Sample records for michaelis-menten-like kinetic model

  1. Relation between pulmonary clearance and particle burden: a Michaelis-Menten-like kinetic model.

    Yu, R. C.; Rappaport, S.M.


    OBJECTIVES: To test the validity of a Michaelis-Menten-like kinetic model of pulmonary clearance of insoluble dusts. METHODS: Data were investigated from studies of pulmonary clearance in F344 rats exposed to antimony trioxide (Sb2O3), photocopy test toner, polyvinyl chloride powder (PVC), and diesel exhaust particles. The Michaelis-Menten-like model was used to develop a relation in which the pulmonary clearance half time was a linear function of lung burden. After combining all data, linear...

  2. Extracting signal from noise: kinetic mechanisms from a Michaelis-Menten-like expression for enzymatic fluctuations.

    Moffitt, Jeffrey R; Bustamante, Carlos


    Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models. © 2013 FEBS.

  3. Characterization of the L-glutamate clearance pathways across the blood-brain barrier and the effect of astrocytes in an in vitro blood-brain barrier model

    Helms, Hans Cc; Aldana, Blanca I; Groth, Simon


    -application of transporter inhibitors and competing amino acids. Endothelial abluminal L-glutamate uptake was almost abolished by co-application of an EAAT-1 specific inhibitor, whereas luminal uptake was inhibited by L-glutamate and L-aspartate (1 mM). L-glutamate uptake followed Michaelis-Menten-like kinetics with high...

  4. A simple theory of motor protein kinetics and energetics. II.

    Qian, H


    A three-state stochastic model of motor protein [Qian, Biophys. Chem. 67 (1997) pp. 263-267] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous solution with various ATP concentrations and its steady-state velocity. A wide variety of dynamic motor behavior are obtained from this simple model. For the particular case of free-load translocation being the most unfavorable step within the hydrolysis cycle, the load-velocity curve is quasi-linear, V/Vmax = (cF/Fmax-c)/(1-c), in contrast to the hyperbolic relationship proposed by A.V. Hill for macroscopic muscle. Significant deviation from the linearity is expected when the velocity is less than 10% of its maximal (free-load) value--a situation under which the processivity of motor diminishes and experimental observations are less certain. We then investigate the dependence of load-velocity curve on ATP (ADP) concentration. It is shown that the free load Vmax exhibits a Michaelis-Menten like behavior, and the isometric Fmax increases linearly with ln([ATP]/[ADP]). However, the quasi-linear region is independent of the ATP concentration, yielding an apparently ATP-independent maximal force below the true isometric force. Finally, the heat production as a function of ATP concentration and external load are calculated. In simple terms and solved with elementary algebra, the present model provides an integrated picture of biochemical kinetics and mechanical energetics of motor proteins.

  5. Kinetics of ethylene and ethylene oxide in subcellular fractions of lungs and livers of male B6C3F1 mice and male fischer 344 rats and of human livers.

    Li, Qiang; Csanády, György András; Kessler, Winfried; Klein, Dominik; Pankratz, Helmut; Pütz, Christian; Richter, Nadine; Filser, Johannes Georg


    Ethylene (ET) is metabolized in mammals to the carcinogenic ethylene oxide (EO). Although both gases are of high industrial relevance, only limited data exist on the toxicokinetics of ET in mice and of EO in humans. Metabolism of ET is related to cytochrome P450-dependent mono-oxygenase (CYP) and of EO to epoxide hydrolase (EH) and glutathione S-transferase (GST). Kinetics of ET metabolism to EO and of elimination of EO were investigated in headspace vessels containing incubations of subcellular fractions of mouse, rat, or human liver or of mouse or rat lung. CYP-associated metabolism of ET and GST-related metabolism of EO were found in microsomes and cytosol, respectively, of each species. EH-related metabolism of EO was not detectable in hepatic microsomes of rats and mice but obeyed saturation kinetics in hepatic microsomes of humans. In ET-exposed liver microsomes, metabolism of ET to EO followed Michaelis-Menten-like kinetics. Mean values of V(max) [nmol/(min·mg protein)] and of the apparent Michaelis constant (K(m) [mmol/l ET in microsomal suspension]) were 0.567 and 0.0093 (mouse), 0.401 and 0.031 (rat), and 0.219 and 0.013 (human). In lung microsomes, V(max) values were 0.073 (mouse) and 0.055 (rat). During ET exposure, the rate of EO production decreased rapidly. By modeling a suicide inhibition mechanism, rate constants for CYP-mediated catalysis and CYP inactivation were estimated. In liver cytosol, mean GST activities to EO expressed as V(max)/K(m) [μl/(min·mg protein)] were 27.90 (mouse), 5.30 (rat), and 1.14 (human). The parameters are most relevant for reducing uncertainties in the risk assessment of ET and EO.

  6. Stochastic kinetics of ribosomes: single motor properties and collective behavior

    Garai, Ashok; Chowdhury, Debashish; Ramakrishnan, T V


    Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a c...

  7. Oxidative desulfurization: kinetic modelling.

    Dhir, S; Uppaluri, R; Purkait, M K


    Increasing environmental legislations coupled with enhanced production of petroleum products demand, the deployment of novel technologies to remove organic sulfur efficiently. This work represents the kinetic modeling of ODS using H(2)O(2) over tungsten-containing layered double hydroxide (LDH) using the experimental data provided by Hulea et al. [V. Hulea, A.L. Maciuca, F. Fajula, E. Dumitriu, Catalytic oxidation of thiophenes and thioethers with hydrogen peroxide in the presence of W-containing layered double hydroxides, Appl. Catal. A: Gen. 313 (2) (2006) 200-207]. The kinetic modeling approach in this work initially targets the scope of the generation of a superstructure of micro-kinetic reaction schemes and models assuming Langmuir-Hinshelwood (LH) and Eley-Rideal (ER) mechanisms. Subsequently, the screening and selection of above models is initially based on profile-based elimination of incompetent schemes followed by non-linear regression search performed using the Levenberg-Marquardt algorithm (LMA) for the chosen models. The above analysis inferred that Eley-Rideal mechanism describes the kinetic behavior of ODS process using tungsten-containing LDH, with adsorption of reactant and intermediate product only taking place on the catalyst surface. Finally, an economic index is presented that scopes the economic aspects of the novel catalytic technology with the parameters obtained during regression analysis to conclude that the cost factor for the catalyst is 0.0062-0.04759 US $ per barrel.

  8. Chemical kinetics modeling

    Westbrook, C.K.; Pitz, W.J. [Lawrence Livermore National Laboratory, CA (United States)


    This project emphasizes numerical modeling of chemical kinetics of combustion, including applications in both practical combustion systems and in controlled laboratory experiments. Elementary reaction rate parameters are combined into mechanisms which then describe the overall reaction of the fuels being studied. Detailed sensitivity analyses are used to identify those reaction rates and product species distributions to which the results are most sensitive and therefore warrant the greatest attention from other experimental and theoretical research programs. Experimental data from a variety of environments are combined together to validate the reaction mechanisms, including results from laminar flames, shock tubes, flow systems, detonations, and even internal combustion engines.

  9. Electrocatalytic Mechanism Involving Michaelis-Menten Kinetics at the Preparative Scale: Theory and Applicability to Photocurrents from a Photosynthetic Algae Suspension With Quinones.

    Longatte, Guillaume; Guille-Collignon, Manon; Lemaître, Frédéric


    In the past years, many strategies have been implemented to benefit from oxygenic photosynthesis to harvest photosynthetic electrons and produce a significant photocurrent. Therefore, electrochemical tools were considered and have globally relied on the electron transfer(s) between the photosynthetic chain and a collecting electrode. In this context, we recently reported the implementation of an electrochemical set-up at the preparative scale to produce photocurrents from a Chlamydomonas reinhardtii algae suspension with an appropriate mediator (2,6-DCBQ) and a carbon gauze as the working electrode. In the present work, we wish to describe a mathematical modeling of the recorded photocurrents to better understand the effects of the experimental conditions on the photosynthetic extraction of electrons. In that way, we established a general model of an electrocatalytic mechanism at the preparative scale (that is, assuming a homogenous bulk solution at any time and a constant diffusion layer, both assumptions being valid under forced convection) in which the chemical step involves a Michaelis-Menten-like behaviour. Dependences of transient and steady-state corresponding currents were analysed as a function of different parameters by means of zone diagrams. This model was tested to our experimental data related to photosynthesis. The corresponding results suggest that competitive pathways beyond photosynthetic harvesting alone should be taken into account. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Modelling heart rate kinetics.

    Zakynthinaki, Maria S


    The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual's cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women).

  11. Modelling heart rate kinetics.

    Maria S Zakynthinaki

    Full Text Available The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise. Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual's cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women.

  12. Modelling Heart Rate Kinetics

    Zakynthinaki, Maria S.


    The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual’s cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women). PMID:25876164

  13. Onsager reciprocity principle for kinetic models and kinetic schemes

    Mahendra, Ajit Kumar


    Boltzmann equation requires some alternative simpler kinetic model like BGK to replace the collision term. Such a kinetic model which replaces the Boltzmann collision integral should preserve the basic properties and characteristics of the Boltzmann equation and comply with the requirements of non equilibrium thermodynamics. Most of the research in development of kinetic theory based methods have focused more on entropy conditions, stability and ignored the crucial aspect of non equilibrium thermodynamics. The paper presents a new kinetic model formulated based on the principles of non equilibrium thermodynamics. The new kinetic model yields correct transport coefficients and satisfies Onsager's reciprocity relationship. The present work also describes a novel kinetic particle method and gas kinetic scheme based on this linkage of non-equilibrium thermodynamics and kinetic theory. The work also presents derivation of kinetic theory based wall boundary condition which complies with the principles of non-equili...

  14. Kinetics Modeling of Cancer Immunology.


    CANCER IMMUNOLOGY -1 DTICS ELECTED SEP 9 8 UNITED STATES NAVAL ACADEMY ANNAPOLIS, MARYLAND V ,1986 %,e docment ha le approved for public A." I and sale...1986 4. TITLE (and Subtitle) S. TYPE OF REPORT & PERIOD COVERED KINETICS MODELING OF CANCER IMMUNOLOGY Final: 1985/1986 6. PERFORMING ORG. REPORT...137 (1986) "Kinetics Modeling of Cancer Immunology " A Trident Scholar Project Report by Midn I/C Scott Helmers, Class of 1986 United States Naval

  15. Crystallization Kinetics within a Generic Modelling Framework

    Meisler, Kresten Troelstrup; von Solms, Nicolas; Gernaey, Krist


    An existing generic modelling framework has been expanded with tools for kinetic model analysis. The analysis of kinetics is carried out within the framework where kinetic constitutive models are collected, analysed and utilized for the simulation of crystallization operations. A modelling...... procedure is proposed to gain the information of crystallization operation kinetic model analysis and utilize this for faster evaluation of crystallization operations....

  16. Characterization of the L-glutamate clearance pathways across the blood-brain barrier and the effect of astrocytes in an in vitro blood-brain barrier model.

    Helms, Hans Cc; Aldana, Blanca I; Groth, Simon; Jensen, Morten M; Waagepetersen, Helle S; Nielsen, Carsten U; Brodin, Birger


    The aim was to characterize the clearance pathways for L-glutamate from the brain interstitial fluid across the blood-brain barrier using a primary in vitro bovine endothelial/rat astrocyte co-culture. Transporter profiling was performed using uptake studies of radiolabeled L-glutamate with co-application of transporter inhibitors and competing amino acids. Endothelial abluminal L-glutamate uptake was almost abolished by co-application of an EAAT-1 specific inhibitor, whereas luminal uptake was inhibited by L-glutamate and L-aspartate (1 mM). L-glutamate uptake followed Michaelis-Menten-like kinetics with high and low affinity at the abluminal and luminal membrane, respectively. This indicated that L-glutamate is taken up via EAAT-1 at the abluminal membrane and exits at the luminal membrane via a low affinity glutamate/aspartate transporter. Metabolism of L-glutamate and transport of metabolites was examined using [U-(13)C] L-glutamate. Intact L-glutamate and metabolites derived from oxidative metabolism were transported through the endothelial cells. High amounts of L-glutamate-derived lactate in the luminal medium indicated cataplerosis via malic enzyme. Thus, L-glutamate can be transported intact from brain to blood via the concerted action of abluminal and luminal transport proteins, but the total brain clearance is highly dependent on metabolism in astrocytes and endothelial cells followed by transport of metabolites.

  17. Chemical kinetics and combustion modeling

    Miller, J.A. [Sandia National Laboratories, Livermore, CA (United States)


    The goal of this program is to gain qualitative insight into how pollutants are formed in combustion systems and to develop quantitative mathematical models to predict their formation rates. The approach is an integrated one, combining low-pressure flame experiments, chemical kinetics modeling, theory, and kinetics experiments to gain as clear a picture as possible of the process in question. These efforts are focused on problems involved with the nitrogen chemistry of combustion systems and on the formation of soot and PAH in flames.

  18. Kinetic Modeling of Biological Systems

    Resat, Haluk; Petzold, Linda; Pettigrew, Michel F.


    The dynamics of how its constituent components interact define the spatio-temporal response of a natural system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided.

  19. Kinetic modelling of enzymatic starch hydrolysis

    Bednarska, K.A.


