinomycin (arm 2). Database (210 patients, including 78 with resistance) was split into 2 sets. A 126-patient training set was initially used to estimate model parameters. Patient hCG kinetics from days 7 to 45 were fit to: [hCG(time)] = hCG7 * exp(-k * time) + hCGres, where hCGres is residual hCG tumor production, hCG7 is the initial hCG level, and k is the elimination rate constant. Receiver operating characteristic (ROC) analyses defined putative hCGRes predictor of resistance. An 84-patient test set was used to assess prediction validity. The hCGres was predictive of outcome in both arms, with no impact of treatment arm on unexplained variability of kinetic parameter estimates. The best hCGres cutoffs to discriminate resistant versus sensitive patients were 7.7 and 74.0 IU/L in arms 1 and 2, respectively. By combining them, 2 predictive groups were defined (ROC area under the curve, 0.82; sensitivity, 93.8%; specificity, 70.5%). The predictive value of hCGres-based groups regarding resistance was reproducible in test set (ROC area under the curve, 0.81; sensitivity, 88.9%; specificity, 73.1%). Both hCGres and treatment arm were associated with resistance by logistic regression analysis. The early predictive value of the modeled kinetic parameter hCGres regarding resistance seems promising in the GOG-174 study. This is the second positive evaluation of this approach. Prospective validation is warranted.

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.

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.

Effect of gamma-irradiation on thermal decomposition kinetics, X-ray diffraction pattern and spectral properties of tris(1,2-diaminoethane)nickel(II)sulphate

NASA Astrophysics Data System (ADS)

Jayashri, T. A.; Krishnan, G.; Rema Rani, N.

2014-12-01

Tris(1,2-diaminoethane)nickel(II)sulphate was prepared, and characterised by various chemical and spectral techniques. The sample was irradiated with 60Co gamma rays for varying doses. Sulphite ion and ammonia were detected and estimated in the irradiated samples. Non-isothermal decomposition kinetics, X-ray diffraction pattern, Fourier transform infrared spectroscopy, electronic, fast atom bombardment mass spectra, and surface morphology of the complex were studied before and after irradiation. Kinetic parameters were evaluated by integral, differential, and approximation methods. Irradiation enhanced thermal decomposition, lowering thermal and kinetic parameters. The mechanism of decomposition is controlled by R3 function. From X-ray diffraction studies, change in lattice parameters and subsequent changes in unit cell volume and average crystallite size were observed. Both unirradiated and irradiated samples of the complex belong to trigonal crystal system. Decrease in the intensity of the peaks was observed in the infrared spectra of irradiated samples. Electronic spectral studies revealed that the M-L interaction is unaffected by irradiation. Mass spectral studies showed that the fragmentation patterns of the unirradiated and irradiated samples are similar. The additional fragment with m/z 256 found in the irradiated sample is attributed to S8+. Surface morphology of the complex changed upon irradiation.

Quantification of tumor perfusion using dynamic contrast-enhanced ultrasound: impact of mathematical modeling

NASA Astrophysics Data System (ADS)

Doury, Maxime; Dizeux, Alexandre; de Cesare, Alain; Lucidarme, Olivier; Pellot-Barakat, Claire; Bridal, S. Lori; Frouin, Frédérique

2017-02-01

Dynamic contrast-enhanced ultrasound has been proposed to monitor tumor therapy, as a complement to volume measurements. To assess the variability of perfusion parameters in ideal conditions, four consecutive test-retest studies were acquired in a mouse tumor model, using controlled injections. The impact of mathematical modeling on parameter variability was then investigated. Coefficients of variation (CV) of tissue blood volume (BV) and tissue blood flow (BF) based-parameters were estimated inside 32 sub-regions of the tumors, comparing the log-normal (LN) model with a one-compartment model fed by an arterial input function (AIF) and improved by the introduction of a time delay parameter. Relative perfusion parameters were also estimated by normalization of the LN parameters and normalization of the one-compartment parameters estimated with the AIF, using a reference tissue (RT) region. A direct estimation (rRTd) of relative parameters, based on the one-compartment model without using the AIF, was also obtained by using the kinetics inside the RT region. Results of test-retest studies show that absolute regional parameters have high CV, whatever the approach, with median values of about 30% for BV, and 40% for BF. The positive impact of normalization was established, showing a coherent estimation of relative parameters, with reduced CV (about 20% for BV and 30% for BF using the rRTd approach). These values were significantly lower (p  <  0.05) than the CV of absolute parameters. The rRTd approach provided the smallest CV and should be preferred for estimating relative perfusion parameters.

Computations and estimates of rate coefficients for hydrocarbon reactions of interest to the atmospheres of outer solar system

NASA Technical Reports Server (NTRS)

Laufer, A. H.; Gardner, E. P.; Kwok, T. L.; Yung, Y. L.

1983-01-01

The rate coefficients, including Arrhenius parameters, have been computed for a number of chemical reactions involving hydrocarbon species for which experimental data are not available and which are important in planetary atmospheric models. The techniques used to calculate the kinetic parameters include the Troe and semiempirical bond energy-bond order (BEBO) or bond strength-bond length (BSBL) methods.

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

Flux estimation of the FIFE planetary boundary layer (PBL) with 10.6 micron Doppler lidar

NASA Technical Reports Server (NTRS)

Gal-Chen, Tzvi; Xu, Mei; Eberhard, Wynn

1990-01-01

A method is devised for calculating wind, momentum, and other flux parameters that characterize the planetary boundary layer (PBL) and thereby facilitate the calibration of spaceborne vs. in situ flux estimates. Single Doppler lidar data are used to estimate the variance of the mean wind and the covariance related to the vertically pointing fluxes of horizontal momentum. The skewness of the vertical velocity and the range of kinetic energy dissipation are also estimated, and the surface heat flux is determined by means of a statistical Navier-Stokes equation. The conclusion shows that the PBL structure combines both 'bottom-up' and 'top-down' processes suggesting that the relevant parameters for the atmospheric boundary layer be revised. The conclusions are of significant interest to the modeling techniques used in General Circulation Models as well as to flux estimation.

Spacecraft structural system identification by modal test

NASA Technical Reports Server (NTRS)

Chen, J.-C.; Peretti, L. F.; Garba, J. A.

1984-01-01

A structural parameter estimation procedure using the measured natural frequencies and kinetic energy distribution as observers is proposed. The theoretical derivation of the estimation procedure is described and its constraints and limitations are explained. This procedure is applied to a large complex spacecraft structural system to identify the inertia matrix using modal test results. The inertia matrix is chosen after the stiffness matrix has been updated by the static test results.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung.

PubMed

Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

2016-04-21

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant (18)F-FDG and (18)F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

NASA Astrophysics Data System (ADS)

Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

2016-04-01

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

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.

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.

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.

Modeling of Tracer Transport Delays for Improved Quantification of Regional Pulmonary ¹⁸F-FDG Kinetics, Vascular Transit Times, and Perfusion.

PubMed

Wellman, Tyler J; Winkler, Tilo; Vidal Melo, Marcos F

2015-11-01

¹⁸F-FDG-PET is increasingly used to assess pulmonary inflammatory cell activity. However, current models of pulmonary ¹⁸F-FDG kinetics do not account for delays in ¹⁸F-FDG transport between the plasma sampling site and the lungs. We developed a three-compartment model of ¹⁸F-FDG kinetics that includes a delay between the right heart and the local capillary blood pool, and used this model to estimate regional pulmonary perfusion. We acquired dynamic ¹⁸F-FDG scans in 12 mechanically ventilated sheep divided into control and lung injury groups (n = 6 each). The model was fit to tracer kinetics in three isogravitational regions-of-interest to estimate regional lung transport delays and regional perfusion. ¹³NN bolus infusion scans were acquired during a period of apnea to measure regional perfusion using an established reference method. The delayed input function model improved description of ¹⁸F-FDG kinetics (lower Akaike Information Criterion) in 98% of studied regions. Local transport delays ranged from 2.0 to 13.6 s, averaging 6.4 ± 2.9 s, and were highest in non-dependent regions. Estimates of regional perfusion derived from model parameters were highly correlated with perfusion measurements based on ¹³NN-PET (R² = 0.92, p < 0.001). By incorporating local vascular transports delays, this model of pulmonary ¹⁸F-FDG kinetics allows for simultaneous assessment of regional lung perfusion, transit times, and inflammation.

Solid-state reaction kinetics of neodymium doped magnesium hydrogen phosphate system

NASA Astrophysics Data System (ADS)

Gupta, Rashmi; Slathia, Goldy; Bamzai, K. K.

2018-05-01

Neodymium doped magnesium hydrogen phosphate (NdMHP) crystals were grown by using gel encapsulation technique. Structural characterization of the grown crystals has been carried out by single crystal X-ray diffraction (XRD) and it revealed that NdMHP crystals crystallize in orthorhombic crystal system with space group Pbca. Kinetics of the decomposition of the grown crystals has been studied by non-isothermal analysis. The estimation of decomposition temperatures and weight loss has been made from the thermogravimetric/differential thermo analytical (TG/DTA) in conjuncture with DSC studies. The various steps involved in the thermal decomposition of the material have been analysed using Horowitz-Metzger, Coats-Redfern and Piloyan-Novikova equations for evaluating various kinetic parameters.

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach

PubMed Central

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M.; El Fakhri, Georges

2013-01-01

Purpose: Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Methods: Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. Results: At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%–29% and 32%–70% for 50 × 106 and 10 × 106 detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40–50 iterations), while more than 500 iterations were needed for CG. Conclusions: The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method. PMID:24089922

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.

Direct reconstruction of cardiac PET kinetic parametric images using a preconditioned conjugate gradient approach.

PubMed

Rakvongthai, Yothin; Ouyang, Jinsong; Guerin, Bastien; Li, Quanzheng; Alpert, Nathaniel M; El Fakhri, Georges

2013-10-01

Our research goal is to develop an algorithm to reconstruct cardiac positron emission tomography (PET) kinetic parametric images directly from sinograms and compare its performance with the conventional indirect approach. Time activity curves of a NCAT phantom were computed according to a one-tissue compartmental kinetic model with realistic kinetic parameters. The sinograms at each time frame were simulated using the activity distribution for the time frame. The authors reconstructed the parametric images directly from the sinograms by optimizing a cost function, which included the Poisson log-likelihood and a spatial regularization terms, using the preconditioned conjugate gradient (PCG) algorithm with the proposed preconditioner. The proposed preconditioner is a diagonal matrix whose diagonal entries are the ratio of the parameter and the sensitivity of the radioactivity associated with parameter. The authors compared the reconstructed parametric images using the direct approach with those reconstructed using the conventional indirect approach. At the same bias, the direct approach yielded significant relative reduction in standard deviation by 12%-29% and 32%-70% for 50 × 10(6) and 10 × 10(6) detected coincidences counts, respectively. Also, the PCG method effectively reached a constant value after only 10 iterations (with numerical convergence achieved after 40-50 iterations), while more than 500 iterations were needed for CG. The authors have developed a novel approach based on the PCG algorithm to directly reconstruct cardiac PET parametric images from sinograms, and yield better estimation of kinetic parameters than the conventional indirect approach, i.e., curve fitting of reconstructed images. The PCG method increases the convergence rate of reconstruction significantly as compared to the conventional CG method.

Strain E?ect on the Instability of Island Formation in Submonolayer Heteroepitaxy

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

Yao, yugui; Li, Maozhi; Wu, Biao

2009-01-01

Strain e ect on the instability of island formation in submonolayer heteroepitaxy is studied in both thermodynamic and kinetic regimes. By using linear stability analysis, the energy change of an island due to small perturbations is analyzed. A phase diagram is constructed to illustrate the interplay between kinetic processes and strain e ect on the shape instability. Critical island sizes beyond which islands grow unstable are also derived for various growth conditions and can be used to estimate energy parameters. The scaling forms of shape instability are also discussed.

Escherichia coli survival in, and release from, white-tailed deer feces.

PubMed

Guber, Andrey K; Fry, Jessica; Ives, Rebecca L; Rose, Joan B

2015-02-01

White-tailed deer are an important reservoir for pathogens that can contribute a large portion of microbial pollution in fragmented agricultural and forest landscapes. The scarcity of experimental data on survival of microorganisms in and release from deer feces makes prediction of their fate and transport less reliable and development of efficient strategies for environment protection more difficult. The goal of this study was to estimate parameters for modeling Escherichia coli survival in and release from deer (Odocoileus virginianus) feces. Our objectives were as follows: (i) to measure survival of E. coli in deer pellets at different temperatures, (ii) to measure kinetics of E. coli release from deer pellets at different rainfall intensities, and (iii) to estimate parameters of models describing survival and release of microorganisms from deer feces. Laboratory experiments were conducted to study E. coli survival in deer pellets at three temperatures and to estimate parameters of Chick's exponential model with temperature correction based on the Arrhenius equation. Kinetics of E. coli release from deer pellets were measured at two rainfall intensities and used to derive the parameters of Bradford-Schijven model of bacterial release. The results showed that parameters of the survival and release models obtained for E. coli in this study substantially differed from those obtained by using other source materials, e.g., feces of domestic animals and manures. This emphasizes the necessity of comprehensive studies of survival of naturally occurring populations of microorganisms in and release from wildlife animal feces in order to achieve better predictions of microbial fate and transport in fragmented agricultural and forest landscapes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dynamic Modeling of the Human Coagulation Cascade Using Reduced Order Effective Kinetic Models (Open Access)

DTIC Science & Technology

2015-03-16

shaded region around each total sensitivity value was the maximum uncertainty in that value estimated by the Sobol method. 2.4. Global Sensitivity...Performance We conducted a global sensitivity analysis, using the variance-based method of Sobol , to estimate which parameters controlled the...Hunter, J.D. Matplotlib: A 2D Graphics Environment. Comput. Sci. Eng. 2007, 9, 90–95. 69. Sobol , I. Global sensitivity indices for nonlinear

Reactivity of fluoroalkanes in reactions of coordinated molecular decomposition

NASA Astrophysics Data System (ADS)

Pokidova, T. S.; Denisov, E. T.

2017-08-01

Experimental results on the coordinated molecular decomposition of RF fluoroalkanes to olefin and HF are analyzed using the model of intersecting parabolas (IPM). The kinetic parameters are calculated to allow estimates of the activation energy ( E) and rate constant ( k) of these reactions, based on enthalpy and IPM algorithms. Parameters E and k are found for the first time for eight RF decomposition reactions. The factors that affect activation energy E of RF decomposition (the enthalpy of the reaction, the electronegativity of the atoms of reaction centers, and the dipole-dipole interaction of polar groups) are determined. The values of E and k for reverse reactions of addition are estimated.

Estimating Arrhenius parameters using temperature programmed molecular dynamics

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

Imandi, Venkataramana; Chatterjee, Abhijit, E-mail: abhijit@che.iitb.ac.in

2016-07-21

Kinetic rates at different temperatures and the associated Arrhenius parameters, whenever Arrhenius law is obeyed, are efficiently estimated by applying maximum likelihood analysis to waiting times collected using the temperature programmed molecular dynamics method. When transitions involving many activated pathways are available in the dataset, their rates may be calculated using the same collection of waiting times. Arrhenius behaviour is ascertained by comparing rates at the sampled temperatures with ones from the Arrhenius expression. Three prototype systems with corrugated energy landscapes, namely, solvated alanine dipeptide, diffusion at the metal-solvent interphase, and lithium diffusion in silicon, are studied to highlight variousmore » aspects of the method. The method becomes particularly appealing when the Arrhenius parameters can be used to find rates at low temperatures where transitions are rare. Systematic coarse-graining of states can further extend the time scales accessible to the method. Good estimates for the rate parameters are obtained with 500-1000 waiting times.« less

Center of pressure based segment inertial parameters validation

PubMed Central

Rezzoug, Nasser; Gorce, Philippe; Isableu, Brice; Venture, Gentiane

2017-01-01

By proposing efficient methods for estimating Body Segment Inertial Parameters’ (BSIP) estimation and validating them with a force plate, it is possible to improve the inverse dynamic computations that are necessary in multiple research areas. Until today a variety of studies have been conducted to improve BSIP estimation but to our knowledge a real validation has never been completely successful. In this paper, we propose a validation method using both kinematic and kinetic parameters (contact forces) gathered from optical motion capture system and a force plate respectively. To compare BSIPs, we used the measured contact forces (Force plate) as the ground truth, and reconstructed the displacements of the Center of Pressure (COP) using inverse dynamics from two different estimation techniques. Only minor differences were seen when comparing the estimated segment masses. Their influence on the COP computation however is large and the results show very distinguishable patterns of the COP movements. Improving BSIP techniques is crucial and deviation from the estimations can actually result in large errors. This method could be used as a tool to validate BSIP estimation techniques. An advantage of this approach is that it facilitates the comparison between BSIP estimation methods and more specifically it shows the accuracy of those parameters. PMID:28662090

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.

PubMed

Penas, David R; González, Patricia; Egea, Jose A; Doallo, Ramón; Banga, Julio R

2017-01-21

The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear dynamic models. Global optimization methods can be used to solve this type of problems but the associated computational cost is very large. Moreover, many of these methods need the tuning of a number of adjustable search parameters, requiring a number of initial exploratory runs and therefore further increasing the computation times. Here we present a novel parallel method, self-adaptive cooperative enhanced scatter search (saCeSS), to accelerate the solution of this class of problems. The method is based on the scatter search optimization metaheuristic and incorporates several key new mechanisms: (i) asynchronous cooperation between parallel processes, (ii) coarse and fine-grained parallelism, and (iii) self-tuning strategies. The performance and robustness of saCeSS is illustrated by solving a set of challenging parameter estimation problems, including medium and large-scale kinetic models of the bacterium E. coli, bakerés yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The results consistently show that saCeSS is a robust and efficient method, allowing very significant reduction of computation times with respect to several previous state of the art methods (from days to minutes, in several cases) even when only a small number of processors is used. The new parallel cooperative method presented here allows the solution of medium and large scale parameter estimation problems in reasonable computation times and with small hardware requirements. Further, the method includes self-tuning mechanisms which facilitate its use by non-experts. We believe that this new method can play a key role in the development of large-scale and even whole-cell dynamic models.

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 of biomolecular interaction by using Newton Iteration Method and Least Squares Method. First, the pseudo first order kinetic model of biomolecular interaction was established. Then the data of molecular interaction of HBsAg and HBsAb was obtained by bioanalyzer. Finally, we used the optical SPR bioanalyzer software which was written by ourselves to make nonlinear fit about the association and dissociation curves. The correlation coefficient R-squared is 0.99229 and 0.99593, respectively. Furthermore, the kinetic parameters and affinity constants were evaluated using the obtained data from the fitting results.

Crystallisation kinetics study in stabilisation treatment of sol-gel derived 45S5 bioglass

NASA Astrophysics Data System (ADS)

Prakrathi, S.; Matin, Mallikarjun; Kiran, P.; Manne, Bhaskar; Ramesh, M. R.

2018-04-01

Solgel gel derived bioglasses require stabilisation heat treatment to decompose nitrates and to improve mechanical stability. While decomposing nitrate phases especially in solgel derived 45S5 bioglass, it is difficult to avoid crystallisation of silicate crystalline phases (Na2CaSi2O6, Na2Ca2Si3O9) due to overlapping of nitrates decomposition and silicates crystallisation temperatures. Control of such crystallinity amount in bioglasses is at most important during stabilisation as it affects the dissolution rates of bioglassesin body fluids. Controlling and quantifying of this crystallinity helps in engineering bioglasses for specific period in application. In this work, synthesis of 45S5 bioglass through solgel method is presented. Here, temperature and time dependent crystallisation kinetics were estimated using a quality parameter derived from X-ray diffraction (XRD) patterns of bioglass during stabilisation treatment. Quality parameter derived from XRD patterns is termed as IPB which is the ratio of integral area of peaks to the integral area of background. It is proposed that IPB can be used as quality parameter to assess crystallinity and to study crystallisation kinetics in bioglasses.

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.

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

Inactivation disinfection property of Moringa Oleifera seed extract: optimization and kinetic studies

NASA Astrophysics Data System (ADS)

Idris, M. A.; Jami, M. S.; Hammed, A. M.

2017-05-01

This paper presents the statistical optimization study of disinfection inactivation parameters of defatted Moringa oleifera seed extract on Pseudomonas aeruginosa bacterial cells. Three level factorial design was used to estimate the optimum range and the kinetics of the inactivation process was also carried. The inactivation process involved comparing different disinfection models of Chicks-Watson, Collins-Selleck and Homs models. The results from analysis of variance (ANOVA) of the statistical optimization process revealed that only contact time was significant. The optimum disinfection range of the seed extract was 125 mg/L, 30 minutes and 120rpm agitation. At the optimum dose, the inactivation kinetics followed the Collin-Selleck model with coefficient of determination (R2) of 0.6320. This study is the first of its kind in determining the inactivation kinetics of pseudomonas aeruginosa using the defatted seed extract.

Calcium tracer kinetics show decreased irreversible flow to bone in glucocorticoid treated patients.

PubMed

Goans, R E; Weiss, G H; Abrams, S A; Perez, M D; Yergey, A L

1995-06-01

Osteopenia resulting from pharmacologic doses of glucocorticoids is well known. Previously, there has been no satisfactory quantitative model describing the kinetics of calcium flow in subjects on chronic steroid use. A mathematical model of calcium isotope interaction with bone is described and applied to determine an estimate of kinetic parameters characterizing these changes. Calcium tracer dilution kinetics after a bolus injection of 42Ca were measured in 14 subjects with juvenile dermatomyositis, 6 on prednisone regimens and 8 on treatment regimens without prednisone. Irreversible tracer loss from plasma bone is found to be significantly reduced (P = 0.043) in the glucocorticoid-treated patients compared with patients on nonsteroid regimens. Reversible flow to bone is noted to be similar in the two groups. These results suggest a direct effect of glucocorticoids on osteoblast function.

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data.

PubMed

Ezer, Daphne; Moignard, Victoria; Göttgens, Berthold; Adryan, Boris

2016-08-01

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics.

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-dependent pharmacological activities. Copyright © 2017 Elsevier Inc. All rights reserved.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Extraction kinetic modelling of total polyphenols and total anthocyanins from saffron floral bio-residues: Comparison of extraction methods.

PubMed

Da Porto, Carla; Natolino, Andrea

2018-08-30

Analysis of the extraction kinetic modelling for natural compounds is essential for industrial application. The second order rate model was applied to estimate the extraction kinetics of conventional solid-liquid extraction (CSLE), ultrasound-assisted extraction (UAE) and microwave-assisted extraction (MAE) of total polyphenols (TPC) from saffron floral bio-residues at different solid-to-liquid ratios (R S/L )(1:10, 1:20, 1:30, 1:50 g ml -1 ), ethanol 59% as solvent and 66 °C temperature. The optimum solid-to-liquid ratios for TPC kinetics were 1:20 for CLSE, 1:30 for UAE and 1:50 for MAE. The kinetics of total anthocyanins (TA) and antioxidant activity (AA) were investigated for the optimum R S/L for each method. The results showed a good prediction of the model for extraction kinetics in all experiments (R 2  > 0.99; NRMS 0.65-3.35%). The kinetic parameters were calculated and discussed. UAE, compared with the other methods, had the greater efficiency for TPC, TA and AA. Copyright © 2018 Elsevier Ltd. All rights reserved.

Three-dimensional whole-brain perfusion quantification using pseudo-continuous arterial spin labeling MRI at multiple post-labeling delays: accounting for both arterial transit time and impulse response function.

PubMed

Qin, Qin; Huang, Alan J; Hua, Jun; Desmond, John E; Stevens, Robert D; van Zijl, Peter C M

2014-02-01

Measurement of the cerebral blood flow (CBF) with whole-brain coverage is challenging in terms of both acquisition and quantitative analysis. In order to fit arterial spin labeling-based perfusion kinetic curves, an empirical three-parameter model which characterizes the effective impulse response function (IRF) is introduced, which allows the determination of CBF, the arterial transit time (ATT) and T(1,eff). The accuracy and precision of the proposed model were compared with those of more complicated models with four or five parameters through Monte Carlo simulations. Pseudo-continuous arterial spin labeling images were acquired on a clinical 3-T scanner in 10 normal volunteers using a three-dimensional multi-shot gradient and spin echo scheme at multiple post-labeling delays to sample the kinetic curves. Voxel-wise fitting was performed using the three-parameter model and other models that contain two, four or five unknown parameters. For the two-parameter model, T(1,eff) values close to tissue and blood were assumed separately. Standard statistical analysis was conducted to compare these fitting models in various brain regions. The fitted results indicated that: (i) the estimated CBF values using the two-parameter model show appreciable dependence on the assumed T(1,eff) values; (ii) the proposed three-parameter model achieves the optimal balance between the goodness of fit and model complexity when compared among the models with explicit IRF fitting; (iii) both the two-parameter model using fixed blood T1 values for T(1,eff) and the three-parameter model provide reasonable fitting results. Using the proposed three-parameter model, the estimated CBF (46 ± 14 mL/100 g/min) and ATT (1.4 ± 0.3 s) values averaged from different brain regions are close to the literature reports; the estimated T(1,eff) values (1.9 ± 0.4 s) are higher than the tissue T1 values, possibly reflecting a contribution from the microvascular arterial blood compartment. Copyright © 2013 John Wiley & Sons, Ltd.

Mathematical modelling of non-stationary fluctuation analysis for studying channel properties of synaptic AMPA receptors

PubMed Central

Benke, Timothy A; Lüthi, Andreas; Palmer, Mary J; Wikström, Martin A; Anderson, William W; Isaac, John T R; Collingridge, Graham L

2001-01-01

The molecular properties of synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptors are an important factor determining excitatory synaptic transmission in the brain. Changes in the number (N) or single-channel conductance (γ) of functional AMPA receptors may underlie synaptic plasticity, such as long-term potentiation (LTP) and long-term depression (LTD). These parameters have been estimated using non-stationary fluctuation analysis (NSFA). The validity of NSFA for studying the channel properties of synaptic AMPA receptors was assessed using a cable model with dendritic spines and a microscopic kinetic description of AMPA receptors. Electrotonic, geometric and kinetic parameters were altered in order to determine their effects on estimates of the underlying γ. Estimates of γ were very sensitive to the access resistance of the recording (RA) and the mean open time of AMPA channels. Estimates of γ were less sensitive to the distance between the electrode and the synaptic site, the electrotonic properties of dendritic structures, recording electrode capacitance and background noise. Estimates of γ were insensitive to changes in spine morphology, synaptic glutamate concentration and the peak open probability (Po) of AMPA receptors. The results obtained using the model agree with biological data, obtained from 91 dendritic recordings from rat CA1 pyramidal cells. A correlation analysis showed that RA resulted in a slowing of the decay time constant of excitatory postsynaptic currents (EPSCs) by approximately 150 %, from an estimated value of 3.1 ms. RA also greatly attenuated the absolute estimate of γ by approximately 50-70 %. When other parameters remain constant, the model demonstrates that NSFA of dendritic recordings can readily discriminate between changes in γvs. changes in N or Po. Neither background noise nor asynchronous activation of multiple synapses prevented reliable discrimination between changes in γ and changes in either N or Po. The model (available online) can be used to predict how changes in the different properties of AMPA receptors may influence synaptic transmission and plasticity. PMID:11731574

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.

Modelling Sublimation of Carbon Dioxide

ERIC Educational Resources Information Center

Winkel, Brian

2012-01-01

In this article, the author reports results in their efforts to model sublimation of carbon dioxide and the associated kinetics order and parameter estimation issues in their model. They have offered the reader two sets of data and several approaches to determine the rate of sublimation of a piece of solid dry ice. They presented several models…

Variability estimation of urban wastewater biodegradable fractions by respirometry.

PubMed

Lagarde, Fabienne; Tusseau-Vuillemin, Marie-Hélène; Lessard, Paul; Héduit, Alain; Dutrop, François; Mouchel, Jean-Marie

2005-11-01

This paper presents a methodology for assessing the variability of biodegradable chemical oxygen demand (COD) fractions in urban wastewaters. Thirteen raw wastewater samples from combined and separate sewers feeding the same plant were characterised, and two optimisation procedures were applied in order to evaluate the variability in biodegradable fractions and related kinetic parameters. Through an overall optimisation on all the samples, a unique kinetic parameter set was obtained with a three-substrate model including an adsorption stage. This method required powerful numerical treatment, but improved the identifiability problem compared to the usual sample-to-sample optimisation. The results showed that the fractionation of samples collected in the combined sewer was much more variable (standard deviation of 70% of the mean values) than the fractionation of the separate sewer samples, and the slowly biodegradable COD fraction was the most significant fraction (45% of the total COD on average). Because these samples were collected under various rain conditions, the standard deviations obtained here on the combined sewer biodegradable fractions could be used as a first estimation of the variability of this type of sewer system.

Anaerobic biodegradability of fish remains: experimental investigation and parameter estimation.

PubMed

Donoso-Bravo, Andres; Bindels, Francoise; Gerin, Patrick A; Vande Wouwer, Alain

2015-01-01

The generation of organic waste associated with aquaculture fish processing has increased significantly in recent decades. The objective of this study is to evaluate the anaerobic biodegradability of several fish processing fractions, as well as water treatment sludge, for tilapia and sturgeon species cultured in recirculated aquaculture systems. After substrate characterization, the ultimate biodegradability and the hydrolytic rate were estimated by fitting a first-order kinetic model with the biogas production profiles. In general, the first-order model was able to reproduce the biogas profiles properly with a high correlation coefficient. In the case of tilapia, the skin/fin, viscera, head and flesh presented a high level of biodegradability, above 310 mLCH₄gCOD⁻¹, whereas the head and bones showed a low hydrolytic rate. For sturgeon, the results for all fractions were quite similar in terms of both parameters, although viscera presented the lowest values. Both the substrate characterization and the kinetic analysis of the anaerobic degradation may be used as design criteria for implementing anaerobic digestion in a recirculating aquaculture system.

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.

Determination of in vivo RNA kinetics using RATE-seq.

PubMed

Neymotin, Benjamin; Athanasiadou, Rodoniki; Gresham, David

2014-10-01

The abundance of a transcript is determined by its rate of synthesis and its rate of degradation; however, global methods for quantifying RNA abundance cannot distinguish variation in these two processes. Here, we introduce RNA approach to equilibrium sequencing (RATE-seq), which uses in vivo metabolic labeling of RNA and approach to equilibrium kinetics, to determine absolute RNA degradation and synthesis rates. RATE-seq does not disturb cellular physiology, uses straightforward normalization with exogenous spike-ins, and can be readily adapted for studies in most organisms. We demonstrate the use of RATE-seq to estimate genome-wide kinetic parameters for coding and noncoding transcripts in Saccharomyces cerevisiae. © 2014 Neymotin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Comparative study on fractal analysis of interferometry images with application to tear film surface quality assessment.

PubMed

Szyperski, Piotr D

2018-06-01

The purpose of this research was to evaluate the applicability of the fractal dimension (FD) estimators to assess lateral shearing interferometric (LSI) measurements of tear film surface quality. Retrospective recordings of tear film measured with LSI were used: 69 from healthy subjects and 41 from patients diagnosed with dry eye syndrome. Five surface quality descriptors were considered, four based on FD and a previously reported descriptor operating in a spatial frequency domain (M 2 ), presenting temporal kinetics of post-blink tear film. A set of 12 regression parameters has been extracted and analyzed for classification purposes. The classifiers are assessed in terms of receiver operating characteristics and areas under their curves (AUC). Also, the computational loads are estimated. The maximum AUC of 82.4% was achieved for M 2 , closely followed by the binary box-counting (BBC) FD estimator with AUC=78.6%. For all descriptors, statistically significant differences between the subject groups were found (p<0.05). The BBC FD estimator was characterized with the highest empirical computational efficiency that was about 30% faster than that of M 2 , while that based on the differential box-counting exhibited the lowest efficiency (4.5 times slower than the best one). Concluding, FD estimators can be utilized for quantitative assessment of tear film kinetics. They provide a viable alternative to previously used spectral counter parameters, and at the same time allow higher computational efficiency.

A pharmacometric case study regarding the sensitivity of structural model parameter estimation to error in patient reported dosing times.

PubMed

Knights, Jonathan; Rohatagi, Shashank

2015-12-01

Although there is a body of literature focused on minimizing the effect of dosing inaccuracies on pharmacokinetic (PK) parameter estimation, most of the work centers on missing doses. No attempt has been made to specifically characterize the effect of error in reported dosing times. Additionally, existing work has largely dealt with cases in which the compound of interest is dosed at an interval no less than its terminal half-life. This work provides a case study investigating how error in patient reported dosing times might affect the accuracy of structural model parameter estimation under sparse sampling conditions when the dosing interval is less than the terminal half-life of the compound, and the underlying kinetics are monoexponential. Additional effects due to noncompliance with dosing events are not explored and it is assumed that the structural model and reasonable initial estimates of the model parameters are known. Under the conditions of our simulations, with structural model CV % ranging from ~20 to 60 %, parameter estimation inaccuracy derived from error in reported dosing times was largely controlled around 10 % on average. Given that no observed dosing was included in the design and sparse sampling was utilized, we believe these error results represent a practical ceiling given the variability and parameter estimates for the one-compartment model. The findings suggest additional investigations may be of interest and are noteworthy given the inability of current PK software platforms to accommodate error in dosing times.

Online optimal experimental re-design in robotic parallel fed-batch cultivation facilities.

PubMed

Cruz Bournazou, M N; Barz, T; Nickel, D B; Lopez Cárdenas, D C; Glauche, F; Knepper, A; Neubauer, P

2017-03-01

We present an integrated framework for the online optimal experimental re-design applied to parallel nonlinear dynamic processes that aims to precisely estimate the parameter set of macro kinetic growth models with minimal experimental effort. This provides a systematic solution for rapid validation of a specific model to new strains, mutants, or products. In biosciences, this is especially important as model identification is a long and laborious process which is continuing to limit the use of mathematical modeling in this field. The strength of this approach is demonstrated by fitting a macro-kinetic differential equation model for Escherichia coli fed-batch processes after 6 h of cultivation. The system includes two fully-automated liquid handling robots; one containing eight mini-bioreactors and another used for automated at-line analyses, which allows for the immediate use of the available data in the modeling environment. As a result, the experiment can be continually re-designed while the cultivations are running using the information generated by periodical parameter estimations. The advantages of an online re-computation of the optimal experiment are proven by a 50-fold lower average coefficient of variation on the parameter estimates compared to the sequential method (4.83% instead of 235.86%). The success obtained in such a complex system is a further step towards a more efficient computer aided bioprocess development. Biotechnol. Bioeng. 2017;114: 610-619. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

PubMed

Villaverde, Alejandro F; Henriques, David; Smallbone, Kieran; Bongard, Sophia; Schmid, Joachim; Cicin-Sain, Damjan; Crombach, Anton; Saez-Rodriguez, Julio; Mauch, Klaus; Balsa-Canto, Eva; Mendes, Pedro; Jaeger, Johannes; Banga, Julio R

2015-02-20

Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The community has already developed many methods and software packages which aim to facilitate these tasks. However, there is a lack of suitable benchmark problems which allow a fair and systematic evaluation and comparison of these contributions. Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area. This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli, baker's yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The level of description includes metabolism, transcription, signal transduction, and development. For each problem we provide (i) a basic description and formulation, (ii) implementations ready-to-run in several formats, (iii) computational results obtained with specific solvers, (iv) a basic analysis and interpretation. This suite of benchmark problems can be readily used to evaluate and compare parameter estimation methods. Further, it can also be used to build test problems for sensitivity and identifiability analysis, model reduction and optimal experimental design methods. The suite, including codes and documentation, can be freely downloaded from the BioPreDyn-bench website, https://sites.google.com/site/biopredynbenchmarks/ .

ESTIMATION OF CONSTANT AND TIME-VARYING DYNAMIC PARAMETERS OF HIV INFECTION IN A NONLINEAR DIFFERENTIAL EQUATION MODEL.

PubMed

Liang, Hua; Miao, Hongyu; Wu, Hulin

2010-03-01

Modeling viral dynamics in HIV/AIDS studies has resulted in deep understanding of pathogenesis of HIV infection from which novel antiviral treatment guidance and strategies have been derived. Viral dynamics models based on nonlinear differential equations have been proposed and well developed over the past few decades. However, it is quite challenging to use experimental or clinical data to estimate the unknown parameters (both constant and time-varying parameters) in complex nonlinear differential equation models. Therefore, investigators usually fix some parameter values, from the literature or by experience, to obtain only parameter estimates of interest from clinical or experimental data. However, when such prior information is not available, it is desirable to determine all the parameter estimates from data. In this paper, we intend to combine the newly developed approaches, a multi-stage smoothing-based (MSSB) method and the spline-enhanced nonlinear least squares (SNLS) approach, to estimate all HIV viral dynamic parameters in a nonlinear differential equation model. In particular, to the best of our knowledge, this is the first attempt to propose a comparatively thorough procedure, accounting for both efficiency and accuracy, to rigorously estimate all key kinetic parameters in a nonlinear differential equation model of HIV dynamics from clinical data. These parameters include the proliferation rate and death rate of uninfected HIV-targeted cells, the average number of virions produced by an infected cell, and the infection rate which is related to the antiviral treatment effect and is time-varying. To validate the estimation methods, we verified the identifiability of the HIV viral dynamic model and performed simulation studies. We applied the proposed techniques to estimate the key HIV viral dynamic parameters for two individual AIDS patients treated with antiretroviral therapies. We demonstrate that HIV viral dynamics can be well characterized and quantified for individual patients. As a result, personalized treatment decision based on viral dynamic models is possible.

A constrained extended Kalman filter for the optimal estimate of kinematics and kinetics of a sagittal symmetric exercise.