    Kinetic modelling of enzymatic starch hydrolysis – a summary K.A. Bednarska The dissertation entitled ‘Kinetic modelling of enzymatic starch hydrolysis’ describes the enzymatic hydrolysis and kinetic modelling of liquefaction and saccharification of wheat starch. A

  20. Kinetic models of conjugated metabolic cycles

    Ershov, Yu. A.


    A general method is developed for the quantitative kinetic analysis of conjugated metabolic cycles in the human organism. This method is used as a basis for constructing a kinetic graph and model of the conjugated citric acid and ureapoiesis cycles. The results from a kinetic analysis of the model for these cycles are given.

  1. A model of reactor kinetics

    Thompson, A.S.; Thompson, B.R.


    The analytical model of nuclear reactor transients, incorporating both mechanical and nuclear effects, simulates reactor kinetics. Linear analysis shows the stability borderline for small power perturbations. In a stable system, initial power disturbances die out with time. With an unstable combination of nuclear and mechanical characteristics, initial disturbances persist and may increase with time. With large instability, oscillations of great magnitude occur. Stability requirements set limits on the power density at which particular reactors can operate. The limiting power density depends largely on the product of two terms: the fraction of delayed neutrons and the frictional damping of vibratory motion in reactor core components. As the fraction of delayed neutrons is essentially fixed, mechanical damping largely determines the maximum power density. A computer program, based on the analytical model, calculates and plots reactor power as a nonlinear function of time in response to assigned values of mechanical and nuclear characteristics.

  2. Kinetics model for lutate dosimetry

    Lima, M.F.; Mesquita, C.H., E-mail:, E-mail: [Instituto de Pesquisas Energeticas (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)


    The use of compartmental analysis to predict the behavior of drugs in the organism is considered the better option among numerous methods employed in pharmacodynamics. A six compartments model was developed to determinate the kinetic constants of 177Lu-DOTATATO biodistribution using data from one published study with 67 patients treated by PRRT (Peptide receptor radionuclide therapy) and followed by CT during 68,25 hours. The compartmental analysis was made using the software AnaComp Registered-Sign . The influence of the time pos-injection over the dose assessment was studied taking into account the renal excretion management by aminoacid coinfusion, whose direct effects persist in the first day. The biodistribution curve was split in five sectors: 0-0.25h; 0-3.25h; 3.25-24.25h; 24.25-68.25h and 3.25-68.25h. After the examination of that influence, the study was concentrated in separate the biodistribution curve in two phases. Phase 1: governed by uptake from the blood, considering the time pos-injection until 3.25h and phase 2: governed by renal excretion, considering the time pos-injection from 3.25h to 68.25h. The model considered the organs and tissues superposition in the CT image acquisition by sampling parameters as the contribution of the the activity concentration in blood and relation between the sizes of the whole body and measured organs. The kinetic constants obtained from each phase (1 and 2) were used in dose assessment to patients in 26 organs and tissues described by MIRD. Dosimetry results were in agreement with the available results from literature, restrict to whole body, kidneys, bone marrow, spleen and liver. The advantage of the proposed model is the compartmental method quickness and power to estimate dose in organs and tissues, including tumor that, in the most part, were not discriminate by voxels of phantoms built using CT images. (author)

  3. Crystallization Kinetics within a Generic Modeling Framework

    Meisler, Kresten Troelstrup; von Solms, Nicolas; Gernaey, Krist V.


    to the modeling of various kinetic phenomena like nucleation, growth, agglomeration, and breakage are discussed in terms of model forms, model parameters, their availability and/or estimation, and their selection and application for specific crystallization operational scenarios under study. The advantages......A new and extended version of a generic modeling framework for analysis and design of crystallization operations is presented. The new features of this framework are described, with focus on development, implementation, identification, and analysis of crystallization kinetic models. Issues related...... of employing a well-structured model library for storage, use/reuse, and analysis of the kinetic models are highlighted. Examples illustrating the application of the modeling framework for kinetic model discrimination related to simulation of specific crystallization scenarios and for kinetic model parameter...

  4. Chemical Kinetic Modeling of 2-Methylhexane Combustion

    Mohamed, Samah Y.


    Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important for investigating the combustion behavior of diesel, gasoline, and aviation fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracy in certain portions of the models. This study focuses on updating thermodynamic data and kinetic model for a gasoline surrogate fuel, 2-methylhexane, with recently published group values and rate rules. These update provides a better agreement with rapid compression machine measurements of ignition delay time, while also strengthening the fundamental basis of the model.

  5. Error correction during DNA replication: DNAP as Dr. Jekyll-and-Mr. Hyde

    Sharma, Ajeet K


    DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\\it polymerase} catalyzing the elongation of a new DNA molecule by adding a monomer. However, it can switch to the role of an {\\it exonuclease} and shorten the same DNA by cleavage of the last incorporated monomer from the nascent DNA. Just as misincorporated nucleotides can escape exonuclease causing replication error, correct nucleotide may get sacrificed unnecessarily by erroneous cleavage. The interplay of polymerase and exonuclease activities of a DNAP is explored here by developing a minimal stochastic kinetic model of DNA replication. Exact analytical expressions are derived for a few key statistical distributions; these characterize the temporal patterns in the mechanical stepping and the chemical (cleavage) reaction. The Michaelis-Menten-like analytical expression derived for the average rates of these two processes not only demonstrate the ef...

  6. Modeling of Reactor Kinetics and Dynamics

    Matthew Johnson; Scott Lucas; Pavel Tsvetkov


    In order to model a full fuel cycle in a nuclear reactor, it is necessary to simulate the short time-scale kinetic behavior of the reactor as well as the long time-scale dynamics that occur with fuel burnup. The former is modeled using the point kinetics equations, while the latter is modeled by coupling fuel burnup equations with the kinetics equations. When the equations are solved simultaneously with a nonlinear equation solver, the end result is a code with the unique capability of modeling transients at any time during a fuel cycle.

  7. An equilibrium and kinetic modeling



    Jun 18, 2007 ... Potato dextrose agar medium was prepared by taking 200 g of peeled and sliced potato with .... of glucose as carbon source and ammonium chloride as nitrogen source each. .... Pore and solid diffusion kinetics in fixed bed ...

  8. Kinetic exchange models for social opinion formation

    Lallouache, Mehdi; Chakrabarti, Bikas K


    We propose a minimal model for the collective dynamics of opinion formation in the society, by modifying kinetic exchange dynamics studied in the context of income, money or wealth distributions in a society.

  9. Chemical Kinetic Modeling of Advanced Transportation Fuels

    PItz, W J; Westbrook, C K; Herbinet, O


    Development of detailed chemical kinetic models for advanced petroleum-based and nonpetroleum based fuels is a difficult challenge because of the hundreds to thousands of different components in these fuels and because some of these fuels contain components that have not been considered in the past. It is important to develop detailed chemical kinetic models for these fuels since the models can be put into engine simulation codes used for optimizing engine design for maximum efficiency and minimal pollutant emissions. For example, these chemistry-enabled engine codes can be used to optimize combustion chamber shape and fuel injection timing. They also allow insight into how the composition of advanced petroleum-based and non-petroleum based fuels affect engine performance characteristics. Additionally, chemical kinetic models can be used separately to interpret important in-cylinder experimental data and gain insight into advanced engine combustion processes such as HCCI and lean burn engines. The objectives are: (1) Develop detailed chemical kinetic reaction models for components of advanced petroleum-based and non-petroleum based fuels. These fuels models include components from vegetable-oil-derived biodiesel, oil-sand derived fuel, alcohol fuels and other advanced bio-based and alternative fuels. (2) Develop detailed chemical kinetic reaction models for mixtures of non-petroleum and petroleum-based components to represent real fuels and lead to efficient reduced combustion models needed for engine modeling codes. (3) Characterize the role of fuel composition on efficiency and pollutant emissions from practical automotive engines.

  10. A kinetic model for predicting biodegradation.

    Dimitrov, S; Pavlov, T; Nedelcheva, D; Reuschenbach, P; Silvani, M; Bias, R; Comber, M; Low, L; Lee, C; Parkerton, T; Mekenyan, O


    Biodegradation plays a key role in the environmental risk assessment of organic chemicals. The need to assess biodegradability of a chemical for regulatory purposes supports the development of a model for predicting the extent of biodegradation at different time frames, in particular the extent of ultimate biodegradation within a '10 day window' criterion as well as estimating biodegradation half-lives. Conceptually this implies expressing the rate of catabolic transformations as a function of time. An attempt to correlate the kinetics of biodegradation with molecular structure of chemicals is presented. A simplified biodegradation kinetic model was formulated by combining the probabilistic approach of the original formulation of the CATABOL model with the assumption of first order kinetics of catabolic transformations. Nonlinear regression analysis was used to fit the model parameters to OECD 301F biodegradation kinetic data for a set of 208 chemicals. The new model allows the prediction of biodegradation multi-pathways, primary and ultimate half-lives and simulation of related kinetic biodegradation parameters such as biological oxygen demand (BOD), carbon dioxide production, and the nature and amount of metabolites as a function of time. The model may also be used for evaluating the OECD ready biodegradability potential of a chemical within the '10-day window' criterion.

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

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


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

  12. Chemical Kinetic Models for Advanced Engine Combustion

    Pitz, William J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mehl, Marco [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Westbrook, Charles K. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    The objectives for this project are as follows: Develop detailed chemical kinetic models for fuel components used in surrogate fuels for compression ignition (CI), homogeneous charge compression ignition (HCCI) and reactivity-controlled compression-ignition (RCCI) engines; and Combine component models into surrogate fuel models to represent real transportation fuels. Use them to model low-temperature combustion strategies in HCCI, RCCI, and CI engines that lead to low emissions and high efficiency.

  13. Kinetic models with randomly perturbed binary collisions

    Bassetti, Federico; Toscani, Giuseppe


    We introduce a class of Kac-like kinetic equations on the real line, with general random collisional rules, which include as particular cases models for wealth redistribution in an agent-based market or models for granular gases with a background heat bath. Conditions on these collisional rules which guarantee both the existence and uniqueness of equilibrium profiles and their main properties are found. We show that the characterization of these stationary solutions is of independent interest, since the same profiles are shown to be solutions of different evolution problems, both in the econophysics context and in the kinetic theory of rarefied gases.

  14. Kinetic and hydrodynamic models of chemotactic aggregation

    Chavanis, Pierre-Henri


    We derive general kinetic and hydrodynamic models of chemotactic aggregation that describe certain features of the morphogenesis of biological colonies (like bacteria, amoebae, endothelial cells or social insects). Starting from a stochastic model defined in terms of N coupled Langevin equations, we derive a nonlinear mean field Fokker-Planck equation governing the evolution of the distribution function of the system in phase space. By taking the successive moments of this kinetic equation and using a local thermodynamic equilibrium condition, we derive a set of hydrodynamic equations involving a damping term. In the limit of small frictions, we obtain a hyperbolic model describing the formation of network patterns (filaments) and in the limit of strong frictions we obtain a parabolic model which is a generalization of the standard Keller-Segel model describing the formation of clusters (clumps). Our approach connects and generalizes several models introduced in the chemotactic literature. We discuss the anal...

  15. A kinetic model of zircon thermoluminescence

    Turkin, A.A.; Es, H.J. van; Vainshtein, D.I.; Hartog, H.W. den

    A kinetic model of zircon thermoluminescence (TL) has been constructed to simulate the processes and stages relevant to thermoluminescent dating such as: filling of electron and hole traps during the excitation stage both for natural and laboratory irradiation; the time dependence of fading after

  16. Kinetic modeling of reactions in Foods

    Boekel, van M.A.J.S.


    The level of quality that food maintains as it travels down the production-to-consumption path is largely determined by the chemical, biochemical, physical, and microbiological changes that take place during its processing and storage. Kinetic Modeling of Reactions in Foods demonstrates how to effec

  17. Gaussian kinetic model for granular gases.

    Dufty, James W; Baskaran, Aparna; Zogaib, Lorena


    A kinetic model for the Boltzmann equation is proposed and explored as a practical means to investigate the properties of a dilute granular gas. It is shown that all spatially homogeneous initial distributions approach a universal "homogeneous cooling solution" after a few collisions. The homogeneous cooling solution (HCS) is studied in some detail and the exact solution is compared with known results for the hard sphere Boltzmann equation. It is shown that all qualitative features of the HCS, including the nature of overpopulation at large velocities, are reproduced by the kinetic model. It is also shown that all the transport coefficients are in excellent agreement with those from the Boltzmann equation. Also, the model is specialized to one having a velocity independent collision frequency and the resulting HCS and transport coefficients are compared to known results for the Maxwell model. The potential of the model for the study of more complex spatially inhomogeneous states is discussed.

  18. Kinetics model development of cocoa bean fermentation

    Kresnowati, M. T. A. P.; Gunawan, Agus Yodi; Muliyadini, Winny


    Although Indonesia is one of the biggest cocoa beans producers in the world, Indonesian cocoa beans are oftenly of low quality and thereby frequently priced low in the world market. In order to improve the quality, adequate post-harvest cocoa processing techniques are required. Fermentation is the vital stage in series of cocoa beans post harvest processing which could improve the quality of cocoa beans, in particular taste, aroma, and colours. During the fermentation process, combination of microbes grow producing metabolites that serve as the precursors for cocoa beans flavour. Microbial composition and thereby their activities will affect the fermentation performance and influence the properties of cocoa beans. The correlation could be reviewed using a kinetic model that includes unstructured microbial growth, substrate utilization and metabolic product formation. The developed kinetic model could be further used to design cocoa bean fermentation process to meet the expected quality. Further the development of kinetic model of cocoa bean fermentation also serve as a good case study of mixed culture solid state fermentation, that has rarely been studied. This paper presents the development of a kinetic model for solid-state cocoa beans fermentation using an empirical approach. Series of lab scale cocoa bean fermentations, either natural fermentations without starter addition or fermentations with mixed yeast and lactic acid bacteria starter addition, were used for model parameters estimation. The results showed that cocoa beans fermentation can be modelled mathematically and the best model included substrate utilization, microbial growth, metabolites production and its transport. Although the developed model still can not explain the dynamics in microbial population, this model can sufficiently explained the observed changes in sugar concentration as well as metabolic products in the cocoa bean pulp.

  19. Computational model for Halorhodopsin photocurrent kinetics

    Bravo, Jaime; Stefanescu, Roxana; Talathi, Sachin


    Optogenetics is a rapidly developing novel optical stimulation technique that employs light activated ion channels to excite (using channelrhodopsin (ChR)) or suppress (using halorhodopsin (HR)) impulse activity in neurons with high temporal and spatial resolution. This technique holds enormous potential to externally control activity states in neuronal networks. The channel kinetics of ChR and HR are well understood and amenable for mathematical modeling. Significant progress has been made in recent years to develop models for ChR channel kinetics. To date however, there is no model to mimic photocurrents produced by HR. Here, we report the first model developed for HR photocurrents based on a four-state model of the HR photocurrent kinetics. The model provides an excellent fit (root-mean-square error of 3.1862x10-4, to an empirical profile of experimentally measured HR photocurrents. In combination, mathematical models for ChR and HR photocurrents can provide effective means to design test light based control systems to regulate neural activity, which in turn may have implications for the development of novel light based stimulation paradigms for brain disease control. I would like to thank the University of Florida and the Physics Research Experience for Undergraduates (REU) program, funded through NSF DMR-1156737. This research was also supported through start-up funds provided to Dr. Sachin Talathi

  20. Modeling inhomogeneous DNA replication kinetics.

    Michel G Gauthier

    Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

  1. Reduced Chemical Kinetic Model for Titan Entries

    Romain Savajano


    Full Text Available A reduced chemical kinetic model for Titan's atmosphere has been developed. This new model with 18 species and 28 reactions includes the mainfeatures of a more complete scheme, respecting the radiative fluxes. It has been verified against three key elements: a sensitivity analysis, the equilibrium chemical composition using shock tube simulations in CHEMKIN, and the results of computational fluid dynamics (CFDs simulations.

  2. Compartmental modeling and tracer kinetics

    Anderson, David H


    This monograph is concerned with mathematical aspects of compartmental an­ alysis. In particular, linear models are closely analyzed since they are fully justifiable as an investigative tool in tracer experiments. The objective of the monograph is to bring the reader up to date on some of the current mathematical prob­ lems of interest in compartmental analysis. This is accomplished by reviewing mathematical developments in the literature, especially over the last 10-15 years, and by presenting some new thoughts and directions for future mathematical research. These notes started as a series of lectures that I gave while visiting with the Division of Applied ~1athematics, Brown University, 1979, and have developed in­ to this collection of articles aimed at the reader with a beginning graduate level background in mathematics. The text can be used as a self-paced reading course. With this in mind, exercises have been appropriately placed throughout the notes. As an aid in reading the material, the e~d of a ...

  3. Thermodynamic and kinetic modelling: creep resistant materials

    Hald, John; Korcakova, L.; Danielsen, Hilmar Kjartansson


    particles and coarsening of MX, M23C6 and Laves phase particles. The modelling provided new insight into the long term stability of new steels. Modelling of the detrimental precipitation of Z phase Cr(V,Nb)N is described, which points to new approaches in alloy development for higher temperatures......The use of thermodynamic and kinetic modelling of microstructure evolution in materials exposed to high temperatures in power plants is demonstrated with two examples. Precipitate stability in martensitic 9–12%Cr steels is modelled including equilibrium phase stability, growth of Laves phase...


    G. T. Justino

    Full Text Available Abstract The high octane number of pyrolysis gasoline (PYGAS explains its insertion in the gasoline pool. However, its use is troublesome due to the presence of gum-forming chemicals which, in turn, can be removed via hydrogenation. The use of Langmuir-Hinshelwood kinetic models was evaluated for hydrogenation of styrene, a typical gum monomer, using Pd/9%Nb2O5-Al2O3 as catalyst. Kinetic models accounting for hydrogen dissociative and non-dissociative adsorption were considered. The availability of one or two kinds of catalytic sites was analyzed. Experiments were carried out in a semi-batch reactor at constant temperature and pressure in the absence of transport limitations. The conditions used in each experiment varied between 16 - 56 bar and 60 - 100 ºC for pressure and temperature, respectively. The kinetic models were evaluated using MATLAB and EMSO software. Models using adsorption of hydrogen and organic molecules on the same type of site fitted the data best.

  5. A kinetic model for chemical neurotransmission

    Ramirez-Santiago, Guillermo; Martinez-Valencia, Alejandro; Fernandez de Miguel, Francisco

    Recent experimental observations in presynaptic terminals at the neuromuscular junction indicate that there are stereotyped patterns of cooperativeness in the fusion of adjacent vesicles. That is, a vesicle in hemifusion process appears on the side of a fused vesicle and which is followed by another vesicle in a priming state while the next one is in a docking state. In this talk we present a kinetic model for this morphological pattern in which each vesicle state previous to the exocytosis is represented by a kinetic state. This chain states kinetic model can be analyzed by means of a Master equation whose solution is simulated with the stochastic Gillespie algorithm. With this approach we have reproduced the responses to the basal release in the absence of stimulation evoked by the electrical activity and the phenomena of facilitation and depression of neuromuscular synapses. This model offers new perspectives to understand the underlying phenomena in chemical neurotransmission based on molecular interactions that result in the cooperativity between vesicles during neurotransmitter release. DGAPA Grants IN118410 and IN200914 and Conacyt Grant 130031.

  6. Kinetic effects in edge plasma: kinetic modeling for edge plasma and detached divertor

    Takizuka, T.


    Detached divertor is considered a solution for the heat control in magnetic-confinement fusion reactors. Numerical simulations using the comprehensive divertor codes based on the plasma fluid modeling are indispensable for the design of the detached divertor in future reactors. Since the agreement in the results between detached-divertor experiments and simulations has been rather fair but not satisfactory, further improvement of the modeling is required. The kinetic effect is one of key issues for improving the modeling. Complete kinetic behaviors are able to be simulated by the kinetic modeling. In this paper at first, major kinetic effects in edge plasma and detached divertor are listed. One of the most powerful kinetic models, particle-in-cell (PIC) model, is described in detail. Several results of PIC simulations of edge-plasma kinetic natures are presented. Future works on PIC modeling and simulation for the deeper understanding of edge plasma and detached divertor are discussed.


    Daniele Penteado Rosa


    Full Text Available Drying of orange seeds representing waste products from juice processing was studied in the temperatures of 40, 50, 60 and 70 °C and drying velocities of 0.6, 1.0 and 1.4 m/s. Experimental drying kinetics of orange seeds were obtained using a convective air forced dryer. Three thin-layer models: Page model, Lewis model, and the Henderson-Pabis model and the diffusive model were used to predict the drying curves. The Henderson-Pabis and the diffusive models show the best fitting performance and statistical evaluations. Moreover, the temperature dependence on the effective diffusivity followed an Arrhenius relationship, and the activation energies ranging from 16.174 to 16.842 kJ/mol

  8. Modelling dimercaptosuccinic acid (DMSA) plasma kinetics in humans

    van Eijkeren, Jan C H; Olie, J Daniël N; Bradberry, Sally M; Vale, J Allister; de Vries, Irma; Meulenbelt, Jan; Hunault, Claudine C


    CONTEXT: No kinetic models presently exist which simulate the effect of chelation therapy on lead blood concentrations in lead poisoning. OBJECTIVE: Our aim was to develop a kinetic model that describes the kinetics of dimercaptosuccinic acid (DMSA; succimer), a commonly used chelating agent, that c

  9. A kinetic model of plasma turbulence

    Servidio, S.; Valentini, F.; Perrone, D.; Greco, A.; Califano, F.; Matthaeus, W. H.; Veltri, P.


    A Hybrid Vlasov-Maxwell (HVM) model is presented and recent results about the link between kinetic effects and turbulence are reviewed. Using five-dimensional (2D in space and 3D in the velocity space) simulations of plasma turbulence, it is found that kinetic effects (or non-fluid effects) manifest through the deformation of the proton velocity distribution function (DF), with patterns of non-Maxwellian features being concentrated near regions of strong magnetic gradients. The direction of the proper temperature anisotropy, calculated in the main reference frame of the distribution itself, has a finite probability of being along or across the ambient magnetic field, in general agreement with the classical definition of anisotropy T ⊥/T ∥ (where subscripts refer to the magnetic field direction). Adopting the latter conventional definition, by varying the global plasma beta (β) and fluctuation level, simulations explore distinct regions of the space given by T ⊥/T ∥ and β∥, recovering solar wind observations. Moreover, as in the solar wind, HVM simulations suggest that proton anisotropy is not only associated with magnetic intermittent events, but also with gradient-type structures in the flow and in the density. The role of alpha particles is reviewed using multi-ion kinetic simulations, revealing a similarity between proton and helium non-Maxwellian effects. The techniques presented here are applied to 1D spacecraft-like analysis, establishing a link between non-fluid phenomena and solar wind magnetic discontinuities. Finally, the dimensionality of turbulence is investigated, for the first time, via 6D HVM simulations (3D in both spaces). These preliminary results provide support for several previously reported studies based on 2.5D simulations, confirming several basic conclusions. This connection between kinetic features and turbulence open a new path on the study of processes such as heating, particle acceleration, and temperature

  10. Mathematical Modelling of Thermal Degradation Kinetics of Ascorbic ...

    However, adequate study has not been conducted to exploit the potential of this ... of ascorbic acid in yeabesha gomen fitted first-order reaction kinetic model ... Activation energy for ascorbic degeneration kinetics of yeabesha gomen was ...

  11. Thermodynamic and kinetic modeling of transcriptional pausing.

    Tadigotla, Vasisht R; O Maoiléidigh, Dáibhid; Sengupta, Anirvan M; Epshtein, Vitaly; Ebright, Richard H; Nudler, Evgeny; Ruckenstein, Andrei E


    We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the associated DNA-RNA hybrid; and (iii) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotranscriptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.

  12. Thermodynamically consistent model calibration in chemical kinetics

    Goutsias John


    Full Text Available Abstract 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 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

  13. Modeling in applied sciences a kinetic theory approach

    Pulvirenti, Mario


    Modeling complex biological, chemical, and physical systems, in the context of spatially heterogeneous mediums, is a challenging task for scientists and engineers using traditional methods of analysis Modeling in Applied Sciences is a comprehensive survey of modeling large systems using kinetic equations, and in particular the Boltzmann equation and its generalizations An interdisciplinary group of leading authorities carefully develop the foundations of kinetic models and discuss the connections and interactions between model theories, qualitative and computational analysis and real-world applications This book provides a thoroughly accessible and lucid overview of the different aspects, models, computations, and methodology for the kinetic-theory modeling process Topics and Features * Integrated modeling perspective utilized in all chapters * Fluid dynamics of reacting gases * Self-contained introduction to kinetic models * Becker–Doring equations * Nonlinear kinetic models with chemical reactions * Kinet...

  14. On Kinetics Modeling of Vibrational Energy Transfer

    Gilmore, John O.; Sharma, Surendra P.; Cavolowsky, John A. (Technical Monitor)


    Two models of vibrational energy exchange are compared at equilibrium to the elementary vibrational exchange reaction for a binary mixture. The first model, non-linear in the species vibrational energies, was derived by Schwartz, Slawsky, and Herzfeld (SSH) by considering the detailed kinetics of vibrational energy levels. This model recovers the result demanded at equilibrium by the elementary reaction. The second model is more recent, and is gaining use in certain areas of computational fluid dynamics. This model, linear in the species vibrational energies, is shown not to recover the required equilibrium result. Further, this more recent model is inconsistent with its suggested rate constants in that those rate constants were inferred from measurements by using the SSH model to reduce the data. The non-linear versus linear nature of these two models can lead to significant differences in vibrational energy coupling. Use of the contemporary model may lead to significant misconceptions, especially when integrated in computer codes considering multiple energy coupling mechanisms.




    Full Text Available The paper presents kinetics modelling of adsorption of fluorine onto modified diatomite, its fundamental characteristics and mathematical derivations. Three models of defluoridation kinetics were used to fit the experimental results on adsorption fluorine onto diatomite: the pseudo-first order model Lagergren, the pseudo-second order model G. McKay and H.S. Ho and intraparticle diffusion model of W.J. Weber and J.C. Morris. Kinetics studies revealed that the adsorption of fluorine followed second-order rate model, complimented by intraparticle diffusion kinetics. The adsorption mechanism of fluorine involved three stages – external surface adsorption, intraparticle diffusion and the stage of equilibrium.