PubMed

Bonnet, V; Dumas, R; Cappozzo, A; Joukov, V; Daune, G; Kulić, D; Fraisse, P; Andary, S; Venture, G

2017-09-06

This paper presents a method for real-time estimation of the kinematics and kinetics of a human body performing a sagittal symmetric motor task, which would minimize the impact of the stereophotogrammetric soft tissue artefacts (STA). The method is based on a bi-dimensional mechanical model of the locomotor apparatus the state variables of which (joint angles, velocities and accelerations, and the segments lengths and inertial parameters) are estimated by a constrained extended Kalman filter (CEKF) that fuses input information made of both stereophotogrammetric and dynamometric measurement data. Filter gains are made to saturate in order to obtain plausible state variables and the measurement covariance matrix of the filter accounts for the expected STA maximal amplitudes. We hypothesised that the ensemble of constraints and input redundant information would allow the method to attenuate the STA propagation to the end results. The method was evaluated in ten human subjects performing a squat exercise. The CEKF estimated and measured skin marker trajectories exhibited a RMS difference lower than 4mm, thus in the range of STAs. The RMS differences between the measured ground reaction force and moment and those estimated using the proposed method (9N and 10Nm) were much lower than obtained using a classical inverse dynamics approach (22N and 30Nm). From the latter results it may be inferred that the presented method allows for a significant improvement of the accuracy with which kinematic variables and relevant time derivatives, model parameters and, therefore, intersegmental moments are estimated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantitative Functional Imaging Using Dynamic Positron Computed Tomography and Rapid Parameter Estimation Techniques

NASA Astrophysics Data System (ADS)

Koeppe, Robert Allen

Positron computed tomography (PCT) is a diagnostic imaging technique that provides both three dimensional imaging capability and quantitative measurements of local tissue radioactivity concentrations in vivo. This allows the development of non-invasive methods that employ the principles of tracer kinetics for determining physiological properties such as mass specific blood flow, tissue pH, and rates of substrate transport or utilization. A physiologically based, two-compartment tracer kinetic model was derived to mathematically describe the exchange of a radioindicator between blood and tissue. The model was adapted for use with dynamic sequences of data acquired with a positron tomograph. Rapid estimation techniques were implemented to produce functional images of the model parameters by analyzing each individual pixel sequence of the image data. A detailed analysis of the performance characteristics of three different parameter estimation schemes was performed. The analysis included examination of errors caused by statistical uncertainties in the measured data, errors in the timing of the data, and errors caused by violation of various assumptions of the tracer kinetic model. Two specific radioindicators were investigated. ('18)F -fluoromethane, an inert freely diffusible gas, was used for local quantitative determinations of both cerebral blood flow and tissue:blood partition coefficient. A method was developed that did not require direct sampling of arterial blood for the absolute scaling of flow values. The arterial input concentration time course was obtained by assuming that the alveolar or end-tidal expired breath radioactivity concentration is proportional to the arterial blood concentration. The scale of the input function was obtained from a series of venous blood concentration measurements. The method of absolute scaling using venous samples was validated in four studies, performed on normal volunteers, in which directly measured arterial concentrations were compared to those predicted from the expired air and venous blood samples. The glucose analog ('18)F-3-deoxy-3-fluoro-D -glucose (3-FDG) was used for quantitating the membrane transport rate of glucose. The measured data indicated that the phosphorylation rate of 3-FDG was low enough to allow accurate estimation of the transport rate using a two compartment model.

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.

Biodrying of sewage sludge: kinetics of volatile solids degradation under different initial moisture contents and air-flow rates.

PubMed

Villegas, Manuel; Huiliñir, Cesar

2014-12-01

This study focuses on the kinetics of the biodegradation of volatile solids (VS) of sewage sludge for biodrying under different initial moisture contents (Mc) and air-flow rates (AFR). For the study, a 3(2) factorial design, whose factors were AFR (1, 2 or 3L/minkgTS) and initial Mc (59%, 68% and 78% w.b.), was used. Using seven kinetic models and a nonlinear regression method, kinetic parameters were estimated and the models were analyzed with two statistical indicators. Initial Mc of around 68% increases the temperature matrix and VS consumption, with higher moisture removal at lower initial Mc values. Lower AFRs gave higher matrix temperatures and VS consumption, while higher AFRs increased water removal. The kinetic models proposed successfully simulate VS biodegradation, with root mean square error (RMSE) between 0.007929 and 0.02744, and they can be used as a tool for satisfactory prediction of VS in biodrying. Copyright © 2014 Elsevier Ltd. All rights reserved.

Systems, methods and computer-readable media to model kinetic performance of rechargeable electrochemical devices

DOEpatents

Gering, Kevin L.

2013-01-01

A system includes an electrochemical cell, monitoring hardware, and a computing system. The monitoring hardware samples performance characteristics of the electrochemical cell. The computing system determines cell information from the performance characteristics. The computing system also analyzes the cell information of the electrochemical cell with a Butler-Volmer (BV) expression modified to determine exchange current density of the electrochemical cell by including kinetic performance information related to pulse-time dependence, electrode surface availability, or a combination thereof. A set of sigmoid-based expressions may be included with the modified-BV expression to determine kinetic performance as a function of pulse time. The determined exchange current density may be used with the modified-BV expression, with or without the sigmoid expressions, to analyze other characteristics of the electrochemical cell. Model parameters can be defined in terms of cell aging, making the overall kinetics model amenable to predictive estimates of cell kinetic performance along the aging timeline.

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

Alvarez-Ramirez, J.; Aguilar, R.; Lopez-Isunza, F.

FCC processes involve complex interactive dynamics which are difficult to operate and control as well as poorly known reaction kinetics. This work concerns the synthesis of temperature controllers for FCC units. The problem is addressed first for the case where perfect knowledge of the reaction kinetics is assumed, leading to an input-output linearizing state feedback. However, in most industrial FCC units, perfect knowledge of reaction kinetics and composition measurements is not available. To address the problem of robustness against uncertainties in the reaction kinetics, an adaptive model-based nonlinear controller with simplified reaction models is presented. The adaptive strategy makes usemore » of estimates of uncertainties derived from calorimetric (energy) balances. The resulting controller is similar in form to standard input-output linearizing controllers and can be tuned analogously. Alternatively, the controller can be tuned using a single gain parameter and is computationally efficient. The performance of the closed-loop system and the controller design procedure are shown with simulations.« less

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.

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.

Abuse behavior of high-power, lithium-ion cells

NASA Astrophysics Data System (ADS)

Spotnitz, R.; Franklin, J.

Published accounts of abuse testing of lithium-ion cells and components are summarized, including modeling work. From this summary, a set of exothermic reactions is selected with corresponding estimates of heats of reaction. Using this set of reactions, along with estimated kinetic parameters and designs for high-rate batteries, models for the abuse behavior (oven, short-circuit, overcharge, nail, crush) are developed. Finally, the models are used to determine that fluorinated binder plays a relatively unimportant role in thermal runaway.

Net growth rate of continuum heterogeneous biofilms with inhibition kinetics.

PubMed

Gonzo, Elio Emilio; Wuertz, Stefan; Rajal, Veronica B

2018-01-01

Biofilm systems can be modeled using a variety of analytical and numerical approaches, usually by making simplifying assumptions regarding biofilm heterogeneity and activity as well as effective diffusivity. Inhibition kinetics, albeit common in experimental systems, are rarely considered and analytical approaches are either lacking or consider effective diffusivity of the substrate and the biofilm density to remain constant. To address this obvious knowledge gap an analytical procedure to estimate the effectiveness factor (dimensionless substrate mass flux at the biofilm-fluid interface) was developed for a continuum heterogeneous biofilm with multiple limiting-substrate Monod kinetics to different types of inhibition kinetics. The simple perturbation technique, previously validated to quantify biofilm activity, was applied to systems where either the substrate or the inhibitor is the limiting component, and cases where the inhibitor is a reaction product or the substrate also acts as the inhibitor. Explicit analytical equations are presented for the effectiveness factor estimation and, therefore, the calculation of biomass growth rate or limiting substrate/inhibitor consumption rate, for a given biofilm thickness. The robustness of the new biofilm model was tested using kinetic parameters experimentally determined for the growth of Pseudomonas putida CCRC 14365 on phenol. Several additional cases have been analyzed, including examples where the effectiveness factor can reach values greater than unity, characteristic of systems with inhibition kinetics. Criteria to establish when the effectiveness factor can reach values greater than unity in each of the cases studied are also presented.

MATLAB-implemented estimation procedure for model-based assessment of hepatic insulin degradation from standard intravenous glucose tolerance test data.

PubMed

Di Nardo, Francesco; Mengoni, Michele; Morettini, Micaela

2013-05-01

Present study provides a novel MATLAB-based parameter estimation procedure for individual assessment of hepatic insulin degradation (HID) process from standard frequently-sampled intravenous glucose tolerance test (FSIGTT) data. Direct access to the source code, offered by MATLAB, enabled us to design an optimization procedure based on the alternating use of Gauss-Newton's and Levenberg-Marquardt's algorithms, which assures the full convergence of the process and the containment of computational time. Reliability was tested by direct comparison with the application, in eighteen non-diabetic subjects, of well-known kinetic analysis software package SAAM II, and by application on different data. Agreement between MATLAB and SAAM II was warranted by intraclass correlation coefficients ≥0.73; no significant differences between corresponding mean parameter estimates and prediction of HID rate; and consistent residual analysis. Moreover, MATLAB optimization procedure resulted in a significant 51% reduction of CV% for the worst-estimated parameter by SAAM II and in maintaining all model-parameter CV% <20%. In conclusion, our MATLAB-based procedure was suggested as a suitable tool for the individual assessment of HID process. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Nucleation kinetics of urea succinic acid –ferroelectric single crystal

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

Dhivya, R.; Voohrees College, Vellore-632014, Tamilnadu; Vizhi, R. Ezhil, E-mail: rezhilvizhi@vit.ac.in, E-mail: revizhi@gmail.com

2015-06-24

Single crystals of Urea Succinic Acid (USA) were grown by slow cooling technique. The crystalline system was confirmed by powder X-ray diffraction. The metastable zonewidth were carried out for various temperatures i.e., 35°, 40°, 45° and 50°C. The induction period is experimentally determined and various nucleation parameters have been estimated.

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

Biofiltration kinetics for volatile organic compounds (VOCs) and development of a structure-biodegradability relationship

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

Govind, R.; Wang, Z.; Bishop, D.F.

1997-12-31

In recent years, regulation of hazardous air pollutants under the Clean Air Act and its amendments, has emerged as a major environmental issue. Major sources of volatile organic compounds (VOCs) in air are chemical production plants, manufacturing sites using common solvents, combustion sources, and waste treatment operations, such as waste water treatment plants, vacuum extraction of contaminated soils, and ground water stripping operations. Biofiltration is an emerging technology for treatment of biodegradable volatile organic compounds (VOCs) present in air. In biofiltration, the contaminants are contacted with active microorganisms present either in naturally bioactive materials, such as soil, peat, compost, etc.,more » or immobilized on an inactive support media. Design of biofilters requires information on biodegradation kinetics which controls biofilter size. In this paper, an experimental microbiofilter system is presented which can be used to measure biofiltration kinetics for any volatile organic compound. A mathematical model is used to derive the Monod biokinetic parameters from the experimental data. Finally, a structure-bioactivity relationship is derived for estimating the biofiltration biokinetic parameters for a variety of VOCs.« less

Economic inequality and mobility in kinetic models for social sciences

NASA Astrophysics Data System (ADS)

Letizia Bertotti, Maria; Modanese, Giovanni

2016-10-01

Statistical evaluations of the economic mobility of a society are more difficult than measurements of the income distribution, because they require to follow the evolution of the individuals' income for at least one or two generations. In micro-to-macro theoretical models of economic exchanges based on kinetic equations, the income distribution depends only on the asymptotic equilibrium solutions, while mobility estimates also involve the detailed structure of the transition probabilities of the model, and are thus an important tool for assessing its validity. Empirical data show a remarkably general negative correlation between economic inequality and mobility, whose explanation is still unclear. It is therefore particularly interesting to study this correlation in analytical models. In previous work we investigated the behavior of the Gini inequality index in kinetic models in dependence on several parameters which define the binary interactions and the taxation and redistribution processes: saving propensity, taxation rates gap, tax evasion rate, welfare means-testing etc. Here, we check the correlation of mobility with inequality by analyzing the mobility dependence from the same parameters. According to several numerical solutions, the correlation is confirmed to be negative.

Kinetic model of water vapour adsorption by gluten-free starch

NASA Astrophysics Data System (ADS)

Ocieczek, Aneta; Kostek, Robert; Ruszkowska, Millena

2015-01-01

This study evaluated the kinetics of water vapour adsorption on the surface of starch molecules derived from wheat. The aim of the study was to determine an equation that would allow estimation of water content in tested material in any timepoint of the adsorption process aimed at settling a balance with the environment. An adsorption isotherm of water vapour on starch granules was drawn. The parameters of the Guggenheim, Anderson, and De Boer equation were determined by characterizing the tested product and adsorption process. The equation of kinetics of water vapour adsorption on the surface of starch was determined based on the Guggenheim, Anderson, and De Boer model describing the state of equilibrium and on the model of a first-order linear inert element describing the changes in water content over time.

Comparison of Mathematical Equation and Neural Network Modeling for Drying Kinetic of Mendong in Microwave Oven

NASA Astrophysics Data System (ADS)

Maulidah, Rifa'atul; Purqon, Acep

2016-08-01

Mendong (Fimbristylis globulosa) has a potentially industrial application. We investigate a predictive model for heat and mass transfer in drying kinetics during drying a Mendong. We experimentally dry the Mendong by using a microwave oven. In this study, we analyze three mathematical equations and feed forward neural network (FNN) with back propagation to describe the drying behavior of Mendong. Our results show that the experimental data and the artificial neural network model has a good agreement and better than a mathematical equation approach. The best FNN for the prediction is 3-20-1-1 structure with Levenberg- Marquardt training function. This drying kinetics modeling is potentially applied to determine the optimal parameters during mendong drying and to estimate and control of drying process.

Kinetic Analysis of the Main Temperature Stage of Fast Pyrolysis

NASA Astrophysics Data System (ADS)

Yang, Xiaoxiao; Zhao, Yuying; Xu, Lanshu; Li, Rui

2017-10-01

Kinetics of the thermal decomposition of eucalyptus chips was evaluated using a high-rate thermogravimetric analyzer (BL-TGA) designed by our research group. The experiments were carried out under non-isothermal condition in order to determine the fast pyrolysis behavior of the main temperature stage (350-540ºC) at heating rates of 60, 120, 180, and 360ºC min-1. The Coats-Redfern integral method and four different reaction mechanism models were adopted to calculate the kinetic parameters including apparent activation energy and pre-exponential factor, and the Flynn-Wall-Ozawa method was employed to testify apparent activation energy. The results showed that estimation value was consistent with the values obtained by linear fitting equations, and the best-fit model for fast pyrolysis was found.

Reciprocal Sliding Friction Model for an Electro-Deposited Coating and Its Parameter Estimation Using Markov Chain Monte Carlo Method

PubMed Central

Kim, Kyungmok; Lee, Jaewook

2016-01-01

This paper describes a sliding friction model for an electro-deposited coating. Reciprocating sliding tests using ball-on-flat plate test apparatus are performed to determine an evolution of the kinetic friction coefficient. The evolution of the friction coefficient is classified into the initial running-in period, steady-state sliding, and transition to higher friction. The friction coefficient during the initial running-in period and steady-state sliding is expressed as a simple linear function. The friction coefficient in the transition to higher friction is described with a mathematical model derived from Kachanov-type damage law. The model parameters are then estimated using the Markov Chain Monte Carlo (MCMC) approach. It is identified that estimated friction coefficients obtained by MCMC approach are in good agreement with measured ones. PMID:28773359

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 real and predicted fertility. Once the accuracy of fertility prediction has been confirmed, the model developed in the present study could be used by artificial insemination centers for bull selection or for elimination of poor fertility ejaculates.

A Graphical User Interface for a Method to Infer Kinetics and Network Architecture (MIKANA)

PubMed Central

Mourão, Márcio A.; Srividhya, Jeyaraman; McSharry, Patrick E.; Crampin, Edmund J.; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis–Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1). PMID:22096591

A graphical user interface for a method to infer kinetics and network architecture (MIKANA).

PubMed

Mourão, Márcio A; Srividhya, Jeyaraman; McSharry, Patrick E; Crampin, Edmund J; Schnell, Santiago

2011-01-01

One of the main challenges in the biomedical sciences is the determination of reaction mechanisms that constitute a biochemical pathway. During the last decades, advances have been made in building complex diagrams showing the static interactions of proteins. The challenge for systems biologists is to build realistic models of the dynamical behavior of reactants, intermediates and products. For this purpose, several methods have been recently proposed to deduce the reaction mechanisms or to estimate the kinetic parameters of the elementary reactions that constitute the pathway. One such method is MIKANA: Method to Infer Kinetics And Network Architecture. MIKANA is a computational method to infer both reaction mechanisms and estimate the kinetic parameters of biochemical pathways from time course data. To make it available to the scientific community, we developed a Graphical User Interface (GUI) for MIKANA. Among other features, the GUI validates and processes an input time course data, displays the inferred reactions, generates the differential equations for the chemical species in the pathway and plots the prediction curves on top of the input time course data. We also added a new feature to MIKANA that allows the user to exclude a priori known reactions from the inferred mechanism. This addition improves the performance of the method. In this article, we illustrate the GUI for MIKANA with three examples: an irreversible Michaelis-Menten reaction mechanism; the interaction map of chemical species of the muscle glycolytic pathway; and the glycolytic pathway of Lactococcus lactis. We also describe the code and methods in sufficient detail to allow researchers to further develop the code or reproduce the experiments described. The code for MIKANA is open source, free for academic and non-academic use and is available for download (Information S1).

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.

Comparison of desiccation tolerance among Listeria monocytogenes, Escherichia coli O157:H7, Salmonella enterica, and Cronobacter sakazakii in powdered infant formula.

PubMed

Koseki, Shigenobu; Nakamura, Nobutaka; Shiina, Takeo

2015-01-01

Bacterial pathogens such as Listeria monocytogenes, Escherichia coli O157:H7, Salmonella enterica, and Cronobacter sakazakii have demonstrated long-term survival in/on dry or low-water activity (aw) foods. However, there have been few comparative studies on the desiccation tolerance among these bacterial pathogens separately in a same food matrix. In the present study, the survival kinetics of the four bacterial pathogens separately inoculated onto powdered infant formula as a model low-aw food was compared during storage at 5, 22, and 35°C. No significant differences in the survival kinetics between E. coli O157:H7 and L. monocytogenes were observed. Salmonella showed significantly higher desiccation tolerance than these pathogens, and C. sakazakii demonstrated significantly higher desiccation tolerance than all other three bacteria studied. Thus, the desiccation tolerance was represented as C. sakazakii > Salmonella > E. coli O157:H7 = L. monocytogenes. The survival kinetics of each bacterium was mathematically analyzed, and the observed kinetics was successfully described using the Weibull model. To evaluate the variability of the inactivation kinetics of the tested bacterial pathogens, the Monte Carlo simulation was performed using assumed probability distribution of the estimated fitted parameters. The simulation results showed that the storage temperature significantly influenced survival of each bacterium under the dry environment, where the bacterial inactivation became faster with increasing storage temperature. Furthermore, the fitted rate and shape parameters of the Weibull model were successfully modelled as a function of temperature. The numerical simulation of the bacterial inactivation was realized using the functions of the parameters under arbitrary fluctuating temperature conditions.

A novel fast and flexible technique of radical kinetic behaviour investigation based on pallet for plasma evaluation structure and numerical analysis

NASA Astrophysics Data System (ADS)

Malinowski, Arkadiusz; Takeuchi, Takuya; Chen, Shang; Suzuki, Toshiya; Ishikawa, Kenji; Sekine, Makoto; Hori, Masaru; Lukasiak, Lidia; Jakubowski, Andrzej

2013-07-01

This paper describes a new, fast, and case-independent technique for sticking coefficient (SC) estimation based on pallet for plasma evaluation (PAPE) structure and numerical analysis. Our approach does not require complicated structure, apparatus, or time-consuming measurements but offers high reliability of data and high flexibility. Thermal analysis is also possible. This technique has been successfully applied to estimation of very low value of SC of hydrogen radicals on chemically amplified ArF 193 nm photoresist (the main goal of this study). Upper bound of our technique has been determined by investigation of SC of fluorine radical on polysilicon (in elevated temperature). Sources of estimation error and ways of its reduction have been also discussed. Results of this study give an insight into the process kinetics, and not only they are helpful in better process understanding but additionally they may serve as parameters in a phenomenological model development for predictive modelling of etching for ultimate CMOS topography simulation.

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

PubMed Central

Kaltenbacher, Barbara; Hasenauer, Jan

2017-01-01

Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation (ODE) models has improved our understanding of small- and medium-scale biological processes. While the same should in principle hold for large- and genome-scale processes, the computational methods for the analysis of ODE models which describe hundreds or thousands of biochemical species and reactions are missing so far. While individual simulations are feasible, the inference of the model parameters from experimental data is computationally too intensive. In this manuscript, we evaluate adjoint sensitivity analysis for parameter estimation in large scale biochemical reaction networks. We present the approach for time-discrete measurement and compare it to state-of-the-art methods used in systems and computational biology. Our comparison reveals a significantly improved computational efficiency and a superior scalability of adjoint sensitivity analysis. The computational complexity is effectively independent of the number of parameters, enabling the analysis of large- and genome-scale models. Our study of a comprehensive kinetic model of ErbB signaling shows that parameter estimation using adjoint sensitivity analysis requires a fraction of the computation time of established methods. The proposed method will facilitate mechanistic modeling of genome-scale cellular processes, as required in the age of omics. PMID:28114351

An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking

PubMed Central

Hoffman, Elizabeth A.; Zaidi, Hussain; Shetty, Savera J.; Bekiranov, Stefan; Auble, David T.

2018-01-01

Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these interactions. We have developed a method to estimate binding kinetic parameters from time-dependent formaldehyde crosslinking data, called crosslinking kinetics (CLK) analysis. Cultures of yeast cells are crosslinked with formaldehyde for various periods of time, yielding the relative ChIP signal at particular loci. We fit the data using the mass-action CLK model to extract kinetic parameters of the TF-chromatin interaction, including the on- and off-rates and crosslinking rate. From the on- and off-rate we obtain the occupancy and residence time. The following protocol is the second iteration of this method, CLKv2, updated with improved crosslinking and quenching conditions, more information about crosslinking rates, and systematic procedures for modeling the observed kinetic regimes. CLKv2 analysis has been applied to investigate the binding behavior of the TATA-binding protein (TBP), and a selected subset of other TFs. The protocol was developed using yeast cells, but may be applicable to cells from other organisms as well. PMID:29682595

Determination of biodegradability kinetics of RCRA compounds using respirometry for structure-activity relationships

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

Tabak, H.H.; Desai, S.; Govind, R.

1990-01-01

Electrolytic respirometry is attaining prominence in biodegradation studies and is becoming one of the more suitable experimental methods for measuring the biodegradability and the kinetics of biodegradation of toxic organic compounds by the sewage, sludge, and soil microbiota and for determining substrate inhibitory effects to microorganisms in wastewater treatment systems. The purpose of the study was to obtain information on biological treatability of the benzene, phenol, phthalate, ketone organics and of the Superfund CERCLA organics bearing wastes in wastewater treatment systems which will support the development of an EPA technical guidance document on the discharge of the above organics tomore » POTWs. The paper discusses the experimental design and procedural steps for the respirometric biodegradation and toxicity testing approach for individual organics or specific industrial wastes at different concentration levels in a mineral salts medium. A developed multi-level protocol is presented for determination of the biodegradability, microbial acclimation to toxic substrates and first order kinetic parameters of biodegradation for estimation of the Monod kinetic parameter of toxic organic compounds, in order to correlate the extent and rate of biodegradation with a predictive model based on chemical properties and molecular structure of these compounds. Respirometric biodegradation/inhibition and biokinetic data are provided for representative RCRA alkyl benzene and ketone organics.« less

Dynamic dual-tracer PET reconstruction.

PubMed

Gao, Fei; Liu, Huafeng; Jian, Yiqiang; Shi, Pengcheng

2009-01-01

Although of important medical implications, simultaneous dual-tracer positron emission tomography reconstruction remains a challenging problem, primarily because the photon measurements from dual tracers are overlapped. In this paper, we propose a simultaneous dynamic dual-tracer reconstruction of tissue activity maps based on guidance from tracer kinetics. The dual-tracer reconstruction problem is formulated in a state-space representation, where parallel compartment models serve as continuous-time system equation describing the tracer kinetic processes of dual tracers, and the imaging data is expressed as discrete sampling of the system states in measurement equation. The image reconstruction problem has therefore become a state estimation problem in a continuous-discrete hybrid paradigm, and H infinity filtering is adopted as the estimation strategy. As H infinity filtering makes no assumptions on the system and measurement statistics, robust reconstruction results can be obtained for the dual-tracer PET imaging system where the statistical properties of measurement data and system uncertainty are not available a priori, even when there are disturbances in the kinetic parameters. Experimental results on digital phantoms, Monte Carlo simulations and physical phantoms have demonstrated the superior performance.

An HMM-based algorithm for evaluating rates of receptor–ligand binding kinetics from thermal fluctuation data

PubMed Central

Ju, Lining; Wang, Yijie Dylan; Hung, Ying; Wu, Chien-Fu Jeff; Zhu, Cheng

2013-01-01

Motivation: Abrupt reduction/resumption of thermal fluctuations of a force probe has been used to identify association/dissociation events of protein–ligand bonds. We show that off-rate of molecular dissociation can be estimated by the analysis of the bond lifetime, while the on-rate of molecular association can be estimated by the analysis of the waiting time between two neighboring bond events. However, the analysis relies heavily on subjective judgments and is time-consuming. To automate the process of mapping out bond events from thermal fluctuation data, we develop a hidden Markov model (HMM)-based method. Results: The HMM method represents the bond state by a hidden variable with two values: bound and unbound. The bond association/dissociation is visualized and pinpointed. We apply the method to analyze a key receptor–ligand interaction in the early stage of hemostasis and thrombosis: the von Willebrand factor (VWF) binding to platelet glycoprotein Ibα (GPIbα). The numbers of bond lifetime and waiting time events estimated by the HMM are much more than those estimated by a descriptive statistical method from the same set of raw data. The kinetic parameters estimated by the HMM are in excellent agreement with those by a descriptive statistical analysis, but have much smaller errors for both wild-type and two mutant VWF-A1 domains. Thus, the computerized analysis allows us to speed up the analysis and improve the quality of estimates of receptor–ligand binding kinetics. Contact: jeffwu@isye.gatech.edu or cheng.zhu@bme.gatech.edu PMID:23599504

Quantifying stream nutrient uptake from ambient to saturation with instantaneous tracer additions

NASA Astrophysics Data System (ADS)

Covino, T. P.; McGlynn, B. L.; McNamara, R.

2009-12-01

Stream nutrient tracer additions and spiraling metrics are frequently used to quantify stream ecosystem behavior. However, standard approaches limit our understanding of aquatic biogeochemistry. Specifically, the relationship between in-stream nutrient concentration and stream nutrient spiraling has not been characterized. The standard constant rate (steady-state) approach to stream spiraling parameter estimation, either through elevating nutrient concentration or adding isotopically labeled tracers (e.g. 15N), provides little information regarding the stream kinetic curve that represents the uptake-concentration relationship analogous to the Michaelis-Menten curve. These standard approaches provide single or a few data points and often focus on estimating ambient uptake under the conditions at the time of the experiment. Here we outline and demonstrate a new method using instantaneous nutrient additions and dynamic analyses of breakthrough curve (BTC) data to characterize the full relationship between spiraling metrics and nutrient concentration. We compare the results from these dynamic analyses to BTC-integrated, and standard steady-state approaches. Our results indicate good agreement between these three approaches but we highlight the advantages of our dynamic method. Specifically, our new dynamic method provides a cost-effective and efficient approach to: 1) characterize full concentration-spiraling metric curves; 2) estimate ambient spiraling metrics; 3) estimate Michaelis-Menten parameters maximum uptake (Umax) and the half-saturation constant (Km) from developed uptake-concentration kinetic curves, and; 4) measure dynamic nutrient spiraling in larger rivers where steady-state approaches are impractical.

Direct reconstruction of pharmacokinetic parameters in dynamic fluorescence molecular tomography by the augmented Lagrangian method

NASA Astrophysics Data System (ADS)

Zhu, Dianwen; Zhang, Wei; Zhao, Yue; Li, Changqing

2016-03-01

Dynamic fluorescence molecular tomography (FMT) has the potential to quantify physiological or biochemical information, known as pharmacokinetic parameters, which are important for cancer detection, drug development and delivery etc. To image those parameters, there are indirect methods, which are easier to implement but tend to provide images with low signal-to-noise ratio, and direct methods, which model all the measurement noises together and are statistically more efficient. The direct reconstruction methods in dynamic FMT have attracted a lot of attention recently. However, the coupling of tomographic image reconstruction and nonlinearity of kinetic parameter estimation due to the compartment modeling has imposed a huge computational burden to the direct reconstruction of the kinetic parameters. In this paper, we propose to take advantage of both the direct and indirect reconstruction ideas through a variable splitting strategy under the augmented Lagrangian framework. Each iteration of the direct reconstruction is split into two steps: the dynamic FMT image reconstruction and the node-wise nonlinear least squares fitting of the pharmacokinetic parameter images. Through numerical simulation studies, we have found that the proposed algorithm can achieve good reconstruction results within a small amount of time. This will be the first step for a combined dynamic PET and FMT imaging in the future.

Exact and approximate solutions for the decades-old Michaelis-Menten equation: Progress-curve analysis through integrated rate equations.

PubMed

Goličnik, Marko

2011-01-01

The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate V, and the Michaelis constant K(M) ) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to understand fully, or can even be misunderstood, by students when based only on the differential form of the Michaelis-Menten equation, and the variety of methods available to calculate the kinetic constants from rate versus substrate concentration "textbook data." Consequently, enzyme kinetics can be confusing if an analytical solution of the Michaelis-Menten equation is not available. Therefore, the still rarely known exact solution to the Michaelis-Menten equation is presented here through the explicit closed-form equation in terms of the Lambert W(x) function. Unfortunately, as the W(x) is not available in standard curve-fitting computer programs, the practical use of this direct solution is limited for most life-science students. Thus, the purpose of this article is to provide analytical approximations to the equation for modeling Michaelis-Menten kinetics. The elementary and explicit nature of these approximations can provide students with direct and simple estimations of kinetic parameters from raw experimental time-course data. The Michaelis-Menten kinetics studied in the latter context can provide an ideal alternative to the 100-year-old problems of data transformation, graphical visualization, and data analysis of enzyme-catalyzed reactions. Hence, the content of the course presented here could gradually become an important component of the modern biochemistry curriculum in the 21st century. Copyright © 2011 Wiley Periodicals, Inc.

Applying constraints on model-based methods: Estimation of rate constants in a second order consecutive reaction

NASA Astrophysics Data System (ADS)

Kompany-Zareh, Mohsen; Khoshkam, Maryam

2013-02-01

This paper describes estimation of reaction rate constants and pure ultraviolet/visible (UV-vis) spectra of the component involved in a second order consecutive reaction between Ortho-Amino benzoeic acid (o-ABA) and Diazoniom ions (DIAZO), with one intermediate. In the described system, o-ABA was not absorbing in the visible region of interest and thus, closure rank deficiency problem did not exist. Concentration profiles were determined by solving differential equations of the corresponding kinetic model. In that sense, three types of model-based procedures were applied to estimate the rate constants of the kinetic system, according to Levenberg/Marquardt (NGL/M) algorithm. Original data-based, Score-based and concentration-based objective functions were included in these nonlinear fitting procedures. Results showed that when there is error in initial concentrations, accuracy of estimated rate constants strongly depends on the type of applied objective function in fitting procedure. Moreover, flexibility in application of different constraints and optimization of the initial concentrations estimation during the fitting procedure were investigated. Results showed a considerable decrease in ambiguity of obtained parameters by applying appropriate constraints and adjustable initial concentrations of reagents.

Kinetic and thermodynamic studies of a novel acid protease from Aspergillus foetidus.

PubMed

Souza, Paula Monteiro; Aliakbarian, Bahar; Filho, Edivaldo Ximenes Ferreira; Magalhães, Pérola Oliveira; Junior, Adalberto Pessoa; Converti, Attilio; Perego, Patrizia

2015-11-01

The kinetics of a thermostable extracellular acid protease produced by an Aspergillus foetidus strain was investigated at different pH, temperatures and substrate concentrations. The enzyme exhibited maximal activity at pH 5.0 and 55°C, and its irreversible deactivation was well described by first-order kinetics. When temperature was raised from 55 to 70°C, the deactivation rate constant increased from 0.018 to 5.06h(-1), while the half-life decreased from 37.6 to 0.13h. The results of activity collected at different temperatures were then used to estimate, the activation energy of the hydrolysis reaction (E*=19.03kJ/mol) and the standard enthalpy variation of reversible enzyme unfolding (ΔH°U=19.03kJ/mol). The results of residual activity tests carried out in the temperature range 55-70°C allowed estimating the activation energy (E(*)d=314.12kJ/mol), enthalpy (311.27≤(ΔH°d≤311.39kJ/mol), entropy (599.59≤ΔS(*)d≤610.49kJ/mol K) and Gibbs free energy (103.18≤ΔG(*)d≤113.87kJ/mol) of the enzyme irreversible denaturation. These thermodynamic parameters suggest that this new protease is highly thermostable and could be important for industrial applications. To the best of our knowledge, this is the first report on thermodynamic parameters of an acid protease produced by A. foetidus. Copyright © 2015 Elsevier B.V. All rights reserved.

Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations

NASA Astrophysics Data System (ADS)

Wu, Hao; Nüske, Feliks; Paul, Fabian; Klus, Stefan; Koltai, Péter; Noé, Frank

2017-04-01

Markov state models (MSMs) and master equation models are popular approaches to approximate molecular kinetics, equilibria, metastable states, and reaction coordinates in terms of a state space discretization usually obtained by clustering. Recently, a powerful generalization of MSMs has been introduced, the variational approach conformation dynamics/molecular kinetics (VAC) and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters. While it is known how to estimate MSMs from trajectories whose starting points are not sampled from an equilibrium ensemble, this has not yet been the case for TICA and the VAC. Previous estimates from short trajectories have been strongly biased and thus not variationally optimal. Here, we employ the Koopman operator theory and the ideas from dynamic mode decomposition to extend the VAC and TICA to non-equilibrium data. The main insight is that the VAC and TICA provide a coefficient matrix that we call Koopman model, as it approximates the underlying dynamical (Koopman) operator in conjunction with the basis set used. This Koopman model can be used to compute a stationary vector to reweight the data to equilibrium. From such a Koopman-reweighted sample, equilibrium expectation values and variationally optimal reversible Koopman models can be constructed even with short simulations. The Koopman model can be used to propagate densities, and its eigenvalue decomposition provides estimates of relaxation time scales and slow collective variables for dimension reduction. Koopman models are generalizations of Markov state models, TICA, and the linear VAC and allow molecular kinetics to be described without a cluster discretization.

Reaction of diazepam and related benzodiazepines with chlorine. Kinetics, transformation products and in-silico toxicological assessment.

PubMed

Carpinteiro, Inmaculada; Rodil, Rosario; Quintana, José Benito; Cela, Rafael

2017-09-01

In this work, the reaction of four benzodiazepines (diazepam, oxazepam, nordazepam and temazepam) during water chlorination was studied by means of liquid chromatography-quadrupole-time of flight-mass spectrometry (LC-QTOF-MS). For those compounds that showed a significant degradation, i.e. diazepam, oxazepam and nordazepam, parameters affecting to the reaction kinetics (pH, chlorine and bromide level) were studied in detail and transformation products were tentatively identified. The oxidation reactions followed pseudofirst-order kinetics with rate constants in the range of 1.8-42.5 M -1  s -1 , 0.13-1.16 M -1  s -1 and 0.04-20.4 M -1  s -1 corresponding to half-life values in the range of 1.9-146 min, 1.8-87 h and 2.5-637 h for oxazepam, nordazepam and diazepam, respectively, depending of the levels of studied parameters. Chlorine and pH affected significantly the reaction kinetics, where an increase of the pH resulted into a decrease of the reaction rate, whereas higher chlorine dosages led to faster kinetics, as expected in this case. The transformation of the studied benzodiazepines occurs mainly at the 1,4-diazepine 7-membered-ring, resulting in ring opening to form benzophenone derivatives or the formation of a 6-membered pyrimidine ring, leading to quinazoline derivatives. The formation of these by-products was also tested in real surface water samples observing kinetics of oxazepam degradation slower in river than in creek water, while the degradation of the two other benzodiazepines occurred only in the simpler sample (creek water). Finally, the acute and chronical toxicity and mutagenicity of precursors and transformation products were estimated using quantitative structure-activity relationship (QSAR) software tools: Ecological Structure Activity Relationships (ECOSAR) and Toxicity Estimation Software Tool (TEST), finding that some transformation products could be more toxic/mutagenic than the precursor drug, but additional test would be needed to confirm this fact. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of the performance of tracer kinetic model-driven registration for dynamic contrast enhanced MRI using different models of contrast enhancement.

PubMed

Buonaccorsi, Giovanni A; Roberts, Caleb; Cheung, Sue; Watson, Yvonne; O'Connor, James P B; Davies, Karen; Jackson, Alan; Jayson, Gordon C; Parker, Geoff J M

2006-09-01

The quantitative analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) data is subject to model fitting errors caused by motion during the time-series data acquisition. However, the time-varying features that occur as a result of contrast enhancement can confound motion correction techniques based on conventional registration similarity measures. We have therefore developed a heuristic, locally controlled tracer kinetic model-driven registration procedure, in which the model accounts for contrast enhancement, and applied it to the registration of abdominal DCE-MRI data at high temporal resolution. Using severely motion-corrupted data sets that had been excluded from analysis in a clinical trial of an antiangiogenic agent, we compared the results obtained when using different models to drive the tracer kinetic model-driven registration with those obtained when using a conventional registration against the time series mean image volume. Using tracer kinetic model-driven registration, it was possible to improve model fitting by reducing the sum of squared errors but the improvement was only realized when using a model that adequately described the features of the time series data. The registration against the time series mean significantly distorted the time series data, as did tracer kinetic model-driven registration using a simpler model of contrast enhancement. When an appropriate model is used, tracer kinetic model-driven registration influences motion-corrupted model fit parameter estimates and provides significant improvements in localization in three-dimensional parameter maps. This has positive implications for the use of quantitative DCE-MRI for example in clinical trials of antiangiogenic or antivascular agents.