  16. Kinetic depletion model for pellet ablation

    Kuteev, Boris V. [State Technical Univ., St. Petersburg (Russian Federation)


    A kinetic model for depletion effect, which determines pellet ablation when the pellet passes a rational magnetic surface, is formulated. The model predicts a moderate decrease of the ablation rate compared with the earlier considered monoenergy versions [1, 2]. For typical T-10 conditions the ablation rate reduces by a reactor of 2.5 when the 1-mm pellet penetrates through the plasma center. A substantial deceleration of pellets -about 15% per centimeter of low shire rational q region; is predicted. Penetration for Low Field Side and High Field Side injections is considered taking into account modification of the electron distribution function by toroidal magnetic field. It is shown that Shafranov shift and toroidal effects yield the penetration length for HFS injection higher by a factor of 1.5. This fact should be taken into account when plasma-shielding effects on penetration are considered. (author)

  17. Holographic kinetic k-essence model

    Cruz, Norman [Departamento de Fisica, Facultad de Ciencia, Universidad de Santiago de Chile, Casilla 307, Santiago (Chile)], E-mail:; Gonzalez-Diaz, Pedro F.; Rozas-Fernandez, Alberto [Colina de los Chopos, Instituto de Fisica Fundamental, Consejo Superior de Investigaciones Cientificas, Serrano 121, 28006 Madrid (Spain)], E-mail:; Sanchez, Guillermo [Departamento de Matematica y Ciencia de la Computacion, Facultad de Ciencia, Universidad de Santiago de Chile, Casilla 307, Santiago (Chile)], E-mail:


    We consider a connection between the holographic dark energy density and the kinetic k-essence energy density in a flat FRW universe. With the choice c{>=}1, the holographic dark energy can be described by a kinetic k-essence scalar field in a certain way. In this Letter we show this kinetic k-essential description of the holographic dark energy with c{>=}1 and reconstruct the kinetic k-essence function F(X)

  18. Population balance modeling of antibodies aggregation kinetics.

    Arosio, Paolo; Rima, Simonetta; Lattuada, Marco; Morbidelli, Massimo


    The aggregates morphology and the aggregation kinetics of a model monoclonal antibody under acidic conditions have been investigated. Growth occurs via irreversible cluster-cluster coagulation forming compact, fractal aggregates with fractal dimension of 2.6. We measured the time evolution of the average radius of gyration, , and the average hydrodynamic radius, , by in situ light scattering, and simulated the aggregation kinetics by a modified Smoluchowski's population balance equations. The analysis indicates that aggregation does not occur under diffusive control, and allows quantification of effective intermolecular interactions, expressed in terms of the Fuchs stability ratio (W). In particular, by introducing a dimensionless time weighed on W, the time evolutions of measured under various operating conditions (temperature, pH, type and concentration of salt) collapse on a single master curve. The analysis applies also to data reported in the literature when growth by cluster-cluster coagulation dominates, showing a certain level of generality in the antibodies aggregation behavior. The quantification of the stability ratio gives important physical insights into the process, including the Arrhenius dependence of the aggregation rate constant and the relationship between monomer-monomer and cluster-cluster interactions. Particularly, it is found that the reactivity of non-native monomers is larger than that of non-native aggregates, likely due to the reduction of the number of available hydrophobic patches during aggregation.

  19. Kinetic modelling of coupled transport across biological membranes.

    Korla, Kalyani; Mitra, Chanchal K


    In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.

  20. Electrothermal Model of Kinetic Inductance Detectors

    Thomas, Christopher N; Goldie, David J


    An electrothermal model of Kinetic Inductance Detectors (KIDs) is described. The non-equilibrium state of the resonator's quasiparticle system is characterized by an effective temperature, which because of readout-power heating is higher than that of the bath. By balancing the flow of energy into the quasiparticle system, it is possible to calculate the steady-state large-signal, small-signal and noise behaviour. Resonance-curve distortion and hysteretic switching appear naturally within the framework. It is shown that an electrothermal feedback process exists, which affects all aspects of behaviour. It is also shown that generation-recombination noise can be interpreted in terms of the thermal fluctuation noise in the effective thermal conductance that links the quasiparticle and phonon systems of the resonator. Because the scheme is based on electrothermal considerations, multiple elements can be added to simulate the behaviour of complex devices, such as resonators on membranes, again taking into account r...

  1. A review on solar wind modeling: kinetic and fluid aspects

    Echim, Marius; Lie-Svendsen, Oystein


    We review the main advantages and limitations of the kinetic exospheric and fluid models of the solar wind (SW). We discuss the hydrostatic model imagined by Chapman, the first supersonic hydrodynamic models published by Parker and the first generation subsonic kinetic model proposed by Chamberlain. It is shown that a correct estimation of the electric field as in the second generation kinetic exospheric models developed by Lemaire and Scherer, provides a supersonic expansion of the corona, reconciling the hydrodynamic and the kinetic approach. The third generation kinetic exospheric models considers kappa velocity distribution function (VDF) instead of a Maxwellian at the exobase and in addition they treat a non-monotonic variation of the electric potential with the radial distance; the fourth generation exospheric models include Coulomb collisions based on the Fokker--Planck collision term. Multi-fluid models of the solar wind provide a coarse grained description and reproduce with success the spatio-tempor...

  2. Chemical Kinetic Modeling of Biofuel Combustion

    Sarathy, Subram Maniam

    Bioalcohols, such as bioethanol and biobutanol, are suitable replacements for gasoline, while biodiesel can replace petroleum diesel. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This study's contribution is experimentally validated chemical kinetic combustion mechanisms for biobutanol and biodiesel. Fundamental combustion data and chemical kinetic mechanisms are presented and discussed to improve our understanding of biofuel combustion. The net environmental impact of biobutanol (i.e., n-butanol) has not been studied extensively, so this study first assesses the sustainability of n-butanol derived from corn. The results indicate that technical advances in fuel production are required before commercializing biobutanol. The primary contribution of this research is new experimental data and a novel chemical kinetic mechanism for n-butanol combustion. The results indicate that under the given experimental conditions, n-butanol is consumed primarily via abstraction of hydrogen atoms to produce fuel radical molecules, which subsequently decompose to smaller hydrocarbon and oxygenated species. The hydroxyl moiety in n-butanol results in the direct production of the oxygenated species such as butanal, acetaldehyde, and formaldehyde. The formation of these compounds sequesters carbon from forming soot precursors, but they may introduce other adverse environmental and health effects. Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents high quality experimental data for one large fatty acid methyl ester, methyl decanoate, and models its combustion using an improved skeletal mechanism. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which ultimately lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular

  3. Thermoluminescence of zircon: a kinetic model

    Turkin, A A; Vainshtein, D I; Hartog, H W D


    The mineral zircon, ZrSiO sub 4 , belongs to a class of promising materials for geochronometry by means of thermoluminescence (TL) dating. The development of a reliable and reproducible method for TL dating with zircon requires detailed knowledge of the processes taking place during exposure to ionizing radiation, long-term storage, annealing at moderate temperatures and heating at a constant rate (TL measurements). To understand these processes one needs a kinetic model of TL. This paper is devoted to the construction of such a model. The goal is to study the qualitative behaviour of the system and to determine the parameters and processes controlling TL phenomena of zircon. The model considers the following processes: (i) Filling of electron and hole traps at the excitation stage as a function of the dose rate and the dose for both (low dose rate) natural and (high dose rate) laboratory irradiation. (ii) Time dependence of TL fading in samples irradiated under laboratory conditions. (iii) Short time anneali...

  4. Kinetic modelling of krypton fluoride laser systems

    Jancaitis, K.S.


    A kinetic model has been developed for the KrF* rare gas halide laser system, specifically for electron-beam pumped mixtures of krypton, fluorine, and either helium or argon. The excitation produced in the laser gas by the e-beam was calculated numerically using an algorithm checked by comparing the predicted ionization yields in the pure rare gases with their experimental values. The excitation of the laser media by multi-kilovolt x-rays was also modeled and shown to be similar to that produced by high energy electrons. A system of equations describing the transfer of the initial gas excitation into the laser upper level was assembled using reaction rate constants from both experiment and theory. A one-dimensional treatment of the interaction of the laser radiation with the gas was formulated which considered spontaneous and stimulated emission and absorption. The predictions of this model were in good agreement with the fluorescence signals and gain and absorption measured experimentally.

  5. Shear-Driven Reconnection in Kinetic Models

    Black, C.; Antiochos, S. K.; Germaschewski, K.; Karpen, J. T.; DeVore, C. R.; Bessho, N.


    The explosive energy release in solar eruptive phenomena is believed to be due to magnetic reconnection. In the standard model for coronal mass ejections (CME) and/or solar flares, the free energy for the event resides in the strongly sheared magnetic field of a filament channel. The pre-eruption force balance consists of an upward force due to the magnetic pressure of the sheared field countered by a downward tension due to overlying unsheared field. Magnetic reconnection disrupts this force balance; therefore, it is critical for understanding CME/flare initiation, to model the onset of reconnection driven by the build-up of magnetic shear. In MHD simulations, the application of a magnetic-field shear is a trivial matter. However, kinetic effects are dominant in the diffusion region and thus, it is important to examine this process with PIC simulations as well. The implementation of such a driver in PIC methods is challenging, however, and indicates the necessity of a true multiscale model for such processes in the solar environment. The field must be sheared self-consistently and indirectly to prevent the generation of waves that destroy the desired system. Plasma instabilities can arise nonetheless. In the work presented here, we show that we can control this instability and generate a predicted out-of-plane magnetic flux. This material is based upon work supported by the National Science Foundation under Award No. AGS-1331356.

  6. Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations

    Washington, K.E.


    The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations.

  7. Fully implicit kinetic modelling of collisional plasmas

    Mousseau, V.A.


    This dissertation describes a numerical technique, Matrix-Free Newton Krylov, for solving a simplified Vlasov-Fokker-Planck equation. This method is both deterministic and fully implicit, and may not have been a viable option before current developments in numerical methods. Results are presented that indicate the efficiency of the Matrix-Free Newton Krylov method for these fully-coupled, nonlinear integro-differential equations. The use and requirement for advanced differencing is also shown. To this end, implementations of Chang-Cooper differencing and flux limited Quadratic Upstream Interpolation for Convective Kinematics (QUICK) are presented. Results are given for a fully kinetic ion-electron problem with a self consistent electric field calculated from the ion and electron distribution functions. This numerical method, including advanced differencing, provides accurate solutions, which quickly converge on workstation class machines. It is demonstrated that efficient steady-state solutions can be achieved to the non-linear integro-differential equation, obtaining quadratic convergence, without incurring the large memory requirements of an integral operator. Model problems are presented which simulate plasma impinging on a plate with both high and low neutral particle recycling typical of a divertor in a Tokamak device. These model problems demonstrate the performance of the new solution method.

  8. Kinetic modeling in pre-clinical positron emission tomography

    Kuntner, Claudia [AIT Austrian Institute of Technology GmbH, Seibersdorf (Austria). Biomedical Systems, Health and Environment Dept.


    Pre-clinical positron emission tomography (PET) has evolved in the last few years from pure visualization of radiotracer uptake and distribution towards quantification of the physiological parameters. For reliable and reproducible quantification the kinetic modeling methods used to obtain relevant parameters of radiotracer tissue interaction are important. Here we present different kinetic modeling techniques with a focus on compartmental models including plasma input models and reference tissue input models. The experimental challenges of deriving the plasma input function in rodents and the effect of anesthesia are discussed. Finally, in vivo application of kinetic modeling in various areas of pre-clinical research is presented and compared to human data.

  9. A Review of Kinetic Modeling Methodologies for Complex Processes

    de Oliveira Luís P.


    Full Text Available In this paper, kinetic modeling techniques for complex chemical processes are reviewed. After a brief historical overview of chemical kinetics, an overview is given of the theoretical background of kinetic modeling of elementary steps and of multistep reactions. Classic lumping techniques are introduced and analyzed. Two examples of lumped kinetic models (atmospheric gasoil hydrotreating and residue hydroprocessing developed at IFP Energies nouvelles (IFPEN are presented. The largest part of this review describes advanced kinetic modeling strategies, in which the molecular detail is retained, i.e. the reactions are represented between molecules or even subdivided into elementary steps. To be able to retain this molecular level throughout the kinetic model and the reactor simulations, several hurdles have to be cleared first: (i the feedstock needs to be described in terms of molecules, (ii large reaction networks need to be automatically generated, and (iii a large number of rate equations with their rate parameters need to be derived. For these three obstacles, molecular reconstruction techniques, deterministic or stochastic network generation programs, and single-event micro-kinetics and/or linear free energy relationships have been applied at IFPEN, as illustrated by several examples of kinetic models for industrial refining processes.


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  11. Innovative first order elimination kinetics working model for easy learning

    Navin Budania


    Conclusions: First order elimination kinetics is easily understood with the help of above working model. More and more working models could be developed for teaching difficult topics. [Int J Basic Clin Pharmacol 2016; 5(3.000: 862-864


    Harerimana, Casimir; Vasel, Jean-Luc; Jupsin, Hugues; Ouali, Amira


    The aim of the study was first to develop a simple and practical model of anaerobic digestion including sulphate-reduction in anaerobic ponds. The basic microbiology of our model consists of three steps, namely, acidogenesis, methanogenesis, and sulphate reduction. This model includes multiple reaction stoichiometry and substrate utilization kinetics. The second aim was to determine some kinetic parameters associated with this model. The values of these parameters for sulfidogenic bacteria ar...