Microbial community composition of a multi-stage moving bed biofilm reactor and its interaction with kinetic model parameters estimation.

PubMed

Wang, Xiaodong; Bi, Xuejun; Hem, Lars John; Ratnaweera, Harsha

2018-07-15

Microbial community diversity determines the function of each chamber of multi-stage moving bed biofilm reactor (MBBR) systems. How the microbial community data can be further used to serve wastewater treatment process modelling and optimization has been rarely studied. In this study, a MBBR system was set up to investigate the microbial community diversity of biofilm in each functional chamber. The compositions of microbial community of biofilm from different chambers of MBBR were quantified by high-throughput sequencing. Significantly higher proportion of autotrophs were found in the second aerobic chamber (15.4%), while 4.3% autotrophs were found in the first aerobic chamber. Autotrophs in anoxic chamber were negligible. Moreover, ratios of active heterotrophic biomass and autotrophic biomass (X H /X A ) were obtained by performing respiration tests. By setting heterotroph/autotroph ratios obtained from sequencing analysis equal to X H /X A , a novel approach for kinetic model parameters estimation was developed. This work not only investigated microbial community of MBBR system, but also it provided an approach to make further use of molecular microbiology analysis results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Amyloplast Sedimentation Kinetics in Corn Roots

NASA Technical Reports Server (NTRS)

Leopold, A. C.; Sack, F.

1985-01-01

Knowledge of the parameters of amyloplast sedimentation is crucial for an evaluation of proposed mechanisms of root graviperception. Early estimates of the rate of root amyloplast sedimentation were as low as 1.2 micron/min which may be too slow for many amyloplasts to reach the vicinity of the new lower wall within the presentation time. On this basis, Haberlandt's classical statolith hypothesis involving amyloplast stimulation of a sensitive surface near the new lower wall was questioned. The aim was to determine the kinetics of amyloplast sedimentation with reference to the presentation time in living and fixed corn rootcap cells as compared with coleoptiles of the same variety.

A new chlorophycean nickel hyperaccumulator.

PubMed

Harish; Sundaramoorthy, S; Kumar, Devendra; Vaijapurkar, S G

2008-06-01

Bioremediation of nickel by chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at various concentrations of Ni2+ were assessed in terms of protein level and 12 mg L(-1) of the Ni2+ is the tolerance limit (46.76% level of growth kinetics). Absorption/adsorption kinetics was estimated after 240 h of Ni2+ treatments. Absorptions were higher than adsorption with maximum accumulation factor (AF) of 1.37. Ni2+ concentration and absorption were linearly related (r=0.98; p>0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to correlate the state of metabolism and these exhibited reduction due to heavy metal stress.

Power-law modeling based on least-squares minimization criteria.

PubMed

Hernández-Bermejo, B; Fairén, V; Sorribas, A

1999-10-01

The power-law formalism has been successfully used as a modeling tool in many applications. The resulting models, either as Generalized Mass Action or as S-systems models, allow one to characterize the target system and to simulate its dynamical behavior in response to external perturbations and parameter changes. The power-law formalism was first derived as a Taylor series approximation in logarithmic space for kinetic rate-laws. The especial characteristics of this approximation produce an extremely useful systemic representation that allows a complete system characterization. Furthermore, their parameters have a precise interpretation as local sensitivities of each of the individual processes and as rate-constants. This facilitates a qualitative discussion and a quantitative estimation of their possible values in relation to the kinetic properties. Following this interpretation, parameter estimation is also possible by relating the systemic behavior to the underlying processes. Without leaving the general formalism, in this paper we suggest deriving the power-law representation in an alternative way that uses least-squares minimization. The resulting power-law mimics the target rate-law in a wider range of concentration values than the classical power-law. Although the implications of this alternative approach remain to be established, our results show that the predicted steady-state using the least-squares power-law is closest to the actual steady-state of the target system.

A kinetic study on sesame cake protein hydrolysis by Alcalase.

PubMed

Demirhan, Elçin; Apar, Dilek Kılıç; Özbek, Belma

2011-01-01

In the present study, the hydrolysis of sesame cake protein was performed by Alcalase, a bacterial protease produced by Bacillus licheniformis, to investigate the reaction kinetics of sesame cake hydrolysis and to determine decay and product inhibition effects for Alcalase. The reactions were carried out for 10 min in 0.1 L of aqueous solutions containing 10, 15, 20, 25, and 30 g protein/L at various temperature and pH values. To determine decay and product inhibition effects for Alcalase, a series of inhibition experiments were conducted with the addition of various amounts of hydrolysate. The reaction kinetics was investigated by initial rate approach. The initial reaction rates were determined from the slopes of the linear models that fitted to the experimental data. The kinetic parameters, K(m) and V(max), were estimated as 41.17 g/L and 9.24 meqv/L x min. The Lineweaver-Burk plots showed that the type of inhibition for Alcalase determined as uncompetitive, and the inhibition constant, K(i), was estimated as 38.24% (hydrolysate/substrate mixture). Practical Application: Plant proteins are increasingly being used as an alternative to proteins from animal sources to perform functional roles in food formulation. Knowledge of the kinetics of the hydrolysis reaction is essential for the optimization of enzymatic protein hydrolysis and for increasing the utilization of plant proteins in food products. Therefore, in the present study, the hydrolysis of sesame cake protein was performed by Alcalase, a bacterial protease produced by B. licheniformis, to investigate the reaction kinetics of sesame cake hydrolysis and to determine decay and product inhibition effects for Alcalase.

Use of a "Super-child" Approach to Assess the Vitamin A Equivalence of Moringa oleifera Leaves, Develop a Compartmental Model for Vitamin A Kinetics, and Estimate Vitamin A Total Body Stores in Young Mexican Children.

PubMed

Lopez-Teros, Veronica; Ford, Jennifer Lynn; Green, Michael H; Tang, Guangwen; Grusak, Michael A; Quihui-Cota, Luis; Muzhingi, Tawanda; Paz-Cassini, Mariela; Astiazaran-Garcia, Humberto

2017-12-01

Background: Worldwide, an estimated 250 million children <5 y old are vitamin A (VA) deficient. In Mexico, despite ongoing efforts to reduce VA deficiency, it remains an important public health problem; thus, food-based interventions that increase the availability and consumption of provitamin A-rich foods should be considered. Objective: The objectives were to assess the VA equivalence of 2 H-labeled Moringa oleifera (MO) leaves and to estimate both total body stores (TBS) of VA and plasma retinol kinetics in young Mexican children. Methods: β-Carotene was intrinsically labeled by growing MO plants in a 2 H 2 O nutrient solution. Fifteen well-nourished children (17-35 mo old) consumed puréed MO leaves (1 mg β-carotene) and a reference dose of [ 13 C 10 ]retinyl acetate (1 mg) in oil. Blood (2 samples/child) was collected 10 times (2 or 3 children each time) over 35 d. The bioefficacy of MO leaves was calculated from areas under the composite "super-child" plasma isotope response curves, and MO VA equivalence was estimated through the use of these values; a compartmental model was developed to predict VA TBS and retinol kinetics through the use of composite plasma [ 13 C 10 ]retinol data. TBS were also estimated with isotope dilution. Results: The relative bioefficacy of β-carotene retinol activity equivalents from MO was 28%; VA equivalence was 3.3:1 by weight (0.56 μmol retinol:1 μmol β-carotene). Kinetics of plasma retinol indicate more rapid plasma appearance and turnover and more extensive recycling in these children than are observed in adults. Model-predicted mean TBS (823 μmol) was similar to values predicted using a retinol isotope dilution equation applied to data from 3 to 6 d after dosing (mean ± SD: 832 ± 176 μmol; n = 7). Conclusions: The super-child approach can be used to estimate population carotenoid bioefficacy and VA equivalence, VA status, and parameters of retinol metabolism from a composite data set. Our results provide initial estimates of retinol kinetics in well-nourished young children with adequate VA stores and demonstrate that MO leaves may be an important source of VA. © 2017 American Society for Nutrition.

Genetic algorithms for the application of Activated Sludge Model No. 1.

PubMed

Kim, S; Lee, H; Kim, J; Kim, C; Ko, J; Woo, H; Kim, S

2002-01-01

The genetic algorithm (GA) has been integrated into the IWA ASM No. 1 to calibrate important stoichiometric and kinetic parameters. The evolutionary feature of GA was used to configure the multiple local optima as well as the global optimum. The objective function of optimization was designed to minimize the difference between estimated and measured effluent concentrations at the activated sludge system. Both steady state and dynamic data of the simulation benchmark were used for calibration using denitrification layout. Depending upon the confidence intervals and objective functions, the proposed method provided distributions of parameter space. Field data have been collected and applied to validate calibration capacity of GA. Dynamic calibration was suggested to capture periodic variations of inflow concentrations. Also, in order to verify this proposed method in real wastewater treatment plant, measured data sets for substrate concentrations were obtained from Haeundae wastewater treatment plant and used to estimate parameters in the dynamic system. The simulation results with calibrated parameters matched well with the observed concentrations of effluent COD.

Development and experimental validation of a frying model to estimate acrylamide levels in French fries.

PubMed

Palazoğlu, T K; Gökmen, V

2008-04-01

In this study, a numerical model was developed to simulate frying of potato strips and estimate acrylamide levels in French fries. Heat and mass transfer parameters determined during frying of potato strips and the formation and degradation kinetic parameters of acrylamide obtained with a sugar-asparagine model system were incorporated within the model. The effect of reducing sugar content (0.3 to 2.15 g/100 g dry matter), strip thickness (8.5 x 8.5 mm and 10 x 10 mm), and frying time (3, 4, 5, and 6 min) and temperature (150, 170, and 190 degrees C) on resultant acrylamide level in French fries was investigated both numerically and experimentally. The model appeared to closely estimate the acrylamide contents, and thereby may potentially save considerable time, money, and effort during the stages of process design and optimization.

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

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

Clarifications regarding the use of model-fitting methods of kinetic analysis for determining the activation energy from a single non-isothermal curve.

PubMed

Sánchez-Jiménez, Pedro E; Pérez-Maqueda, Luis A; Perejón, Antonio; Criado, José M

2013-02-05

This paper provides some clarifications regarding the use of model-fitting methods of kinetic analysis for estimating the activation energy of a process, in response to some results recently published in Chemistry Central journal. The model fitting methods of Arrhenius and Savata are used to determine the activation energy of a single simulated curve. It is shown that most kinetic models correctly fit the data, each providing a different value for the activation energy. Therefore it is not really possible to determine the correct activation energy from a single non-isothermal curve. On the other hand, when a set of curves are recorded under different heating schedules are used, the correct kinetic parameters can be clearly discerned. Here, it is shown that the activation energy and the kinetic model cannot be unambiguously determined from a single experimental curve recorded under non isothermal conditions. Thus, the use of a set of curves recorded under different heating schedules is mandatory if model-fitting methods are employed.

Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores

NASA Astrophysics Data System (ADS)

Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

2015-11-01

We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.

Equilibrium and kinetic adsorption study of a cationic dye by a natural adsorbent--silkworm pupa.

PubMed

Noroozi, B; Sorial, G A; Bahrami, H; Arami, M

2007-01-02

In this work the use of silkworm pupa, which is the waste of silk spinning industries has been investigated as an adsorbent for the removal of C.I. Basic Blue 41. The amino acid nature of the pupa provided a reasonable capability for dye removal. Equilibrium adsorption isotherms and kinetics were investigated. The adsorption equilibrium data were analyzed by using various adsorption isotherm models and the results have shown that adsorption behavior of the dye could be described reasonably well by either Langmuir or Freundlich models. The characteristic parameters for each isotherm have been determined. The monolayer adsorption capacity was determined to be 555 mg/g. Kinetic studies indicated that the adsorption follows pseudo-second-order kinetics with a rate constant of 0.0434 and 0.0572 g/min mg for initial dye concentration of 200 mg/l at 20 and 40 degrees C, respectively. Kinetic studies showed that film diffusion and intra-particle diffusion were simultaneously operating during the adsorption process. The rate constant for intra-particle diffusion was estimated to be 1.985 mg/g min(0.5).

Kinetic energy offsets for multicharged ions from an electron beam ion source.

PubMed

Kulkarni, D D; Ahl, C D; Shore, A M; Miller, A J; Harriss, J E; Sosolik, C E; Marler, J P

2017-08-01

Using a retarding field analyzer, we have measured offsets between the nominal and measured kinetic energy of multicharged ions extracted from an electron beam ion source (EBIS). By varying source parameters, a shift in ion kinetic energy was attributed to the trapping potential produced by the space charge of the electron beam within the EBIS. The space charge of the electron beam depends on its charge density, which in turn depends on the amount of negative charge (electron beam current) and its velocity (electron beam energy). The electron beam current and electron beam energy were both varied to obtain electron beams of varying space charge and these were related to the observed kinetic energy offsets for Ar 4+ and Ar 8+ ion beams. Knowledge of these offsets is important for studies that seek to utilize slow, i.e., low kinetic energy, multicharged ions to exploit their high potential energies for processes such as surface modification. In addition, we show that these offsets can be utilized to estimate the effective radius of the electron beam inside the trap.

Calcium kinetics with microgram stable isotope doses and saliva sampling

NASA Technical Reports Server (NTRS)

Smith, S. M.; Wastney, M. E.; Nyquist, L. E.; Shih, C. Y.; Wiesmann, H.; Nillen, J. L.; Lane, H. W.

1996-01-01

Studies of calcium kinetics require administration of tracer doses of calcium and subsequent repeated sampling of biological fluids. This study was designed to develop techniques that would allow estimation of calcium kinetics by using small (micrograms) doses of isotopes instead of the more common large (mg) doses to minimize tracer perturbation of the system and reduce cost, and to explore the use of saliva sampling as an alternative to blood sampling. Subjects received an oral dose (133 micrograms) of 43Ca and an i.v. dose (7.7 micrograms) of 46Ca. Isotopic enrichment in blood, urine, saliva and feces was well above thermal ionization mass spectrometry measurement precision up to 170 h after dosing. Fractional calcium absorptions determined from isotopic ratios in blood, urine and saliva were similar. Compartmental modeling revealed that kinetic parameters determined from serum or saliva data were similar, decreasing the necessity for blood samples. It is concluded from these results that calcium kinetics can be assessed with micrograms doses of stable isotopes, thereby reducing tracer costs and with saliva samples, thereby reducing the amount of blood needed.

Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis.

PubMed

Hock, Sabrina; Hasenauer, Jan; Theis, Fabian J

2013-01-01

Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed in-vitro and in-vivo using microscopy based imaging techniques. The resulting time-series of two dimensional, high-resolutions images in combination with mechanistic models enable the quantitative analysis of the underlying mechanisms. However, such a model-based analysis is still challenging due to measurement noise and sparse observations, which result in uncertainties of the model parameters. We introduce a likelihood function for image-based measurements with log-normal distributed noise. Based upon this likelihood function we formulate the maximum likelihood estimation problem, which is solved using PDE-constrained optimization methods. To assess the uncertainty and practical identifiability of the parameters we introduce profile likelihoods for diffusion processes. As proof of concept, we model certain aspects of the guidance of dendritic cells towards lymphatic vessels, an example for haptotaxis. Using a realistic set of artificial measurement data, we estimate the five kinetic parameters of this model and compute profile likelihoods. Our novel approach for the estimation of model parameters from image data as well as the proposed identifiability analysis approach is widely applicable to diffusion processes. The profile likelihood based method provides more rigorous uncertainty bounds in contrast to local approximation methods.

Radiation processed polychloroprene-co-ethylene-propene diene terpolymer blends: Effect of radiation vulcanization on solvent transport kinetics

NASA Astrophysics Data System (ADS)

Dubey, K. A.; Bhardwaj, Y. K.; Chaudhari, C. V.; Kumar, Virendra; Goel, N. K.; Sabharwal, S.

2009-03-01

Blends of polychloroprene rubber (PCR) and ethylene propylene diene terpolymer rubber (EPDM) of different compositions were made and exposed to different gamma radiation doses. The radiation sensitivity and radiation vulcanization efficiency of blends was estimated by gel-content analysis, Charlesby-Pinner parameter determination and crosslinking density measurements. Gamma radiation induced crosslinking was most efficient for EPDM ( p0/ q0 ˜ 0.08), whereas it was the lowest for blends containing 40% PCR ( p0/ q0 ˜ 0.34). The vulcanized blends were characterized for solvent diffusion characteristics by following the swelling dynamics. Blends with higher PCR content showed anomalous swelling. The sorption and permeability of the solvent were not strictly in accordance with each other and the extent of variation in two parameters was found to be a function of blend composition. The Δ G values for solvent diffusion were in the range -2.97 to -9.58 kJ/mol and indicated thermodynamically favorable sorption for all blends. These results were corroborated by dynamic swelling, experimental as well as simulated profiles and have been explained on the basis of correlation between crosslinking density, diffusion kinetics, thermodynamic parameters and polymer-polymer interaction parameter.

ATOMIC-SCALE DESIGN OF IRON FISCHER-TROPSCH CATALYSTS: A COMBINED COMPUTATIONAL CHEMISTRY, EXPERIMENTAL, AND MICROKINETIC MODELING APPROACH

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

Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale

2005-03-22

Efforts during this first year focused on four areas: (1) searching/summarizing published FTS mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) construction of mass spectrometer-TPD and Berty CSTR reactor systems; (3) preparation and characterization of unsupported iron and alumina-supported iron catalysts at various iron loadings (4) Determination of thermochemical parameters such as binding energies of reactive intermediates, heat of FTS elementary reaction steps, and kinetic parameters such as activation energies, and frequency factors of FTS elementary reaction steps on a number of model surfaces. Literature describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts wasmore » compiled in a draft review. Construction of the mass spectrometer-TPD system is 90% complete and of a Berty CSTR reactor system 98% complete. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by nonaqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2}, thus ideal for kinetic and mechanistic studies. The alumina-supported iron catalysts will be used for kinetic and mechanistic studies. In the coming year, adsorption/desorption properties, rates of elementary steps, and global reaction rates will be measured for these catalysts, with and without promoters, providing a database for understanding effects of dispersion, metal loading, and support on elementary kinetic parameters and for validation of computational models that incorporate effects of surface structure and promoters. Furthermore, using state-of-the-art self-consistent Density Functional Theory (DFT) methods, we have extensively studied the thermochemistry and kinetics of various elementary steps on three different model surfaces: (1) Fe(110), (2) Fe(110) modified by subsurface C, and (3) Fe surface modified with Pt adatoms. These studies have yielded valuable insights into the reactivity of Fe surfaces for FTS, and provided accurate estimates for the effect of Fe modifiers such as subsurface C and surface Pt.« less

Simultaneous removal of SO2 and trace SeO2 from flue gas: effect of SO2 on selenium capture and kinetics study.

PubMed

Li, Yuzhong; Tong, Huiling; Zhuo, Yuqun; Wang, Shujuan; Xu, Xuchang

2006-12-15

Sulfur dioxide (SO2) and trace elements are all pollutants derived from coal combustion. This study relates to the simultaneous removal of SO2 and trace selenium dioxide (SeO2) from flue gas by calcium oxide (CaO) adsorption in the moderate temperature range, especially the effect of SO2 presence on selenium capture. Experiments performed on a thermogravimetric analyzer (TGA) can reach the following conclusions. When the CaO conversion is relatively low and the reaction rate is controlled by chemical kinetics, the SO2 presence does not affect the selenium capture. When the CaO conversion is very high and the reaction rate is controlled by product layer diffusion, the SO2 presence and the product layer diffusion resistance jointly reduce the selenium capture. On the basis of the kinetics study, a method to estimate the trace selenium removal efficiency using kinetic parameters and the sulfur removal efficiency is developed.

Experimental Design for Parameter Estimation of Gene Regulatory Networks

PubMed Central

Timmer, Jens

2012-01-01

Systems biology aims for building quantitative models to address unresolved issues in molecular biology. In order to describe the behavior of biological cells adequately, gene regulatory networks (GRNs) are intensively investigated. As the validity of models built for GRNs depends crucially on the kinetic rates, various methods have been developed to estimate these parameters from experimental data. For this purpose, it is favorable to choose the experimental conditions yielding maximal information. However, existing experimental design principles often rely on unfulfilled mathematical assumptions or become computationally demanding with growing model complexity. To solve this problem, we combined advanced methods for parameter and uncertainty estimation with experimental design considerations. As a showcase, we optimized three simulated GRNs in one of the challenges from the Dialogue for Reverse Engineering Assessment and Methods (DREAM). This article presents our approach, which was awarded the best performing procedure at the DREAM6 Estimation of Model Parameters challenge. For fast and reliable parameter estimation, local deterministic optimization of the likelihood was applied. We analyzed identifiability and precision of the estimates by calculating the profile likelihood. Furthermore, the profiles provided a way to uncover a selection of most informative experiments, from which the optimal one was chosen using additional criteria at every step of the design process. In conclusion, we provide a strategy for optimal experimental design and show its successful application on three highly nonlinear dynamic models. Although presented in the context of the GRNs to be inferred for the DREAM6 challenge, the approach is generic and applicable to most types of quantitative models in systems biology and other disciplines. PMID:22815723

Biosorption of formic and acetic acids from aqueous solution using activated carbon from shea butter seed shells

NASA Astrophysics Data System (ADS)

Adekola, Folahan A.; Oba, Ismaila A.

2017-10-01

The efficiency of prepared activated carbon from shea butter seed shells (SB-AC) for the adsorption of formic acid (FA) and acetic acid (AA) from aqueous solution was investigated. The effect of optimization parameters including initial concentration, agitation time, adsorbent dosage and temperature of adsorbate solution on the sorption capacity were studied. The SB-AC was characterized for the following parameters: bulk density, moisture content, ash content, pH, Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The optimal conditions for the adsorption were established and the adsorption data for AA fitted Dubinin-Radushkevich (D-R) isotherm well, whereas FA followed Langmuir isotherm. The kinetic data were examined. It was found that pseudo-second-order kinetic model was found to adequately explain the sorption kinetic of AA and FA from aqueous solution. It was again found that intraparticle diffusion was found to explain the adsorption mechanism. Adsorption thermodynamic parameters were estimated and the negative values of Δ G showed that the adsorption process was feasible and spontaneous in nature, while the negative values of Δ H indicate that the adsorption process was exothermic. It is therefore established that SB-AC has good potential for the removal of AA and FA from aqueous solution. Hence, it should find application in the regular treatment of polluted water in aquaculture and fish breeding system.

A critical evaluation of the experimental design of studies of mechanism based enzyme inhibition, with implications for in vitro-in vivo extrapolation.

PubMed

Ghanbari, F; Rowland-Yeo, K; Bloomer, J C; Clarke, S E; Lennard, M S; Tucker, G T; Rostami-Hodjegan, A

2006-04-01

The published literature on mechanism based inhibition (MBI) of CYPs was evaluated with respect to experimental design, methodology and data analysis. Significant variation was apparent in the dilution factor, ratio of preincubation to incubation times and probe substrate concentrations used, and there were some anomalies in the estimation of associated kinetic parameters (k(inact), K(I), r). The impact of the application of inaccurate values of k(inact) and K(I) when extrapolating to the extent of inhibition in vivo is likely to be greatest for those compounds of intermediate inhibitory potency, but this also depends on the fraction of the net clearance of substrate subject to MBI and the pre-systemic and systemic exposure to the inhibitor. For potent inhibitors, the experimental procedure is unlikely to have a material influence on the maximum inhibition. Nevertheless, the bias in the values of the kinetic parameters may influence the time for recovery of enzyme activity following re-synthesis of the enzyme. Careful attention to the design of in vitro experiments to obtain accurate kinetic parameters is necessary for a reliable prediction of different aspects of the in vivo consequences of MBI. The review calls for experimental studies to quantify the impact of study design in studies of MBI, with a view to better harmonisation of protocols.

Experiments and Reaction Models of Fundamental Combustion Properties

DTIC Science & Technology

2010-05-31

in liquid hydrocarbon flames Lennard - Jones 12-6 potential parameters were estimated for n-alkanes and 1-alkenes with carbon numbers ranging from 5...hydrocarbons, were studied both experimentally and numerically. The fuel mixtures were chosen in order to gain insight into potential kinetic couplings...initio electronic structure theory, transition state theory, and master equation modelling. The potential energy surface was examined with the coupled

A physiology-based parametric imaging method for FDG-PET data

NASA Astrophysics Data System (ADS)

Scussolini, Mara; Garbarino, Sara; Sambuceti, Gianmario; Caviglia, Giacomo; Piana, Michele

2017-12-01

Parametric imaging is a compartmental approach that processes nuclear imaging data to estimate the spatial distribution of the kinetic parameters governing tracer flow. The present paper proposes a novel and efficient computational method for parametric imaging which is potentially applicable to several compartmental models of diverse complexity and which is effective in the determination of the parametric maps of all kinetic coefficients. We consider applications to [18 F]-fluorodeoxyglucose positron emission tomography (FDG-PET) data and analyze the two-compartment catenary model describing the standard FDG metabolization by an homogeneous tissue and the three-compartment non-catenary model representing the renal physiology. We show uniqueness theorems for both models. The proposed imaging method starts from the reconstructed FDG-PET images of tracer concentration and preliminarily applies image processing algorithms for noise reduction and image segmentation. The optimization procedure solves pixel-wise the non-linear inverse problem of determining the kinetic parameters from dynamic concentration data through a regularized Gauss-Newton iterative algorithm. The reliability of the method is validated against synthetic data, for the two-compartment system, and experimental real data of murine models, for the renal three-compartment system.

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.

Spatio-temporal diffusion of dynamic PET images

NASA Astrophysics Data System (ADS)

Tauber, C.; Stute, S.; Chau, M.; Spiteri, P.; Chalon, S.; Guilloteau, D.; Buvat, I.

2011-10-01

Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.

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

Santhanagopalan, Shriram; White, Ralph E.

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

Aqueous extraction kinetics of soluble solids, phenolics and flavonoids from sage (Salvia fruticosa Miller) leaves.

PubMed

Torun, Mehmet; Dincer, Cuneyt; Topuz, Ayhan; Sahin-Nadeem, Hilal; Ozdemir, Feramuz

2015-05-01

In the present study, aqueous extraction kinetics of total soluble solids (TSS), total phenolic content (TPC) and total flavonoid content (TFC) from Salvia fruticosa leaves were investigated throughout 150 min. of extraction period against temperature (60-80 °C), particle size (2-8 mm) and loading percentage (1-4 %). The extract yielded 25 g/100 g TSS which contained 30 g/100 g TPC and 25 g/100 g TFC. The extraction data in time course fit with reversible first order kinetic model. All tested variables showed significant effect on the estimated kinetic parameters except equilibrium concentration. Increasing the extraction temperature resulted high extraction rate constants and equilibrium concentrations of the tested variables notably above 70 °C. By using the Arrhenius relationship, activation energy of the TSS, TPC and TFC were determined as 46.11 ± 5.61, 36.80 ± 3.12 and 33.52 ± 2.23 kj/mol, respectively. By decreasing the particle size, the extraction rate constants and diffusion coefficients exponentially increased whereas equilibrium concentrations did not change significantly. The equilibrium concentrations of the tested parameters showed linear behavior with increasing the loading percentage of the sage, however; the change in extraction rates did not show linear behavior due to submerging effect of 4 % loading.

An analysis of OH excited state absorption lines in DR 21 and K3-50

NASA Astrophysics Data System (ADS)

Jones, K. N.; Doel, R. C.; Field, D.; Gray, M. D.; Walker, R. N. F.

1992-10-01

We present an analysis of the OH absorption line zones observed toward the compact H II regions DR 21 and K3-50. Using as parameters the kinetic and dust temperatures, the H2 number density and the ratio of OH-H2 number densities to the velocity gradient, the model quantitatively reproduces the absorption line data for the six main line transitions in 2 Pi3/2 J = 5/2, 7/2, and 9/2. Observed upper limits for the absorption or emission in the satellite lines of 2 Pi3/2 J = 5/2 are crucial in constraining the range of derived parameters. Physical conditions derived for DR 21 show that the kinetic temperature centers around 140 K, the H2 number density around 10 exp 7/cu cm, and that the OH column density in the excited state absorption zone lies between 1 x 10 exp 15/sq cm and 2 x 10 exp 15/sq cm. Including contributions from a J = 3/2 absorption zone, the total OH column density is more than a factor of 2 lower than estimates based upon LTE (Walmsley et al., 1986). The OH absorption zone in K3-50 tends toward higher density and displays a larger column density, while the kinetic temperature is similar. For both sources, the dust temperature is found to be significantly lower than the kinetic temperature.

Simulation of aerobic and anaerobic biodegradation processes at a crude oil spill site

USGS Publications Warehouse

Essaid, Hedeff I.; Bekins, Barbara A.; Godsy, E. Michael; Warren, Ean; Baedecker, Mary Jo; Cozzarelli, Isabelle M.

1995-01-01

A two-dimensional, multispecies reactive solute transport model with sequential aerobic and anaerobic degradation processes was developed and tested. The model was used to study the field-scale solute transport and degradation processes at the Bemidji, Minnesota, crude oil spill site. The simulations included the biodegradation of volatile and nonvolatile fractions of dissolved organic carbon by aerobic processes, manganese and iron reduction, and methanogenesis. Model parameter estimates were constrained by published Monod kinetic parameters, theoretical yield estimates, and field biomass measurements. Despite the considerable uncertainty in the model parameter estimates, results of simulations reproduced the general features of the observed groundwater plume and the measured bacterial concentrations. In the simulation, 46% of the total dissolved organic carbon (TDOC) introduced into the aquifer was degraded. Aerobic degradation accounted for 40% of the TDOC degraded. Anaerobic processes accounted for the remaining 60% of degradation of TDOC: 5% by Mn reduction, 19% by Fe reduction, and 36% by methanogenesis. Thus anaerobic processes account for more than half of the removal of DOC at this site.

Turbulent Kinetic Energy (TKE) Budgets Using 5-beam Doppler Profilers

NASA Astrophysics Data System (ADS)

Guerra, M. A.; Thomson, J. M.

2016-12-01

Field observations of turbulence parameters are important for the development of hydrodynamic models, understanding contaminant mixing, and predicting sediment transport. The turbulent kinetic energy (TKE) budget quantifies where turbulence is being produced, dissipated or transported at a specific site. The Nortek Signature 5-beam AD2CP was used to measure velocities at high sampling rates (up to 8 Hz) at Admiralty Inlet and Rich Passage in Puget Sound, WA, USA. Raw along-beam velocity data is quality controlled and is used to estimate TKE spectra, spatial structure functions, and Reynolds stress tensors. Exceptionally low Doppler noise in the data enables clear observations of the inertial sub-range of isotropic turbulence in both the frequency TKE spectra and the spatial structure functions. From these, TKE dissipation rates are estimated following Kolmogorov's theory of turbulence. The TKE production rates are estimated using Reynolds stress tensors together with the vertical shear in the mean flow. The Reynolds stress tensors are estimated following the methodology of Dewey and Stinger (2007), which is significantly improved by inclusion of the 5th beam (as opposed to the conventional 4). These turbulence parameters are used to study the TKE budget along the water column at the two sites. Ebb and flood production and dissipation rates are compared through the water column at both sites. At Admiralty Inlet, dissipation exceeds production during ebb while the opposite occurs during flood because the proximity to a lateral headland. At Rich Passage, production exceeds dissipation through the water column for all tidal conditions due to a vertical sill in the vicinity of the measurement site.

Kinetic Monte Carlo simulations of the effect of the exchange control layer thickness in CoPtCrB/CoPtCrSiO granular media

NASA Astrophysics Data System (ADS)

Almudallal, Ahmad M.; Mercer, J. I.; Whitehead, J. P.; Plumer, M. L.; van Ek, J.

2018-05-01

A hybrid Landau Lifshitz Gilbert/kinetic Monte Carlo algorithm is used to simulate experimental magnetic hysteresis loops for dual layer exchange coupled composite media. The calculation of the rate coefficients and difficulties arising from low energy barriers, a fundamental problem of the kinetic Monte Carlo method, are discussed and the methodology used to treat them in the present work is described. The results from simulations are compared with experimental vibrating sample magnetometer measurements on dual layer CoPtCrB/CoPtCrSiO media and a quantitative relationship between the thickness of the exchange control layer separating the layers and the effective exchange constant between the layers is obtained. Estimates of the energy barriers separating magnetically reversed states of the individual grains in zero applied field as well as the saturation field at sweep rates relevant to the bit write speeds in magnetic recording are also presented. The significance of this comparison between simulations and experiment and the estimates of the material parameters obtained from it are discussed in relation to optimizing the performance of magnetic storage media.

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.

Complete kinetic mechanism for recycling of the bacterial ribosome

PubMed Central

Borg, Anneli; Pavlov, Michael

2016-01-01

How EF-G and RRF act together to split a post-termination ribosomal complex into its subunits has remained obscure. Here, using stopped-flow experiments with Rayleigh light scattering detection and quench-flow experiments with radio-detection of GTP hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. Ribosome splitting requires that EF-G binds to an already RRF-containing ribosome. EF-G binding to RRF-free ribosomes induces futile rounds of GTP hydrolysis and inhibits ribosome splitting, implying that while RRF is purely an activator of recycling, EF-G acts as both activator and competitive inhibitor of RRF in recycling of the post-termination ribosome. The ribosome splitting rate and the number of GTPs consumed per splitting event depend strongly on the free concentrations of EF-G and RRF. The maximal recycling rate, here estimated as 25 sec−1, is approached at very high concentrations of EF-G and RRF with RRF in high excess over EF-G. The present in vitro results, suggesting an in vivo ribosome recycling rate of ∼5 sec−1, are discussed in the perspective of rapidly growing bacterial cells. PMID:26527791

Bioreactors with immobilized lipases: state of the art.

PubMed

Balcão, V M; Paiva, A L; Malcata, F X

1996-05-01

This review attempts to provide an updated compilation of studies reported in the literature pertaining to reactors containing lipases in immobilized forms, in a way that helps the reader direct a bibliographic search and develop an integrated perspective of the subject. Highlights are given to industrial applications of lipases (including control and economic considerations), as well as to methods of immobilization and configurations of reactors in which lipases are used. Features associated with immobilized lipase kinetics such as enzyme activities, adsorption properties, optimum operating conditions, and estimates of the lumped parameters in classical kinetic formulations (Michaelis-Menten model for enzyme action and first-order model for enzyme decay) are presented in the text in a systematic tabular form.

Toxicokinetics of perfluorooctane sulfonate in birds under environmentally realistic exposure conditions and development of a kinetic predictive model.

PubMed

Tarazona, J V; Rodríguez, C; Alonso, E; Sáez, M; González, F; San Andrés, M D; Jiménez, B; San Andrés, M I

2015-01-22

This article describes the toxicokinetics of perfluorooctane sulfonate (PFOS) in birds under low repeated dosing, equivalent to 0.085 μg/kg per day, representing environmentally realistic exposure conditions. The best fitting was provided by a simple pseudo monocompartmental first-order kinetics model, regulated by two rates, with a pseudo first-order dissipation half-life of 230 days, accounting for real elimination as well as binding of PFOS to non-exchangeable structures. The calculated assimilation efficiency was 0.66 with confidence intervals of 0.64 and 0.68. The model calculations confirmed that the measured maximum concentrations were still far from the steady state situation, which for this dose regime, was estimated at a value of about 65 μg PFOS/L serum achieved after a theoretical 210 weeks continuous exposure. The results confirm a very different kinetics than that observed in single-dose experiments confirming clear dose-related differences in apparent elimination rates in birds, as described for humans and monkeys; suggesting that a capacity-limited saturable process should also be considered in the kinetic behavior of PFOS in birds. Pseudo first-order kinetic models are highly convenient and frequently used for predicting bioaccumulation of chemicals in livestock and wildlife; the study suggests that previous bioaccumulation models using half-lives obtained at high doses are expected to underestimate the biomagnification potential of PFOS. The toxicokinetic parameters presented here can be used for higher-tier bioaccumulation estimations of PFOS in chickens and as surrogate values for modeling PFOS kinetics in wild bird species. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Extraction of Antioxidant Phenolic Compounds from Brewer’s Spent Grain: Optimization and Kinetics Modeling

PubMed Central

Sologubik, Carlos A.; Fernández, María B.; Manrique, Guillermo D.

2018-01-01

The kinetics of polyphenol extraction from brewer’s spent grain (BSG), using a batch system, ultrasound assistance, and microwave assistance and the evolution of antioxidant capacity of these extracts over time, were studied. The main parameters of extraction employed in the batch system were evaluated, and, by applying response surface analysis, the following optimal conditions were obtained: Liquid/solid ratio of 30:1 mL/g at 80 °C, using 72% (v/v) ethanol:water as the solvent system. Under these optimized conditions, ultrasound assistance demonstrated the highest extraction rate and equilibrium yield, as well as shortest extraction times, followed by microwave assistance. Among the mathematical models used, Patricelli’s model proved the most suitable for describing the extraction kinetics for each method tested, and is therefore able to predict the response values and estimate the extraction rates and potential maximum yields in each case. PMID:29570683

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.

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.

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

Human Leg Model Predicts Muscle Forces, States, and Energetics during Walking.