  13. A kinetic model for the penicillin biosynthetic pathway in

    Nielsen, Jens; Jørgensen, Henrik


    A kinetic model for the first two steps in the penicillin biosynthetic pathway, i.e. the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS) is proposed. The model is based on Michaelis-Menten type kinetics with non-competitive inhibition of the ACVS by ACV, and competitive inhibition...... of the IPNS by glutathione. The model predicted flux through the pathway corresponds well with the measured rate of penicillin biosynthesis. From the kinetic model the elasticity coefficients and the flux control coefficients are calculated throughout a fed-batch cultivation, and it is found...

  14. Kinetic models in spin chemistry. 1. The hyperfine interaction

    Mojaza, M.; Pedersen, J. B.


    Kinetic models for quantum systems are quite popular due to their simplicity, although they are difficult to justify. We show that the transformation from quantum to kinetic description can be done exactly for the hyperfine interaction of one nuclei with arbitrary spin; more spins are described w...

  15. Modeling the kinetics of essential oil hydrodistillation from plant materials

    Milojević Svetomir Ž.


    Full Text Available The present work deals with modeling the kinetics of essential oils extraction from plant materials by water and steam distillation. The experimental data were obtained by studying the hydrodistillation kinetics of essential oil from juniper berries. The literature data on the kinetics of essential oils hydrodistillation from different plant materials were also included into the modeling. A physical model based on simultaneous washing and diffusion of essential oil from plant materials were developed to describe the kinetics of essential oils hydrodistillation, and two other simpler models were derived from this physical model assuming either instantaneous washing followed by diffusion or diffusion with no washing (i.e. the first-order kinetics. The main goal was to compare these models and suggest the optimum ones for water and steam distillation and for different plant materials. All three models described well the experimental kinetic data on water distillation irrespective of the type of distillation equipment and its scale, the type of plant materials and the operational conditions. The most applicable one is the model involving simultaneous washing and diffusion of the essential oil. However, this model was generally inapplicable for steam distillation of essential oils, except for juniper berries. For this hydrodistillation technique, the pseudo first-order model was shown to be the best one. In a few cases, a variation of the essential oil yield with time was observed to be sigmoidal and was modeled by the Boltzmann sigmoid function.

  16. Aromatization of light naphtha fractions on zeolites 1: Kinetic model

    Rovenskaja Svetlana A.


    Full Text Available On the basis of analyzing kinetic experimental data performed in laboratory integral reactors a lumping kinetic model of the "Zeoforming" process was developed. A reaction scheme of the lumped components was proposed, that was adapted to the technological requirements. The reaction rate constants and activation energies were estimated, that are valid for certain feed compositions. The model is intended for further modeling and optimization of the process.

  17. Kinetic derivation of a Hamilton-Jacobi traffic flow model

    Borsche, Raul; Kimathi, Mark


    Kinetic models for vehicular traffic are reviewed and considered from the point of view of deriving macroscopic equations. A derivation of the associated macroscopic traffic flow equations leads to different types of equations: in certain situations modified Aw-Rascle equations are obtained. On the other hand, for several choices of kinetic parameters new Hamilton-Jacobi type traffic equations are found. Associated microscopic models are discussed and numerical experiments are presented discussing several situations for highway traffic and comparing the different models.

  18. Lumping procedure for a kinetic model of catalytic naphtha reforming

    H. M. Arani


    Full Text Available A lumping procedure is developed for obtaining kinetic and thermodynamic parameters of catalytic naphtha reforming. All kinetic and deactivation parameters are estimated from industrial data and thermodynamic parameters are calculated from derived mathematical expressions. The proposed model contains 17 lumps that include the C6 to C8+ hydrocarbon range and 15 reaction pathways. Hougen-Watson Langmuir-Hinshelwood type reaction rate expressions are used for kinetic simulation of catalytic reactions. The kinetic parameters are benchmarked with several sets of plant data and estimated by the SQP optimization method. After calculation of deactivation and kinetic parameters, plant data are compared with model predictions and only minor deviations between experimental and calculated data are generally observed.

  19. Modelling atypical CYP3A4 kinetics: principles and pragmatism.

    Houston, J Brian; Galetin, Aleksandra


    The Michaelis-Menten model, and the existence of a single active site for the interaction of substrate with drug metabolizing enzyme, adequately describes a substantial number of in vitro metabolite kinetic data sets for both clearance and inhibition determination. However, in an increasing number of cases (involving most notably, but not exclusively, CYP3A4), atypical kinetic features are observed, e.g., auto- and heteroactivation; partial, cooperative, and substrate inhibition; concentration-dependent effector responses (activation/inhibition); limited substrate substitution and inhibitory reciprocity necessitating sub-group classification. The phenomena listed above cannot be readily interpreted using single active site models and the literature indicates that three types of approaches have been adopted. First the 'nai ve' approach of using the Michaelis-Menten model regardless of the kinetic behaviour, second the 'empirical' approach (e.g., employing the Hill or uncompetitive inhibition equations to model homotropic phenomena of sigmoidicity and substrate inhibition, respectively) and finally, the 'mechanistic' approach. The later includes multisite kinetic models derived using the same rapid equilibrium/steady-state assumptions as the single-site model. These models indicate that 2 or 3 binding sites exist for a given CYP3A4 substrate and/or effector. Multisite kinetic models share common features, depending on the substrate kinetics and the nature of the effector response observed in vitro, which allow a generic model to be proposed. Thus although more complex than the other two approaches, they show more utility and can be comprehensively applied in relatively simple versions that can be readily generated from generic model. Multisite kinetic features, observed in isolated hepatocytes as well as in microsomes from hepatic tissue and heterologous expression systems, may be evident in substrate depletion-time profiles as well as in metabolite formation rates

  20. Modeling Biodegradation Kinetics on Benzene and Toluene and Their Mixture

    Aparecido N. Módenes


    Full Text Available The objective of this work was to model the biodegradation kinetics of toxic compounds toluene and benzene as pure substrates and in a mixture. As a control, Monod and Andrews models were used. To predict substrates interactions, more sophisticated models of inhibition and competition, and SKIP (sum kinetics interactions parameters model were applied. The models evaluation was performed based on the experimental data from Pseudomonas putida F1 activities published in the literature. In parameter identification procedure, the global method of particle swarm optimization (PSO was applied. The simulation results show that the better description of the biodegradation process of pure toxic substrate can be achieved by Andrews' model. The biodegradation process of a mixture of toxic substrates is modeled the best when modified competitive inhibition and SKIP models are used. The developed software can be used as a toolbox of a kinetics model catalogue of industrial wastewater treatment for process design and optimization.

  1. Biomass torrefaction: modeling of volatile and solid product evolution kinetics.

    Bates, Richard B; Ghoniem, Ahmed F


    The aim of this work is the development of a kinetics model for the evolution of the volatile and solid product composition during torrefaction conditions between 200 and 300°C. Coupled to an existing two step solid mass loss kinetics mechanism, this model describes the volatile release kinetics in terms of a set of identifiable chemical components, permitting the solid product composition to be estimated by mass conservation. Results show that most of the volatiles released during the first stage include highly oxygenated species such as water, acetic acid, and carbon dioxide, while volatiles released during the second step are composed primarily of lactic acid, methanol, and acetic acid. This kinetics model will be used in the development of a model to describe reaction energy balance and heat release dynamics.

  2. Kinetic, equilibrium and thermodynamic modelling of the sorption of ...

    Kinetic, equilibrium and thermodynamic modelling of the sorption of metals ... Batch sorption studies were conducted to assess the potential of a ... negative Ea values, indicating their preference to bind to low-energy sites. ... Article Metrics.

  3. Jellium-with-gap model applied to semilocal kinetic functionals

    Constantin, Lucian A.; Fabiano, Eduardo; Śmiga, Szymon; Della Sala, Fabio


    We investigate a highly nonlocal generalization of the Lindhard function, given by the jellium-with-gap model. We find a band-gap-dependent gradient expansion of the kinetic energy, which performs noticeably well for large atoms. Using the static linear response theory and the simplest semilocal model for the local band gap, we derive a nonempirical generalized gradient approximation (GGA) of the kinetic energy. This GGA kinetic-energy functional is remarkably accurate for the description of weakly interacting molecular systems within the subsystem formulation of density functional theory.

  4. Kinetic models in industrial biotechnology - Improving cell factory performance.

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


    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.

  5. An integral representation of functions in gas-kinetic models

    Perepelitsa, Misha


    Motivated by the theory of kinetic models in gas dynamics, we obtain an integral representation of lower semicontinuous functions on {{{R}}^d,} {d≥1}. We use the representation to study the problem of compactness of a family of the solutions of the discrete time BGK model for the compressible Euler equations. We determine sufficient conditions for strong compactness of moments of kinetic densities, in terms of the measures from their integral representations.

  6. Kinetic Modelling of Pesticidal Degradation and Microbial Growth in Soil



    This paper discusses such models for the degradation kinetics of pesticides in soil as the model expressing the degradation rate as a function of two varables:the pesticide concentration and the number of pesticide degrading microorganisms,the model expressing the pesticide concentration as explicit or implicit function of time ,and the model exprssing the pesticide loss rate constants as functions of temperature,These models may interpret the degradation curves with an inflection point.A Kinetic model describing the growth processes of microbial populations in a closed system is reported as well.

  7. New mass loss kinetic model for thermal decomposition of biomass


    Based on non-isothermal experimental results for eight Chinese biomass species, a new kinetic model,named as the "pseudo bi-component separate-stage model (PBSM)", is developed in this note to describe the mass loss behavior of biomass thermal decomposition. This model gains an advantage over the commonly used "pseudo single-component overall model (PSOM)" and "pseudo multi-component overall model (PMOM)". By means of integral analysis it is indicated that the new model is suitable to describe the mass loss kinetics of wood and leaf samples under relatively low heating rates (e.g. 10°C/rin, used in this work).``

  8. Detailed Chemical Kinetic Modeling of Cyclohexane Oxidation

    Silke, E J; Pitz, W J; Westbrook, C K; Ribaucour, M


    A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Reaction rate constant rules are developed for the low temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Since cyclohexane produces only one type of cyclohexyl radical, much of the low temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical + O{sub 2} through five, six and seven membered ring transition states. The direct elimination of cyclohexene and HO{sub 2} from RO{sub 2} is included in the treatment using a modified rate constant of Cavallotti et al. Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies on cyclohexane. Calculations indicated that the production of 1,2-epoxycyclohexane observed in the experiments can not be simulated based on the current understanding of low temperature chemistry. Possible 'alternative' H-atom isomerizations leading to different products from the parent O{sub 2}QOOH radical were included in the low temperature chemical kinetic mechanism and were found to play a significant role.

  9. Kinetic modelling of the Fischer-Tropsch synthesis

    Gambaro, C.; Pollesel, P.; Zennaro, R. [Eni S.p.A., San Donato Milanese (Italy); Lietti, L.; Tronconi, E. [Politecnico di Milano (Italy)


    In this work the development of a CO conversion kinetic model of the Fischer-Tropsch process will be presented. Kinetic data were produced testing a Co-based catalyst on two lab units, equipped with a slurry autoclave and a fixed bed reactor respectively. Accordingly, information on the catalytic performances of the same catalyst in two reactor configurations were also obtained. The experimental results were then analyzed with different kinetic models, available in the literature: two mechanistic models, derived by Sarup-Wojciechowski and Yates-Satterfield, and a simple power law rate expression were compared. The parameters of the different rate expressions were estimated by non-linear regression of the kinetic data collected on the two lab units. (orig.)

  10. Modelling of the Kinetics of Sulfure Compounds in Desulfurisation Processes Based on Industry Data of Plant

    Krivtcova Nadezhda


    Full Text Available Modelling of sulfur compounds kinetics was performed, including kinetics of benzothiophene and dibenzothiophene homologues. Modelling is based on experimental data obtained from monitoring of industrial hydrotreating set. Obtained results include kinetic parameters of reactions.

  11. Chemical Kinetic Models for HCCI and Diesel Combustion

    Pitz, W J; Westbrook, C K; Mehl, M; Sarathy, S M


    Predictive engine simulation models are needed to make rapid progress towards DOE's goals of increasing combustion engine efficiency and reducing pollutant emissions. These engine simulation models require chemical kinetic submodels to allow the prediction of the effect of fuel composition on engine performance and emissions. Chemical kinetic models for conventional and next-generation transportation fuels need to be developed so that engine simulation tools can predict fuel effects. The objectives are to: (1) Develop detailed chemical kinetic models for fuel components used in surrogate fuels for diesel and HCCI engines; (2) Develop surrogate fuel models to represent real fuels and model low temperature combustion strategies in HCCI and diesel engines that lead to low emissions and high efficiency; and (3) Characterize the role of fuel composition on low temperature combustion modes of advanced combustion engines.

  12. Hybrid fluid/kinetic model for parallel heat conduction

    Callen, J.D.; Hegna, C.C.; Held, E.D. [Univ. of Wisconsin, Madison, WI (United States)


    It is argued that in order to use fluid-like equations to model low frequency ({omega} < {nu}) phenomena such as neoclassical tearing modes in low collisionality ({nu} < {omega}{sub b}) tokamak plasmas, a Chapman-Enskog-like approach is most appropriate for developing an equation for the kinetic distortion (F) of the distribution function whose velocity-space moments lead to the needed fluid moment closure relations. Further, parallel heat conduction in a long collision mean free path regime can be described through a combination of a reduced phase space Chapman-Enskog-like approach for the kinetics and a multiple-time-scale analysis for the fluid and kinetic equations.

  13. Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

    Li, Yulan; Hu, Shenyang Y.; Sun, Xin; Khaleel, Mohammad A.


    Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubble evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink

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

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


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

  15. Kinetic Modelling of Macroscopic Properties Changes during Crosslinked Polybutadiene Oxidation

    Audouin, Ludmila; Coquillat, Marie; Colin, Xavier; Verdu, Jacques; Nevière, Robert


    The thermal oxidation of additive free hydroxyl-terminated polybutadiene (HTPB) isocyanate crosslinked rubber bulk samples has been studied at 80, 100 and 120 °C in air. The oxidation kinetics has been monitored by gravimetry and thickness distribution of oxidation products was determined by FTIR mapping. Changes of elastic shear modulus G' during oxidation were followed during oxidation at the same temperatures. The kinetic model established previously for HTPB has been adapted for bulk sample oxidation using previously determined set of kinetic parameters. Oxygen diffusion control of oxidation has been introduced into the model. The mass changes kinetic curves and oxidation products profiles were simulated and adequate fit was obtained. Using the rubber elasticity theory the elastic modulus changes were simulated taking into account the elastically active chains concentration changes due to chain scission and crosslinking reactions. The reasonable fit of G' as a function of oxidation time experimental curves was obtained.

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

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


    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.

  17. A Kinetic Model of Chromium in a Flame


    Chromium has been identified as a carcinogenic metal.Incineration is the useful method for disposal of toxic chromium hazard waste and a chromium kinetic model in a flame is very important to study chromium oxidation.Chromium chemical kinetics over a range of temperatures of a hydrogen/air flame is proposed.Nine chromium compounds and fifty-eight reversible chemical reactions were considered The forward reaction rates are calculated based on the molecular collision approach for unknown ones and Arrhenius's Law for known ones.The backward reaction rates were calculated according to forward reaction rates, the equilibrium constants and chemical thermodynamics.It is verified by several equilibrium cases and is tested by a hydrogen/air diffusion flame.The results show that the kinetic model could be used in cases in which the chromium kinetics play an important role in a flame

  18. Kinetic exchange models: From molecular physics to social science

    Patriarca, Marco; Chakraborti, Anirban


    We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.

  19. Kinetic exchange models: From molecular physics to social science

    Patriarca, Marco


    We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.

  20. Physiologically based kinetic modeling of the bioactivation of myristicin

    Al-Malahmeh, Amer J.; Al-Ajlouni, Abdelmajeed; Wesseling, Sebastiaan; Soffers, Ans E.M.F.; Al-Subeihi, A.; Kiwamoto, Reiko; Vervoort, Jacques; Rietjens, Ivonne M.C.M.


    The present study describes physiologically based kinetic (PBK) models for the alkenylbenzene myristicin that were developed by extension of the PBK models for the structurally related alkenylbenzene safrole in rat and human. The newly developed myristicin models revealed that the formation of th

  1. Chemical kinetic modeling of H{sub 2} applications

    Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D. [Lawrence Livermore National Lab., CA (United States)] [and others


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

  2. A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions

    Chang, Ivan; Baldi, Pierre


    Motivation: Oxidoreductases are a fundamental class of enzymes responsible for the catalysis of oxidation–reduction reactions, crucial in most bioenergetic metabolic pathways. From their common root in the ancient prebiotic environment, oxidoreductases have evolved into diverse and elaborate protein structures with specific kinetic properties and mechanisms adapted to their individual functional roles and environmental conditions. While accurate kinetic modeling of oxidoreductases is thus imp...

  3. The Nonlinear Magnetosphere: Expressions in MHD and in Kinetic Models

    Hesse, Michael; Birn, Joachim


    Like most plasma systems, the magnetosphere of the Earth is governed by nonlinear dynamic evolution equations. The impact of nonlinearities ranges from large scales, where overall dynamics features are exhibiting nonlinear behavior, to small scale, kinetic, processes, where nonlinear behavior governs, among others, energy conversion and dissipation. In this talk we present a select set of examples of such behavior, with a specific emphasis on how nonlinear effects manifest themselves in MHD and in kinetic models of magnetospheric plasma dynamics.

  4. Application of Detailed Chemical Kinetics to Combustion Instability Modeling


    under two different conditions corresponding to marginally stable and unstable operation in order to evaluate the performance of the chemical kinetics...instability is a complex interaction between acoustics and the heat release due to combustion.In rocket engines, which are acoustically compact, there is...and amplitudes remains a challenge. The present article is an attempt towards addressing such discrepancies by enhancing the chemical kinetics model

  5. Kinetic model for hydroisomerization reaction of C8-aromatics

    Ouguan XU; Hongye SU; Xiaoming JIN; Jian CHU


    Based on the reported reaction networks, a novel six-component hydroisomerization reaction net-work with a new lumped species including C8-naphthenes and Cs-paraffins is proposed and a kinetic model for a commercial unit is also developed. An empirical catalyst deactivation function is incorporated into the model accounting for the loss in activity because of coke forma-tion on the catalyst surface during the long-term opera-tion. The Runge-Kutta method is used to solve the ordinary differential equations of the model. The reaction kinetic parameters are benchmarked with several sets of balanced plant data and estimated by the differential vari-able metric optimization method (BFGS). The kinetic model is validated by an industrial unit with sets of plant data under different operating conditions and simulation results show a good agreement between the model predic-tions and the plant observations.

  6. A tool model for predicting atmospheric kinetics with sensitivity analysis


    A package( a tool model) for program of predicting atmospheric chemical kinetics with sensitivity analysis is presented. The new direct method of calculating the first order sensitivity coefficients using sparse matrix technology to chemical kinetics is included in the tool model, it is only necessary to triangularize the matrix related to the Jacobian matrix of the model equation. The Gear type procedure is used to integrate amodel equation and its coupled auxiliary sensitivity coefficient equations. The FORTRAN subroutines of the model equation, the sensitivity coefficient equations, and their Jacobian analytical expressions are generated automatically from a chemical mechanism. The kinetic representation for the model equation and its sensitivity coefficient equations, and their Jacobian matrix is presented. Various FORTRAN subroutines in packages, such as SLODE, modified MA28, Gear package, with which the program runs in conjunction are recommended.The photo-oxidation of dimethyl disulfide is used for illustration.

  7. Kinetics of ethylcyclohexane pyrolysis and oxidation: An experimental and detailed kinetic modeling study

    Wang, Zhandong


    Ethylcyclohexane (ECH) is a model compound for cycloalkanes with long alkyl side-chains. A preliminary investigation on ECH (Wang et al., Proc. Combust. Inst., 35, 2015, 367-375) revealed that an accurate ECH kinetic model with detailed fuel consumption mechanism and aromatic growth pathways, as well as additional ECH pyrolysis and oxidation data with detailed species concentration covering a wide pressure and temperature range are required to understand the ECH combustion kinetics. In this work, the flow reactor pyrolysis of ECH at various pressures (30, 150 and 760Torr) was studied using synchrotron vacuum ultraviolet (VUV) photoionization mass spectrometry (PIMS) and gas chromatography (GC). The mole fraction profiles of numerous major and minor species were evaluated, and good agreement was observed between the PIMS and GC data sets. Furthermore, a fuel-rich burner-stabilized laminar premixed ECH/O2/Ar flame at 30Torr was studied using synchrotron VUV PIMS. A detailed kinetic model for ECH high temperature pyrolysis and oxidation was developed and validated against the pyrolysis and flame data performed in this work. Further validation of the kinetic model is presented against literature data including species concentrations in jet-stirred reactor oxidation, ignition delay times in a shock tube, and laminar flame speeds at various pressures and equivalence ratios. The model well predicts the consumption of ECH, the growth of aromatics, and the global combustion properties. Reaction flux and sensitivity analysis were utilized to elucidate chemical kinetic features of ECH combustion under various reaction conditions. © 2015 The Combustion Institute.

  8. Repopulation Kinetics and the Linear-Quadratic Model

    O'Rourke, S. F. C.; McAneney, H.; Starrett, C.; O'Sullivan, J. M.


    The standard Linear-Quadratic (LQ) survival model for radiotherapy is used to investigate different schedules of radiation treatment planning for advanced head and neck cancer. We explore how these treament protocols may be affected by different tumour repopulation kinetics between treatments. The laws for tumour cell repopulation include the logistic and Gompertz models and this extends the work of Wheldon et al. [1], which was concerned with the case of exponential repopulation between treatments. Treatment schedules investigated include standarized and accelerated fractionation. Calculations based on the present work show, that even with growth laws scaled to ensure that the repopulation kinetics for advanced head and neck cancer are comparable, considerable variation in the survival fraction to orders of magnitude emerged. Calculations show that application of the Gompertz model results in a significantly poorer prognosis for tumour eradication. Gaps in treatment also highlight the differences in the LQ model with the effect of repopulation kinetics included.

  9. Kinetic modeling of the Townsend breakdown in argon

    Macheret, S. O.; Shneider, M. N.


    Kinetic modeling of the Townsend breakdown in argon was performed in the "forward-back" approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.

  10. Hard-sphere kinetic models for inert and reactive mixtures

    Polewczak, Jacek


    I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A *, B *, in which the chemical reactions are of the type A+B\\rightleftharpoons {{A}\\ast}+{{B}\\ast} , with A * and B * being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided.

  11. Strain in the mesoscale kinetic Monte Carlo model for sintering

    Bjørk, Rasmus; Frandsen, Henrik Lund; Tikare, V.


    Shrinkage strains measured from microstructural simulations using the mesoscale kinetic Monte Carlo (kMC) model for solid state sintering are discussed. This model represents the microstructure using digitized discrete sites that are either grain or pore sites. The algorithm used to simulate...

  12. Some models for the adsorption kinetics of pesticides in soil

    Leistra, M.; Dekkers, W.A.


    Three models describing adsorption‐desorption kinetics of pesticides in soil, that could be incorporated into computer programs on pesticide movement in soil, were discussed, the first model involved single first‐order rate equations for adsorption and desorption. Results from an analytical and a

  13. Simplified kinetic models of methanol oxidation on silver

    Andreasen, Anders; Lynggaard, Hasse Harloff; Stegelmann, Carsten;


    Recently the authors developed a microkinetic model of methanol oxidation on silver [A. Andreasen, H. Lynggaard, C. Stegelmann, P. Stoltze, Surf. Sci. 544 (2003) 5–23]. The model successfully explains both surface science experiments and kinetic experiments at industrial conditions applying...

  14. Simplified kinetic models of methanol oxidation on silver

    Andreasen, A.; Lynggaard, H.; Stegelmann, C.;


    Recently the authors developed a microkinetic model of methanol oxidation on silver [A. Andreasen, H. Lynggaard, C. Stegelmann, P. Stoltze, Surf. Sci. 544 (2003) 5-23]. The model successfully explains both surface science experiments and kinetic experiments at industrial conditions applying...

  15. Computer-Aided Construction of Chemical Kinetic Models

    Green, William H. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)


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

  16. Information cascade, Kirman's ant colony model, and kinetic Ising model

    Hisakado, Masato


    In this paper, we discuss a voting model in which voters can obtain information from a finite number of previous voters. There exist three groups of voters: (i) digital herders and independent voters, (ii) analog herders and independent voters, and (iii) tanh-type herders. In our previous paper, we used the mean field approximation for case (i). In that study, if the reference number r is above three, phase transition occurs and the solution converges to one of the equilibria. In contrast, in the current study, the solution oscillates between the two equilibria, that is, good and bad equilibria. In this paper, we show that there is no phase transition when r is finite. If the annealing schedule is adequately slow from finite r to infinite r, the voting rate converges only to the good equilibrium. In case (ii), the state of reference votes is equivalent to that of Kirman's ant colony model, and it follows beta binomial distribution. In case (iii), we show that the model is equivalent to the finite-size kinetic...

  17. Comparison of linear modes in kinetic plasma models

    Camporeale, Enrico


    We compare, in an extensive and systematic way, linear theory results obtained with the hybrid (ion-kinetic and electron-fluid), the gyrokinetic and the fully-kinetic plasma models. We present a test case with parameters that are relevant for solar wind turbulence at small scales, which is a topic now recognized to need a kinetic treatment, to a certain extent. We comment on the comparison of low-frequency single modes (Alfv\\'{e}n/ion-cyclotron, ion-acoustic, and fast modes) for a wide range of propagation angles, and on the overall spectral properties of the linear operators, for quasi-perpendicular propagation. The methodology and the results presented in this paper will be valuable when choosing which model should be used in regimes where the assumptions of each model are not trivially satisfied.

  18. Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica

    Oboh, I., E-mail: [Department of Chemical and Petroleum Engineering, University of Uyo, Uyo (Nigeria); Aluyor, E.; Audu, T. [Department of Chemical Engineering, University of Uyo, BeninCity, BeninCity (Nigeria)


    The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R{sup 2}), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.

  19. A Detailed Chemical Kinetic Model for TNT

    Pitz, W J; Westbrook, C K


    A detailed chemical kinetic mechanism for 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and soot formation during the destruction of munitions. The TNT mechanism treats only gas-phase reactions. Reactions for the decomposition of TNT and for the consumption of intermediate products formed from TNT are assembled based on information from the literature and on current understanding of aromatic chemistry. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reaction paths are developed based on similar paths for aromatic hydrocarbons. Reaction-rate constant expressions are estimated from the literature and from analogous reactions where the rate constants are available. The detailed reaction mechanism for TNT is added to existing reaction mechanisms for RDX and for hydrocarbons. Computed results show the effect of oxygen concentration on the amount of soot precursors that are formed in the combustion of RDX and TNT mixtures in N{sub 2}/O{sub 2} mixtures.