PubMed

Markowitz, Jared; Herr, Hugh

2016-05-01

Humans employ a high degree of redundancy in joint actuation, with different combinations of muscle and tendon action providing the same net joint torque. Both the resolution of these redundancies and the energetics of such systems depend on the dynamic properties of muscles and tendons, particularly their force-length relations. Current walking models that use stock parameters when simulating muscle-tendon dynamics tend to significantly overestimate metabolic consumption, perhaps because they do not adequately consider the role of elasticity. As an alternative, we posit that the muscle-tendon morphology of the human leg has evolved to maximize the metabolic efficiency of walking at self-selected speed. We use a data-driven approach to evaluate this hypothesis, utilizing kinematic, kinetic, electromyographic (EMG), and metabolic data taken from five participants walking at self-selected speed. The kinematic and kinetic data are used to estimate muscle-tendon lengths, muscle moment arms, and joint moments while the EMG data are used to estimate muscle activations. For each subject we perform an optimization using prescribed skeletal kinematics, varying the parameters that govern the force-length curve of each tendon as well as the strength and optimal fiber length of each muscle while seeking to simultaneously minimize metabolic cost and maximize agreement with the estimated joint moments. We find that the metabolic cost of transport (MCOT) values of our participants may be correctly matched (on average 0.36±0.02 predicted, 0.35±0.02 measured) with acceptable joint torque fidelity through application of a single constraint to the muscle metabolic budget. The associated optimal muscle-tendon parameter sets allow us to estimate the forces and states of individual muscles, resolving redundancies in joint actuation and lending insight into the potential roles and control objectives of the muscles of the leg throughout the gait cycle.

Cardiorespiratory Kinetics Determined by Pseudo-Random Binary Sequences - Comparisons between Walking and Cycling.

PubMed

Koschate, J; Drescher, U; Thieschäfer, L; Heine, O; Baum, K; Hoffmann, U

2016-12-01

This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O 2 ) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O 2 of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O 2 kinetics were estimated from heart rate and pulmonary V̇O 2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O 2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O 2 showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O 2 during walking, the assessment of muscular V̇O 2 kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry. © Georg Thieme Verlag KG Stuttgart · New York.

Fitting integrated enzyme rate equations to progress curves with the use of a weighting matrix.

PubMed Central

Franco, R; Aran, J M; Canela, E I

1991-01-01

A method is presented for fitting the pairs of values product formed-time taken from progress curves to the integrated rate equation. The procedure is applied to the estimation of the kinetic parameters of the adenosine deaminase system. Simulation studies demonstrate the capabilities of this strategy. A copy of the FORTRAN77 program used can be obtained from the authors by request. PMID:2006914

Migration of antioxidants from polylactic acid films: A parameter estimation approach and an overview of the current mass transfer models.

PubMed

Samsudin, Hayati; Auras, Rafael; Mishra, Dharmendra; Dolan, Kirk; Burgess, Gary; Rubino, Maria; Selke, Susan; Soto-Valdez, Herlinda

2018-01-01

Migration studies of chemicals from contact materials have been widely conducted due to their importance in determining the safety and shelf life of a food product in their packages. The US Food and Drug Administration (FDA) and the European Food Safety Authority (EFSA) require this safety assessment for food contact materials. So, migration experiments are theoretically designed and experimentally conducted to obtain data that can be used to assess the kinetics of chemical release. In this work, a parameter estimation approach was used to review and to determine the mass transfer partition and diffusion coefficients governing the migration process of eight antioxidants from poly(lactic acid), PLA, based films into water/ethanol solutions at temperatures between 20 and 50°C. Scaled sensitivity coefficients were calculated to assess simultaneously estimation of a number of mass transfer parameters. An optimal experimental design approach was performed to show the importance of properly designing a migration experiment. Additional parameters also provide better insights on migration of the antioxidants. For example, the partition coefficients could be better estimated using data from the early part of the experiment instead at the end. Experiments could be conducted for shorter periods of time saving time and resources. Diffusion coefficients of the eight antioxidants from PLA films were between 0.2 and 19×10 -14 m 2 /s at ~40°C. The use of parameter estimation approach provided additional and useful insights about the migration of antioxidants from PLA films. Copyright © 2017 Elsevier Ltd. All rights reserved.

Feasibility of Rapid Multitracer PET Tumor Imaging

NASA Astrophysics Data System (ADS)

Kadrmas, D. J.; Rust, T. C.

2005-10-01

Positron emission tomography (PET) can characterize different aspects of tumor physiology using various tracers. PET scans are usually performed using only one tracer since there is no explicit signal for distinguishing multiple tracers. We tested the feasibility of rapidly imaging multiple PET tracers using dynamic imaging techniques, where the signals from each tracer are separated based upon differences in tracer half-life, kinetics, and distribution. Time-activity curve populations for FDG, acetate, ATSM, and PTSM were simulated using appropriate compartment models, and noisy dual-tracer curves were computed by shifting and adding the single-tracer curves. Single-tracer components were then estimated from dual-tracer data using two methods: principal component analysis (PCA)-based fits of single-tracer components to multitracer data, and parallel multitracer compartment models estimating single-tracer rate parameters from multitracer time-activity curves. The PCA analysis found that there is information content present for separating multitracer data, and that tracer separability depends upon tracer kinetics, injection order and timing. Multitracer compartment modeling recovered rate parameters for individual tracers with good accuracy but somewhat higher statistical uncertainty than single-tracer results when the injection delay was >10 min. These approaches to processing rapid multitracer PET data may potentially provide a new tool for characterizing multiple aspects of tumor physiology in vivo.

Cell shape characterization and classification with discrete Fourier transforms and self-organizing maps.

PubMed

Kriegel, Fabian L; Köhler, Ralf; Bayat-Sarmadi, Jannike; Bayerl, Simon; Hauser, Anja E; Niesner, Raluca; Luch, Andreas; Cseresnyes, Zoltan

2018-03-01

Cells in their natural environment often exhibit complex kinetic behavior and radical adjustments of their shapes. This enables them to accommodate to short- and long-term changes in their surroundings under physiological and pathological conditions. Intravital multi-photon microscopy is a powerful tool to record this complex behavior. Traditionally, cell behavior is characterized by tracking the cells' movements, which yields numerous parameters describing the spatiotemporal characteristics of cells. Cells can be classified according to their tracking behavior using all or a subset of these kinetic parameters. This categorization can be supported by the a priori knowledge of experts. While such an approach provides an excellent starting point for analyzing complex intravital imaging data, faster methods are required for automated and unbiased characterization. In addition to their kinetic behavior, the 3D shape of these cells also provide essential clues about the cells' status and functionality. New approaches that include the study of cell shapes as well may also allow the discovery of correlations amongst the track- and shape-describing parameters. In the current study, we examine the applicability of a set of Fourier components produced by Discrete Fourier Transform (DFT) as a tool for more efficient and less biased classification of complex cell shapes. By carrying out a number of 3D-to-2D projections of surface-rendered cells, the applied method reduces the more complex 3D shape characterization to a series of 2D DFTs. The resulting shape factors are used to train a Self-Organizing Map (SOM), which provides an unbiased estimate for the best clustering of the data, thereby characterizing groups of cells according to their shape. We propose and demonstrate that such shape characterization is a powerful addition to, or a replacement for kinetic analysis. This would make it especially useful in situations where live kinetic imaging is less practical or not possible at all. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

Multi-wavelength campaign on NGC 7469. II. Column densities and variability in the X-ray spectrum

NASA Astrophysics Data System (ADS)

Peretz, U.; Behar, E.; Kriss, G. A.; Kaastra, J.; Arav, N.; Bianchi, S.; Branduardi-Raymont, G.; Cappi, M.; Costantini, E.; De Marco, B.; Di Gesu, L.; Ebrero, J.; Kaspi, S.; Mehdipour, M.; Middei, R.; Paltani, S.; Petrucci, P. O.; Ponti, G.; Ursini, F.

2018-01-01

We have investigated the ionic column density variability of the ionized outflows associated with NGC 7469, to estimate their location and power. This could allow a better understanding of galactic feedback of AGNs to their host galaxies. Analysis of seven XMM-Newton grating observations from 2015 is reported. We used an individual-ion spectral fitting approach, and compared different epochs to accurately determine variability on timescales of years, months, and days. We find no significant column density variability in a ten-year period implying that the outflow is far from the ionizing source. The implied lower bound on the ionization equilibrium time, ten years, constrains the lower limit on the distance to be at least 12 pc, and up to 31 pc, much less but consistent with the 1 kpc wide starburst ring. The ionization distribution of column density is reconstructed from measured column densities, nicely matching results of two 2004 observations, with one large high ionization parameter (ξ) component at 2 < log ξ< 3.5, and one at 0.5 < log ξ< 1 in cgs units. The strong dependence of the expression for kinetic power, ∝ 1 /ξ, hampers tight constraints on the feedback mechanism of outflows with a large range in ionization parameter, which is often observed and indicates a non-conical outflow. The kinetic power of the outflow is estimated here to be within 0.4 and 60% of the Eddington luminosity, depending on the ion used to estimate ξ.

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 Ea with only routine open-system Rock-Eval data, which will allow for better estimating hydrocarbon generation.

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.

A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons

PubMed Central

Vavoulis, Dimitrios V.; Straub, Volko A.; Aston, John A. D.; Feng, Jianfeng

2012-01-01

Traditional approaches to the problem of parameter estimation in biophysical models of neurons and neural networks usually adopt a global search algorithm (for example, an evolutionary algorithm), often in combination with a local search method (such as gradient descent) in order to minimize the value of a cost function, which measures the discrepancy between various features of the available experimental data and model output. In this study, we approach the problem of parameter estimation in conductance-based models of single neurons from a different perspective. By adopting a hidden-dynamical-systems formalism, we expressed parameter estimation as an inference problem in these systems, which can then be tackled using a range of well-established statistical inference methods. The particular method we used was Kitagawa's self-organizing state-space model, which was applied on a number of Hodgkin-Huxley-type models using simulated or actual electrophysiological data. We showed that the algorithm can be used to estimate a large number of parameters, including maximal conductances, reversal potentials, kinetics of ionic currents, measurement and intrinsic noise, based on low-dimensional experimental data and sufficiently informative priors in the form of pre-defined constraints imposed on model parameters. The algorithm remained operational even when very noisy experimental data were used. Importantly, by combining the self-organizing state-space model with an adaptive sampling algorithm akin to the Covariance Matrix Adaptation Evolution Strategy, we achieved a significant reduction in the variance of parameter estimates. The algorithm did not require the explicit formulation of a cost function and it was straightforward to apply on compartmental models and multiple data sets. Overall, the proposed methodology is particularly suitable for resolving high-dimensional inference problems based on noisy electrophysiological data and, therefore, a potentially useful tool in the construction of biophysical neuron models. PMID:22396632

Practical limits for reverse engineering of dynamical systems: a statistical analysis of sensitivity and parameter inferability in systems biology models.

PubMed

Erguler, Kamil; Stumpf, Michael P H

2011-05-01

The size and complexity of cellular systems make building predictive models an extremely difficult task. In principle dynamical time-course data can be used to elucidate the structure of the underlying molecular mechanisms, but a central and recurring problem is that many and very different models can be fitted to experimental data, especially when the latter are limited and subject to noise. Even given a model, estimating its parameters remains challenging in real-world systems. Here we present a comprehensive analysis of 180 systems biology models, which allows us to classify the parameters with respect to their contribution to the overall dynamical behaviour of the different systems. Our results reveal candidate elements of control in biochemical pathways that differentially contribute to dynamics. We introduce sensitivity profiles that concisely characterize parameter sensitivity and demonstrate how this can be connected to variability in data. Systematically linking data and model sloppiness allows us to extract features of dynamical systems that determine how well parameters can be estimated from time-course measurements, and associates the extent of data required for parameter inference with the model structure, and also with the global dynamical state of the system. The comprehensive analysis of so many systems biology models reaffirms the inability to estimate precisely most model or kinetic parameters as a generic feature of dynamical systems, and provides safe guidelines for performing better inferences and model predictions in the context of reverse engineering of mathematical models for biological systems.

Reducing the Anaerobic Digestion Model No. 1 for its application to an industrial wastewater treatment plant treating winery effluent wastewater.

PubMed

García-Diéguez, Carlos; Bernard, Olivier; Roca, Enrique

2013-03-01

The Anaerobic Digestion Model No. 1 (ADM1) is a complex model which is widely accepted as a common platform for anaerobic process modeling and simulation. However, it has a large number of parameters and states that hinder its calibration and use in control applications. A principal component analysis (PCA) technique was extended and applied to simplify the ADM1 using data of an industrial wastewater treatment plant processing winery effluent. The method shows that the main model features could be obtained with a minimum of two reactions. A reduced stoichiometric matrix was identified and the kinetic parameters were estimated on the basis of representative known biochemical kinetics (Monod and Haldane). The obtained reduced model takes into account the measured states in the anaerobic wastewater treatment (AWT) plant and reproduces the dynamics of the process fairly accurately. The reduced model can support on-line control, optimization and supervision strategies for AWT plants. Copyright © 2013 Elsevier Ltd. All rights reserved.

Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms

NASA Astrophysics Data System (ADS)

Tokar, M. Z.

2016-12-01

Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 % - 30 % . This discrepancy can be significantly reduced if after the convergence of coupled plasma-neutral calculations, the final computation for c-x atoms is done kinetically.

Optimal experimental design for parameter estimation of a cell signaling model.

PubMed

Bandara, Samuel; Schlöder, Johannes P; Eils, Roland; Bock, Hans Georg; Meyer, Tobias

2009-11-01

Differential equation models that describe the dynamic changes of biochemical signaling states are important tools to understand cellular behavior. An essential task in building such representations is to infer the affinities, rate constants, and other parameters of a model from actual measurement data. However, intuitive measurement protocols often fail to generate data that restrict the range of possible parameter values. Here we utilized a numerical method to iteratively design optimal live-cell fluorescence microscopy experiments in order to reveal pharmacological and kinetic parameters of a phosphatidylinositol 3,4,5-trisphosphate (PIP(3)) second messenger signaling process that is deregulated in many tumors. The experimental approach included the activation of endogenous phosphoinositide 3-kinase (PI3K) by chemically induced recruitment of a regulatory peptide, reversible inhibition of PI3K using a kinase inhibitor, and monitoring of the PI3K-mediated production of PIP(3) lipids using the pleckstrin homology (PH) domain of Akt. We found that an intuitively planned and established experimental protocol did not yield data from which relevant parameters could be inferred. Starting from a set of poorly defined model parameters derived from the intuitively planned experiment, we calculated concentration-time profiles for both the inducing and the inhibitory compound that would minimize the predicted uncertainty of parameter estimates. Two cycles of optimization and experimentation were sufficient to narrowly confine the model parameters, with the mean variance of estimates dropping more than sixty-fold. Thus, optimal experimental design proved to be a powerful strategy to minimize the number of experiments needed to infer biological parameters from a cell signaling assay.

The kinetic study of hydrogen bacteria and methanotrophs in pure and defined mixed cultures

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

Arora, D.K.

The kinetics of pure and mixed cultures of Alcaligenes eutrophus H 16 and Methylobacterium organophilum CRL 26 under double substrate limited conditions were studied. In pure culture growth kinetics, a non-interactive model was found to fit the experimental data best. The yield of biomass on limiting substrate was found to vary with the dilution rate. The variation in the biomass yield may be attributed to the change in metabolic pathways resulting from a shift in the limiting substrates. Both species exhibited wall growth in the chemostat under dark conditions. However, under illuminated conditions, there was significant reduction in wall growth.more » Poly-{beta}-hydroxybutyric acid was synthesized by both species under ammonia and oxygen limiting conditions. The feed gas mixture was optimized to achieve the steady-state coexistence of these two species in a chemostate for the first time. In mixed cultures, the biomass species assays were differentiated on the basis of their selective growth on particular compounds: Sarcosine and D-arabinose were selected for hydrogen bacteria and methylotrophs, respectively. The kinetics parameters estimated from pure cultures were used to predict the growth kinetics of these species in defined mixed cultures.« less

Virtual parameter-estimation experiments in Bioprocess-Engineering education.

PubMed

Sessink, Olivier D T; Beeftink, Hendrik H; Hartog, Rob J M; Tramper, Johannes

2006-05-01

Cell growth kinetics and reactor concepts constitute essential knowledge for Bioprocess-Engineering students. Traditional learning of these concepts is supported by lectures, tutorials, and practicals: ICT offers opportunities for improvement. A virtual-experiment environment was developed that supports both model-related and experimenting-related learning objectives. Students have to design experiments to estimate model parameters: they choose initial conditions and 'measure' output variables. The results contain experimental error, which is an important constraint for experimental design. Students learn from these results and use the new knowledge to re-design their experiment. Within a couple of hours, students design and run many experiments that would take weeks in reality. Usage was evaluated in two courses with questionnaires and in the final exam. The faculties involved in the two courses are convinced that the experiment environment supports essential learning objectives well.

Lactate threshold by muscle electrical impedance in professional rowers

NASA Astrophysics Data System (ADS)

Jotta, B.; Coutinho, A. B. B.; Pino, A. V.; Souza, M. N.

2017-04-01

Lactate threshold (LT) is one of the physiological parameters usually used in rowing sport training prescription because it indicates the transitions from aerobic to anaerobic metabolism. Assessment of LT is classically based on a series of values of blood lactate concentrations obtained during progressive exercise tests and thus has an invasive aspect. The feasibility of noninvasive LT estimative through bioelectrical impedance spectroscopy (BIS) data collected in thigh muscles during rowing ergometer exercise tests was investigated. Nineteen professional rowers, age 19 (mean) ± 4.8 (standard deviation) yr, height 187.3 ± 6.6 cm, body mass 83 ± 7.7 kg, and training experience of 7 ± 4 yr, were evaluated in a rowing ergometer progressive test with paired measures of blood lactate concentration and BIS in thigh muscles. Bioelectrical impedance data were obtained by using a bipolar method of spectroscopy based on the current response to a voltage step. An electrical model was used to interpret BIS data and to derive parameters that were investigated to estimate LT noninvasively. From the serial blood lactate measurements, LT was also determined through Dmax method (LTDmax). The zero crossing of the second derivative of kinetic of the capacitance electrode (Ce), one of the BIS parameters, was used to estimate LT. The agreement between the LT estimates through BIS (LTBIS) and through Dmax method (LTDmax) was evaluated using Bland-Altman plots, leading to a mean difference between the estimates of just 0.07 W and a Pearson correlation coefficient r = 0.85. This result supports the utilization of the proposed method based on BIS parameters for estimating noninvasively the lactate threshold in rowing.

Diverse Data Sets Can Yield Reliable Information through Mechanistic Modeling: Salicylic Acid Clearance.

PubMed

Raymond, G M; Bassingthwaighte, J B

This is a practical example of a powerful research strategy: putting together data from studies covering a diversity of conditions can yield a scientifically sound grasp of the phenomenon when the individual observations failed to provide definitive understanding. The rationale is that defining a realistic, quantitative, explanatory hypothesis for the whole set of studies, brings about a "consilience" of the often competing hypotheses considered for individual data sets. An internally consistent conjecture linking multiple data sets simultaneously provides stronger evidence on the characteristics of a system than does analysis of individual data sets limited to narrow ranges of conditions. Our example examines three very different data sets on the clearance of salicylic acid from humans: a high concentration set from aspirin overdoses; a set with medium concentrations from a research study on the influences of the route of administration and of sex on the clearance kinetics, and a set on low dose aspirin for cardiovascular health. Three models were tested: (1) a first order reaction, (2) a Michaelis-Menten (M-M) approach, and (3) an enzyme kinetic model with forward and backward reactions. The reaction rates found from model 1 were distinctly different for the three data sets, having no commonality. The M-M model 2 fitted each of the three data sets but gave a reliable estimates of the Michaelis constant only for the medium level data (K m = 24±5.4 mg/L); analyzing the three data sets together with model 2 gave K m = 18±2.6 mg/L. (Estimating parameters using larger numbers of data points in an optimization increases the degrees of freedom, constraining the range of the estimates). Using the enzyme kinetic model (3) increased the number of free parameters but nevertheless improved the goodness of fit to the combined data sets, giving tighter constraints, and a lower estimated K m = 14.6±2.9 mg/L, demonstrating that fitting diverse data sets with a single model improves confidence in the results. This modeling effort is also an example of reproducible science available at html://www.physiome.org/jsim/models/webmodel/NSR/SalicylicAcidClearance.

Kinetic Analysis of Isothermal Decomposition Process of Sodium Bicarbonate Using the Weibull Probability Function—Estimation of Density Distribution Functions of the Apparent Activation Energies

NASA Astrophysics Data System (ADS)

Janković, Bojan

2009-10-01

The decomposition process of sodium bicarbonate (NaHCO3) has been studied by thermogravimetry in isothermal conditions at four different operating temperatures (380 K, 400 K, 420 K, and 440 K). It was found that the experimental integral and differential conversion curves at the different operating temperatures can be successfully described by the isothermal Weibull distribution function with a unique value of the shape parameter ( β = 1.07). It was also established that the Weibull distribution parameters ( β and η) show independent behavior on the operating temperature. Using the integral and differential (Friedman) isoconversional methods, in the conversion (α) range of 0.20 ≤ α ≤ 0.80, the apparent activation energy ( E a ) value was approximately constant ( E a, int = 95.2 kJmol-1 and E a, diff = 96.6 kJmol-1, respectively). The values of E a calculated by both isoconversional methods are in good agreement with the value of E a evaluated from the Arrhenius equation (94.3 kJmol-1), which was expressed through the scale distribution parameter ( η). The Málek isothermal procedure was used for estimation of the kinetic model for the investigated decomposition process. It was found that the two-parameter Šesták-Berggren (SB) autocatalytic model best describes the NaHCO3 decomposition process with the conversion function f(α) = α0.18(1-α)1.19. It was also concluded that the calculated density distribution functions of the apparent activation energies ( ddfE a ’s) are not dependent on the operating temperature, which exhibit the highly symmetrical behavior (shape factor = 1.00). The obtained isothermal decomposition results were compared with corresponding results of the nonisothermal decomposition process of NaHCO3.

Toxicokinetics of perfluorooctane sulfonate in rabbits under environmentally realistic exposure conditions and comparative assessment between mammals and birds.

PubMed

Tarazona, J V; Rodríguez, C; Alonso, E; Sáez, M; González, F; San Andrés, M D; Jiménez, B; San Andrés, M I

2016-01-22

This article describes the toxicokinetics of perfluorooctane sulfonate (PFOS) in rabbits under low repeated dosing, equivalent to 0.085μg/kg per day, and the observed differences between rabbits and chickens. The best fitting for both species was provided by a simple pseudo monocompartmental first-order kinetics model, regulated by two rates, and accounting for real elimination as well as binding of PFOS to non-exchangeable structures. Elimination was more rapid in rabbits, with a pseudo first-order dissipation half-life of 88 days compared to the 230 days observed for chickens. By contrast, the calculated assimilation efficiency for rabbits was almost 1, very close to full absorption, significantly higher than the 0.66 with confidence intervals of 0.64 and 0.68 observed for chickens. The results confirm a very different kinetics than that observed in single-dose experiments confirming clear dose-related differences in apparent elimination rates in rabbits, as previously described for humans and other mammals; suggesting the role of a capacity-limited saturable process resulting in different kinetic behaviours for PFOS in high dose versus environmentally relevant low dose exposure conditions. The model calculations confirmed that the measured maximum concentrations were still far from the steady state situation, and that the different kinetics between birds and mammals should may play a significant role in the biomagnifications assessment and potential exposure for humans and predators. For the same dose regime, the steady state concentration was estimated at about 36μg PFOS/L serum for rabbits, slightly above one-half of the 65μg PFOS/L serum estimated for chickens. The toxicokinetic parameters presented here can be used for higher-tier bioaccumulation estimations of PFOS in rabbits and chickens as starting point for human health exposure assessments and as surrogate values for modeling PFOS kinetics in wild mammals and bird in exposure assessment of predatory species. Published by Elsevier Ireland Ltd.

Application of ADM1 for modeling of biogas production from anaerobic digestion of Hydrilla verticillata.

PubMed

Chen, Xiaojuan; Chen, Zhihua; Wang, Xun; Huo, Chan; Hu, Zhiquan; Xiao, Bo; Hu, Mian

2016-07-01

The present study focused on the application of anaerobic digestion model no. 1 (ADM1) to simulate biogas production from Hydrilla verticillata. Model simulation was carried out by implementing ADM1 in AQUASIM 2.0 software. Sensitivity analysis was used to select the most sensitive parameters for estimation using the absolute-relative sensitivity function. Among all the kinetic parameters, disintegration constant (kdis), hydrolysis constant of protein (khyd_pr), Monod maximum specific substrate uptake rate (km_aa, km_ac, km_h2) and half-saturation constants (Ks_aa, Ks_ac) affect biogas production significantly, which were optimized by fitting of the model equations to the data obtained from batch experiments. The ADM1 model after parameter estimation was able to well predict the experimental results of daily biogas production and biogas composition. The simulation results of evolution of organic acids, bacteria concentrations and inhibition effects also helped to get insight into the reaction mechanisms. Copyright © 2016. Published by Elsevier Ltd.

Biochemical methane potential (BMP) tests: Reducing test time by early parameter estimation.

PubMed

Da Silva, C; Astals, S; Peces, M; Campos, J L; Guerrero, L

2018-01-01

Biochemical methane potential (BMP) test is a key analytical technique to assess the implementation and optimisation of anaerobic biotechnologies. However, this technique is characterised by long testing times (from 20 to >100days), which is not suitable for waste utilities, consulting companies or plants operators whose decision-making processes cannot be held for such a long time. This study develops a statistically robust mathematical strategy using sensitivity functions for early prediction of BMP first-order model parameters, i.e. methane yield (B 0 ) and kinetic constant rate (k). The minimum testing time for early parameter estimation showed a potential correlation with the k value, where (i) slowly biodegradable substrates (k≤0.1d -1 ) have a minimum testing times of ≥15days, (ii) moderately biodegradable substrates (0.1

Combined pressure-thermal inactivation kinetics of Bacillus amyloliquefaciens spores in egg patty mince.

PubMed

Rajan, S; Ahn, J; Balasubramaniam, V M; Yousef, A E

2006-04-01

Bacillus amyloliquefaciens is a potential surrogate for Clostridium botulinum in validation studies involving bacterial spore inactivation by pressure-assisted thermal processing. Spores of B. amyloliquefaciens Fad 82 were inoculated into egg patty mince (approximately 1.4 x 10(8) spores per g), and the product was treated with combinations of pressure (0.1 to 700 MPa) and heat (95 to 121 degrees C) in a custom-made high-pressure kinetic tester. The values for the inactivation kinetic parameter (D), temperature coefficient (zT), and pressure coefficient (zP) were determined with a linear model. Inactivation parameters from the nonlinear Weibull model also were estimated. An increase in process pressure decreased the D-value at 95, 105, and 110 degrees C; however, at 121 degrees C the contribution of pressure to spore lethality was less pronounced. The zP-value increased from 170 MPa at 95 degrees C to 332 MPa at 121 degrees C, suggesting that B. amyloliquefaciens spores became less sensitive to pressure changes at higher temperatures. Similarly, the zT-value increased from 8.2 degrees C at 0.1 MPa to 26.8 degrees C at 700 MPa, indicating that at elevated pressures, the spores were less sensitive to changes in temperature. The nonlinear Weibull model parameter b increased with increasing pressure or temperature and was inversely related to the D-value. Pressure-assisted thermal processing is a potential alternative to thermal processing for producing shelf-stable egg products.

Kinetics of CLL cells in tissues and blood during therapy with the BTK inhibitor ibrutinib.

PubMed

Wodarz, Dominik; Garg, Naveen; Komarova, Natalia L; Benjamini, Ohad; Keating, Michael J; Wierda, William G; Kantarjian, Hagop; James, Danelle; O'Brien, Susan; Burger, Jan A

2014-06-26

The Bruton tyrosine kinase (BTK) inhibitor ibrutinib has excellent clinical activity in patients with chronic lymphocytic leukemia (CLL). Characteristically, ibrutinib causes CLL cell redistribution from tissue sites into the peripheral blood during the initial weeks of therapy. To better characterize the dynamics of this redistribution phenomenon, we correlated serial lymphocyte counts with volumetric changes in lymph node and spleen sizes during ibrutinib therapy. Kinetic parameters were estimated by applying a mathematical model to the data. We found that during ibrutinib therapy, 1.7% ± 1.1% of blood CLL cells and 2.7% ± 0.99% of tissue CLL cells die per day. The fraction of the tissue CLL cells that was redistributed into the blood during therapy was estimated to be 23.3% ± 17% of the total tissue disease burden. These data indicate that the reduction of tissue disease burden by ibrutinib is due more to CLL cell death and less to egress from nodal compartments. © 2014 by The American Society of Hematology.

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.

Inter- and intra-species variability in heat resistance and the effect of heat treatment intensity on subsequent growth of Byssochlamys fulva and Byssochlamys nivea.

PubMed

Santos, Juliana L P; Samapundo, Simbarashe; Gülay, Sonay M; Van Impe, Jan; Sant'Ana, Anderson S; Devlieghere, Frank

2018-04-21

The major aims of this study were to assess inter- and intra-species variability of heat resistant moulds (HRMs), Byssochlamys fulva and Byssochlamys nivea, with regards to (i) heat resistance and (ii) effect of heat treatment intensity on subsequent outgrowth. Four-week-old ascospores were suspended in buffered glucose solution (13° Brix, pH 3.5) and heat treated in a thermal cycler adjusted at 85 °C, 90 °C and 93 °C. Two variants of the Weibull model were fitted to the survival data and the following inactivation parameters estimated: b (inactivation rate, min -1 ), n (curve shape) and δ (the time taken for first decimal reduction, min). In addition to the assessment of heat resistance, outgrowth of Byssochlamys sp. from ascospores heated at 70 °C, 75 °C, 80 °C, 85 °C and 90 °C for 10 min and at 93 °C for 30 and 70 s was determined at 22 °C for up to 30 days. The Baranyi and Roberts model was fitted to the growth data to estimate the radial growth rates (μ max , mm.day -1 ) and lag times (λ, days). Inter-species variability and significant differences (p < 0.05) were observed for both inactivation and growth estimated parameters among B. fulva and B. nivea strains. The effect of heat treatment intensity on outgrowth of B. fulva strains was more apparent at the most intense heat treatment evaluated (90 °C/10 min), which was also the condition in which greater dispersion of the estimated kinetic parameters was observed. On the other hand, B. nivea strains were more affected by heating, resulting in greater variability of growth parameters estimated at different heating intensities and in very long lag phases (up to 25 days). The results show that inter- and intra-species variability in the kinetic parameters of Byssochlamys sp. needs to be taken into account for more accurate spoilage prediction. Furthermore, the effect of thermal treatments on subsequent outgrowth from ascospores should be explored in combination with other relevant factors such as °Brix and oxygen to develop thermal processes and storage conditions which can prevent the growth of HRMs and spoilage of heat treated food products. Copyright © 2018 Elsevier B.V. All rights reserved.

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)

Chemical Kinetics of the TPS and Base Bleeding During Flight Test

NASA Technical Reports Server (NTRS)

Osipov, Viatcheslav; Ponizhovskaya, Ekaterina; Hafiychuck, Halyna; Luchinsky, Dmitry; Smelyanskiy, Vadim; Dagostino, Mark; Canabal, Francisco; Mobley, Brandon L.

2012-01-01

The present research deals with thermal degradation of polyurethane foam (PUF) during flight test. Model of thermal decomposition was developed that accounts for polyurethane kinetics parameters extracted from thermogravimetric analyses and radial heat losses to the surrounding environment. The model predicts mass loss of foam, the temperature and kinetic of release of the exhaust gases and char as function of heat and radiation loads. When PUF is heated, urethane bond break into polyol and isocyanate. In the first stage, isocyanate pyrolyses and oxidizes. As a result, the thermo-char and oil droplets (yellow smoke) are released. In the second decomposition stage, pyrolysis and oxidization of liquid polyol occur. Next, the kinetics of chemical compound release and the information about the reactions occurring in the base area are coupled to the CFD simulations of the base flow in a single first stage motor vertically stacked vehicle configuration. The CFD simulations are performed to estimate the contribution of the hot out-gassing, chemical reactions, and char oxidation to the temperature rise of the base flow. The results of simulations are compared with the flight test data.

Kinetics of hydrogen consumption by methanogenic consortia and cultures of hydrogen-consuming anaerobes. [Methanospirillum PM1, M. hungatei JF-1, Methanosarcina barkeri MS, Methanobacterium PM2, Desulfovibrio G11 and PS1

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

Robinson, J.A.

1982-01-01

Hydrogen plays a central role in the breakdown of organic matter in anaerobic habitats, influencing the nature of the fermentation end products and possibly, rates at which the initial substrates are degraded. The kinetics were examined for H/sub 2/ consumption by samples from natural anaerobic habitats, pure cultures of H/sub 2/-consuming anaerobes, and co-cultures comprised of methanogenic and sulfate-reducing bacteria. These kinetic studies were performed using a gas-recirculation system that allowed precise measurements of gaseous phase H/sub 2/ and CH/sub 4/. Uptake and growth kinetic parameters were estimated for the natural samples and suspensions of H/sub 2/-consumers by fitting H/submore » 2/ depletion (progress curve) data to integrated forms of Michaelis-Menten and Monod equations. Samples included eutrophic lake sediments, anaerobic digestor sludge, and rumen fluid. The bacteria studied were methanospirillum PM1, Methanosarcina barkeri MS, Methanospirillum hungatei JF-1, Methanohbacterium PM2, and Desulfovibrio strains G11 and PS1.« less

Kinetic study on the effect of temperature on biogas production using a lab scale batch reactor.

PubMed

Deepanraj, B; Sivasubramanian, V; Jayaraj, S

2015-11-01

In the present study, biogas production from food waste through anaerobic digestion was carried out in a 2l laboratory-scale batch reactor operating at different temperatures with a hydraulic retention time of 30 days. The reactors were operated with a solid concentration of 7.5% of total solids and pH 7. The food wastes used in this experiment were subjected to characterization studies before and after digestion. Modified Gompertz model and Logistic model were used for kinetic study of biogas production. The kinetic parameters, biogas yield potential of the substrate (B), the maximum biogas production rate (Rb) and the duration of lag phase (λ), coefficient of determination (R(2)) and root mean square error (RMSE) were estimated in each case. The effect of temperature on biogas production was evaluated experimentally and compared with the results of kinetic study. The results demonstrated that the reactor with operating temperature of 50°C achieved maximum cumulative biogas production of 7556ml with better biodegradation efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

Kinetic model-based feed-forward controlled fed-batch fermentation of Lactobacillus rhamnosus for the production of lactic acid from Arabic date juice.

PubMed

Choi, Minsung; Al-Zahrani, Saeed M; Lee, Sang Yup

2014-06-01

Arabic date is overproduced in Arabic countries such as Saudi Arabia and Iraq and is mostly composed of sugars (70-80 wt%). Here we developed a fed-batch fermentation process by using a kinetic model for the efficient production of lactic acid to a high concentration from Arabic date juice. First, a kinetic model of Lactobacillus rhamnosus grown on date juice in batch fermentation was constructed in EXCEL so that the estimation of parameters and simulation of the model can be easily performed. Then, several fed-batch fermentations were conducted by employing different feeding strategies including pulsed feeding, exponential feeding, and modified exponential feeding. Based on the results of fed-batch fermentations, the kinetic model for fed-batch fermentation was also developed. This new model was used to perform feed-forward controlled fed-batch fermentation, which resulted in the production of 171.79 g l(-1) of lactic acid with the productivity and yield of 1.58 and 0.87 g l(-1) h(-1), respectively.

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 initial target concentration. Model 1 was found to be slightly more robust than model 2 giving better estimates of initial target concentration when estimation of parameters was done for qPCR curves with very different initial target concentration. Both models may be used to estimate the initial absolute concentration of target sequence when a standard curve is not available. It is argued that the kinetic approach to modeling and interpreting quantitative PCR data has the potential to give more precise estimates of the true initial target concentrations than other methods currently used for analysis of qPCR data. The two models presented here give a unified model of the qPCR process in that they explain the shape of the qPCR curve for a wide variety of initial target concentrations.

Astrocytic tracer dynamics estimated from [1-¹¹C]-acetate PET measurements.

PubMed

Arnold, Andrea; Calvetti, Daniela; Gjedde, Albert; Iversen, Peter; Somersalo, Erkki

2015-12-01

We address the problem of estimating the unknown parameters of a model of tracer kinetics from sequences of positron emission tomography (PET) scan data using a statistical sequential algorithm for the inference of magnitudes of dynamic parameters. The method, based on Bayesian statistical inference, is a modification of a recently proposed particle filtering and sequential Monte Carlo algorithm, where instead of preassigning the accuracy in the propagation of each particle, we fix the time step and account for the numerical errors in the innovation term. We apply the algorithm to PET images of [1-¹¹C]-acetate-derived tracer accumulation, estimating the transport rates in a three-compartment model of astrocytic uptake and metabolism of the tracer for a cohort of 18 volunteers from 3 groups, corresponding to healthy control individuals, cirrhotic liver and hepatic encephalopathy patients. The distribution of the parameters for the individuals and for the groups presented within the Bayesian framework support the hypothesis that the parameters for the hepatic encephalopathy group follow a significantly different distribution than the other two groups. The biological implications of the findings are also discussed. © The Authors 2014. Published by Oxford University Press on behalf of the Institute of Mathematics and its Applications. All rights reserved.

Long-term Kinetics of Uranyl Desorption from Sediments Under Advective Conditions

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

Shang, Jianying; Liu, Chongxuan; Wang, Zheming

2014-02-15

Long-term (> 4 months) column experiments were performed to investigate the kinetics of uranyl (U(VI)) desorption in sediments collected from the Integrated Field Research Challenge (IFRC) site at the US Department of Energy (DOE) Hanford 300 Area. The experimental results were used to evaluate alternative multi-rate surface complexation reaction (SCR) approaches to describe the short- and long-term kinetics of U(VI) desorption under flow conditions. The SCR stoichiometry, equilibrium constants, and multi-rate parameters were independently characterized in batch and stirred flow-cell reactors. Multi-rate SCR models that were either additively constructed using the SCRs for individual size fractions (e.g., Shang et al.,more » 2011), or composite in nature could effectively describe short-term U(VI) desorption under flow conditions. The long-term desorption results, however, revealed that using a labile U concentration measured by carbonate extraction under-estimated desorbable U(VI) and the long-term rate of U(VI) desorption. An alternative modeling approach using total U as the desorbable U(VI) concentration was proposed to overcome this difficulty. This study also found that the gravel size fraction (2-8 mm), which is typically treated as non-reactive in modeling U(VI) reactive transport because of low external surface area, can have an important effect on the U(VI) desorption in the sediment. This study demonstrates an approach to effectively extrapolate U(VI) desorption kinetics for field-scale application, and identifies important parameters and uncertainties affecting model predictions.« less

Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Shu, Yao-Gen; Zhou, Xin; Ou-Yang, Zhong-Can; Li, Ming

2017-01-01

The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models. However, all these models did not systematically investigate the dominant factor on DNAP fidelity, i.e. the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.

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.

Kinetic parameters of the GUINEVERE reference configuration in VENUS-F reactor obtained from a pile noise experiment using Rossi and Feynman methods

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

Geslot, Benoit; Pepino, Alexandra; Blaise, Patrick

A pile noise measurement campaign has been conducted by the CEA in the VENUS-F reactor (SCK-CEN, Mol Belgium) in April 2011 in the reference critical configuration of the GUINEVERE experimental program. The experimental setup made it possible to estimate the core kinetic parameters: the prompt neutron decay constant, the delayed neutron fraction and the generation time. A precise assessment of these constants is of prime importance. In particular, the effective delayed neutron fraction is used to normalize and compare calculated reactivities of different subcritical configurations, obtained by modifying either the core layout or the control rods position, with experimental onesmore » deduced from the analysis of measurements. This paper presents results obtained with a CEA-developed time stamping acquisition system. Data were analyzed using Rossi-α and Feynman-α methods. Results were normalized to reactor power using a calibrated fission chamber with a deposit of Np-237. Calculated factors were necessary to the analysis: the Diven factor was computed by the ENEA (Italy) and the power calibration factor by the CNRS/IN2P3/LPC Caen. Results deduced with both methods are consistent with respect to calculated quantities. Recommended values are given by the Rossi-α estimator, that was found to be the most robust. The neutron generation time was found equal to 0.438 ± 0.009 μs and the effective delayed neutron fraction is 765 ± 8 pcm. Discrepancies with the calculated value (722 pcm, calculation from ENEA) are satisfactory: -5.6% for the Rossi-α estimate and -2.7% for the Feynman-α estimate. (authors)« less

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.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

NASA Astrophysics Data System (ADS)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

A low-cost Mr compatible ergometer to assess post-exercise phosphocreatine recovery kinetics.

PubMed

Naimon, Niels D; Walczyk, Jerzy; Babb, James S; Khegai, Oleksandr; Che, Xuejiao; Alon, Leeor; Regatte, Ravinder R; Brown, Ryan; Parasoglou, Prodromos

2017-06-01

To develop a low-cost pedal ergometer compatible with ultrahigh (7 T) field MR systems to reliably quantify metabolic parameters in human lower leg muscle using phosphorus magnetic resonance spectroscopy. We constructed an MR compatible ergometer using commercially available materials and elastic bands that provide resistance to movement. We recruited ten healthy subjects (eight men and two women, mean age ± standard deviation: 32.8 ± 6.0 years, BMI: 24.1 ± 3.9 kg/m 2 ). All subjects were scanned on a 7 T whole-body magnet. Each subject was scanned on two visits and performed a 90 s plantar flexion exercise at 40% maximum voluntary contraction during each scan. During the first visit, each subject performed the exercise twice in order for us to estimate the intra-exam repeatability, and once during the second visit in order to estimate the inter-exam repeatability of the time constant of phosphocreatine recovery kinetics. We assessed the intra and inter-exam reliability in terms of the within-subject coefficient of variation (CV). We acquired reliable measurements of PCr recovery kinetics with an intra- and inter-exam CV of 7.9% and 5.7%, respectively. We constructed a low-cost pedal ergometer compatible with ultrahigh (7 T) field MR systems, which allowed us to quantify reliably PCr recovery kinetics in lower leg muscle using 31 P-MRS.

Estimating Tropical Cyclone Surface Wind Field Parameters with the CYGNSS Constellation

NASA Astrophysics Data System (ADS)

Morris, M.; Ruf, C. S.

2016-12-01

A variety of parameters can be used to describe the wind field of a tropical cyclone (TC). Of particular interest to the TC forecasting and research community are the maximum sustained wind speed (VMAX), radius of maximum wind (RMW), 34-, 50-, and 64-kt wind radii, and integrated kinetic energy (IKE). The RMW is the distance separating the storm center and the VMAX position. IKE integrates the square of surface wind speed over the entire storm. These wind field parameters can be estimated from observations made by the Cyclone Global Navigation Satellite System (CYGNSS) constellation. The CYGNSS constellation consists of eight small satellites in a 35-degree inclination circular orbit. These satellites will be operating in standard science mode by the 2017 Atlantic TC season. CYGNSS will provide estimates of ocean surface wind speed under all precipitating conditions with high temporal and spatial sampling in the tropics. TC wind field data products can be derived from the level-2 CYGNSS wind speed product. CYGNSS-based TC wind field science data products are developed and tested in this paper. Performance of these products is validated using a mission simulator prelaunch.

Explicit least squares system parameter identification for exact differential input/output models

NASA Technical Reports Server (NTRS)

Pearson, A. E.

1993-01-01

The equation error for a class of systems modeled by input/output differential operator equations has the potential to be integrated exactly, given the input/output data on a finite time interval, thereby opening up the possibility of using an explicit least squares estimation technique for system parameter identification. The paper delineates the class of models for which this is possible and shows how the explicit least squares cost function can be obtained in a way that obviates dealing with unknown initial and boundary conditions. The approach is illustrated by two examples: a second order chemical kinetics model and a third order system of Lorenz equations.

Cosmological evolution of supermassive black holes in the centres of galaxies

NASA Astrophysics Data System (ADS)

Kapinska, Anna D.

2012-06-01

Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large scale structure. Their jets inject a significant amount of energy into the surrounding medium, hence they can provide useful information in the study of the density and evolution of the intergalactic and intracluster medium. The jet activity is also believed to regulate the growth of massive galaxies via the AGN feedback. In this thesis I explore the intrinsic and extrinsic physical properties of the population of Fanaroff-Riley II (FR II) objects, i.e. their kinetic luminosities, lifetimes, and central densities of their environments. In particular, the radio and kinetic luminosity functions of these powerful radio sources are investigated using the complete, flux limited radio catalogues of 3CRR and BRL. I construct multidimensional Monte Carlo simulations using semi-analytical models of FR II source time evolution to create artificial samples of radio galaxies. Unlike previous studies, I compare radio luminosity functions found with both the observed and simulated data to explore the best-fitting fundamental source parameters. The Monte Carlo method presented here allows one to: (i) set better limits on the predicted fundamental parameters of which confidence intervals estimated over broad ranges are presented, and (ii) generate the most plausible underlying parent populations of these radio sources. Moreover, I allow the source physical properties to co-evolve with redshift, and I find that all the investigated parameters most likely undergo cosmological evolution; however these parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. Furthermore, since it has been suggested that low luminosity FR IIs may be distinct from their powerful equivalents, I attempt to investigate fundamental properties of a sample of low redshift, low radio luminosity density radio galaxies. Based on SDSS-FIRST-NVSS radio sample I construct a low frequency (325 MHz) sample of radio galaxies and attempt to explore the fundamental properties of these low luminosity radio sources. The results are discussed through comparison with the results from the powerful radio sources of the 3CRR and BRL samples. Finally, I investigate the total power injected by populations of these powerful radio sources at various cosmological epochs and discuss the significance of the impact of these sources on the evolving Universe. Remarkably, sets of two degenerate fundamental parameters, the kinetic luminosity and maximum lifetimes of radio sources, despite the degeneracy provide particularly robust estimates of the total power produced by FR IIs during their lifetimes. This can be also used for robust estimations of the quenching of the cooling flows in cluster of galaxies.

Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics

NASA Astrophysics Data System (ADS)

Arani, Babak M. S.; Mahmoudi, Mahdi; Lahti, Leo; González, Javier; Wit, Ernst C.

2018-06-01

Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

Estimation of the growth kinetics for the cooling crystallisation of paracetamol and ethanol solutions

NASA Astrophysics Data System (ADS)

Mitchell, Niall A.; Ó'Ciardhá, Clifford T.; Frawley, Patrick J.

2011-08-01

This work details the estimation of the growth kinetics of paracetamol in ethanol solutions for cooling crystallisation processes, by means of isothermal seeded batch experiments. The growth kinetics of paracetamol crystals were evaluated in isolation, with the growth rate assumed to be size independent. Prior knowledge of the Metastable Zone Width (MSZW) was required, so that supersaturation ratios of 1.7-1.1 could be induced in solution without the occurrence of nucleation. The technique involved the utilisation of two in-situ Process Analytical Techniques (PATs), with a Focused Beam Reflectance Measurement (FBRM ®) utilised to ensure that negligible nucleation occurred and an Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) probe employed for online monitoring of solute concentration. Initial Particle Size Distributions (PSDs) were used in conjunction with desupersaturation profiles to determine the growth rate as a function of temperature and supersaturation. Furthermore, the effects of seed loading and size on the crystal growth rate were investigated. A numerical model, incorporating the population balance equation and the method of moments, was utilised to describe the crystal growth process. Experimental parameters were compared to the model simulation, with the accuracy of the model validated by means of the final product PSDs and solute concentration.

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

Spectral Rate Theory for Two-State Kinetics

NASA Astrophysics Data System (ADS)

Prinz, Jan-Hendrik; Chodera, John D.; Noé, Frank

2014-02-01

Classical rate theories often fail in cases where the observable(s) or order parameter(s) used is a poor reaction coordinate or the observed signal is deteriorated by noise, such that no clear separation between reactants and products is possible. Here, we present a general spectral two-state rate theory for ergodic dynamical systems in thermal equilibrium that explicitly takes into account how the system is observed. The theory allows the systematic estimation errors made by standard rate theories to be understood and quantified. We also elucidate the connection of spectral rate theory with the popular Markov state modeling approach for molecular simulation studies. An optimal rate estimator is formulated that gives robust and unbiased results even for poor reaction coordinates and can be applied to both computer simulations and single-molecule experiments. No definition of a dividing surface is required. Another result of the theory is a model-free definition of the reaction coordinate quality. The reaction coordinate quality can be bounded from below by the directly computable observation quality, thus providing a measure allowing the reaction coordinate quality to be optimized by tuning the experimental setup. Additionally, the respective partial probability distributions can be obtained for the reactant and product states along the observed order parameter, even when these strongly overlap. The effects of both filtering (averaging) and uncorrelated noise are also examined. The approach is demonstrated on numerical examples and experimental single-molecule force-probe data of the p5ab RNA hairpin and the apo-myoglobin protein at low pH, focusing here on the case of two-state kinetics.

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. Funding: R01 CA136927.« less

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.

Motion prediction of a non-cooperative space target

NASA Astrophysics Data System (ADS)

Zhou, Bang-Zhao; Cai, Guo-Ping; Liu, Yun-Meng; Liu, Pan

2018-01-01

Capturing a non-cooperative space target is a tremendously challenging research topic. Effective acquisition of motion information of the space target is the premise to realize target capture. In this paper, motion prediction of a free-floating non-cooperative target in space is studied and a motion prediction algorithm is proposed. In order to predict the motion of the free-floating non-cooperative target, dynamic parameters of the target must be firstly identified (estimated), such as inertia, angular momentum and kinetic energy and so on; then the predicted motion of the target can be acquired by substituting these identified parameters into the Euler's equations of the target. Accurate prediction needs precise identification. This paper presents an effective method to identify these dynamic parameters of a free-floating non-cooperative target. This method is based on two steps, (1) the rough estimation of the parameters is computed using the motion observation data to the target, and (2) the best estimation of the parameters is found by an optimization method. In the optimization problem, the objective function is based on the difference between the observed and the predicted motion, and the interior-point method (IPM) is chosen as the optimization algorithm, which starts at the rough estimate obtained in the first step and finds a global minimum to the objective function with the guidance of objective function's gradient. So the speed of IPM searching for the global minimum is fast, and an accurate identification can be obtained in time. The numerical results show that the proposed motion prediction algorithm is able to predict the motion of the target.

Age and sex affect protein metabolism at protein intakes that span the range of adequacy: comparison of leucine kinetics and nitrogen balance data.

PubMed

Conley, Travis B; McCabe, George P; Lim, Eunjung; Yarasheski, Kevin E; Johnson, Craig A; Campbell, Wayne W

2013-04-01

Research suggests that changes in leucine oxidation (leuox) with feeding may reflect adult protein requirements. We evaluated this possibility by assessing the effects of age, sex, and different protein intakes on whole-body leucine kinetics and nitrogen balance. Thirty-four young (n=18, 22-46 years) and old (n=16, 63-81 years) men and women completed three 18-day trials with protein intakes of 0.50, 0.75 and 1.00 g protein·kg body weight(-1)·d(-1). Fasting and fed-state leucine kinetics were quantified on day 12 of each trial using a primed, constant infusion of L-[1-13C]leucine. Protein requirement was estimated using classical nitrogen balance measurements and calculations. Leucine kinetics parameters were influenced by age and sex across all protein intakes. With feeding, leuox increased more in old vs. young adults. Independent of age, fasting and fed-state leuox were lower, and net leucine balance (fasting+fed-state) was higher in women vs. men. Among all subjects and protein intakes, nitrogen balance was correlated with fed-state leuox (r=0.39), fed-state leucine balance (r=0.60), net leucine balance (r=0.49) and the change in leuox from the fasting to fed state (r=0.49) (P<.05 for all results). At the highest protein intake, the change in leuox with feeding was inversely correlated with protein requirement (r=-0.39). These findings indicate that leucine kinetics, especially leuox, reflect nitrogen balance-based estimates of the need for dietary protein and generally support the view that protein requirement is comparable between young and old adults. Copyright © 2013 Elsevier Inc. All rights reserved.

Age and sex affect protein metabolism at protein intakes that span the range of adequacy: comparison of leucine kinetics and nitrogen balance data☆

PubMed Central

Conley, Travis B.; McCabe, George P.; Lim, Eunjung; Yarasheski, Kevin E.; Johnson, Craig A.; Campbell, Wayne W.

2012-01-01

Research suggests that changes in leucine oxidation (leuox) with feeding may reflect adult protein requirements. We evaluated this possibility by assessing the effects of age, sex, and different protein intakes on whole-body leucine kinetics and nitrogen balance. Thirty-four young (n = 18, 22–46 years) and old (n= 16, 63–81 years) men and women completed three 18-day trials with protein intakes of 0.50, 0.75 and 1.00 g protein·kg body weight−1·d−1. Fasting and fed-state leucine kinetics were quantified on day 12 of each trial using a primed, constant infusion of L-[1-13C]leucine. Protein requirement was estimated using classical nitrogen balance measurements and calculations. Leucine kinetics parameters were influenced by age and sex across all protein intakes. With feeding, leuox increased more in old vs. young adults. Independent of age, fasting and fed-state leuox were lower, and net leucine balance (fasting+fed-state) was higher in women vs. men. Among all subjects and protein intakes, nitrogen balance was correlated with fed-state leuox (r=0.39), fed-state leucine balance (r=0.60), net leucine balance (r=0.49) and the change in leuox from the fasting to fed state (r=0.49) (P<.05 for all results). At the highest protein intake, the change in leuox with feeding was inversely correlated with protein requirement (r=−0.39). These findings indicate that leucine kinetics, especially leuox, reflect nitrogen balance-based estimates of the need for dietary protein and generally support the view that protein requirement is comparable between young and old adults. PMID:22841544

Uncertainty for calculating transport on Titan: A probabilistic description of bimolecular diffusion parameters

NASA Astrophysics Data System (ADS)

Plessis, S.; McDougall, D.; Mandt, K.; Greathouse, T.; Luspay-Kuti, A.

2015-11-01

Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's upper atmosphere. Our results show that, after propagating uncertainty through the Massman model, the uncertainty in molecular diffusion is highly correlated to temperature and we observe no noticeable correlation with pressure. We propagate the calibrated molecular diffusion estimate and associated uncertainty to obtain an estimate with uncertainty due to bimolecular diffusion for the methane molar fraction as a function of altitude. Results show that the uncertainty in methane abundance due to molecular diffusion is in general small compared to eddy diffusion and the chemical kinetics description. However, methane abundance is most sensitive to uncertainty in molecular diffusion above 1200 km where the errors are nontrivial and could have important implications for scientific research based on diffusion models in this altitude range.

A NIST Kinetic Data Base for PAH Reaction and Soot Particle Inception During Combusion

DTIC Science & Technology

2007-12-01

in Computational Fluid Dynamics (CFD) codes hat have lead to the capability of describing complex reactive flow problems and thus simulating... parameters . However in the absence of data estimates must be made. Since the chemistry of combustion is extremely complex and for proper description...118:381-389 9. Babushok, V. and Tsang, W., J. Prop. and Pwr . 20 (2004) 403-414. 10. . Fournet, R., Warth, V., Glaude, P.A., Battin-Leclerc, F

Estimations of ABL fluxes and other turbulence parameters from Doppler lidar data

NASA Technical Reports Server (NTRS)

Gal-Chen, Tzvi; Xu, Mei; Eberhard, Wynn

1989-01-01

Techniques for extraction boundary layer parameters from measurements of a short-pulse CO2 Doppler lidar are described. The measurements are those collected during the First International Satellites Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE). By continuously operating the lidar for about an hour, stable statistics of the radial velocities can be extracted. Assuming that the turbulence is horizontally homogeneous, the mean wind, its standard deviations, and the momentum fluxes were estimated. Spectral analysis of the radial velocities is also performed from which, by examining the amplitude of the power spectrum at the inertial range, the kinetic energy dissipation was deduced. Finally, using the statistical form of the Navier-Stokes equations, the surface heat flux is derived as the residual balance between the vertical gradient of the third moment of the vertical velocity and the kinetic energy dissipation. Combining many measurements would normally reduce the error provided that, it is unbiased and uncorrelated. The nature of some of the algorithms however, is such that, biased and correlated errors may be generated even though the raw measurements are not. Data processing procedures were developed that eliminate bias and minimize error correlation. Once bias and error correlations are accounted for, the large sample size is shown to reduce the errors substantially. The principal features of the derived turbulence statistics for two case studied are presented.

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.

Investigation of the first-order phase transition kinetics using the method of pulsed photothermal surface deformation: radial measurements

NASA Astrophysics Data System (ADS)

Vintzentz, S. V.; Sandomirsky, V. B.

1992-09-01

An extension of the photothermal surface deformation (PTSD) method to study the macroscopic kinetics of the first-order phase transition (PTr) is given. The movement of the phase interface (PI) over a surface with a PTr locally induced in the subsurface volume by a focused laser pulse is investigated for the first time using radial measurements of the PTSD kinetics. For the known metal-to-semiconductor PTr in VO 2 (a good model system) a procedure is suggested for measuring the maximum size rsm of the "hot" (metal) phase on the surface (a parameter most difficult to determine) as well as for estimating the velocity of the PI movement over the surface, vs, and in the bulk, vb. Besides, it is shown that the PTSD method may be used to determine the "local" threshold energy E0 needed for the laser-induced PTr and the "local" latent heat L of the PTr. This demonstrates the feasibility of scanning surface E0- and L-microscopy.

Combustion and kinetic parameters estimation of torrefied pine, acacia and Miscanthus giganteus using experimental and modelling techniques.

PubMed

Wilk, Małgorzata; Magdziarz, Aneta; Gajek, Marcin; Zajemska, Monika; Jayaraman, Kandasamy; Gokalp, Iskender

2017-11-01

A novel approach, linking both experiments and modelling, was applied to obtain a better understanding of combustion characteristics of torrefied biomass. Therefore, Pine, Acacia and Miscanthus giganteus have been investigated under 260°C, 1h residence time and argon atmosphere. A higher heating value and carbon content corresponding to a higher fixed carbon, lower volatile matter, moisture content, and ratio O/C were obtained for all torrefied biomass. TGA analysis was used in order to proceed with the kinetics study and Chemkin calculations. The kinetics analysis demonstrated that the torrefaction process led to a decrease in Ea compared to raw biomass. The average Ea of pine using the KAS method changed from 169.42 to 122.88kJ/mol. The changes in gaseous products of combustion were calculated by Chemkin, which corresponded with the TGA results. The general conclusion based on these investigations is that torrefaction improves the physical and chemical properties of biomass. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mathematical modeling of enzyme production using Trichoderma harzianum P49P11 and sugarcane bagasse as carbon source.

PubMed

Gelain, Lucas; da Cruz Pradella, José Geraldo; da Costa, Aline Carvalho

2015-12-01

A mathematical model to describe the kinetics of enzyme production by the filamentous fungus Trichoderma harzianum P49P11 was developed using a low cost substrate as main carbon source (pretreated sugarcane bagasse). The model describes the cell growth, variation of substrate concentration and production of three kinds of enzymes (cellulases, beta-glucosidase and xylanase) in different sugarcane bagasse concentrations (5; 10; 20; 30; 40 gL(-1)). The 10 gL(-1) concentration was used to validate the model and the other to parameter estimation. The model for enzyme production has terms implicitly representing induction and repression. Substrate variation was represented by a simple degradation rate. The models seem to represent well the kinetics with a good fit for the majority of the assays. Validation results indicate that the models are adequate to represent the kinetics for a biotechnological process. Copyright © 2015 Elsevier Ltd. All rights reserved.

The comparative kinetic analysis of Acetocell and Lignoboost® lignin pyrolysis: the estimation of the distributed reactivity models.

PubMed

Janković, Bojan

2011-10-01

The non-isothermal pyrolysis kinetics of Acetocell (the organosolv) and Lignoboost® (kraft) lignins, in an inert atmosphere, have been studied by thermogravimetric analysis. Using isoconversional analysis, it was concluded that the apparent activation energy for all lignins strongly depends on conversion, showing that the pyrolysis of lignins is not a single chemical process. It was identified that the pyrolysis process of Acetocell and Lignoboost® lignin takes place over three reaction steps, which was confirmed by appearance of the corresponding isokinetic relationships (IKR). It was found that major pyrolysis stage of both lignins is characterized by stilbene pyrolysis reactions, which were subsequently followed by decomposition reactions of products derived from the stilbene pyrolytic process. It was concluded that non-isothermal pyrolysis of Acetocell and Lignoboost® lignins can be best described by n-th (n>1) reaction order kinetics, using the Weibull mixture model (as distributed reactivity model) with alternating shape parameters. Copyright © 2011 Elsevier Ltd. All rights reserved.

Removal of ammonium ions by laboratory-synthesized zeolite linde type A adsorption from water samples affected by mining activities in Ghana.

PubMed

Kwakye-Awuah, Bright; Labik, Linus Kweku; Nkrumah, Isaac; Williams, Craig

2014-03-01

Ammonium ion adsorption by laboratory-synthesized zeolite (linde type A; LTA) was investigated in batch kinetics experiments. Synthesized zeolite LTA was characterized by X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, thermogravimetric analysis, Fourier transform infrared spectroscopy and particle size analysis. Water samples were taken from the Nyam and Tano rivers in Ghana, and 0.8 g of zeolite was added to 100 ml portions of each sample. Portions of the samples were withdrawn every 30 min for 150 min and the concentration of ammonia in each sample was determined. The removal efficiency of zeolite LTA was evaluated by retrieving the zeolite from the water samples and adding to a fresh sample to repeat the process. Equilibrium data were fitted by Langmuir and Freundlich isotherms. Maximum adsorption capacities were 72.99 mg g(-1) for samples from the River Nyam and 72.87 mg g(-1) for samples from the River Tano. The equilibrium kinetic data were analysed using adsorption kinetic models: pseudo-first order and pseudo-second order kinetic models. Linear regression was used to estimate the adsorption and kinetic parameters. The results showed that the adsorption followed pseudo-second order kinetics and suggest that zeolite LTA is a good adsorbent for the removal of nitrogen ammonia from water.

Characterization of breast lesion using T1-perfusion magnetic resonance imaging: Qualitative vs. quantitative analysis.

PubMed

Thakran, S; Gupta, P K; Kabra, V; Saha, I; Jain, P; Gupta, R K; Singh, A

2018-06-14

The objective of this study was to quantify the hemodynamic parameters using first pass analysis of T 1 -perfusion magnetic resonance imaging (MRI) data of human breast and to compare these parameters with the existing tracer kinetic parameters, semi-quantitative and qualitative T 1 -perfusion analysis in terms of lesion characterization. MRI of the breast was performed in 50 women (mean age, 44±11 [SD] years; range: 26-75) years with a total of 15 benign and 35 malignant breast lesions. After pre-processing, T 1 -perfusion MRI data was analyzed using qualitative approach by two radiologists (visual inspection of the kinetic curve into types I, II or III), semi-quantitative (characterization of kinetic curve types using empirical parameters), generalized-tracer-kinetic-model (tracer kinetic parameters) and first pass analysis (hemodynamic-parameters). Chi-squared test, t-test, one-way analysis-of-variance (ANOVA) using Bonferroni post-hoc test and receiver-operating-characteristic (ROC) curve were used for statistical analysis. All quantitative parameters except leakage volume (Ve), qualitative (type-I and III) and semi-quantitative curves (type-I and III) provided significant differences (P<0.05) between benign and malignant lesions. Kinetic parameters, particularly volume transfer coefficient (K trans ) provided a significant difference (P<0.05) between all grades except grade-II vs III. The hemodynamic parameter (relative-leakage-corrected-breast-blood-volume [rBBVcorr) provided a statistically significant difference (P<0.05) between all grades. It also provided highest sensitivity and specificity among all parameters in differentiation between different grades of malignant breast lesions. Quantitative parameters, particularly rBBVcorr and K trans provided similar sensitivity and specificity in differentiating benign from malignant breast lesions for this cohort. Moreover, rBBVcorr provided better differentiation between different grades of malignant breast lesions among all the parameters. Copyright © 2018. Published by Elsevier Masson SAS.

Generic Schemes for Single-Molecule Kinetics. 2: Information Content of the Poisson Indicator.

PubMed

Avila, Thomas R; Piephoff, D Evan; Cao, Jianshu

2017-08-24

Recently, we described a pathway analysis technique (paper 1) for analyzing generic schemes for single-molecule kinetics based upon the first-passage time distribution. Here, we employ this method to derive expressions for the Poisson indicator, a normalized measure of stochastic variation (essentially equivalent to the Fano factor and Mandel's Q parameter), for various renewal (i.e., memoryless) enzymatic reactions. We examine its dependence on substrate concentration, without assuming all steps follow Poissonian kinetics. Based upon fitting to the functional forms of the first two waiting time moments, we show that, to second order, the non-Poissonian kinetics are generally underdetermined but can be specified in certain scenarios. For an enzymatic reaction with an arbitrary intermediate topology, we identify a generic minimum of the Poisson indicator as a function of substrate concentration, which can be used to tune substrate concentration to the stochastic fluctuations and to estimate the largest number of underlying consecutive links in a turnover cycle. We identify a local maximum of the Poisson indicator (with respect to substrate concentration) for a renewal process as a signature of competitive binding, either between a substrate and an inhibitor or between multiple substrates. Our analysis explores the rich connections between Poisson indicator measurements and microscopic kinetic mechanisms.

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. Copyright © 2018 Elsevier Ltd. All rights reserved.

Kinetic analysis of non-isothermal solid-state reactions: multi-stage modeling without assumptions in the reaction mechanism.

PubMed

Pomerantsev, Alexey L; Kutsenova, Alla V; Rodionova, Oxana Ye

2017-02-01

A novel non-linear regression method for modeling non-isothermal thermogravimetric data is proposed. Experiments for several heating rates are analyzed simultaneously. The method is applicable to complex multi-stage processes when the number of stages is unknown. Prior knowledge of the type of kinetics is not required. The main idea is a consequent estimation of parameters when the overall model is successively changed from one level of modeling to another. At the first level, the Avrami-Erofeev functions are used. At the second level, the Sestak-Berggren functions are employed with the goal to broaden the overall model. The method is tested using both simulated and real-world data. A comparison of the proposed method with a recently published 'model-free' deconvolution method is presented.

Evolution of a terrestrial magma ocean: Thermodynamics, kinetics, rheology, convection, differentiation

NASA Technical Reports Server (NTRS)

Solomatov, V. S.; Stevenson, D. J.

1992-01-01

The evolution of an initially totally molten magma ocean is constrained on the basis of analysis of various physical problems in the magma ocean. First of all an equilibrium thermodynamics of the magma ocean is developed in the melting temperature range. The equilibrium thermodynamical parameters are found as functions only of temperature and pressure and are used in the subsequent models of kinetics and convection. Kinematic processes determine the crystal size and also determine a non-equilibrium thermodynamics of the system. Rheology controls all dynamical regimes of the magma ocean. The thermal convection models for different rheological laws are developed for both the laminar convection and for turbulent convection in the case of equilibrium thermodynamics of the multiphase system. The evolution is estimated on the basis of all the above analysis.

Metronidazole removal in powder-activated carbon and concrete-containing graphene adsorption systems: Estimation of kinetic, equilibrium and thermodynamic parameters and optimization of adsorption by a central composite design.

PubMed

Manjunath, S V; Kumar, S Mathava; Ngo, Huu Hao; Guo, Wenshan

2017-12-06

Metronidazole (MNZ) removal by two adsorbents, i.e., concrete-containing graphene (CG) and powder-activated carbon (PAC), was investigated via batch-mode experiments and the outcomes were used to analyze the kinetics, equilibrium and thermodynamics of MNZ adsorption. MNZ sorption on CG and PAC has followed the pseudo-second-order kinetic model, and the thermodynamic parameters revealed that MNZ adsorption was spontaneous on PAC and non-spontaneous on CG. Subsequently, two-parameter isotherm models, i.e., Langmuir, Freundlich, Temkin, Dubinin-Radushkevich and Elovich models, were applied to evaluate the MNZ adsorption capacity. The maximum MNZ adsorption capacities ([Formula: see text]) of PAC and CG were found to be between 25.5-32.8 mg/g and 0.41-0.002 mg/g, respectively. Subsequently, the effects of pH, temperature and adsorbent dosage on MNZ adsorption were evaluated by a central composite design (CCD) approach. The CCD experiments have pointed out the complete removal of MNZ at a much lower PAC dosage by increasing the system temperature (i.e., from 20°C to 40°C). On the other hand, a desorption experiment has shown 3.5% and 1.7% MNZ removal from the surface of PAC and CG, respectively, which was insignificant compared to the sorbed MNZ on the surface by adsorption. The overall findings indicate that PAC and CG with higher graphene content could be useful in MNZ removal from aqueous systems.

Phenol biodegradation by immobilized Pseudomonas putida FNCC-0071 cells in alginate beads

NASA Astrophysics Data System (ADS)

Hakim, Lukman Nul; Rochmadi, Sutijan

2017-06-01

Phenol is one of industrial liquid waste which is harmful to the environment, so it must be degraded. It can be degraded by immobilized Pseudomonas putida FNCC-0071 cells. It needs the kinetics and mass transfer data to design this process which can be estimated by the proposed dynamic model in this study. This model involves simultaneous diffusion and reaction in the alginate bead and liquid bulk. The preliminary stage of phenol biodegradation process was acclimatization cells. This is the stage where cells were acclimated to phenol as carbon source (substrate). Then the acclimated cells were immobilized in alginate beads by extrusion method. The variation of the initial phenol concentration in the solution is 350 to 850 ppm where 60 g alginate bead contained by cells loaded into its solution in reactor batch, so then biodegradation occurs. In this study, the average radius of alginate bead was 0.152 cm. The occurred kinetic reaction process can be explained by Blanch kinetic model with the decreasing of parameter μmax' while the increasing values of initial phenol concentration in the same time, but the parameters KM, KM', and kt were increasing by the rising values of initial phenol concentration. The value of the parameter β is almost zero. Effective diffusivity of phenol and cells are 1.11 × 10-5±4.5% cm2 s-1 and 1.39 × 10-7± 0.04% cm2 s-1. The partition coefficient of phenol and cells are 0.39 ± 15% and 2.22 ± 18%.

A SCR Model Calibration Approach with Spatially Resolved Measurements and NH 3 Storage Distributions

DOE PAGES

Song, Xiaobo; Parker, Gordon G.; Johnson, John H.; ...

2014-11-27

The selective catalytic reduction (SCR) is a technology used for reducing NO x emissions in the heavy-duty diesel (HDD) engine exhaust. In this study, the spatially resolved capillary inlet infrared spectroscopy (Spaci-IR) technique was used to study the gas concentration and NH 3 storage distributions in a SCR catalyst, and to provide data for developing a SCR model to analyze the axial gaseous concentration and axial distributions of NH 3 storage. A two-site SCR model is described for simulating the reaction mechanisms. The model equations and a calculation method was developed using the Spaci-IR measurements to determine the NH 3more » storage capacity and the relationships between certain kinetic parameters of the model. Moreover, a calibration approach was then applied for tuning the kinetic parameters using the spatial gaseous measurements and calculated NH3 storage as a function of axial position instead of inlet and outlet gaseous concentrations of NO, NO 2, and NH 3. The equations and the approach for determining the NH 3 storage capacity of the catalyst and a method of dividing the NH 3 storage capacity between the two storage sites are presented. It was determined that the kinetic parameters of the adsorption and desorption reactions have to follow certain relationships for the model to simulate the experimental data. Finally, the modeling results served as a basis for developing full model calibrations to SCR lab reactor and engine data and state estimator development as described in the references (Song et al. 2013a, b; Surenahalli et al. 2013).« less

Assimilation of Biophysical Neuronal Dynamics in Neuromorphic VLSI.

PubMed

Wang, Jun; Breen, Daniel; Akinin, Abraham; Broccard, Frederic; Abarbanel, Henry D I; Cauwenberghs, Gert

2017-12-01

Representing the biophysics of neuronal dynamics and behavior offers a principled analysis-by-synthesis approach toward understanding mechanisms of nervous system functions. We report on a set of procedures assimilating and emulating neurobiological data on a neuromorphic very large scale integrated (VLSI) circuit. The analog VLSI chip, NeuroDyn, features 384 digitally programmable parameters specifying for 4 generalized Hodgkin-Huxley neurons coupled through 12 conductance-based chemical synapses. The parameters also describe reversal potentials, maximal conductances, and spline regressed kinetic functions for ion channel gating variables. In one set of experiments, we assimilated membrane potential recorded from one of the neurons on the chip to the model structure upon which NeuroDyn was designed using the known current input sequence. We arrived at the programmed parameters except for model errors due to analog imperfections in the chip fabrication. In a related set of experiments, we replicated songbird individual neuron dynamics on NeuroDyn by estimating and configuring parameters extracted using data assimilation from intracellular neural recordings. Faithful emulation of detailed biophysical neural dynamics will enable the use of NeuroDyn as a tool to probe electrical and molecular properties of functional neural circuits. Neuroscience applications include studying the relationship between molecular properties of neurons and the emergence of different spike patterns or different brain behaviors. Clinical applications include studying and predicting effects of neuromodulators or neurodegenerative diseases on ion channel kinetics.

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches

PubMed Central

Guedich, Sondés; Puffer-Enders, Barbara; Baltzinger, Mireille; Hoffmann, Guillaume; Da Veiga, Cyrielle; Jossinet, Fabrice; Thore, Stéphane; Bec, Guillaume; Ennifar, Eric; Burnouf, Dominique; Dumas, Philippe

2016-01-01

ABSTRACT Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations. PMID:26932506

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches.

PubMed

Guedich, Sondés; Puffer-Enders, Barbara; Baltzinger, Mireille; Hoffmann, Guillaume; Da Veiga, Cyrielle; Jossinet, Fabrice; Thore, Stéphane; Bec, Guillaume; Ennifar, Eric; Burnouf, Dominique; Dumas, Philippe

2016-01-01

Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.

Kinetic modeling of electron transfer reactions in photosystem I complexes of various structures with substituted quinone acceptors.

PubMed

Milanovsky, Georgy E; Petrova, Anastasia A; Cherepanov, Dmitry A; Semenov, Alexey Yu

2017-09-01

The reduction kinetics of the photo-oxidized primary electron donor P 700 in photosystem I (PS I) complexes from cyanobacteria Synechocystis sp. PCC 6803 were analyzed within the kinetic model, which considers electron transfer (ET) reactions between P 700 , secondary quinone acceptor A 1 , iron-sulfur clusters and external electron donor and acceptors - methylviologen (MV), 2,3-dichloro-naphthoquinone (Cl 2 NQ) and oxygen. PS I complexes containing various quinones in the A 1 -binding site (phylloquinone PhQ, plastoquinone-9 PQ and Cl 2 NQ) as well as F X -core complexes, depleted of terminal iron-sulfur F A /F B clusters, were studied. The acceleration of charge recombination in F X -core complexes by PhQ/PQ substitution indicates that backward ET from the iron-sulfur clusters involves quinone in the A 1 -binding site. The kinetic parameters of ET reactions were obtained by global fitting of the P 700 + reduction with the kinetic model. The free energy gap ΔG 0 between F X and F A /F B clusters was estimated as -130 meV. The driving force of ET from A 1 to F X was determined as -50 and -220 meV for PhQ in the A and B cofactor branches, respectively. For PQ in A 1A -site, this reaction was found to be endergonic (ΔG 0  = +75 meV). The interaction of PS I with external acceptors was quantitatively described in terms of Michaelis-Menten kinetics. The second-order rate constants of ET from F A /F B , F X and Cl 2 NQ in the A 1 -site of PS I to external acceptors were estimated. The side production of superoxide radical in the A 1 -site by oxygen reduction via the Mehler reaction might comprise ≥0.3% of the total electron flow in PS I.