  20. Kinetic models for irreversible processes on a lattice

    Wolf, N.O.


    The development and application of kinetic lattice models are considered. For the most part, the discussions are restricted to lattices in one-dimension. In Chapter 1, a brief overview of kinetic lattice model formalisms and an extensive literature survey are presented. A review of the kinetic models for non-cooperative lattice events is presented in Chapter 2. The development of cooperative lattice models and solution of the resulting kinetic equations for an infinite and a semi-infinite lattice are thoroughly discussed in Chapters 3 and 4. The cooperative models are then applied to the problem of theoretically dtermining the sticking coefficient for molecular chemisorption in Chapter 5. In Chapter 6, other possible applications of these models and several model generalizations are considered. Finally, in Chapter 7, an experimental study directed toward elucidating the mechanistic factors influencing the chemisorption of methane on single crystal tungsten is reported. In this it differs from the rest of the thesis which deals with the statistical distributions resulting from a given mechanism.

  1. Transperitoneal transport of creatinine. A comparison of kinetic models

    Fugleberg, S; Graff, J; Joffe, P;


    Six kinetic models of transperitoneal creatinine transport were formulated and validated on the basis of experimental results obtained from 23 non-diabetic patients undergoing peritoneal dialysis. The models were designed to elucidate the presence or absence of diffusive, non-lymphatic convective...... including all three forms of transport is superior to other models. We conclude that the best model of transperitoneal creatinine transport includes diffusion, non-lymphatic convective transport and lymphatic convective transport....

  2. Plasma interfacial mixing layers: Comparisons of fluid and kinetic models

    Vold, Erik; Yin, Lin; Taitano, William; Albright, B. J.; Chacon, Luis; Simakov, Andrei; Molvig, Kim


    We examine plasma transport across an initial discontinuity between two species by comparing fluid and kinetic models. The fluid model employs a kinetic theory approximation for plasma transport in the limit of small Knudsen number. The kinetic simulations include explicit particle-in-cell simulations (VPIC) and a new implicit Vlasov-Fokker-Planck code, iFP. The two kinetic methods are shown to be in close agreement for many aspects of the mixing dynamics at early times (to several hundred collision times). The fluid model captures some of the earliest time dynamic behavior seen in the kinetic results, and also generally agrees with iFP at late times when the total pressure gradient relaxes and the species transport is dominated by slow diffusive processes. The results show three distinct phases of the mixing: a pressure discontinuity forms across the initial interface (on times of a few collisions), the pressure perturbations propagate away from the interfacial mixing region (on time scales of an acoustic transit) and at late times the pressure relaxes in the mix region leaving a non-zero center of mass flow velocity. The center of mass velocity associated with the outward propagating pressure waves is required to conserve momentum in the rest frame. Work performed under the auspices of the U.S. DOE by the LANS, LLC, Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396. Funding provided by the Advanced Simulation and Computing (ASC) Program.

  3. Thermodynamic and Kinetic Modeling of Transcriptional Pausing

    Vasisht R. Tadigotla; Dáibhid Ó. Maoiléidigh; Anirvan M. Sengupta; Vitaly Epshtein; Richard H. Ebright; Evgeny Nudler; Andrei E. Ruckenstein


    We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC...

  4. Bayesian inference of chemical kinetic models from proposed reactions

    Galagali, Nikhil


    © 2014 Elsevier Ltd. Bayesian inference provides a natural framework for combining experimental data with prior knowledge to develop chemical kinetic models and quantify the associated uncertainties, not only in parameter values but also in model structure. Most existing applications of Bayesian model selection methods to chemical kinetics have been limited to comparisons among a small set of models, however. The significant computational cost of evaluating posterior model probabilities renders traditional Bayesian methods infeasible when the model space becomes large. We present a new framework for tractable Bayesian model inference and uncertainty quantification using a large number of systematically generated model hypotheses. The approach involves imposing point-mass mixture priors over rate constants and exploring the resulting posterior distribution using an adaptive Markov chain Monte Carlo method. The posterior samples are used to identify plausible models, to quantify rate constant uncertainties, and to extract key diagnostic information about model structure-such as the reactions and operating pathways most strongly supported by the data. We provide numerical demonstrations of the proposed framework by inferring kinetic models for catalytic steam and dry reforming of methane using available experimental data.

  5. 3D Building Model Fitting Using A New Kinetic Framework

    Brédif, Mathieu; Pierrot-Deseilligny, Marc; Maître, Henri


    We describe a new approach to fit the polyhedron describing a 3D building model to the point cloud of a Digital Elevation Model (DEM). We introduce a new kinetic framework that hides to its user the combinatorial complexity of determining or maintaining the polyhedron topology, allowing the design of a simple variational optimization. This new kinetic framework allows the manipulation of a bounded polyhedron with simple faces by specifying the target plane equations of each of its faces. It proceeds by evolving continuously from the polyhedron defined by its initial topology and its initial plane equations to a polyhedron that is as topologically close as possible to the initial polyhedron but with the new plane equations. This kinetic framework handles internally the necessary topological changes that may be required to keep the faces simple and the polyhedron bounded. For each intermediate configurations where the polyhedron looses the simplicity of its faces or its boundedness, the simplest topological mod...

  6. A kinetic model of carbon burnout in pulverized coal combustion

    Hurt, R.; Jian-Kuan Sun; Lunden, M. [Brown University, Providence, RI (United States). Division of Engineering


    The degree of carbon burnout is an important operating characteristic of full-scale suspension-fired coal combustion systems affecting boiler efficiency, electrostatic precipitator operation and the value of fly ash as a saleable product. Prediction of carbon loss requires special char combustion kinetics valid through the very high conversions targeted in industry (typically {gt} 99.5%), and valid for a wide-range of particle temperature histories occurring in full-scale furnaces. The paper presents high-temperature kinetic data for five coal chars in the form of time-resolved burning profiles that include the late stages of combustion. It then describes the development and validation of the Carbon Burnout Kinetic Model (CBK), a coal-general kinetics package that is specifically designed to predict the total extent of carbon burnout and ultimate fly ash carbon content for prescribed temperature/oxygen histories typical of pulverized coal combustion systems. The model combines the single-film treatment of cha oxidation with quantitative descriptions of thermal annealing, statistical kinetics, statistical densities, and ash inhibition in the late stages of combustion. In agreement with experimental observations, the CBK model predicts (1) low reactivities for unburned carbon residues extracted from commercial ash samples, (2) reactivity loss in the late stages of laboratory combustion, (3) the observed sensitivity of char reactivity to high-temperature heat treatment on second and subsecond time scales, and (4) the global reaction inhibition by mineral matter in the late stages of combustion observed in single-particle imaging studies. The model ascribes these various char deactivation phenomena to the combined effects of thermal annealing, ash inhibition, and the preferential consumption of more reactive particles (statistical kinetics), the relative contributions of which vary greatly with combustion conditions. 39 refs., 4 figs., 4 tabs., 1 app.

  7. Modeling uptake kinetics of cadmium by field-grown lettuce

    Chen Weiping [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States)], E-mail:; Li Lianqing [Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095 (China); Chang, Andrew C.; Wu Laosheng [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States); Kwon, Soon-Ik [Agricultural Environmental and Ecology Division, National Institute of Agricultural Science and Technology, Suwon 441-707 (Korea, Republic of); Bottoms, Rick [Desert Research and Extension Center, 1004 East Holton Road, El Centro, CA 92243 (United States)


    Cadmium uptake by field grown Romaine lettuce treated with P-fertilizers of different Cd levels was investigated over an entire growing season. Results indicated that the rate of Cd uptake at a given time of the season can be satisfactorily described by the Michaelis-Menten kinetics, that is, plant uptake increases as the Cd concentration in soil solution increases, and it gradually approaches a saturation level. However, the rate constant of the Michaelis-Menten kinetics changes over the growing season. Under a given soil Cd level, the cadmium content in plant tissue decreases exponentially with time. To account for the dynamic nature of Cd uptake, a kinetic model integrating the time factor was developed to simulate Cd plant uptake over the growing season: C{sub Plant} = C{sub Solution} . PUF{sub max} . exp[-b . t], where C{sub Plant} and C{sub Solution} refer to the Cd content in plant tissue and soil solution, respectively, PUF{sub max} and b are kinetic constants. - A kinetic model was developed to evaluate the uptake of Cd under field conditions.

  8. A physical model of nicotinic ACh receptor kinetics

    Nurowska, Ewa; Bratiichuk, Mykola; Dworakowska, Beata; Nowak, Roman J.


    We present a new approach to nicotinic receptor kinetics and a new model explaining random variabilities in the duration of open events. The model gives new interpretation on brief and long receptor openings and predicts (for two identical binding sites) the presence of three components in the open time distribution: two brief and a long. We also present the physical model of the receptor block. This picture naturally and universally explains receptor desensitization, the phenomenon of centra...

  9. A Discrete Velocity Traffic Kinetic Model Including Desired Speed

    Shoufeng Lu


    Full Text Available We introduce the desired speed variable into the table of games and formulate a new table of games and the corresponding discrete traffic kinetic model. We use the hybrid programming technique of VB and MATLAB to develop the program. Lastly, we compared the proposed model result and the detector data. The results show that the proposed model can describe the traffic flow evolution.

  10. Exploring the chemical kinetics of partially oxidized intermediates by combining experiments, theory, and kinetic modeling.

    Hoyermann, Karlheinz; Mauß, Fabian; Olzmann, Matthias; Welz, Oliver; Zeuch, Thomas


    Partially oxidized intermediates play a central role in combustion and atmospheric chemistry. In this perspective, we focus on the chemical kinetics of alkoxy radicals, peroxy radicals, and Criegee intermediates, which are key species in both combustion and atmospheric environments. These reactive intermediates feature a broad spectrum of chemical diversity. Their reactivity is central to our understanding of how volatile organic compounds are degraded in the atmosphere and converted into secondary organic aerosol. Moreover, they sensitively determine ignition timing in internal combustion engines. The intention of this perspective article is to provide the reader with information about the general mechanisms of reactions initiated by addition of atomic and molecular oxygen to alkyl radicals and ozone to alkenes. We will focus on critical branching points in the subsequent reaction mechanisms and discuss them from a consistent point of view. As a first example of our integrated approach, we will show how experiment, theory, and kinetic modeling have been successfully combined in the first infrared detection of Criegee intermediates during the gas phase ozonolysis. As a second example, we will examine the ignition timing of n-heptane/air mixtures at low and intermediate temperatures. Here, we present a reduced, fuel size independent kinetic model of the complex chemistry initiated by peroxy radicals that has been successfully applied to simulate standard n-heptane combustion experiments.

  11. A Kinetic Model for Vapor-liquid Flows


    A Kinetic Model for Vapor-liquid Flows Aldo Frezzotti, Livio Gibelli and Silvia Lorenzani Dipartimento di Matematica del Politecnico di Milano Piazza...ES) Dipartimento di Matematica del Politecnico di Milano Piazza Leonardo da Vinci 32 - 20133 Milano - Italy 8. PERFORMING ORGANIZATION REPORT NUMBER

  12. Development of simple kinetic models and parameter estimation for ...


    Key words: Exponential feed, growth modeling, Monod kinetic equation, Pichia pastoris, recombinant human ... Author(s) agree that this article remains permanently open access under the terms of the Creative Commons .... Methanol was the only energy and carbon source ..... A potential explanation for the decline in cell.

  13. Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling.

    Noé, Frank; Banisch, Ralf; Clementi, Cecilia


    Identification of the main reaction coordinates and building of kinetic models of macromolecular systems require a way to measure distances between molecular configurations that can distinguish slowly interconverting states. Here we define the commute distance that can be shown to be closely related to the expected commute time needed to go from one configuration to the other, and back. A practical merit of this quantity is that it can be easily approximated from molecular dynamics data sets when an approximation of the Markov operator eigenfunctions is available, which can be achieved by the variational approach to approximate eigenfunctions of Markov operators, also called variational approach of conformation dynamics (VAC) or the time-lagged independent component analysis (TICA). The VAC or TICA components can be scaled such that a so-called commute map is obtained in which Euclidean distance corresponds to the commute distance, and thus kinetic models such as Markov state models can be computed based on Euclidean operations, such as standard clustering. In addition, the distance metric gives rise to a quantity we call total kinetic content, which is an excellent score to rank input feature sets and kinetic model quality.

  14. Estimation of Kinetic Parameters in an Automotive SCR Catalyst Model

    Åberg, Andreas; Widd, Anders; Abildskov, Jens;


    A challenge during the development of models for simulation of the automotive Selective Catalytic Reduction catalyst is the parameter estimation of the kinetic parameters, which can be time consuming and problematic. The parameter estimation is often carried out on small-scale reactor tests, or p...

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

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


    In the context of limiting the environmental impact of transportation, this critical review discusses new directions which are being followed in the development of more predictive and more accurate detailed chemical kinetic models for the combustion of fuels. In the first part, the performance of current models, especially in terms of the prediction of pollutant formation, is evaluated. In the next parts, recent methods and ways to improve these models are described. An emphasis is given on the development of detailed models based on elementary reactions, on the production of the related thermochemical and kinetic parameters, and on the experimental techniques available to produce the data necessary to evaluate model predictions under well defined conditions (212 references). This journal is © The Royal Society of Chemistry 2011

  16. Second order kinetic Kohn-Sham lattice model

    Solorzano, Sergio; Herrmann, Hans


    In this work we introduce a new semi-implicit second order correction scheme to the kinetic Kohn-Sham lattice model. The new approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the periodic table finding good agreement with the expected values. Additionally we simulate the ethane molecule where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.