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

Garcia, Andres

Transport and reaction in zeolites and other porous materials, such as mesoporous silica particles, has been a focus of interest in recent years. This is in part due to the possibility of anomalous transport effects (e.g. single-file diffusion) and its impact in the reaction yield in catalytic processes. Computational simulations are often used to study these complex nonequilibrium systems. Computer simulations using Molecular Dynamics (MD) techniques are prohibitive, so instead coarse grained one-dimensional models with the aid of Kinetic Monte Carlo (KMC) simulations are used. Both techniques can be computationally expensive, both time and resource wise. These coarse-grained systems canmore » be exactly described by a set of coupled stochastic master equations, that describe the reaction-diffusion kinetics of the system. The equations can be written exactly, however, coupling between the equations and terms within the equations make it impossible to solve them exactly; approximations must be made. One of the most common methods to obtain approximate solutions is to use Mean Field (MF) theory. MF treatments yield reasonable results at high ratios of reaction rate k to hop rate h of the particles, but fail completely at low k=h due to the over-estimation of fluxes of particles within the pore. We develop a method to estimate fluxes and intrapore diffusivity in simple one- dimensional reaction-diffusion models at high and low k=h, where the pores are coupled to an equilibrated three-dimensional fluid. We thus successfully describe analytically these simple reaction-diffusion one-dimensional systems. Extensions to models considering behavior with long range steric interactions and wider pores require determination of multiple boundary conditions. We give a prescription to estimate the required parameters for these simulations. For one dimensional systems, if single-file diffusion is relaxed, additional parameters to describe particle exchange have to be introduced. We use Langevin Molecular Dynamics (MD) simulations to assess these parameters.« less

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 identification that assumes that FDG blood input in the brain can be modeled as a function of time and several parameters (IFM) is analyzed also. Nonuniform sampling SLS (NSLS) is developed due to the rapid change of the FDG concentration in the blood during the early postinjection stage. Comparisons of accuracy of EVAM, SLS, NSLS and IFM identification techniques are made.

Synthesis and Characterization of Liquid Crystalline Epoxy Resins

DTIC Science & Technology

2014-01-01

Temperature dependence of the four parameters in the Burgers model. ......... 81 Figure 4.7 Dependence of creep compliance on creep time at different...Kinetic parameters for LCERs. ......................................................................... 65 Table 3.4 Kinetic parameters for non-LCERs...curing in a high strength magnetic field. The orientation was quantified by an orientation parameter determined with two-dimensional X-ray diffraction

A case study of real-time monitoring of solid-state phase transformations in acoustically levitated particles using near infrared and Raman spectroscopy.

PubMed

Rehder, Sönke; Wu, Jian X; Laackmann, Julian; Moritz, Hans-Ulrich; Rantanen, Jukka; Rades, Thomas; Leopold, Claudia S

2013-01-23

The objective of this study was to monitor the amorphous-to-crystalline solid-state phase transformation kinetics of the model drug ibuprofen with spectroscopic methods during acoustic levitation. Chemical and physical information was obtained by real-time near infrared (NIRS) and Raman spectroscopy measurements. The recrystallisation kinetic parameters (overall recrystallisation rate constant β and the time needed to reach 50% of the equilibrated level t(50)), were determined using a multivariate curve resolution approach. The acoustic levitation device coupled with non-invasive spectroscopy enabled monitoring of the recrystallisation process of the difficult-to-handle (adhesive) amorphous sample. The application of multivariate curve resolution enabled isolation of the underlying pure spectra, which corresponded well with the reference spectra of amorphous and crystalline ibuprofen. The recrystallisation kinetic parameters were estimated from the recrystallisation profiles. While the empirical recrystallisation rate constant determined by NIR and Raman spectroscopy were comparable, the lag time for recrystallisation was significantly lower with Raman spectroscopy as compared to NIRS. This observation was explained by the high energy density of the Raman laser beam, which might have led to local heating effects of the sample and thus reduced the recrystallisation onset time. It was concluded that acoustic levitation with NIR and Raman spectroscopy combined with multivariate curve resolution allowed direct determination of the recrystallisation kinetics of amorphous drugs and thus is a promising technique for monitoring solid-state phase transformations of adhesive small-sized samples during the early phase of drug development. Copyright © 2012 Elsevier B.V. All rights reserved.

Tracer kinetic modelling for DCE-MRI quantification of subtle blood-brain barrier permeability.

PubMed

Heye, Anna K; Thrippleton, Michael J; Armitage, Paul A; Valdés Hernández, Maria Del C; Makin, Stephen D; Glatz, Andreas; Sakka, Eleni; Wardlaw, Joanna M

2016-01-15

There is evidence that subtle breakdown of the blood-brain barrier (BBB) is a pathophysiological component of several diseases, including cerebral small vessel disease and some dementias. Dynamic contrast-enhanced MRI (DCE-MRI) combined with tracer kinetic modelling is widely used for assessing permeability and perfusion in brain tumours and body tissues where contrast agents readily accumulate in the extracellular space. However, in diseases where leakage is subtle, the optimal approach for measuring BBB integrity is likely to differ since the magnitude and rate of enhancement caused by leakage are extremely low; several methods have been reported in the literature, yielding a wide range of parameters even in healthy subjects. We hypothesised that the Patlak model is a suitable approach for measuring low-level BBB permeability with low temporal resolution and high spatial resolution and brain coverage, and that normal levels of scanner instability would influence permeability measurements. DCE-MRI was performed in a cohort of mild stroke patients (n=201) with a range of cerebral small vessel disease severity. We fitted these data to a set of nested tracer kinetic models, ranking their performance according to the Akaike information criterion. To assess the influence of scanner drift, we scanned 15 healthy volunteers that underwent a "sham" DCE-MRI procedure without administration of contrast agent. Numerical simulations were performed to investigate model validity and the effect of scanner drift. The Patlak model was found to be most appropriate for fitting low-permeability data, and the simulations showed vp and K(Trans) estimates to be reasonably robust to the model assumptions. However, signal drift (measured at approximately 0.1% per minute and comparable to literature reports in other settings) led to systematic errors in calculated tracer kinetic parameters, particularly at low permeabilities. Our findings justify the growing use of the Patlak model in low-permeability states, which has the potential to provide valuable information regarding BBB integrity in a range of diseases. However, absolute values of the resulting tracer kinetic parameters should be interpreted with extreme caution, and the size and influence of signal drift should be measured where possible. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Tracer kinetic modelling for DCE-MRI quantification of subtle blood–brain barrier permeability

PubMed Central

Heye, Anna K.; Thrippleton, Michael J.; Armitage, Paul A.; Valdés Hernández, Maria del C.; Makin, Stephen D.; Glatz, Andreas; Sakka, Eleni; Wardlaw, Joanna M.

2016-01-01

There is evidence that subtle breakdown of the blood–brain barrier (BBB) is a pathophysiological component of several diseases, including cerebral small vessel disease and some dementias. Dynamic contrast-enhanced MRI (DCE-MRI) combined with tracer kinetic modelling is widely used for assessing permeability and perfusion in brain tumours and body tissues where contrast agents readily accumulate in the extracellular space. However, in diseases where leakage is subtle, the optimal approach for measuring BBB integrity is likely to differ since the magnitude and rate of enhancement caused by leakage are extremely low; several methods have been reported in the literature, yielding a wide range of parameters even in healthy subjects. We hypothesised that the Patlak model is a suitable approach for measuring low-level BBB permeability with low temporal resolution and high spatial resolution and brain coverage, and that normal levels of scanner instability would influence permeability measurements. DCE-MRI was performed in a cohort of mild stroke patients (n = 201) with a range of cerebral small vessel disease severity. We fitted these data to a set of nested tracer kinetic models, ranking their performance according to the Akaike information criterion. To assess the influence of scanner drift, we scanned 15 healthy volunteers that underwent a “sham” DCE-MRI procedure without administration of contrast agent. Numerical simulations were performed to investigate model validity and the effect of scanner drift. The Patlak model was found to be most appropriate for fitting low-permeability data, and the simulations showed vp and KTrans estimates to be reasonably robust to the model assumptions. However, signal drift (measured at approximately 0.1% per minute and comparable to literature reports in other settings) led to systematic errors in calculated tracer kinetic parameters, particularly at low permeabilities. Our findings justify the growing use of the Patlak model in low-permeability states, which has the potential to provide valuable information regarding BBB integrity in a range of diseases. However, absolute values of the resulting tracer kinetic parameters should be interpreted with extreme caution, and the size and influence of signal drift should be measured where possible. PMID:26477653

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.

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.

Effect of temperature on Brettanomyces bruxellensis: metabolic and kinetic aspects.

PubMed

Brandam, Cédric; Castro-Martínez, Claudia; Délia, Marie-Line; Ramón-Portugal, Felipe; Strehaiano, Pierre

2008-01-01

The effect of temperatures ranging from 15 to 35 degrees C on a culture of Brettanomyces bruxellensis was investigated in regards to thermodynamics, metabolism, and kinetics. In this temperature range, we observed an increase in growth and production rates. The growth behavior was well represented using the Arrhenius model, and an apparent activation energy of 16.61 kcal/mol was estimated. A stuck fermentation was observed at 35 degrees C as represented by high cell death. The carbon balance established that temperature had no effect on repartition of the glucose consumption between biomass and products. Hence, the same biomass concentration was obtained for all temperatures, except at 35 degrees C. Moreover, using logistic and Luedeking-Piret models, we demonstrated that production rates of ethanol and acetic acid were partially growth associated. Parameters associated with growth (alpha eth and alpha aa) remained constant with changing temperature, whereas, parameters associated with the population (beta eth and beta aa) varied. Optimal values were obtained at 32 degrees C for ethanol and at 25 degrees C for acetic acid.

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

Experimental and theoretical studies of the thermal behavior of titanium dioxide-SnO2 based composites.

PubMed

Voga, G P; Coelho, M G; de Lima, G M; Belchior, J C

2011-04-07

In this paper we report experimental and theoretical studies concerning the thermal behavior of some organotin-Ti(IV) oxides employed as precursors for TiO(2)/SnO(2) semiconducting based composites, with photocatalytic properties. The organotin-TiO(2) supported materials were obtained by chemical reactions of SnBu(3)Cl (Bu = butyl), TiCl(4) with NH(4)OH in ethanol, in order to impregnate organotin oxide in a TiO(2) matrix. A theoretical model was developed to support experimental procedures. The kinetics parameters: frequency factor (A), activation energy, and reaction order (n) can be estimated through artificial intelligence methods. Genetic algorithm, fuzzy logic, and Petri neural nets were used in order to determine the kinetic parameters as a function of temperature. With this in mind, three precursors were prepared in order to obtain composites with Sn/TiO(2) ratios of 0% (1), 15% (2), and 30% (3) in weight, respectively. The thermal behavior of products (1-3) was studied by thermogravimetric experiments in oxygen.

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.

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

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

PubMed

Liu, Kuan-Miao; Liu, Kuan-Ju

2016-01-01

Enzymatic syntheses of fatty acid anilides are important owing to their wide range of industrial applications in detergents, shampoo, cosmetics, and surfactant formulations. The amidation reaction of Mucor miehei lipase Lipozyme IM20 was investigated for direct amidation of triacylglycerol in organic solvents. The process parameters (reaction temperature, substrate molar ratio, enzyme amount) were optimized to achieve the highest yield of anilide. The maximum yield of palmitanilide (88.9%) was achieved after 24 h of reaction at 40 °C at an enzyme concentration of 1.4% (70 mg). Kinetics of lipase-catalyzed amidation of aniline with tripalmitin has been investigated. The reaction rate could be described in terms of the Michaelis-Menten equation with a Ping-Pong Bi-Bi mechanism and competitive inhibition by both the substrates. The kinetic constants were estimated by using non-linear regression method using enzyme kinetic modules. The enzyme operational stability study showed that Lipozyme IM20 retained 38.1% of the initial activity for the synthesis of palmitanilide (even after repeated use for 48 h). Palmitanilide, a fatty acid amide, exhibited potent antimicrobial activity toward Bacillus cereus. Copyright © 2015 Elsevier Inc. All rights reserved.

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.

Kinetic approach to the study of froth flotation applied to a lepidolite ore

NASA Astrophysics Data System (ADS)

Vieceli, Nathália; Durão, Fernando O.; Guimarães, Carlos; Nogueira, Carlos A.; Pereira, Manuel F. C.; Margarido, Fernanda

2016-07-01

The number of published studies related to the optimization of lithium extraction from low-grade ores has increased as the demand for lithium has grown. However, no study related to the kinetics of the concentration stage of lithium-containing minerals by froth flotation has yet been reported. To establish a factorial design of batch flotation experiments, we conducted a set of kinetic tests to determine the most selective alternative collector, define a range of pulp pH values, and estimate a near-optimum flotation time. Both collectors (Aeromine 3000C and Armeen 12D) provided the required flotation selectivity, although this selectivity was lost in the case of pulp pH values outside the range between 2 and 4. Cumulative mineral recovery curves were used to adjust a classical kinetic model that was modified with a non-negative parameter representing a delay time. The computation of the near-optimum flotation time as the maximizer of a separation efficiency (SE) function must be performed with caution. We instead propose to define the near-optimum flotation time as the time interval required to achieve 95%-99% of the maximum value of the SE function.

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 would occur during natural maturation. Kinetic parameters derived from hydrous pyrolysis show good correlations with one another (compensation effect) and kerogen organic-sulfur contents. These correlations allow for indirect determination of hydrous-pyrolysis kinetic parameters on the basis of the organic-sulfur mole fraction of an immature Type-II or -IIS kerogen. ?? 2006 Elsevier Inc. All rights reserved.

Skin friction and heat transfer correlations for high-speed low-density flow past a flat plate

NASA Technical Reports Server (NTRS)

Woronowicz, Michael S.; Baganoff, Donald

1991-01-01

The independent and dependent variables associated with drag and heat transfer to a flat plate at zero incidence in high-speed, rarefied flow are analyzed anew to reflect the importance of kinetic effects occurring near the plate surface on energy and momentum transfer, rather than following arguments normally used to describe continuum, higher density flowfields. A new parameter, the wall Knudsen number Knx,w, based on an estimate of the mean free path length of molecules having just interacted with the surface of the plate, is introduced and used to correlate published drag and heat transfer data. The new parameter is shown to provide better correlation than either the viscous interaction parameter X or the widely-used slip parameter Voo for drag and heat transfer data over a wide range of Mach numbers, Reynolds numbers, and plate-to-freestream stagnation temperature ratios.

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

PubMed Central

Golightly, Andrew; Wilkinson, Darren J.

2011-01-01

Computational systems biology is concerned with the development of detailed mechanistic models of biological processes. Such models are often stochastic and analytically intractable, containing uncertain parameters that must be estimated from time course data. In this article, we consider the task of inferring the parameters of a stochastic kinetic model defined as a Markov (jump) process. Inference for the parameters of complex nonlinear multivariate stochastic process models is a challenging problem, but we find here that algorithms based on particle Markov chain Monte Carlo turn out to be a very effective computationally intensive approach to the problem. Approximations to the inferential model based on stochastic differential equations (SDEs) are considered, as well as improvements to the inference scheme that exploit the SDE structure. We apply the methodology to a Lotka–Volterra system and a prokaryotic auto-regulatory network. PMID:23226583

Tracer kinetics of forearm endothelial function: comparison of an empirical method and a quantitative modeling technique.

PubMed

Zhao, Xueli; Arsenault, Andre; Lavoie, Kim L; Meloche, Bernard; Bacon, Simon L

2007-01-01

Forearm Endothelial Function (FEF) is a marker that has been shown to discriminate patients with cardiovascular disease (CVD). FEF has been assessed using several parameters: the Rate of Uptake Ratio (RUR), EWUR (Elbow-to-Wrist Uptake Ratio) and EWRUR (Elbow-to-Wrist Relative Uptake Ratio). However, the modeling functions of FEF require more robust models. The present study was designed to compare an empirical method with quantitative modeling techniques to better estimate the physiological parameters and understand the complex dynamic processes. The fitted time activity curves of the forearms, estimating blood and muscle components, were assessed using both an empirical method and a two-compartment model. Although correlational analyses suggested a good correlation between the methods for RUR (r=.90) and EWUR (r=.79), but not EWRUR (r=.34), Altman-Bland plots found poor agreement between the methods for all 3 parameters. These results indicate that there is a large discrepancy between the empirical and computational method for FEF. Further work is needed to establish the physiological and mathematical validity of the 2 modeling methods.

Evaluation and simulation of nitrogen mineralization of paddy soils in Mollisols area of Northeast China under waterlogged incubation

PubMed Central

Zhang, Yuling; Xu, Wenjing; Duan, Pengpeng; Cong, Yaohui; An, Tingting; Yu, Na; Zou, Hongtao; Dang, Xiuli; An, Jing; Fan, Qingfeng; Zhang, Yulong

2017-01-01

Background Understanding the nitrogen (N) mineralization process and applying appropriate model simulation are key factors in evaluating N mineralization. However, there are few studies of the N mineralization characteristics of paddy soils in Mollisols area of Northeast China. Materials and methods The soils were sampled from the counties of Qingan and Huachuan, which were located in Mollisols area of Northeast China. The sample soil was incubated under waterlogged at 30°C in a controlled temperature cabinet for 161 days (a 2: 1 water: soil ratio was maintained during incubation). Three models, i.e. the single first-order kinetics model, the double first-order kinetics model and the mixed first-order and zero-order kinetics model were used to simulate the cumulative mineralised N (NH4+-N and TSN) in the laboratory and waterlogged incubation. Principal results During 161 days of waterlogged incubation, the average cumulative total soluble N (TSN), ammonium N (NH4+-N), and soluble organic N (SON) was 122.2 mg kg-1, 85.9 mg kg-1, and 36.3 mg kg-1, respectively. Cumulative NH4+-N was significantly (P < 0.05) positively correlated with organic carbon (OC), total N (TN), pH, and exchangeable calcium (Ca), and cumulative TSN was significantly (P < 0.05) positively correlated with OC, TN, and exchangeable Ca, but was not significantly (P > 0.05) correlated with C/N ratio, cation exchange capacity (CEC), extractable iron (Fe), clay, and sand. When the cumulative NH4+-N and TSN were simulated, the single first-order kinetics model provided the least accurate simulation. The parameter of the double first-order kinetics model also did not represent the actual data well, but the mixed first-order and zero-order kinetics model provided the most accurate simulation, as demonstrated by the estimated standard error, F statistic values, parameter accuracy, and fitting effect. Conclusions Overall, the results showed that SON was involved with N mineralization process, and the mixed first-order and zero-order kinetics model accurately simulates the N mineralization process of paddy soil in Mollisols area of Northeast China under waterlogged incubation. PMID:28170409

Evaluation and simulation of nitrogen mineralization of paddy soils in Mollisols area of Northeast China under waterlogged incubation.

PubMed

Zhang, Yuling; Xu, Wenjing; Duan, Pengpeng; Cong, Yaohui; An, Tingting; Yu, Na; Zou, Hongtao; Dang, Xiuli; An, Jing; Fan, Qingfeng; Zhang, Yulong

2017-01-01

Understanding the nitrogen (N) mineralization process and applying appropriate model simulation are key factors in evaluating N mineralization. However, there are few studies of the N mineralization characteristics of paddy soils in Mollisols area of Northeast China. The soils were sampled from the counties of Qingan and Huachuan, which were located in Mollisols area of Northeast China. The sample soil was incubated under waterlogged at 30°C in a controlled temperature cabinet for 161 days (a 2: 1 water: soil ratio was maintained during incubation). Three models, i.e. the single first-order kinetics model, the double first-order kinetics model and the mixed first-order and zero-order kinetics model were used to simulate the cumulative mineralised N (NH4+-N and TSN) in the laboratory and waterlogged incubation. During 161 days of waterlogged incubation, the average cumulative total soluble N (TSN), ammonium N (NH4+-N), and soluble organic N (SON) was 122.2 mg kg-1, 85.9 mg kg-1, and 36.3 mg kg-1, respectively. Cumulative NH4+-N was significantly (P < 0.05) positively correlated with organic carbon (OC), total N (TN), pH, and exchangeable calcium (Ca), and cumulative TSN was significantly (P < 0.05) positively correlated with OC, TN, and exchangeable Ca, but was not significantly (P > 0.05) correlated with C/N ratio, cation exchange capacity (CEC), extractable iron (Fe), clay, and sand. When the cumulative NH4+-N and TSN were simulated, the single first-order kinetics model provided the least accurate simulation. The parameter of the double first-order kinetics model also did not represent the actual data well, but the mixed first-order and zero-order kinetics model provided the most accurate simulation, as demonstrated by the estimated standard error, F statistic values, parameter accuracy, and fitting effect. Overall, the results showed that SON was involved with N mineralization process, and the mixed first-order and zero-order kinetics model accurately simulates the N mineralization process of paddy soil in Mollisols area of Northeast China under waterlogged incubation.

New techniques for positron emission tomography in the study of human neurological disorders for the period June 15, 1987 through December 14, 1987

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

Kuhl, D.E.

1987-09-01

A brief progress report is presented describing the preparation of /sup 11/C-scopolamine, /sup 17/F-fluoromethane and /sup 18/F-tetraalkylammonium fluoride. The application of /sup 11/C-scopolamine to map cholinergic receptors in normal human brain. Additional studies entitled ''The Automated Arterial Blood Sampling Systems for PET'' and ''Investigations of Array Processor Based High-Speed Parameter Estimation for Tracer Kinetic Modeling'' are also described. (DT)

Radiation reaction in fusion plasmas.

PubMed

Hazeltine, R D; Mahajan, S M

2004-10-01

The effects of a radiation reaction on thermal electrons in a magnetically confined plasma, with parameters typical of planned burning plasma experiments, are studied. A fully relativistic kinetic equation that includes the radiation reaction is derived. The associated rate of phase-space contraction is computed and the relative importance of the radiation reaction in phase space is estimated. A consideration of the moments of the radiation reaction force show that its effects are typically small in reactor-grade confined plasmas, but not necessarily insignificant.

On real statistics of relaxation in gases

NASA Astrophysics Data System (ADS)

Kuzovlev, Yu. E.

2016-02-01

By example of a particle interacting with ideal gas, it is shown that the statistics of collisions in statistical mechanics at any value of the gas rarefaction parameter qualitatively differ from that conjugated with Boltzmann's hypothetical molecular chaos and kinetic equation. In reality, the probability of collisions of the particle in itself is random. Because of that, the relaxation of particle velocity acquires a power-law asymptotic behavior. An estimate of its exponent is suggested on the basis of simple kinematic reasons.

On firework blasts and qualitative parameter dependency.

PubMed

Zohdi, T I

2016-01-01

In this paper, a mathematical model is developed to qualitatively simulate the progressive time-evolution of a blast from a simple firework. Estimates are made for the blast radius that one can expect for a given amount of detonation energy and pyrotechnic display material. The model balances the released energy from the initial blast pulse with the subsequent kinetic energy and then computes the trajectory of the material under the influence of the drag from the surrounding air, gravity and possible buoyancy. Under certain simplifying assumptions, the model can be solved for analytically. The solution serves as a guide to identifying key parameters that control the evolving blast envelope. Three-dimensional examples are given.

On firework blasts and qualitative parameter dependency

PubMed Central

Zohdi, T. I.

2016-01-01

In this paper, a mathematical model is developed to qualitatively simulate the progressive time-evolution of a blast from a simple firework. Estimates are made for the blast radius that one can expect for a given amount of detonation energy and pyrotechnic display material. The model balances the released energy from the initial blast pulse with the subsequent kinetic energy and then computes the trajectory of the material under the influence of the drag from the surrounding air, gravity and possible buoyancy. Under certain simplifying assumptions, the model can be solved for analytically. The solution serves as a guide to identifying key parameters that control the evolving blast envelope. Three-dimensional examples are given. PMID:26997903

Kinetic quantitation of cerebral PET-FDG studies without concurrent blood sampling: statistical recovery of the arterial input function.

PubMed

O'Sullivan, F; Kirrane, J; Muzi, M; O'Sullivan, J N; Spence, A M; Mankoff, D A; Krohn, K A

2010-03-01

Kinetic quantitation of dynamic positron emission tomography (PET) studies via compartmental modeling usually requires the time-course of the radio-tracer concentration in the arterial blood as an arterial input function (AIF). For human and animal imaging applications, significant practical difficulties are associated with direct arterial sampling and as a result there is substantial interest in alternative methods that require no blood sampling at the time of the study. A fixed population template input function derived from prior experience with directly sampled arterial curves is one possibility. Image-based extraction, including requisite adjustment for spillover and recovery, is another approach. The present work considers a hybrid statistical approach based on a penalty formulation in which the information derived from a priori studies is combined in a Bayesian manner with information contained in the sampled image data in order to obtain an input function estimate. The absolute scaling of the input is achieved by an empirical calibration equation involving the injected dose together with the subject's weight, height and gender. The technique is illustrated in the context of (18)F -Fluorodeoxyglucose (FDG) PET studies in humans. A collection of 79 arterially sampled FDG blood curves are used as a basis for a priori characterization of input function variability, including scaling characteristics. Data from a series of 12 dynamic cerebral FDG PET studies in normal subjects are used to evaluate the performance of the penalty-based AIF estimation technique. The focus of evaluations is on quantitation of FDG kinetics over a set of 10 regional brain structures. As well as the new method, a fixed population template AIF and a direct AIF estimate based on segmentation are also considered. Kinetics analyses resulting from these three AIFs are compared with those resulting from radially sampled AIFs. The proposed penalty-based AIF extraction method is found to achieve significant improvements over the fixed template and the segmentation methods. As well as achieving acceptable kinetic parameter accuracy, the quality of fit of the region of interest (ROI) time-course data based on the extracted AIF, matches results based on arterially sampled AIFs. In comparison, significant deviation in the estimation of FDG flux and degradation in ROI data fit are found with the template and segmentation methods. The proposed AIF extraction method is recommended for practical use.

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 estimated from IIF times in the early stages of isothermal periods, while the osmotic state of the cell was relatively constant. In bovine oocytes, the parameters were estimated from linear cooling data. Without further calibration, the model was used to predict total IIF incidence under different cooling regimes. For protoplasts, D. melanogaster embryos, and bovine oocytes, the model's predictions were quite accurate compared to the actual data. In mouse oocytes, adjustment of the hydraulic permeability coefficient (Lp) at 0 degree C was required to yield realistic behavior.(ABSTRACT TRUNCATED AT 400 WORDS)

Global sensitivity analysis in stochastic simulators of uncertain reaction networks.

PubMed

Navarro Jimenez, M; Le Maître, O P; Knio, O M

2016-12-28

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol's decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

Global sensitivity analysis in stochastic simulators of uncertain reaction networks

DOE PAGES

Navarro Jimenez, M.; Le Maître, O. P.; Knio, O. M.

2016-12-23

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol’s decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes thatmore » the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. Here, a sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.« less

Global sensitivity analysis in stochastic simulators of uncertain reaction networks

NASA Astrophysics Data System (ADS)

Navarro Jimenez, M.; Le Maître, O. P.; Knio, O. M.

2016-12-01

Stochastic models of chemical systems are often subjected to uncertainties in kinetic parameters in addition to the inherent random nature of their dynamics. Uncertainty quantification in such systems is generally achieved by means of sensitivity analyses in which one characterizes the variability with the uncertain kinetic parameters of the first statistical moments of model predictions. In this work, we propose an original global sensitivity analysis method where the parametric and inherent variability sources are both treated through Sobol's decomposition of the variance into contributions from arbitrary subset of uncertain parameters and stochastic reaction channels. The conceptual development only assumes that the inherent and parametric sources are independent, and considers the Poisson processes in the random-time-change representation of the state dynamics as the fundamental objects governing the inherent stochasticity. A sampling algorithm is proposed to perform the global sensitivity analysis, and to estimate the partial variances and sensitivity indices characterizing the importance of the various sources of variability and their interactions. The birth-death and Schlögl models are used to illustrate both the implementation of the algorithm and the richness of the proposed analysis method. The output of the proposed sensitivity analysis is also contrasted with a local derivative-based sensitivity analysis method classically used for this type of systems.

Mixing-controlled reactive transport on travel times in heterogeneous media

NASA Astrophysics Data System (ADS)

Luo, J.; Cirpka, O.

2008-05-01

Modeling mixing-controlled reactive transport using traditional spatial discretization of the domain requires identifying the spatial distributions of hydraulic and reactive parameters including mixing-related quantities such as dispersivities and kinetic mass-transfer coefficients. In most applications, breakthrough curves of conservative and reactive compounds are measured at only a few locations and models are calibrated by matching these breakthrough curves, which is an ill posed inverse problem. By contrast, travel-time based transport models avoid costly aquifer characterization. By considering breakthrough curves measured on different scales, one can distinguish between mixing, which is a prerequisite for reactions, and spreading, which per se does not foster reactions. In the travel-time based framework, the breakthrough curve of a solute crossing an observation plane, or ending in a well, is interpreted as the weighted average of concentrations in an ensemble of non-interacting streamtubes, each of which is characterized by a distinct travel-time value. Mixing is described by longitudinal dispersion and/or kinetic mass transfer along individual streamtubes, whereas spreading is characterized by the distribution of travel times which also determines the weights associated to each stream tube. Key issues in using the travel-time based framework include the description of mixing mechanisms and the estimation of the travel-time distribution. In this work, we account for both apparent longitudinal dispersion and kinetic mass transfer as mixing mechanisms, thus generalizing the stochastic-convective model with or without inter-phase mass transfer and the advective-dispersive streamtube model. We present a nonparametric approach of determining the travel-time distribution, given a breakthrough curve integrated over an observation plane and estimated mixing parameters. The latter approach is superior to fitting parametric models in cases where the true travel-time distribution exhibits multiple peaks or long tails. It is demonstrated that there is freedom for the combinations of mixing parameters and travel-time distributions to fit conservative breakthrough curves and describe the tailing. Reactive transport cases with a bimolecular instantaneous irreversible reaction and a dual Michaelis-Menten problem demonstrate that the mixing introduced by local dispersion and mass transfer may be described by apparent mean mass transfer with coefficients evaluated by local breakthrough curves.

Two-compartment modeling of tissue microcirculation revisited.

PubMed

Brix, Gunnar; Salehi Ravesh, Mona; Griebel, Jürgen

2017-05-01

Conventional two-compartment modeling of tissue microcirculation is used for tracer kinetic analysis of dynamic contrast-enhanced (DCE) computed tomography or magnetic resonance imaging studies although it is well-known that the underlying assumption of an instantaneous mixing of the administered contrast agent (CA) in capillaries is far from being realistic. It was thus the aim of the present study to provide theoretical and computational evidence in favor of a conceptually alternative modeling approach that makes it possible to characterize the bias inherent to compartment modeling and, moreover, to approximately correct for it. Starting from a two-region distributed-parameter model that accounts for spatial gradients in CA concentrations within blood-tissue exchange units, a modified lumped two-compartment exchange model was derived. It has the same analytical structure as the conventional two-compartment model, but indicates that the apparent blood flow identifiable from measured DCE data is substantially overestimated, whereas the three other model parameters (i.e., the permeability-surface area product as well as the volume fractions of the plasma and interstitial distribution space) are unbiased. Furthermore, a simple formula was derived to approximately compute a bias-corrected flow from the estimates of the apparent flow and permeability-surface area product obtained by model fitting. To evaluate the accuracy of the proposed modeling and bias correction method, representative noise-free DCE curves were analyzed. They were simulated for 36 microcirculation and four input scenarios by an axially distributed reference model. As analytically proven, the considered two-compartment exchange model is structurally identifiable from tissue residue data. The apparent flow values estimated for the 144 simulated tissue/input scenarios were considerably biased. After bias-correction, the deviations between estimated and actual parameter values were (11.2 ± 6.4) % (vs. (105 ± 21) % without correction) for the flow, (3.6 ± 6.1) % for the permeability-surface area product, (5.8 ± 4.9) % for the vascular volume and (2.5 ± 4.1) % for the interstitial volume; with individual deviations of more than 20% being the exception and just marginal. Increasing the duration of CA administration only had a statistically significant but opposite effect on the accuracy of the estimated flow (declined) and intravascular volume (improved). Physiologically well-defined tissue parameters are structurally identifiable and accurately estimable from DCE data by the conceptually modified two-compartment model in combination with the bias correction. The accuracy of the bias-corrected flow is nearly comparable to that of the three other (theoretically unbiased) model parameters. As compared to conventional two-compartment modeling, this feature constitutes a major advantage for tracer kinetic analysis of both preclinical and clinical DCE imaging studies. © 2017 American Association of Physicists in Medicine.

Muscular Oxygen Uptake Kinetics in Aged Adults.

PubMed

Koschate, J; Drescher, U; Baum, K; Eichberg, S; Schiffer, T; Latsch, J; Brixius, K; Hoffmann, U

2016-06-01

Pulmonary oxygen uptake (V˙O2) kinetics and heart rate kinetics are influenced by age and fitness. Muscular V˙O2 kinetics can be estimated from heart rate and pulmonary V˙O2. In this study the applicability of a test using pseudo-random binary sequences in combination with a model to estimate muscular V˙O2 kinetics was tested. Muscular V˙O2 kinetics were expected to be faster than pulmonary V˙O2 kinetics, slowed in aged subjects and correlated with maximum V˙O2 and heart rate kinetics. 27 elderly subjects (73±3 years; 81.1±8.2 kg; 175±4.7 cm) participated. Cardiorespiratory kinetics were assessed using the maximum of cross-correlation functions, higher maxima implying faster kinetics. Muscular V˙O2 kinetics were faster than pulmonary V˙O2 kinetics (0.31±0.1 vs. 0.29±0.1 s; p=0.004). Heart rate kinetics were not correlated with muscular or pulmonary V˙O2 kinetics or maximum V˙O2. Muscular V˙O2 kinetics correlated with maximum V˙O2 (r=0.35; p=0.033). This suggests, that muscular V˙O2 kinetics are faster than estimates from pulmonary V˙O2 and related to maximum V˙O2 in aged subjects. In the future this experimental approach may help to characterize alterations in muscular V˙O2 under various conditions independent of motivation and maximal effort. © Georg Thieme Verlag KG Stuttgart · New York.

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.

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

Improving the quantification of contrast enhanced ultrasound using a Bayesian approach

NASA Astrophysics Data System (ADS)

Rizzo, Gaia; Tonietto, Matteo; Castellaro, Marco; Raffeiner, Bernd; Coran, Alessandro; Fiocco, Ugo; Stramare, Roberto; Grisan, Enrico

2017-03-01

Contrast Enhanced Ultrasound (CEUS) is a sensitive imaging technique to assess tissue vascularity, that can be useful in the quantification of different perfusion patterns. This can be particularly important in the early detection and staging of arthritis. In a recent study we have shown that a Gamma-variate can accurately quantify synovial perfusion and it is flexible enough to describe many heterogeneous patterns. Moreover, we have shown that through a pixel-by-pixel analysis the quantitative information gathered characterizes more effectively the perfusion. However, the SNR ratio of the data and the nonlinearity of the model makes the parameter estimation difficult. Using classical non-linear-leastsquares (NLLS) approach the number of unreliable estimates (those with an asymptotic coefficient of variation greater than a user-defined threshold) is significant, thus affecting the overall description of the perfusion kinetics and of its heterogeneity. In this work we propose to solve the parameter estimation at the pixel level within a Bayesian framework using Variational Bayes (VB), and an automatic and data-driven prior initialization. When evaluating the pixels for which both VB and NLLS provided reliable estimates, we demonstrated that the parameter values provided by the two methods are well correlated (Pearson's correlation between 0.85 and 0.99). Moreover, the mean number of unreliable pixels drastically reduces from 54% (NLLS) to 26% (VB), without increasing the computational time (0.05 s/pixel for NLLS and 0.07 s/pixel for VB). When considering the efficiency of the algorithms as computational time per reliable estimate, VB outperforms NLLS (0.11 versus 0.25 seconds per reliable estimate respectively).

Fuzzy Performance between Surface Fitting and Energy Distribution in Turbulence Runner

PubMed Central

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

2012-01-01

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

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.

Transfer of radiocarbon liquid releases from the AREVA La Hague spent fuel reprocessing plant in the English Channel.

PubMed

Fiévet, Bruno; Voiseux, Claire; Rozet, Marianne; Masson, Michel; Bailly du Bois, Pascal

2006-01-01

The recent risk assessment by the North-Cotentin Radioecology Group (, 1999) outlined that (14)C has become one of the major sources of the low dose to man through seafood consumption. It was recommended that more data should be collected about (14)C in the local marine environment. The present study aims to respond to this recommendation. The estimation of (14)C activity in marine species is based on concentration factor values. The values reported here ranged from 1x10(3) to 5x10(3)Bqkg(-1)ww/BqL(-1). A comparison was made between the observed and predicted values. The accuracy of (14)C activity calculations was estimated between underestimation by a factor of 2 and over-estimation by 50% (95% confidence interval). However, the use of the concentration factor parameter is based on the biological and seawater compartments being in steady state. This assumption may not be met at short distances from the point of release of discharges, where rapid changes in seawater concentration may be smoothed out in living organisms due to transfer kinetics. The data processing technique, previously published by Fiévet and Plet (2003. Estimating biological half-lives of radionuclides in marine compartments from environmental time-series measurements. Journal of Environmental Radioactivity 65, 91-107), was used to deal with (14)C transfer kinetics, and carbon half-lives between seawater and a few biological compartments were thus estimated.

Computational analysis of liquid chromatography-tandem mass spectrometric steroid profiling in NCI H295R cells following angiotensin II, forskolin and abiraterone treatment.

PubMed

Mangelis, Anastasios; Dieterich, Peter; Peitzsch, Mirko; Richter, Susan; Jühlen, Ramona; Hübner, Angela; Willenberg, Holger S; Deussen, Andreas; Lenders, Jacques W M; Eisenhofer, Graeme

2016-01-01

Adrenal steroid hormones, which regulate a plethora of physiological functions, are produced via tightly controlled pathways. Investigations of these pathways, based on experimental data, can be facilitated by computational modeling for calculations of metabolic rate alterations. We therefore used a model system, based on mass balance and mass reaction equations, to kinetically evaluate adrenal steroidogenesis in human adrenal cortex-derived NCI H295R cells. For this purpose a panel of 10 steroids was measured by liquid chromatographic-tandem mass spectrometry. Time-dependent changes in cell incubate concentrations of steroids - including cortisol, aldosterone, dehydroepiandrosterone and their precursors - were measured after incubation with angiotensin II, forskolin and abiraterone. Model parameters were estimated based on experimental data using weighted least square fitting. Time-dependent angiotensin II- and forskolin-induced changes were observed for incubate concentrations of precursor steroids with peaks that preceded maximal increases in aldosterone and cortisol. Inhibition of 17-alpha-hydroxylase/17,20-lyase with abiraterone resulted in increases in upstream precursor steroids and decreases in downstream products. Derived model parameters, including rate constants of enzymatic processes, appropriately quantified observed and expected changes in metabolic pathways at multiple conversion steps. Our data demonstrate limitations of single time point measurements and the importance of assessing pathway dynamics in studies of adrenal cortical cell line steroidogenesis. Our analysis provides a framework for evaluation of steroidogenesis in adrenal cortical cell culture systems and demonstrates that computational modeling-derived estimates of kinetic parameters are an effective tool for describing perturbations in associated metabolic pathways. Copyright © 2015 Elsevier Ltd. All rights reserved.

Predictive Modeling for the Growth of Salmonella Enteritidis in Chicken Juice by Real-Time Polymerase Chain Reaction.

PubMed

Noviyanti, Fia; Hosotani, Yukie; Koseki, Shigenobu; Inatsu, Yasuhiro; Kawasaki, Susumu

2018-04-02

The goals of this study were to monitor the growth kinetics of Salmonella Enteritidis in chicken juice using real-time polymerase chain reaction (PCR) and to evaluate its efficacy by comparing the results with an experimental database. Salmonella Enteritidis was inoculated in chicken juice samples at an initial inoculum of 10 4 CFU/mL with inoculated samples incubated at six different temperatures (10, 15, 20, 25, 30, and 35°C). Sampling was carried out for 36 h to observe the growth of Salmonella Enteritidis. The total DNA was extracted from the samples, and the copy number of the Salmonella invasion gene (invA) was quantified by real-time PCR and converted to Salmonella Enteritidis cell concentration. Growth kinetics data were analyzed by the Baranyi and Roberts model to obtain growth parameters, whereas the Ratkowsky's square-root model was used to describe the effect of the interactions between growth parameters and temperature on the growth of Salmonella Enteritidis. The growth parameters of Salmonella Enteritidis obtained from an experiment conducted at a constant temperature were validated with growth data from chicken juice samples that were incubated under fluctuating temperature conditions between 5°C and 30°C for 30-min periods. A high correlation was observed between maximum growth rate (μ max ) and storage temperature, indicating that the real-time PCR-monitoring method provides a precise estimation of Salmonella Enteritidis growth in food material with a microbial flora. Moreover, the μ max data reflected data from microbial responses viewer database and ComBase. The results of this study suggested that real-time PCR monitoring provides a precise estimation of Salmonella Enteritidis growth in food materials with a background microbial flora.

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).

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.

PubMed

Fröhlich, Fabian; Thomas, Philipp; Kazeroonian, Atefeh; Theis, Fabian J; Grima, Ramon; Hasenauer, Jan

2016-07-01

Quantitative mechanistic models are valuable tools for disentangling biochemical pathways and for achieving a comprehensive understanding of biological systems. However, to be quantitative the parameters of these models have to be estimated from experimental data. In the presence of significant stochastic fluctuations this is a challenging task as stochastic simulations are usually too time-consuming and a macroscopic description using reaction rate equations (RREs) is no longer accurate. In this manuscript, we therefore consider moment-closure approximation (MA) and the system size expansion (SSE), which approximate the statistical moments of stochastic processes and tend to be more precise than macroscopic descriptions. We introduce gradient-based parameter optimization methods and uncertainty analysis methods for MA and SSE. Efficiency and reliability of the methods are assessed using simulation examples as well as by an application to data for Epo-induced JAK/STAT signaling. The application revealed that even if merely population-average data are available, MA and SSE improve parameter identifiability in comparison to RRE. Furthermore, the simulation examples revealed that the resulting estimates are more reliable for an intermediate volume regime. In this regime the estimation error is reduced and we propose methods to determine the regime boundaries. These results illustrate that inference using MA and SSE is feasible and possesses a high sensitivity.

Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion

PubMed Central

Thomas, Philipp; Kazeroonian, Atefeh; Theis, Fabian J.; Grima, Ramon; Hasenauer, Jan

2016-01-01

Quantitative mechanistic models are valuable tools for disentangling biochemical pathways and for achieving a comprehensive understanding of biological systems. However, to be quantitative the parameters of these models have to be estimated from experimental data. In the presence of significant stochastic fluctuations this is a challenging task as stochastic simulations are usually too time-consuming and a macroscopic description using reaction rate equations (RREs) is no longer accurate. In this manuscript, we therefore consider moment-closure approximation (MA) and the system size expansion (SSE), which approximate the statistical moments of stochastic processes and tend to be more precise than macroscopic descriptions. We introduce gradient-based parameter optimization methods and uncertainty analysis methods for MA and SSE. Efficiency and reliability of the methods are assessed using simulation examples as well as by an application to data for Epo-induced JAK/STAT signaling. The application revealed that even if merely population-average data are available, MA and SSE improve parameter identifiability in comparison to RRE. Furthermore, the simulation examples revealed that the resulting estimates are more reliable for an intermediate volume regime. In this regime the estimation error is reduced and we propose methods to determine the regime boundaries. These results illustrate that inference using MA and SSE is feasible and possesses a high sensitivity. PMID:27447730

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.

Modelling the growth and ethanol production of Brettanomyces bruxellensis at different glucose concentrations.

PubMed

Aguilar-Uscanga, M G; Garcia-Alvarado, Y; Gomez-Rodriguez, J; Phister, T; Delia, M L; Strehaiano, P

2011-08-01

To study the effect of glucose concentrations on the growth by Brettanomyces bruxellensis yeast strain in batch experiments and develop a mathematical model for kinetic behaviour analysis of yeast growing in batch culture. A Matlab algorithm was developed for the estimation of model parameters. Glucose fermentation by B. bruxellensis was studied by varying its concentration (5, 9.3, 13.8, 16.5, 17.6 and 21.4%). The increase in substrate concentration up to a certain limit was accompanied by an increase in ethanol and biomass production; at a substrate concentration of 50-138 g l(-1), the ethanol and biomass production were 24, 59 and 6.3, 11.4 g l(-1), respectively. However, an increase in glucose concentration to 165 g l(-1) led to a drastic decrease in product formation and substrate utilization. The model successfully simulated the batch kinetic observed in all cases. The confidence intervals were also estimated at each phase at a 0.95 probability level in a t-Student distribution for f degrees of freedom. The maximum ethanol and biomass yields were obtained with an initial glucose concentration of 138 g l(-1). These experiments illustrate the importance of using a mathematical model applied to kinetic behaviour on glucose concentration by B. bruxellensis. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

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.

Laminated helmet materials characterization by terahertz kinetics spectroscopy

NASA Astrophysics Data System (ADS)

Rahman, Anis; Rahman, Aunik K.

2015-05-01

High speed acquisition of reflected terahertz energy constitutes a kinetics spectrum that is an effective tool for layered materials' deformation characterization under ballistic impact. Here we describe utilizing the kinetics spectrum for quantifying a deformation event due to impact in material used for Soldier's helmet. The same technique may be utilized for real-time assessment of trauma by measuring the helmet wore by athletes. The deformation of a laminated material (e.g., a helmet) is dependent on the nature of impact and projectile; thus can uniquely characterize the impact condition leading to a diagnostic procedure based on the energy received by an athlete during an impact. We outline the calibration process for a given material under ballistic impact and then utilize the calibration for extracting physical parameters from the measured kinetics spectrum. Measured kinetics spectra are used to outline the method and rationale for extending the concept to a diagnosis tool. In particular, captured kinetics spectra from multilayered plates subjected to ballistic hit under experimental conditions by high speed digital acquisition system. An algorithm was devised to extract deformation and deformation velocity from which the energy received on the skull was estimated via laws of nonrelativistic motion. This energy is assumed to be related to actual injury conditions, thus forming a basis for determining whether the hit would cause concussion, trauma, or stigma. Such quantification may be used for diagnosing a Soldier's trauma condition in the field or that of an athlete's.

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.

Kinetic models in industrial biotechnology - Improving cell factory performance.

PubMed

Almquist, Joachim; Cvijovic, Marija; Hatzimanikatis, Vassily; Nielsen, Jens; Jirstrand, Mats

2014-07-01

An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance of such production systems is the development and application of mathematical models. To be of value for industrial biotechnology, mathematical models should be able to assist in the rational design of cell factory properties or in the production processes in which they are utilized. Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models. They can, at least in principle, be used to in detail understand, predict, and evaluate the effects of adding, removing, or modifying molecular components of a cell factory and for supporting the design of the bioreactor or fermentation process. However, several challenges still remain before kinetic modeling will reach the degree of maturity required for routine application in industry. Here we review the current status of kinetic cell factory modeling. Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model validation, but several applications of kinetic models for the improvement of cell factories are also discussed. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Multi-process herbicide transport in structured soil columns: Experiments and model analysis

NASA Astrophysics Data System (ADS)

Köhne, J. Maximilian; Köhne, Sigrid; Šimůnek, Jirka

2006-05-01

Model predictions of pesticide transport in structured soils are complicated by multiple processes acting concurrently. In this study, the hydraulic, physical, and chemical nonequilibrium (HNE, PNE, and CNE, respectively) processes governing herbicide transport under variably saturated flow conditions were studied. Bromide (Br -), isoproturon (IPU, 3-(4-isoprpylphenyl)-1,1-dimethylurea) and terbuthylazine (TER, N2-tert-butyl-6-chloro- N4-ethyl-1,3,5-triazine-2,4-diamine) were applied to two soil columns. An aggregated Ap soil column and a macroporous, aggregated Ah soil column were irrigated at a rate of 1 cm h - 1 for 3 h. Two more irrigations at the same rate and duration followed in weekly intervals. Nonlinear (Freundlich) equilibrium and two-site kinetic sorption parameters were determined for IPU and TER using batch experiments. The observed water flow and Br - transport were inversely simulated using mobile-immobile (MIM), dual-permeability (DPM), and combined triple-porosity (DP-MIM) numerical models implemented in HYDRUS-1D, with improving correspondence between empirical data and model results. Using the estimated HNE and PNE parameters together with batch-test derived equilibrium sorption parameters, the preferential breakthrough of the weakly adsorbed IPU in the Ah soil could be reasonably well predicted with the DPM approach, whereas leaching of the strongly adsorbed TER was predicted less well. The transport of IPU and TER through the aggregated Ap soil could be described consistently only when HNE, PNE, and CNE were simultaneously accounted for using the DPM. Inverse parameter estimation suggested that two-site kinetic sorption in inter-aggregate flow paths was reduced as compared to within aggregates, and that large values for the first-order degradation rate were an artifact caused by irreversible sorption. Overall, our results should be helpful to enhance the understanding and modeling of multi-process pesticide transport through structured soils during variably saturated water flow.

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.

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.

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.

Methodology for modeling the devolatilization of refuse-derived fuel from thermogravimetric analysis of municipal solid waste components

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

Fritsky, K.J.; Miller, D.L.; Cernansky, N.P.

1994-09-01

A methodology was introduced for modeling the devolatilization characteristics of refuse-derived fuel (RFD) in terms of temperature-dependent weight loss. The basic premise of the methodology is that RDF is modeled as a combination of select municipal solid waste (MSW) components. Kinetic parameters are derived for each component from thermogravimetric analyzer (TGA) data measured at a specific set of conditions. These experimentally derived parameters, along with user-derived parameters, are inputted to model equations for the purpose of calculating thermograms for the components. The component thermograms are summed to create a composite thermogram that is an estimate of the devolatilization for themore » as-modeled RFD. The methodology has several attractive features as a thermal analysis tool for waste fuels. 7 refs., 10 figs., 3 tabs.« less

Kinetics and thermodynamics of oxidation mediated reaction in L-cysteine and its methyl and ethyl esters in dimethyl sulfoxide-d6 by NMR spectroscopy

NASA Astrophysics Data System (ADS)

Dougherty, Ryan J.; Singh, Jaideep; Krishnan, V. V.

2017-03-01

L-Cysteine (L-Cys), L-Cysteine methyl ester (L-CysME) or L-Cysteine ethyl ester (L-CysEE), when dissolved in dimethyl sulfoxide, undergoes an oxidation process. This process is slow enough and leads to nuclear magnetic resonance (NMR) spectral changes that could be monitored in real time. The oxidation mediated transition is modeled as a pseudo-first order kinetics and the thermodynamic parameters are estimated using the Eyring's formulation. L-Cysteine and their esters are often used as biological models due to the remarkable thiol group that can be found in different oxidation states. This oxidation mediated transition is due to the combination of thiol oxidation to a disulfide followed by solvent-induced effects may be relevant in designing cysteine-based molecular models.

Thermoluminescence properties of gamma-irradiated nano-structure hydroxyapatite.

PubMed

Shafaei, M; Ziaie, F; Sardari, D; Larijani, M M

2016-02-01

The suitability of nano-structured hydroxyapatite (HAP) for use as a thermoluminescence dosimeter was investigated. HAP samples were synthesized using a hydrolysis method. The formation of nanoparticles was confirmed by X-ray diffraction and average particle size was estimated to be ~30 nm. The glow curve exhibited a peak centered at around 200 °C. The additive dose method was applied and this showed that the thermoluminescence (TL) glow curves follow first-order kinetics due to the non-shifting nature of Tm after different doses. The numbers of overlapping peaks and related kinetic parameters were identified from Tm -Tstop through computerized glow curve deconvolution methods. The dependence of the TL responses on radiation dose was studied and a linear dose response up to 1000 Gy was observed for the samples. Copyright © 2015 John Wiley & Sons, Ltd.

Phenol oxidation by mushroom waste extracts: a kinetic and thermodynamic study.

PubMed

Pigatto, Gisele; Lodi, Alessandra; Aliakbarian, Bahar; Converti, Attilio; da Silva, Regildo Marcio Gonçalves; Palma, Mauri Sérgio Alves

2013-09-01

Tyrosinase activity of mushroom extracts was checked for their ability to degrade phenol. Phenol oxidation kinetics was investigated varying temperature from 10 to 60 °C and the initial values of pH, enzyme activity and phenol concentration in the ranges 4.5-8.5, 1.43-9.54 U/mL and 50-600 mg/L, respectively. Thermodynamic parameters of phenol oxidation and tyrosinase reversible inactivation were estimated. Tyrosinase thermostability was also investigated through residual activity tests after extracts exposition at 20-50 °C, whose results allowed exploring the thermodynamics of enzyme irreversible thermoinactivation. This study is the first attempt to separate the effects of reversible unfolding and irreversible denaturation of tyrosinase on its activity. Extracts were finally tested on a real oil mill wastewater. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Faster heart rate and muscular oxygen uptake kinetics in type 2 diabetes patients following endurance training.

PubMed

Koschate, Jessica; Drescher, Uwe; Brinkmann, Christian; Baum, Klaus; Schiffer, Thorsten; Latsch, Joachim; Brixius, Klara; Hoffmann, Uwe

2016-11-01

Cardiorespiratory kinetics were analyzed in type 2 diabetes patients before and after a 12-week endurance exercise-training intervention. It was hypothesized that muscular oxygen uptake and heart rate (HR) kinetics would be faster after the training intervention and that this would be detectable using a standardized work rate protocol with pseudo-random binary sequences. The cardiorespiratory kinetics of 13 male sedentary, middle-aged, overweight type 2 diabetes patients (age, 60 ± 8 years; body mass index, 33 ± 4 kg·m -2 ) were tested before and after the 12-week exercise intervention. Subjects performed endurance training 3 times a week on nonconsecutive days. Pseudo-random binary sequences exercise protocols in combination with time series analysis were used to estimate kinetics. Greater maxima in cross-correlation functions (CCF max ) represent faster kinetics of the respective parameter. CCF max of muscular oxygen uptake (pre-training: 0.31 ± 0.03; post-training: 0.37 ± 0.1, P = 0.024) and CCF max of HR (pre-training: 0.25 ± 0.04; post-training: 0.29 ± 0.06, P = 0.007) as well as peak oxygen uptake (pre-training: 24.4 ± 4.7 mL·kg -1 ·min -1 ; post-training: 29.3 ± 6.5 mL·kg -1 ·min -1 , P = 0.004) increased significantly over the course of the exercise intervention. In conclusion, kinetic responses to changing work rates in the moderate-intensity range are similar to metabolic demands occurring in everyday habitual activities. Moderate endurance training accelerated the kinetic responses of HR and muscular oxygen uptake. Furthermore, the applicability of the used method to detect these accelerations was demonstrated.

Influence of exercise intensity on skeletal muscle blood flow, O2 extraction and O2 uptake on-kinetics

PubMed Central

Jones, Andrew M; Krustrup, Peter; Wilkerson, Daryl P; Berger, Nicolas J; Calbet, José A; Bangsbo, Jens

2012-01-01

Following the start of low-intensity exercise in healthy humans, it has been established that the kinetics of skeletal muscle O2 delivery is faster than, and does not limit, the kinetics of muscle O2 uptake (). Direct data are lacking, however, on the question of whether O2 delivery might limit kinetics during high-intensity exercise. Using multiple exercise transitions to enhance confidence in parameter estimation, we therefore investigated the kinetics of, and inter-relationships between, muscle blood flow (), a– difference and following the onset of low-intensity (LI) and high-intensity (HI) exercise. Seven healthy males completed four 6 min bouts of LI and four 6 min bouts of HI single-legged knee-extension exercise. Blood was frequently drawn from the femoral artery and vein during exercise and , a– difference and were calculated and subsequently modelled using non-linear regression techniques. For LI, the fundamental component mean response time (MRTp) for kinetics was significantly shorter than kinetics (mean ± SEM, 18 ± 4 vs. 30 ± 4 s; P < 0.05), whereas for HI, the MRTp for and was not significantly different (27 ± 5 vs. 29 ± 4 s, respectively). There was no difference in the MRTp for either or between the two exercise intensities; however, the MRTp for a– difference was significantly shorter for HI compared with LI (17 ± 3 vs. 28 ± 4 s; P < 0.05). Excess O2, i.e. oxygen not taken up (×), was significantly elevated within the first 5 s of exercise and remained unaltered thereafter, with no differences between LI and HI. These results indicate that bulk O2 delivery does not limit kinetics following the onset of LI or HI knee-extension exercise. PMID:22711961

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.

Kinetic and metabolic profiles of synthetic cannabinoids NNEI and MN-18.

PubMed

Kevin, Richard C; Lefever, Timothy W; Snyder, Rodney W; Patel, Purvi R; Gamage, Thomas F; Fennell, Timothy R; Wiley, Jenny L; McGregor, Iain S; Thomas, Brian F

2018-01-01

In 2014 and 2015, synthetic cannabinoid receptor agonists NNEI (N-1-naphthalenyl-1-pentyl-1H-indole-3-carboxamide) and MN-18 (N-1-naphthalenyl-1-pentyl-1H-indazole-3-carboxamide) were detected in recreationally used and abused products in multiple countries, and were implicated in episodes of poisoning and toxicity. Despite this, the pharmacokinetic profiles of NNEI and MN-18 have not been characterized. In the present study NNEI and MN-18 were incubated in rat and human liver microsomes and hepatocytes, to estimate kinetic parameters and to identify potential metabolic pathways, respectively. These parameters and pathways were then examined in vivo, via analysis of blood and urine samples from catheterized male rats following intraperitoneal (3 mg/kg) administration of NNEI and MN-18. Both NNEI and MN-18 were rapidly cleared by rat and human liver microsomes, and underwent a range of oxidative transformations during incubation with rat and human hepatocytes. Several unique metabolites were identified for the forensic identification of NNEI and MN-18 intake. Interestingly, NNEI underwent a greater number of biotransformations (20 NNEI metabolites versus 10 MN-18 metabolites), yet parent MN-18 was eliminated at a faster rate than NNEI in vivo. Additionally, in vivo elimination was more rapid than in vitro estimates. These data highlight that even closely related synthetic cannabinoids can possess markedly distinct pharmacokinetic profiles, which can vary substantially between in vitro and in vivo models. Copyright © 2017 John Wiley & Sons, Ltd.

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

Aviles-Ramos, Cuauhtemoc

A thermal decomposition model for PBX 9501 (95% HMX, 2.5% Estane® binder, 2.5% BDNPA/F nitro-plasticizer) was implemented by Dickson, et. al. The objective in this study is to estimate parameters associated with this kinetics model so it can be applied to carry out thermal ignition predictions for LX-07 (90% HMX, 10% Viton binder). LX-07 thermal ignition experiments have been carried out using the “Sandia Instrumented Thermal Ignition Apparatus”, SITI. The SITI design consists of solid cylinders (1” diameter × 1” height) of high explosive (HE) confined by a cylindrical aluminum case. An electric heater is wrapped around the outer surfacemore » of the case. This heater produces a temperature heating ramp on the outer surface of the case. Internal thermocouples measure the HE temperature rise from the center to locations close to the HE-aluminum interface. The energetic material is heated until thermal ignition occurs. A two–dimensional axisymmetric heat conduction finite element model is used to simulate these experiments. The HE thermal decomposition kinetics is coupled to a heat conduction model trough the definition of an energy source term. The parameters used to define the HE thermal decomposition model are optimized to obtain a good agreement with the experimental time to thermal ignition and temperatures. Also, heat capacity and thermal conductivity of the LX-07 mixture were estimated using temperatures measured at the center of the HE before the solid to solid HMX phase transition occurred.« less

CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

PubMed

Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J; Hasenauer, Jan

2016-01-01

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/.

CERENA: ChEmical REaction Network Analyzer—A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics

PubMed Central

Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J.; Hasenauer, Jan

2016-01-01

Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/. PMID:26807911

Covalent binding of aniline to humic substances. 1. Kinetic studies

USGS Publications Warehouse

Weber, E.J.; Spidle, D.L.; Thorn, K.A.

1996-01-01

The reaction kinetics for the covalent binding of aniline with reconstituted IHSS humic and fulvic acids, unfractionated DOM isolated from Suwannee River water, and whole samples of Suwannee River water have been investigated. The reaction kinetics in each of these systems can be adequately described by a simple second-order rate expression. The effect of varying the initial concentration of aniline on reaction kinetics suggested that approximately 10% of the covalent binding sites associated with Suwannee River fulvic acid are highly reactive sites that are quickly saturated. Based on the kinetic parameters determined for the binding of aniline with the Suwannee River fulvic and humic acid isolates, it was estimated that 50% of the aniline concentration decrease in a Suwannee River water sample could be attributed to reaction with the fulvic and humic acid components of the whole water sample. Studies with Suwannee River fulvic acid demonstrated that the rate of binding decreased with decreasing pH, which parallels the decrease in the effective concentration of the neutral form, or reactive nucleophilic species of aniline. The covalent binding of aniline with Suwannee River fulvic acid was inhibited by prior treatment of the fulvic acid with hydrogen sulfide, sodium borohydride, or hydroxylamine. These observations are consistent with a reaction pathway involving nucleophilic addition of aniline to carbonyl moieties present in the fulvic acid.

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.

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)

Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics.

PubMed

Vaas, Lea A I; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.

Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics

PubMed Central

Vaas, Lea A. I.; Sikorski, Johannes; Michael, Victoria; Göker, Markus; Klenk, Hans-Peter

2012-01-01

Background The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed ‘-omics’ techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. Methodology The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. Conclusions We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data. PMID:22536335

Electron transfer complex between nitrous oxide reductase and cytochrome c552 from Pseudomonas nautica: kinetic, nuclear magnetic resonance, and docking studies.

PubMed

Dell'acqua, Simone; Pauleta, Sofia R; Monzani, Enrico; Pereira, Alice S; Casella, Luigi; Moura, José J G; Moura, Isabel

2008-10-14

The multicopper enzyme nitrous oxide reductase (N 2OR) catalyzes the final step of denitrification, the two-electron reduction of N 2O to N 2. This enzyme is a functional homodimer containing two different multicopper sites: CuA and CuZ. CuA is a binuclear copper site that transfers electrons to the tetranuclear copper sulfide CuZ, the catalytic site. In this study, Pseudomonas nautica cytochrome c 552 was identified as the physiological electron donor. The kinetic data show differences when physiological and artificial electron donors are compared [cytochrome vs methylviologen (MV)]. In the presence of cytochrome c 552, the reaction rate is dependent on the ET reaction and independent of the N 2O concentration. With MV, electron donation is faster than substrate reduction. From the study of cytochrome c 552 concentration dependence, we estimate the following kinetic parameters: K m c 552 = 50.2 +/- 9.0 muM and V max c 552 = 1.8 +/- 0.6 units/mg. The N 2O concentration dependence indicates a K mN 2 O of 14.0 +/- 2.9 muM using MV as the electron donor. The pH effect on the kinetic parameters is different when MV or cytochrome c 552 is used as the electron donor (p K a = 6.6 or 8.3, respectively). The kinetic study also revealed the hydrophobic nature of the interaction, and direct electron transfer studies showed that CuA is the center that receives electrons from the physiological electron donor. The formation of the electron transfer complex was observed by (1)H NMR protein-protein titrations and was modeled with a molecular docking program (BiGGER). The proposed docked complexes corroborated the ET studies giving a large number of solutions in which cytochrome c 552 is placed near a hydrophobic patch located around the CuA center.

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.

Effect of light on the kinetics and equilibrium of the textile dye (Reactive Red 120) adsorption by Helianthus annuus hairy roots.

PubMed

Srikantan, Chitra; Suraishkumar, G K; Srivastava, Smita

2018-06-01

The study demonstrates for the first time that light influences the adsorption equilibrium and kinetics of a dye by root culture system. The azo dye (Reactive Red 120) adsorption by the hairy roots of H. annuus followed a pseudo first-order kinetic model and the adsorption equilibrium parameters were best estimated using Langmuir isotherm. The maximum dye adsorption capacity of the roots increased 6-fold, from 0.26 mg g -1 under complete dark conditions to 1.51 mg g -1 under 16/8 h light/dark photoperiod. Similarly, adsorption rate of the dye and removal (%) also increased in the presence of light, irrespective of the initial concentration of the dye (20-110 mg L -1 ). The degradation of the azo dye upon adsorption by the hairy roots of H. annuus was also confirmed. In addition, a strategy for simultaneous dye removal and increased alpha-tocopherol (industrially relevant) production by H. annuus hairy root cultures has been proposed and demonstrated. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physiochemical properties and kinetics of glucoamylase produced from deoxy-d-glucose resistant mutant of Aspergillus niger for soluble starch hydrolysis.

PubMed

Riaz, Muhammad; Rashid, Muhammad Hamid; Sawyer, Lindsay; Akhtar, Saeed; Javed, Muhammad Rizwan; Nadeem, Habibullah; Wear, Martin

2012-01-01

Glucoamylases (GAs) from a wild and a deoxy-d-glucose-resistant mutant of a locally isolated Aspergillus niger were purified to apparent homogeneity. The subunit molecular mass estimated by SDS-PAGE was 93 kDa for both strains, while the molecular masses determined by MALDI-TOF for wild and mutant GAs were 72.876 and 72.063 kDa, respectively. The monomeric nature of the enzymes was confirmed through activity staining. Significant improvement was observed in the kinetic properties of the mutant GA relative to the wild type enzyme. Kinetic constants of starch hydrolysis for A. niger parent and mutant GAs calculated on the basis of molecular masses determined through MALDI-TOF were as follows: k cat = 343 and 727 s -1 , K m = 0.25 and 0.16 mg mL -1 , k cat / K m (specificity constant) = 1374 and 4510 mg mL -1 s -1 , respectively. Thermodynamic parameters for soluble starch hydrolysis also suggested that mutant GA was more efficient compared to the parent enzyme.

Model development and parameter estimation for a hybrid submerged membrane bioreactor treating Ametryn.

PubMed

Navaratna, Dimuth; Shu, Li; Baskaran, Kanagaratnam; Jegatheesan, Veeriah

2012-06-01

A lab-scale membrane bioreactor (MBR) was used to remove Ametryn from synthetic wastewater. It was found that concentrations of MLSS and extra-cellular polymeric substances (EPS) in MBR mixed liquor fluctuated (production and decay) differently for about 40 days (transition period) after the introduction of Ametryn. During the subsequent operations with higher organic loading rates, it was also found that a low net biomass yield (higher death rate) and a higher rate of fouling of membrane (a very high rate during the first 48 h) due to increased levels of bound EPS (eEPS) in MBR mixed liquor. A mathematical model was developed to estimate the kinetic parameters before and after the introduction of Ametryn. This model will be useful in simulating the performance of a MBR treating Ametryn in terms of flux, rate of fouling (in terms of transmembrane pressure and membrane resistance) as well as treatment efficiency. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

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 based on the influent COD fraction contributed by the test compound.

Bayesian Calibration of Thermodynamic Databases and the Role of Kinetics

NASA Astrophysics Data System (ADS)

Wolf, A. S.; Ghiorso, M. S.

2017-12-01

Self-consistent thermodynamic databases of geologically relevant materials (like Berman, 1988; Holland and Powell, 1998, Stixrude & Lithgow-Bertelloni 2011) are crucial for simulating geological processes as well as interpreting rock samples from the field. These databases form the backbone of our understanding of how fluids and rocks interact at extreme planetary conditions. Considerable work is involved in their construction from experimental phase reaction data, as they must self-consistently describe the free energy surfaces (including relative offsets) of potentially hundreds of interacting phases. Standard database calibration methods typically utilize either linear programming or least squares regression. While both produce a viable model, they suffer from strong limitations on the training data (which must be filtered by hand), along with general ignorance of many of the sources of experimental uncertainty. We develop a new method for calibrating high P-T thermodynamic databases for use in geologic applications. The model is designed to handle pure solid endmember and free fluid phases and can be extended to include mixed solid solutions and melt phases. This new calibration effort utilizes Bayesian techniques to obtain optimal parameter values together with a full family of statistically acceptable models, summarized by the posterior. Unlike previous efforts, the Bayesian Logistic Uncertain Reaction (BLUR) model directly accounts for both measurement uncertainties and disequilibrium effects, by employing a kinetic reaction model whose parameters are empirically determined from the experiments themselves. Thus, along with the equilibrium free energy surfaces, we also provide rough estimates of the activation energies, entropies, and volumes for each reaction. As a first application, we demonstrate this new method on the three-phase aluminosilicate system, illustrating how it can produce superior estimates of the phase boundaries by incorporating constraints from all available data, while automatically handling variable data quality due to a combination of measurement errors and kinetic effects.

Evaluation of limited blood sampling population input approaches for kinetic quantification of [18F]fluorothymidine PET data.

PubMed

Contractor, Kaiyumars B; Kenny, Laura M; Coombes, Charles R; Turkheimer, Federico E; Aboagye, Eric O; Rosso, Lula

2012-03-24

Quantification of kinetic parameters of positron emission tomography (PET) imaging agents normally requires collecting arterial blood samples which is inconvenient for patients and difficult to implement in routine clinical practice. The aim of this study was to investigate whether a population-based input function (POP-IF) reliant on only a few individual discrete samples allows accurate estimates of tumour proliferation using [18F]fluorothymidine (FLT). Thirty-six historical FLT-PET data with concurrent arterial sampling were available for this study. A population average of baseline scans blood data was constructed using leave-one-out cross-validation for each scan and used in conjunction with individual blood samples. Three limited sampling protocols were investigated including, respectively, only seven (POP-IF7), five (POP-IF5) and three (POP-IF3) discrete samples of the historical dataset. Additionally, using the three-point protocol, we derived a POP-IF3M, the only input function which was not corrected for the fraction of radiolabelled metabolites present in blood. The kinetic parameter for net FLT retention at steady state, Ki, was derived using the modified Patlak plot and compared with the original full arterial set for validation. Small percentage differences in the area under the curve between all the POP-IFs and full arterial sampling IF was found over 60 min (4.2%-5.7%), while there were, as expected, larger differences in the peak position and peak height.A high correlation between Ki values calculated using the original arterial input function and all the population-derived IFs was observed (R2 = 0.85-0.98). The population-based input showed good intra-subject reproducibility of Ki values (R2 = 0.81-0.94) and good correlation (R2 = 0.60-0.85) with Ki-67. Input functions generated using these simplified protocols over scan duration of 60 min estimate net PET-FLT retention with reasonable accuracy.

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.

Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling.

PubMed

Modenese, Luca; Montefiori, Erica; Wang, Anqi; Wesarg, Stefan; Viceconti, Marco; Mazzà, Claudia

2018-05-17

The generation of subject-specific musculoskeletal models of the lower limb has become a feasible task thanks to improvements in medical imaging technology and musculoskeletal modelling software. Nevertheless, clinical use of these models in paediatric applications is still limited for what concerns the estimation of muscle and joint contact forces. Aiming to improve the current state of the art, a methodology to generate highly personalized subject-specific musculoskeletal models of the lower limb based on magnetic resonance imaging (MRI) scans was codified as a step-by-step procedure and applied to data from eight juvenile individuals. The generated musculoskeletal models were used to simulate 107 gait trials using stereophotogrammetric and force platform data as input. To ensure completeness of the modelling procedure, muscles' architecture needs to be estimated. Four methods to estimate muscles' maximum isometric force and two methods to estimate musculotendon parameters (optimal fiber length and tendon slack length) were assessed and compared, in order to quantify their influence on the models' output. Reported results represent the first comprehensive subject-specific model-based characterization of juvenile gait biomechanics, including profiles of joint kinematics and kinetics, muscle forces and joint contact forces. Our findings suggest that, when musculotendon parameters were linearly scaled from a reference model and the muscle force-length-velocity relationship was accounted for in the simulations, realistic knee contact forces could be estimated and these forces were not sensitive the method used to compute muscle maximum isometric force. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Linear prediction and single-channel recording.

PubMed

Carter, A A; Oswald, R E

1995-08-01

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

A Study of Wake Development and Structure in Constant Pressure Gradients

NASA Technical Reports Server (NTRS)

Thomas, Flint O.; Nelson, R. C.; Liu, Xiaofeng

2000-01-01

Motivated by the application to high-lift aerodynamics for commercial transport aircraft, a systematic investigation into the response of symmetric/asymmetric planar turbulent wake development to constant adverse, zero, and favorable pressure gradients has been conducted. The experiments are performed at a Reynolds number of 2.4 million based on the chord of the wake generator. A unique feature of this wake study is that the pressure gradients imposed on the wake flow field are held constant. The experimental measurements involve both conventional LDV and hot wire flow field surveys of mean and turbulent quantities including the turbulent kinetic energy budget. In addition, similarity analysis and numerical simulation have also been conducted for this wake study. A focus of the research has been to isolate the effects of both pressure gradient and initial wake asymmetry on the wake development. Experimental results reveal that the pressure gradient has a tremendous influence on the wake development, despite the relatively modest pressure gradients imposed. For a given pressure gradient, the development of an initially asymmetric wake is different from the initially symmetric wake. An explicit similarity solution for the shape parameters of the symmetric wake is obtained and agrees with the experimental results. The turbulent kinetic energy budget measurements of the symmetric wake demonstrate that except for the convection term, the imposed pressure gradient does not change the fundamental flow physics of turbulent kinetic energy transport. Based on the turbulent kinetic energy budget measurements, an approach to correct the bias error associated with the notoriously difficult dissipation estimate is proposed and validated through the comparison of the experimental estimate with a direct numerical simulation result.

A novel approach for calculating shelf life of minimally processed vegetables.

PubMed

Corbo, Maria Rosaria; Del Nobile, Matteo Alessandro; Sinigaglia, Milena

2006-01-15

Shelf life of minimally processed vegetables is often calculated by using the kinetic parameters of Gompertz equation as modified by Zwietering et al. [Zwietering, M.H., Jongenburger, F.M., Roumbouts, M., van't Riet, K., 1990. Modelling of the bacterial growth curve. Applied and Environmental Microbiology 56, 1875-1881.] taking 5x10(7) CFU/g as the maximum acceptable contamination value consistent with acceptable quality of these products. As this method does not allow estimation of the standard errors of the shelf life, in this paper the modified Gompertz equation was re-parameterized to directly include the shelf life as a fitting parameter among the Gompertz parameters. Being the shelf life a fitting parameter is possible to determine its confidence interval by fitting the proposed equation to the experimental data. The goodness-of-fit of this new equation was tested by using mesophilic bacteria cell loads from different minimally processed vegetables (packaged fresh-cut lettuce, fennel and shredded carrots) that differed for some process operations or for package atmosphere. The new equation was able to describe the data well and to estimate the shelf life. The results obtained emphasize the importance of using the standard errors for the shelf life value to show significant differences among the samples.

Growth of non-toxigenic Clostridium botulinum mutant LNT01 in cooked beef: One-step kinetic analysis and comparison with C. sporogenes and C. perfringens.

PubMed

Huang, Lihan

2018-05-01

The objective of this study was to investigate the growth kinetics of Clostridium botulinum LNT01, a non-toxigenic mutant of C. botulinum 62A, in cooked ground beef. The spores of C. botulinum LNT01 were inoculated to ground beef and incubated anaerobically under different temperature conditions to observe growth and develop growth curves. A one-step kinetic analysis method was used to analyze the growth curves simultaneously to minimize the global residual error. The data analysis was performed using the USDA IPMP-Global Fit, with the Huang model as the primary model and the cardinal parameters model as the secondary model. The results of data analysis showed that the minimum, optimum, and maximum growth temperatures of this mutant are 11.5, 36.4, and 44.3 °C, and the estimated optimum specific growth rate is 0.633 ln CFU/g per h, or 0.275 log CFU/g per h. The maximum cell density is 7.84 log CFU/g. The models and kinetic parameters were validated using additional isothermal and dynamic growth curves. The resulting residual errors of validation followed a Laplace distribution, with about 60% of the residual errors within ±0.5 log CFU/g of experimental observations, suggesting that the models could predict the growth of C. botulinum LNT01 in ground beef with reasonable accuracy. Comparing with C. perfringens, C. botulinum LNT01 grows at much slower rates and with much longer lag times. Its growth kinetics is also very similar to C. sporogenes in ground beef. The results of computer simulation using kinetic models showed that, while prolific growth of C. perfringens may occur in ground beef during cooling, no growth of C. botulinum LNT01 or C. sporogenes would occur under the same cooling conditions. The models developed in this study may be used for prediction of the growth and risk assessments of proteolytic C. botulinum in cooked meats. Published by Elsevier Ltd.

Study of Metal-NH[subscript 3] Interfaces (Metal= Cu, Ni, Ag) Using Potentiostatic Curves

ERIC Educational Resources Information Center

Nunes, Nelson; Martins, Angela; Leitao, Ruben Elvas

2007-01-01

Experiment is conducted to determine the kinetic parameters of metal-solution interfaces. During the experiment the kinetic parameters for the interfaces Cu-NH[subscript 3], Ag-NH[subscript 3] and Ni-NH[subscript 3] is easily determined.

Photodegradation of naproxen and its photoproducts in aqueous solution at 254 nm: a kinetic investigation.

PubMed

Marotta, Raffaele; Spasiano, Danilo; Di Somma, Ilaria; Andreozzi, Roberto

2013-01-01

The kinetics of photodegradation of the non steroidal anti-inflammatory drug naproxen (+)-S-2-(6-methoxynaphthalen-2-yl)propanoic acid, an emerging organic pollutant, was studied in aqueous solutions under deaerated and aerated conditions. The photolysis experiments were carried out under monochromatic irradiation (λ = 254 nm) at pH = 7.0 and T = 25 °C. Simplified reaction schemes of photodegradation of naproxen are proposed in absence and in presence of oxygen respectively. The schemes take into account the photolysis of naproxen and its photoproducts and the reactions of the measured species with oxygen dissolved in the liquid bulk. According to these schemes, two kinetic models were developed which correlate the experimental data, for runs performed in absence and in presence of oxygen, with a fair accuracy and allowed to estimate the best values for the unknown kinetic parameters. The calculated quantum yield of direct photolysis of naproxen under deaerated media is in good agreement with the one previously reported. Under aerated conditions, the generation of singlet oxygen has also been taken into account. The obtained results, under the adopted conditions, indicated a marked influence of dissolved oxygen on the photodegradation rates of naproxen and the relative distribution of the major reaction intermediates. Copyright © 2012 Elsevier Ltd. All rights reserved.

Characteristics of SME biodiesel-fueled diesel particle emissions and the kinetics of oxidation.

PubMed

Jung, Heejung; Kittelson, David B; Zachariah, Michael R

2006-08-15

Biodiesel is one of the most promising alternative diesel fuels. As diesel emission regulations have become more stringent, the diesel particulate filter (DPF) has become an essential part of the aftertreatment system. Knowledge of kinetics of exhaust particle oxidation for alternative diesel fuels is useful in estimating the change in regeneration behavior of a DPF with such fuels. This study examines the characteristics of diesel particulate emissions as well as kinetics of particle oxidation using a 1996 John Deere T04045TF250 off-highway engine and 100% soy methyl ester (SME) biodiesel (B100) as fuel. Compared to standard D2 fuel, this B100 reduced particle size, number, and volume in the accumulation mode where most of the particle mass is found. At 75% load, number decreased by 38%, DGN decreased from 80 to 62 nm, and volume decreased by 82%. Part of this decrease is likely associated with the fact that the particles were more easily oxidized. Arrhenius parameters for the biodiesel fuel showed a 2-3times greater frequency factor and approximately 6 times higher oxidation rate compared to regular diesel fuel in the range of 700-825 degrees C. The faster oxidation kinetics should facilitate regeneration when used with a DPF.

Kinetics of aerobic cometabolic biodegradation of chlorinated and brominated aliphatic hydrocarbons: A review.

PubMed

Jesus, João; Frascari, Dario; Pozdniakova, Tatiana; Danko, Anthony S

2016-05-15

This review analyses kinetic studies of aerobic cometabolism (AC) of halogenated aliphatic hydrocarbons (HAHs) from 2001-2015 in order to (i) compare the different kinetic models proposed, (ii) analyse the estimated model parameters with a focus on novel HAHs and the identification of general trends, and (iii) identify further research needs. The results of this analysis show that aerobic cometabolism can degrade a wide range of HAHs, including HAHs that were not previously tested such as chlorinated propanes, highly chlorinated ethanes and brominated methanes and ethanes. The degree of chlorine mineralization was very high for the chlorinated HAHs. Bromine mineralization was not determined for studies with brominated aliphatics. The examined research period led to the identification of novel growth substrates of potentially high interest. Decreasing performance of aerobic cometabolism were found with increasing chlorination, indicating the high potential of aerobic cometabolism in the presence of medium- and low-halogenated HAHs. Further research is needed for the AC of brominated aliphatic hydrocarbons, the potential for biofilm aerobic cometabolism processes, HAH-HAH mutual inhibition and the identification of the enzymes responsible for each aerobic cometabolism process. Lastly, some indications for a possible standardization of future kinetic studies of HAH aerobic cometabolism are provided. Copyright © 2016 Elsevier B.V. All rights reserved.

An Analysis Method for Superconducting Resonator Parameter Extraction with Complex Baseline Removal

NASA Technical Reports Server (NTRS)

Cataldo, Giuseppe

2014-01-01

A new semi-empirical model is proposed for extracting the quality (Q) factors of arrays of superconducting microwave kinetic inductance detectors (MKIDs). The determination of the total internal and coupling Q factors enables the computation of the loss in the superconducting transmission lines. The method used allows the simultaneous analysis of multiple interacting discrete resonators with the presence of a complex spectral baseline arising from reflections in the system. The baseline removal allows an unbiased estimate of the device response as measured in a cryogenic instrumentation setting.

Application of a metabolic balancing technique to the analysis of microbial fermentation data.

PubMed

de Hollander, J A

1991-01-01

A general method for the development of fermentation models, based on elemental and metabolic balances, is illustrated with three examples from the literature. Physiological parameters such as the (maximal) yield on ATP, the energetic maintenance coefficient, the P/O ratio and others are estimated by fitting model equations to experimental data. Further, phenomenological relations concerning kinetics of product formation and limiting enzyme activities are assessed. The results are compared with the conclusions of the original articles, and differences due to the application of improved models are discussed.

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.

On the Jet Properties of γ-Ray-loud Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Chen, Liang

2018-04-01

Based on broadband spectral energy distributions (SEDs), we estimate the jet physical parameters of 1392 γ-ray-loud active galactic nuclei (AGNs), the largest sample so far. The (SED) jet power and magnetization parameter are derived for these AGNs. Out of these sources, the accretion disk luminosity of 232 sources and (extended) kinetic jet powers of 159 sources are compiled from archived papers. We find the following. (1) Flat-spectrum radio quasars (FSRQs) and BL Lacs are well separated by {{Γ }}=-0.127{log}{L}γ +8.18 in the γ-ray luminosity versus photon index plane with a success rate of 88.6%. (2) Most FSRQs present a (SED) jet power larger than the accretion power, which suggests that the relativistic jet-launching mechanism is dominated by the Blandford–Znajek process. This result confirms previous findings. (3) There is a significant anticorrelation between jet magnetization and a ratio of the (SED) jet power to the (extended) kinetic jet power, which, for the first time, provides supporting evidence for the jet energy transportation theory: a high-magnetization jet may more easily transport energy to a large scale than a low-magnetization jet.

Estimation of turbulence characteristics of the low-level eyewall and outer-core regions in intense Hurricanes Allen (1980) and Hugo (1989)

NASA Astrophysics Data System (ADS)

Zhang, J. A.; Marks, F. D.; Montgomery, M.; Lorsolo, S.

2010-12-01

Turbulent transport processes in the atmospheric boundary layer play an important role in the intensification and maintenance of a hurricane vortex. However, direct measurement of turbulence in the hurricane boundary layer has been scarce. This study analyzes the flight-level data collected by research aircraft that penetrated the eyewalls of Category 5 Hurricane Hugo (1989) and Category 4 Hurricane Allen (1980) between 1 km and the sea surface. Momentum flux, turbulent kinetic energy (TKE) and vertical eddy diffusivity are estimated before and during the eyewall penetrations. Spatial scales of turbulent eddies are determined through spectral analysis. The turbulence parameters estimated for the eyewall penetration leg are found to be nearly an order of magnitude larger than those for the leg outside the eyewall at similar altitudes. In the low-level intense eyewall region, the horizontal length scale of dominant turbulent eddies is found to be between 500 - 3000 m and the corresponding vertical length scale is approximately 100 - 200 m. The results suggest also that it is unwise to include the eyewall vorticity maximum (EVM) in the turbulence parameter estimation, since the EVMs are likely to be quasi two-dimensional vortex structures that are embedded within the three dimensional turbulence on the inside edge of the eyewall.

Event-by-Event Continuous Respiratory Motion Correction for Dynamic PET Imaging.

PubMed

Yu, Yunhan; Chan, Chung; Ma, Tianyu; Liu, Yaqiang; Gallezot, Jean-Dominique; Naganawa, Mika; Kelada, Olivia J; Germino, Mary; Sinusas, Albert J; Carson, Richard E; Liu, Chi

2016-07-01

Existing respiratory motion-correction methods are applied only to static PET imaging. We have previously developed an event-by-event respiratory motion-correction method with correlations between internal organ motion and external respiratory signals (INTEX). This method is uniquely appropriate for dynamic imaging because it corrects motion for each time point. In this study, we applied INTEX to human dynamic PET studies with various tracers and investigated the impact on kinetic parameter estimation. The use of 3 tracers-a myocardial perfusion tracer, (82)Rb (n = 7); a pancreatic β-cell tracer, (18)F-FP(+)DTBZ (n = 4); and a tumor hypoxia tracer, (18)F-fluoromisonidazole ((18)F-FMISO) (n = 1)-was investigated in a study of 12 human subjects. Both rest and stress studies were performed for (82)Rb. The Anzai belt system was used to record respiratory motion. Three-dimensional internal organ motion in high temporal resolution was calculated by INTEX to guide event-by-event respiratory motion correction of target organs in each dynamic frame. Time-activity curves of regions of interest drawn based on end-expiration PET images were obtained. For (82)Rb studies, K1 was obtained with a 1-tissue model using a left-ventricle input function. Rest-stress myocardial blood flow (MBF) and coronary flow reserve (CFR) were determined. For (18)F-FP(+)DTBZ studies, the total volume of distribution was estimated with arterial input functions using the multilinear analysis 1 method. For the (18)F-FMISO study, the net uptake rate Ki was obtained with a 2-tissue irreversible model using a left-ventricle input function. All parameters were compared with the values derived without motion correction. With INTEX, K1 and MBF increased by 10% ± 12% and 15% ± 19%, respectively, for (82)Rb stress studies. CFR increased by 19% ± 21%. For studies with motion amplitudes greater than 8 mm (n = 3), K1, MBF, and CFR increased by 20% ± 12%, 30% ± 20%, and 34% ± 23%, respectively. For (82)Rb rest studies, INTEX had minimal effect on parameter estimation. The total volume of distribution of (18)F-FP(+)DTBZ and Ki of (18)F-FMISO increased by 17% ± 6% and 20%, respectively. Respiratory motion can have a substantial impact on dynamic PET in the thorax and abdomen. The INTEX method using continuous external motion data substantially changed parameters in kinetic modeling. More accurate estimation is expected with INTEX. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Toxicokinetics/toxicodynamics links bioavailability for assessing arsenic uptake and toxicity in three aquaculture species.

PubMed

Chen, Wei-Yu; Liao, Chung-Min

2012-11-01

The purpose of this study was to link toxicokinetics/toxicodynamics (TK/TD) and bioavailability-based metal uptake kinetics to assess arsenic (As) uptake and bioaccumulation in three common farmed species of tilapia (Oreochromis mossambicus), milkfish (Chanos chanos), and freshwater clam (Corbicula fluminea). We developed a mechanistic framework by linking damage assessment model (DAM) and bioavailability-based Michaelis-Menten model for describing TK/TD and As uptake mechanisms. The proposed model was verified with published acute toxicity data. The estimated TK/TD parameters were used to simulate the relationship between bioavailable As uptake and susceptibility probability. The As toxicity was also evaluated based on a constructed elimination-recovery scheme. Absorption rate constants were estimated to be 0.025, 0.016, and 0.175 mL g(-1) h(-1) and As uptake rate constant estimates were 22.875, 63.125, and 788.318 ng g(-1) h(-1) for tilapia, milkfish, and freshwater clam, respectively. Here we showed that a potential trade-off between capacities of As elimination and damage recovery was found among three farmed species. Moreover, the susceptibility probability can also be estimated by the elimination-recovery relations. This study suggested that bioavailability-based uptake kinetics and TK/TD-based DAM could be integrated for assessing metal uptake and toxicity in aquatic organisms. This study is useful to quantitatively assess the complex environmental behavior of metal uptake and implicate to risk assessment of metals in aquaculture systems.

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.

Evolution of a mini-scale biphasic dissolution model: Impact of model parameters on partitioning of dissolved API and modelling of in vivo-relevant kinetics.

PubMed

Locher, Kathrin; Borghardt, Jens M; Frank, Kerstin J; Kloft, Charlotte; Wagner, Karl G

2016-08-01

Biphasic dissolution models are proposed to have good predictive power for the in vivo absorption. The aim of this study was to improve our previously introduced mini-scale dissolution model to mimic in vivo situations more realistically and to increase the robustness of the experimental model. Six dissolved APIs (BCS II) were tested applying the improved mini-scale biphasic dissolution model (miBIdi-pH-II). The influence of experimental model parameters including various excipients, API concentrations, dual paddle and its rotation speed was investigated. The kinetics in the biphasic model was described applying a one- and four-compartment pharmacokinetic (PK) model. The improved biphasic dissolution model was robust related to differing APIs and excipient concentrations. The dual paddle guaranteed homogenous mixing in both phases; the optimal rotation speed was 25 and 75rpm for the aqueous and the octanol phase, respectively. A one-compartment PK model adequately characterised the data of fully dissolved APIs. A four-compartment PK model best quantified dissolution, precipitation, and partitioning also of undissolved amounts due to realistic pH profiles. The improved dissolution model is a powerful tool for investigating the interplay between dissolution, precipitation and partitioning of various poorly soluble APIs (BCS II). In vivo-relevant PK parameters could be estimated applying respective PK models. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

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

Influence of P-Glycoprotein Inhibition or Deficiency at the Blood-Brain Barrier on (18)F-2-Fluoro-2-Deoxy-D-glucose ( (18)F-FDG) Brain Kinetics.

PubMed

Tournier, Nicolas; Saba, Wadad; Goutal, Sébastien; Gervais, Philippe; Valette, Héric; Scherrmann, Jean-Michel; Bottlaender, Michel; Cisternino, Salvatore

2015-05-01

The fluorinated D-glucose analog (18)F-2-fluoro-2-deoxy-D-glucose ((18)F-FDG) is the most prevalent radiopharmaceutical for positron emission tomography (PET) imaging. P-Glycoprotein's (P-gp, MDR1, and ABCB1) function in various cancer cell lines and tumors was shown to impact (18)F-FDG incorporation, suggesting that P-gp function at the blood-brain barrier may also modulate (18)F-FDG brain kinetics. We tested the influence of P-gp inhibition using the cyclosporine analog valspodar (PSC833; 5 μM) on the uptake of (18)F-FDG in standardized human P-gp-overexpressing cells (MDCKII-MDR1). Consequences for (18)F-FDG brain kinetics were then assessed using (i) (18)F-FDG PET imaging and suitable kinetic modelling in baboons without or with P-gp inhibition by intravenous cyclosporine infusion (15 mg kg(-1) h(-1)) and (ii) in situ brain perfusion in wild-type and P-gp/Bcrp (breast cancer resistance protein) knockout mice and controlled D-glucose exposure to the brain. In vitro, the time course of (18)F-FDG uptake in MDR1 cells was influenced by the presence of valspodar in the absence of D-glucose but not in the presence of high D-glucose concentration. PET analysis revealed that P-gp inhibition had no significant impact on estimated brain kinetics parameters K 1, k 2, k 3, V T , and CMRGlc. The lack of P-gp effect on in vivo (18)F-FDG brain distribution was confirmed in P-gp/Bcrp-deficient mice. P-gp inhibition indirectly modulates (18)F-FDG uptake into P-gp-overexpressing cells, possibly through differences in the energetic cell level state. (18)F-FDG is not a P-gp substrate at the BBB and (18)F-FDG brain kinetics as well as estimated brain glucose metabolism are influenced by neither P-gp inhibition nor P-gp/Bcrp deficiencies in baboon and mice, respectively.

Sampling errors in the measurement of rain and hail parameters

NASA Technical Reports Server (NTRS)

Gertzman, H. S.; Atlas, D.

1977-01-01

Attention is given to a general derivation of the fractional standard deviation (FSD) of any integrated property X such that X(D) = cD to the n. This work extends that of Joss and Waldvogel (1969). The equation is applicable to measuring integrated properties of cloud, rain or hail populations (such as water content, precipitation rate, kinetic energy, or radar reflectivity) which are subject to statistical sampling errors due to the Poisson distributed fluctuations of particles sampled in each particle size interval and the weighted sum of the associated variances in proportion to their contribution to the integral parameter to be measured. Universal curves are presented which are applicable to the exponential size distribution permitting FSD estimation of any parameters from n = 0 to n = 6. The equations and curves also permit corrections for finite upper limits in the size spectrum and a realistic fall speed law.

Crystallization kinetics of the borax decahydrate

NASA Astrophysics Data System (ADS)

Ceyhan, A. A.; Sahin, Ö.; Bulutcu, A. N.

2007-03-01

The growth and dissolution rates of borax decahydrate have been measured as a function of supersaturation for various particle sizes at different temperature ranges of 13 and 50 °C in a laboratory-scale fluidized bed crystallizer. The values of mass transfer coefficient, K, reaction rate constant, kr and reaction rate order, r were determined. The relative importances of diffusion and integration resistance were described by new terms named integration and diffusion concentration fraction. It was found that the overall growth rate of borax decahydrate is mainly controlled by integration (reaction) steps. It was also estimated that the dissolution region of borax decahydrate, apart from other materials, is controlled by diffusion and surface reaction. Increasing the temperature and particle size cause an increase in the values of kinetic parameters ( Kg, kr and K). The activation energies of overall, reaction and mass transfer steps were determined as 18.07, 18.79 and 8.26 kJmol -1, respectively.

Kinetic model of mitochondrial Krebs cycle: unraveling the mechanism of salicylate hepatotoxic effects.

PubMed

Mogilevskaya, Ekaterina; Demin, Oleg; Goryanin, Igor

2006-10-01

This paper studies the effect of salicylate on the energy metabolism of mitochondria using in silico simulations. A kinetic model of the mitochondrial Krebs cycle is constructed using information on the individual enzymes. Model parameters for the rate equations are estimated using in vitro experimental data from the literature. Enzyme concentrations are determined from data on respiration in mitochondrial suspensions containing glutamate and malate. It is shown that inhibition in succinate dehydrogenase and alpha-ketoglutarate dehydrogenase by salicylate contributes substantially to the cumulative inhibition of the Krebs cycle by salicylates. Uncoupling of oxidative phosphorylation has little effect and coenzyme A consumption in salicylates transformation processes has an insignificant effect on the rate of substrate oxidation in the Krebs cycle. It is found that the salicylate-inhibited Krebs cycle flux can be increased by flux redirection through addition of external glutamate and malate, and depletion in external alpha-ketoglutarate and glycine concentrations.

A B-B-G-K-Y framework for fluid turbulence

NASA Technical Reports Server (NTRS)

Montgomery, D.

1975-01-01

A kinetic theory for fluid turbulence is developed from the Liouville equation and the associated BBGKY hierarchy. Real and imaginary parts of Fourier coefficients of fluid variables play the roles of particles. Closure is achieved by the assumption of negligible five-coefficient correlation functions and probability distributions of Fourier coefficients are the basic variables of the theory. An additional approximation leads to a closed-moment description similar to the so-called eddy-damped Markovian approximation. A kinetic equation is derived for which conservation laws and an H-theorem can be rigorously established, the H-theorem implying relaxation of the absolute equilibrium of Kraichnan. The equation can be cast in the Fokker-Planck form, and relaxation times estimated from its friction and diffusion coefficients. An undetermined parameter in the theory is the free decay time for triplet correlations. Some attention is given to the inclusion of viscous damping and external driving forces.

Kinetics and mechanism of degradation of some 2-sulfanilamidopyrimidine derivatives. Part VI. The use of Hammett equation for kinetic investigation of 2-sulfanilamidopyrimidine derivatives hydrolysis.

PubMed

Zajac, M

1977-01-01

General, k, and specific, k1 and k2, first-order rate constants for the parallel reaction of hydrolysis catalized by H+ ions were estimated for sulfadiazine (I), sulfamerazine (II), sulfadimidine (III), sulfaperine (IV) and sulfamethoxydiazine (V), hydrolyzed in 1 mole/dm3 HCl at 333, 343, 355 and 363 K. General first-order rate constants for the spontaneous hydrolysis of I--V in borate buffer pH 9.20 at 403, 411 and 418 K were also determined. Thermodynamic parameters of the reaction (delta Ha, deltaH not equal to, deltaS not equal to, deltaG not equal to and log A) were calculated. The effect of substituents in positions 4, 5 and 6 of the pyrimidine ring on the rate of hydrolysis was interpreted in terms of Hammett equation.

A novel approach of modeling continuous dark hydrogen fermentation.

PubMed

Alexandropoulou, Maria; Antonopoulou, Georgia; Lyberatos, Gerasimos

2018-02-01

In this study a novel modeling approach for describing fermentative hydrogen production in a continuous stirred tank reactor (CSTR) was developed, using the Aquasim modeling platform. This model accounts for the key metabolic reactions taking place in a fermentative hydrogen producing reactor, using fixed stoichiometry but different reaction rates. Biomass yields are determined based on bioenergetics. The model is capable of describing very well the variation in the distribution of metabolic products for a wide range of hydraulic retention times (HRT). The modeling approach is demonstrated using the experimental data obtained from a CSTR, fed with food industry waste (FIW), operating at different HRTs. The kinetic parameters were estimated through fitting to the experimental results. Hydrogen and total biogas production rates were predicted very well by the model, validating the basic assumptions regarding the implicated stoichiometric biochemical reactions and their kinetic rates. Copyright © 2017 Elsevier Ltd. All rights reserved.

Polypeptide Translocation Through the Mitochondrial TOM Channel: Temperature-Dependent Rates at the Single-Molecule Level.

PubMed

Mahendran, Kozhinjampara R; Lamichhane, Usha; Romero-Ruiz, Mercedes; Nussberger, Stephan; Winterhalter, Mathias

2013-01-03

The TOM protein complex facilitates the transfer of nearly all mitochondrial preproteins across outer mitochondrial membranes. Here we characterized the effect of temperature on facilitated translocation of a mitochondrial presequence peptide pF1β. Ion current fluctuations analysis through single TOM channels revealed thermodynamic and kinetic parameters of substrate binding and allowed determining the energy profile of peptide translocation. The activation energy for the on-rate and off-rate of the presequence peptide into the TOM complex was symmetric with respect to the electric field and estimated to be about 15 and 22 kT per peptide. These values are above that expected for free diffusion of ions in water (6 kT) and reflect the stronger interaction in the channel. Both values are in the range for typical enzyme kinetics and suggest one process without involving large conformational changes within the channel protein.

Kinetics of monomer biodegradation in soil.

PubMed

Siotto, Michela; Sezenna, Elena; Saponaro, Sabrina; Innocenti, Francesco Degli; Tosin, Maurizio; Bonomo, Luca; Mezzanotte, Valeria

2012-01-01

In modern intensive agriculture, plastics are used in several applications (i.e. mulch films, drip irrigation tubes, string, clips, pots, etc.). Interest towards applying biodegradable plastics to replace the conventional plastics is promising. Ten monomers, which can be applied in the synthesis of potentially biodegradable polyesters, were tested according to ASTM 5988-96 (standard respirometric test to evaluate aerobic biodegradation in soil by measuring the carbon dioxide evolution): adipic acid, azelaic acid, 1,4-butanediol, 1,2-ethanediol, 1,6-hexanediol, lactic acid, glucose, sebacic acid, succinic acid and terephthalic acid. Eight replicates were carried out for each monomer for 27-45 days. The numerical code AQUASIM was applied to process the CO₂ experimental data in order to estimate values for the parameters describing the different mechanisms occurring to the monomers in soil: i) the first order solubilization kinetic constant, K(sol) (d⁻¹); ii) the first order biodegradation kinetic constant, K(b) (d⁻¹); iii) the lag time in biodegradation, t(lag) (d); and iv) the carbon fraction biodegraded but not transformed into CO₂, Y (-). The following range of values were obtained: [0.006 d⁻¹, 6.9 d⁻¹] for K(sol), [0.1 d⁻¹, 1.2 d⁻¹] for K(b), and [0.32-0.58] for Y; t(lag) was observed for azelaic acid, 1,2-ethanediol, and terephthalic acid, with estimated values between 3.0 e 4.9 d. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

Development and validation of chemistry agnostic flow battery cost performance model and application to nonaqueous electrolyte systems: Chemistry agnostic flow battery cost performance model

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

Crawford, Alasdair; Thomsen, Edwin; Reed, David

2016-04-20

A chemistry agnostic cost performance model is described for a nonaqueous flow battery. The model predicts flow battery performance by estimating the active reaction zone thickness at each electrode as a function of current density, state of charge, and flow rate using measured data for electrode kinetics, electrolyte conductivity, and electrode-specific surface area. Validation of the model is conducted using a 4kW stack data at various current densities and flow rates. This model is used to estimate the performance of a nonaqueous flow battery with electrode and electrolyte properties used from the literature. The optimized cost for this system ismore » estimated for various power and energy levels using component costs provided by vendors. The model allows optimization of design parameters such as electrode thickness, area, flow path design, and operating parameters such as power density, flow rate, and operating SOC range for various application duty cycles. A parametric analysis is done to identify components and electrode/electrolyte properties with the highest impact on system cost for various application durations. A pathway to 100$kWh -1 for the storage system is identified.« less

Modeling of submicrometer aerosol penetration through sintered granular membrane filters.

PubMed

Marre, Sonia; Palmeri, John; Larbot, André; Bertrand, Marielle

2004-06-01

We present a deep-bed aerosol filtration model that can be used to estimate the efficiency of sintered granular membrane filters in the region of the most penetrating particle size. In this region the capture of submicrometer aerosols, much smaller than the filter pore size, takes place mainly via Brownian diffusion and direct interception acting in synergy. By modeling the disordered sintered grain packing of such filters as a simple cubic lattice, and mapping the corresponding 3D connected pore volume onto a discrete cylindrical pore network, the efficiency of a granular filter can be estimated, using new analytical results for the efficiency of cylindrical pores. This model for aerosol penetration in sintered granular filters includes flow slip and the kinetics of particle capture by the pore surface. With a unique choice for two parameters, namely the structural tortuosity and effective kinetic coefficient of particle adsorption, this semiempirical model can account for the experimental efficiency of a new class of "high-efficiency particulate air" ceramic membrane filters as a function of particle size over a wide range of filter thickness and texture (pore size and porosity) and operating conditions (face velocity).

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...

Traveltime-based descriptions of transport and mixing in heterogeneous domains

NASA Astrophysics Data System (ADS)

Luo, Jian; Cirpka, Olaf A.

2008-09-01

Modeling mixing-controlled reactive transport using traditional spatial discretization of the domain requires identifying the spatial distributions of hydraulic and reactive parameters including mixing-related quantities such as dispersivities and kinetic mass transfer coefficients. In most applications, breakthrough curves (BTCs) of conservative and reactive compounds are measured at only a few locations and spatially explicit models are calibrated by matching these BTCs. A common difficulty in such applications is that the individual BTCs differ too strongly to justify the assumption of spatial homogeneity, whereas the number of observation points is too small to identify the spatial distribution of the decisive parameters. The key objective of the current study is to characterize physical transport by the analysis of conservative tracer BTCs and predict the macroscopic BTCs of compounds that react upon mixing from the interpretation of conservative tracer BTCs and reactive parameters determined in the laboratory. We do this in the framework of traveltime-based transport models which do not require spatially explicit, costly aquifer characterization. By considering BTCs of a conservative tracer measured on different scales, one can distinguish between mixing, which is a prerequisite for reactions, and spreading, which per se does not foster reactions. In the traveltime-based framework, the BTC of a solute crossing an observation plane, or ending in a well, is interpreted as the weighted average of concentrations in an ensemble of non-interacting streamtubes, each of which is characterized by a distinct traveltime value. Mixing is described by longitudinal dispersion and/or kinetic mass transfer along individual streamtubes, whereas spreading is characterized by the distribution of traveltimes, which also determines the weights associated with each stream tube. Key issues in using the traveltime-based framework include the description of mixing mechanisms and the estimation of the traveltime distribution. In this work, we account for both apparent longitudinal dispersion and kinetic mass transfer as mixing mechanisms, thus generalizing the stochastic-convective model with or without inter-phase mass transfer and the advective-dispersive streamtube model. We present a nonparametric approach of determining the traveltime distribution, given a BTC integrated over an observation plane and estimated mixing parameters. The latter approach is superior to fitting parametric models in cases wherein the true traveltime distribution exhibits multiple peaks or long tails. It is demonstrated that there is freedom for the combinations of mixing parameters and traveltime distributions to fit conservative BTCs and describe the tailing. A reactive transport case of a dual Michaelis-Menten problem demonstrates that the reactive mixing introduced by local dispersion and mass transfer may be described by apparent mean mass transfer with coefficients evaluated by local BTCs.

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

Dynamic modeling of sludge compaction and consolidation processes in wastewater secondary settling tanks.

PubMed

Abusam, A; Keesman, K J

2009-01-01

The double exponential settling model is the widely accepted model for wastewater secondary settling tanks. However, this model does not estimate accurately solids concentrations in the settler underflow stream, mainly because sludge compression and consolidation processes are not considered. In activated sludge systems, accurate estimation of the solids in the underflow stream will facilitate the calibration process and can lead to correct estimates of particularly kinetic parameters related to biomass growth. Using principles of compaction and consolidation, as in soil mechanics, a dynamic model of the sludge consolidation processes taking place in the secondary settling tanks is developed and incorporated to the commonly used double exponential settling model. The modified double exponential model is calibrated and validated using data obtained from a full-scale wastewater treatment plant. Good agreement between predicted and measured data confirmed the validity of the modified model.

Photocatalytic mineralization of commercial herbicides in a pilot-scale solar CPC reactor: photoreactor modeling and reaction kinetics constants independent of radiation field.

PubMed

Colina-Márquez, Jose; Machuca-Martínez, Fiderman; Li Puma, Gianluca

2009-12-01

The six-flux absorption-scattering model (SFM) of the radiation field in the photoreactor, combined with reaction kinetics and fluid-dynamic models, has proved to be suitable to describe the degradation of water pollutants in heterogeneous photocatalytic reactors, combining simplicity and accuracy. In this study, the above approach was extended to model the photocatalytic mineralization of a commercial herbicides mixture (2,4-D, diuron, and ametryne used in Colombian sugar cane crops) in a solar, pilot-scale, compound parabolic collector (CPC) photoreactor using a slurry suspension of TiO(2). The ray-tracing technique was used jointly with the SFM to determine the direction of both the direct and diffuse solar photon fluxes and the spatial profile of the local volumetric rate of photon absorption (LVRPA) in the CPC reactor. Herbicides mineralization kinetics with explicit photon absorption effects were utilized to remove the dependence of the observed rate constants from the reactor geometry and radiation field in the photoreactor. The results showed that the overall model fitted the experimental data of herbicides mineralization in the solar CPC reactor satisfactorily for both cloudy and sunny days. Using the above approach kinetic parameters independent of the radiation field in the reactor can be estimated directly from the results of experiments carried out in a solar CPC reactor. The SFM combined with reaction kinetics and fluid-dynamic models proved to be a simple, but reliable model, for solar photocatalytic applications.

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

Ahmed, K.; Tonks, M.; Zhang, Y.

A detailed phase field model for the effect of pore drag on grain growth kinetics was implemented in MARMOT. The model takes into consideration both the curvature-driven grain boundary motion and pore migration by surface diffusion. As such, the model accounts for the interaction between pore and grain boundary kinetics, which tends to retard the grain growth process. Our 2D and 3D simulations demonstrate that the model capture all possible pore-grain boundary interactions proposed in theoretical models. For high enough surface mobility, the pores move along with the migrating boundary as a quasi-rigid-body, albeit hindering its migration rate compared tomore » the pore-free case. For less mobile pores, the migrating boundary can separate from the pores. For the pore-controlled grain growth kinetics, the model predicts a strong dependence of the growth rate on the number of pores, pore size, and surface diffusivity in agreement with theroretical models. An evolution equation for the grain size that includes these parameters was derived and showed to agree well with numerical solution. It shows a smooth transition from boundary-controlled kinetics to pore-controlled kinetics as the surface diffusivity decreases or the number of pores or their size increases. This equation can be utilized in BISON to give accurate estimate for the grain size evolution. This will be accomplished in the near future. The effect of solute drag and anisotropy of grain boundary on grain growth will be investigated in future studies.« less

EMG-Torque correction on Human Upper extremity using Evolutionary Computation

NASA Astrophysics Data System (ADS)

JL, Veronica; Parasuraman, S.; Khan, M. K. A. Ahamed; Jeba DSingh, Kingsly

2016-09-01

There have been many studies indicating that control system of rehabilitative robot plays an important role in determining the outcome of the therapy process. Existing works have done the prediction of feedback signal in the controller based on the kinematics parameters and EMG readings of upper limb's skeletal system. Kinematics and kinetics based control signal system is developed by reading the output of the sensors such as position sensor, orientation sensor and F/T (Force/Torque) sensor and there readings are to be compared with the preceding measurement to decide on the amount of assistive force. There are also other works that incorporated the kinematics parameters to calculate the kinetics parameters via formulation and pre-defined assumptions. Nevertheless, these types of control signals analyze the movement of the upper limb only based on the movement of the upper joints. They do not anticipate the possibility of muscle plasticity. The focus of the paper is to make use of the kinematics parameters and EMG readings of skeletal system to predict the individual torque of upper extremity's joints. The surface EMG signals are fed into different mathematical models so that these data can be trained through Genetic Algorithm (GA) to find the best correlation between EMG signals and torques acting on the upper limb's joints. The estimated torque attained from the mathematical models is called simulated output. The simulated output will then be compared with the actual individual joint which is calculated based on the real time kinematics parameters of the upper movement of the skeleton when the muscle cells are activated. The findings from this contribution are extended into the development of the active control signal based controller for rehabilitation robot.

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

Adsorption equilibrium and kinetics of Immunoglobulin G on a mixed-mode adsorbent in batch and packed bed configuration.

PubMed

Gomes, Pedro Ferreira; Loureiro, José Miguel; Rodrigues, Alírio E

2017-11-17

It is commonly accepted that efficient protein separation and purification to the desired level of purity is one bottleneck in pharmaceutical industries. MabDirect MM is a new type of mixed mode adsorbent, especially designed to operate in expanded bed adsorption (EBA) mode. In this study, equilibrium and kinetics experiments were carried out for the adsorption of Human Immunoglobulin G (hIgG) protein on this new adsorbent. The effects of ionic strength and pH are assessed. Langmuir isotherms parameters are obtained along with the estimation of the effective pore diffusion coefficient (D pe ) by fitting the batch adsorption kinetics experiments with the pore diffusion model. The maximum adsorption of the IgG protein on the MabDirect MM adsorbent, 149.7±7.1mg·g dry -1 , was observed from a pH 5.0 buffer solution without salt addition. Adding salt to the buffer solution, and/or increasing pH, decreases the adsorption capacity which is 4.7±0.4mg·g dry -1 for pH 7.0 with 0.4M NaCl in solution. Regarding the D pe estimation, a value of 15.4×10 -6 cm 2 ·min -1 was obtained for a pH 5.0 solution without salt. Increasing the salt concentration and/or the pH value will decrease the effective pore diffusion, the lowest D pe (0.16×10 -6 cm 2 ·min -1 ) value being observed for an IgG solution at pH 7.0 with 0.4M NaCl. Fixed bed experiments were conducted with the purpose to validate the equilibrium and kinetic parameters obtained in batch. For a feed concentration of 0.5 g·L -1 of IgG in pH 5.0 buffer solution with 0.4M NaCl, a dynamic binding capacity at 10% of breakthrough of 5.3mg·g wet -1 (15.4mg IgG ·mL resin -1 ) was obtained, representing 62% of the saturation capacity. As far as the authors know, this study is the first one concerning the adsorption of hIgG on this type of mixed mode chromatography adsorbent. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Effects of time-temperature profiles on glow curves of germanium-doped optical fibre

NASA Astrophysics Data System (ADS)

Lam, S. E.; Alawiah, A.; Bradley, D. A.; Mohd Noor, N.

2017-08-01

The Germanium (Ge) doped silica optical fibres have demonstrated the great potential to be developed as a thermoluminescent (TL) dosimeter that can be used in various applications in radiotherapy, diagnostic radiology, UV dosimetry system and food irradiation industry. Different time-temperature profile (TTP) parameters of the TL reader have been employed by many researchers in various of TL studies. Nevertheless, none of those studies adequately addressed the effects of the reader's preheat temperature and heating rate on the kinetic parameters of the TL glow curve specifically, the Ge-doped silica optical fibres. This research addresses the issue of TTP parameters with special attention to the determination of the kinetic parameters of the glow curve. The glow curve responses were explored and the kinetic parameters were analyzed by the WinGCF software, to show the effect of the preheat temperature and heating rate of the reader on Ge-doped fibre irradiated with 18 Gy of 6 MV photons radiation. The effect of TTP parameters was discussed and compared against the commercial fibre and tailored made fibre of 6 mol% Ge-doped of flat and cylindrical shape. The deconvolution of glow peaks and the kinetic parameters were obtained by the WinGCF software. This enables to fit accurately (1.5%