  17. Chemical kinetics and combustion modelling with CFX 4

    Stopford, P. [AEA Technology, Computational Fluid Dynamics Services Harwell, Oxfordshire (United Kingdom)


    The presentation describes some recent developments in combustion and kinetics models used in the CFX software of AEA Technology. Three topics are highlighted: the development of coupled solvers in a traditional `SIMPLE`-based CFD code, the use of detailed chemical kinetics mechanism via `look-up` tables and the application of CFD to large-scale multi-burner combustion plant. The aim is identify those physical approximations and numerical methods that are likely to be most useful in the future and those areas where further developments are required. (author) 6 refs.

  18. Kinetics and modeling of anaerobic digestion process


    Anaerobic digestion modeling started in the early 1970s when the need for design and efficient operation of anaerobic systems became evident. At that time not only was the knowledge about the complex process of anaerobic digestion inadequate but also there were computational limitations. Thus...

  19. Laplace transform in tracer kinetic modeling

    Hauser, Eliete B., E-mail: [Instituto do Cerebro (InsCer/FAMAT/PUC-RS), Porto Alegre, RS, (Brazil). Faculdade de Matematica


    The main objective this paper is to quantify the pharmacokinetic processes: absorption, distribution and elimination of radiopharmaceutical(tracer), using Laplace transform method. When the drug is administered intravenously absorption is complete and is available in the bloodstream to be distributed throughout the whole body in all tissues and fluids, and to be eliminated. Mathematical modeling seeks to describe the processes of distribution and elimination through compartments, where distinct pools of tracer (spatial location or chemical state) are assigned to different compartments. A compartment model is described by a system of differential equations, where each equation represents the sum of all the transfer rates to and from a specific compartment. In this work a two-tissue irreversible compartment model is used for description of tracer, [{sup 18}F]2-fluor-2deoxy-D-glucose. In order to determine the parameters of the model, it is necessary to have information about the tracer delivery in the form of an input function representing the time-course of tracer concentration in arterial blood or plasma. We estimate the arterial input function in two stages and apply the Levenberg-Marquardt Method to solve nonlinear regressions. The transport of FDG across de arterial blood is very fast in the first ten minutes and then decreases slowly. We use de Heaviside function to represent this situation and this is the main contribution of this study. We apply the Laplace transform and the analytical solution for two-tissue irreversible compartment model is obtained. The only approach is to determinate de arterial input function. (author)

  20. Ensemble Kinetic Modeling of Metabolic Networks from Dynamic Metabolic Profiles

    Gengjie Jia


    Full Text Available Kinetic modeling of metabolic pathways has important applications in metabolic engineering, but significant challenges still remain. The difficulties faced vary from finding best-fit parameters in a highly multidimensional search space to incomplete parameter identifiability. To meet some of these challenges, an ensemble modeling method is developed for characterizing a subset of kinetic parameters that give statistically equivalent goodness-of-fit to time series concentration data. The method is based on the incremental identification approach, where the parameter estimation is done in a step-wise manner. Numerical efficacy is achieved by reducing the dimensionality of parameter space and using efficient random parameter exploration algorithms. The shift toward using model ensembles, instead of the traditional “best-fit” models, is necessary to directly account for model uncertainty during the application of such models. The performance of the ensemble modeling approach has been demonstrated in the modeling of a generic branched pathway and the trehalose pathway in Saccharomyces cerevisiae using generalized mass action (GMA kinetics.

  1. Intrinsic Kinetic Modeling of Thermal Dimerization of C5 Fraction

    Guo Liang; Wang Tiefeng; Li Dongfeng; Wang Jinfu


    This work aims to investigate the intrinsic kinetics of thermal dimerization of C5 fraction in the reactive distilla-tion process. Experiments are conducted in an 1000-mL stainless steel autoclave under some selected design conditions. By means of the weighted least squares method, the intrinsic kinetics of thermal dimerization of C5 fraction is established, and the corresponding pre-exponential factor as well as the activation energy are determined. For example, the pre-exponential factor A is equal to 4.39×105 and the activation energy Ea is equal to 6.58×104 J/mol for the cyclopentadiene dimerization re-action. The comparison between the experimental and calculated results shows that the kinetics model derived in this work is accurate and reliable, which can be used in the design of reactive distillation columns.

  2. Kinetics of Model Reactions for Interfacial Polymerization

    Henry Hall


    Full Text Available To model the rates of interfacial polycondensations, the rates of reaction of benzoyl chloride and methyl chloroformate with various aliphatic monoamines in acetonitrile were determined at 25 °C. Buffering with picric acid slowed these extremely fast reactions so the rate constants could be determined from the rate of disappearance of picrate ion. The rates of the amine reactions correlated linearly with their Swain-Scott nucleophilicities.

  3. Thermodynamic and kinetic modeling of transcriptional pausing

    Tadigotla, Vasisht R.; Maoiléidigh, Dáibhid Ó; Sengupta, Anirvan M.; Epshtein, Vitaly; Ebright, Richard H.; Nudler, Evgeny; Ruckenstein, Andrei E.


    We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA–DNA, DNA–RNA, and RNA–RNA base pairing associated with (i) the translocational and size fluctuations of the transcription bubble; (ii) changes in the as...

  4. Homogeneous gas phase models of relaxation kinetics in neon afterglow

    Marković Vidosav Lj.


    Full Text Available The homogeneous gas phase models of relaxation kinetics (application of the gas phase effective coefficients to represent surface losses are applied for the study of charged and neutral active particles decay in neon afterglow. The experimental data obtained by the breakdown time delay measurements as a function of the relaxation time td (τ (memory curve is modeled in early, as well as in late afterglow. The number density decay of metastable states can explain neither the early, nor the late afterglow kinetics (memory effect, because their effective lifetimes are of the order of milliseconds and are determined by numerous collision quenching processes. The afterglow kinetics up to hundreds of milliseconds is dominated by the decay of molecular neon Ne2 + and nitrogen ions N2 + (present as impurities and the approximate value of N2 + ambipolar diffusion coefficient is determined. After the charged particle decay, the secondary emitted electrons from the surface catalyzed excitation of nitrogen atoms on the cathode determine the breakdown time delay down to the cosmic rays and natural radioactivity level. Due to the neglecting of number density spatial profiles, the homogeneous gas phase models give only the approximate values of the corresponding coefficients, but reproduce correctly other characteristics of afterglow kinetics from simple fits to the experimental data.

  5. Enzymatic hydrolysis of protein:mechanism and kinetic model

    Qi Wei; He Zhimin


    The bioreaction mechanism and kinetic behavior of protein enzymatic hydrolysis for preparing active peptides were investigated to model and characterize the enzymatic hydrolysis curves.Taking into account single-substrate hydrolysis,enzyme inactivation and substrate or product inhibition,the reaction mechanism could be deduced from a series of experimental results carried out in a stirred tank reactor at different substrate concentrations,enzyme concentrations and temperatures based on M-M equation.An exponential equation dh/dt = aexp(-bh) was also established,where parameters a and b have different expressions according to different reaction mechanisms,and different values for different reaction systems.For BSA-trypsin model system,the regressive results agree with the experimental data,i.e.the average relative error was only 4.73%,and the reaction constants were determined as Km = 0.0748 g/L,Ks = 7.961 g/L,kd = 9.358/min,k2 =38.439/min,Ea= 64.826 kJ/mol,Ed= 80.031 kJ/mol in accordance with the proposed kinetic mode.The whole set of exponential kinetic equations can be used to model the bioreaction process of protein enzymatic hydrolysis,to calculate the thermodynamic and kinetic constants,and to optimize the operating parameters for bioreactor design.

  6. Vlasov models for kinetic Weibel-type instabilities

    Ghizzo, A.; Sarrat, M.; Del Sarto, D.


    The Weibel instability, driven by a temperature anisotropy, is investigated within different kinetic descriptions based on the semi-Lagrangian full kinetic and relativistic Vlasov-Maxwell model, on the multi-stream approach, which is based on a Hamiltonian reduction technique, and finally, with the full pressure tensor fluid-type description. Dispersion relations of the Weibel instability are derived using the three different models. A qualitatively different regime is observed in Vlasov numerical experiments depending on the excitation of a longitudinal plasma electric field driven initially by the combined action of the stream symmetry breaking and weak relativistic effects, in contrast with the existing theories of the Weibel instability based on their purely transverse characters. The multi-stream model offers an alternate way to simulate easily the coupling with the longitudinal electric field and particularly the nonlinear regime of saturation, making numerical experiments more tractable, when only a few moments of the distribution are considered. Thus a numerical comparison between the reduced Hamiltonian model (the multi-stream model) and full kinetic (relativistic) Vlasov simulations has been investigated in that regime. Although nonlinear simulations of the fluid model, including the dynamics of the pressure tensor, have not been carried out here, the model is strongly relevant even in the three-dimensional case.

  7. Developments in kinetic modelling of chalcocite particle oxidation

    Jaervi, J.; Ahokainen, T.; Jokilaakso, A. [Helsinki Univ. of Technology, Otaniemi (Finland). Lab. of Materials Processing and Powder Metallurgy


    A mathematical model for simulating chalcocite particle oxidation is presented. Combustion of pure chalcocite with oxygen is coded as a kinetic module which can be connected as a separate part of commercial CFD-package, PHOENICS. Heat transfer, fluid flow and combustion phenomena can be simulated using CFD-calculation together with the kinetic model. Interaction between gas phase and particles are taken into account by source terms. The aim of the kinetic model is to calculate the particle temperature, contents of species inside the particle, oxygen consumption and formation of sulphur dioxide. Four oxidation reactions are considered and the shrinking core model is used to describe the rate of the oxidation reactions. The model is verified by simulating the particle oxidation reactions in a laboratory scale laminar-flow furnace under different conditions and the model predicts the effects of charges correctly. In the future, the model validation will be done after experimental studies in the laminar flow-furnace. (author) 18 refs.

  8. Modeling Kinetics of Distortion in Porous Bi-layered Structures

    Tadesse Molla, Tesfaye; Frandsen, Henrik Lund; Bjørk, Rasmus;


    Shape distortions during constrained sintering experiment of bi-layer porous and dense cerium gadolinium oxide (CGO) structures have been modeled. Technologies like solid oxide fuel cells require co-firing thin layers with different green densities, which often exhibit differential shrinkage...... because of different sintering rates of the materials resulting in undesired distortions of the component. An analytical model based on the continuum theory of sintering has been developed to describe the kinetics of densification and distortion in the sintering processes. A new approach is used...... to extract the material parameters controlling shape distortion through optimizing the model to experimental data of free shrinkage strains. The significant influence of weight of the sample (gravity) on the kinetics of distortion is taken in to consideration. The modeling predictions indicate good agreement...

  9. Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives

    Vitello, P A; Fried, L E; Howard, W M; Levesque, G; Souers, P C


    Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. They use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. They term their model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. A HE-validation suite of model simulations compared to experiments at ambient, hot, and cold temperatures has been developed. They present here a new rate model and comparison with experimental data.

  10. Ab initio and kinetic modeling studies of formic acid oxidation

    Marshall, Paul; Glarborg, Peter


    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute....... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...

  11. Kinetic model for the pathogenesis of radiation lung damage

    Collis, C.H. (Institute of Cancer Research, Sutton (UK). Surrey Branch)


    The development of radiation-induced lung damage can be explained by a kinetic model, based on the assumption that this damage becomes manifest only when a critical proportion (K) of essential cells have ceased to function, and that the rate of loss of these cells following irradiation is linear and dose-dependent. The kinetic model relates the surviving fraction to the time to manifestation of radiation-induced lung damage and to constants, K and the cell cycle time, T. Predictions made from the model about the nature of the response to irradiation are, for the most part, fulfilled. The model can also be used to interpret the response to combined treatment with irradiation and cytotoxic drugs, including the much earlier manifestation of lung damage sometimes seen with such treatment.

  12. Study on Kinetics for Desulfurization of Model Diesel

    Qian Jianhua; Zhou Yuenan; Liu Lin; Wang Yue; Xing Jinjuan; Lü Hong


    In this study, by means of the experiments for desulfurization of model diesel through oxi-dative extraction, the changes associated with the rate of desulfurization of diesel and the mechanism for oxidation of sulfides in diesel were explored. Through studying the mechanism for oxidation of sulfides and the principle of solvent extraction, the kinetic equation of desulfurization via oxidative extraction were determined. By means of the evaluation of model parameters and curve fitting, the reaction order between organic sulfide and sulfone, the intrinsic oxidation rate constant of organic sulfide and sulfone, and the equilibrium constant between suifone in model diesel and extractive sol-vent were determined. The experimental values of the desulfurization rate and the theoretical values of the corresponding model equation had closely demonstrated that the desulfurization reaction rate had high accuracy. And the reaction kinetics could provide an important basis for diesel desulfurization process in the future.

  13. Cleaner combustion developing detailed chemical kinetic models

    Battin-Leclerc, Frédérique; Blurock, Edward


    This overview compiles the on-going research in Europe to enlarge and deepen the understanding of the reaction mechanisms and pathways associated with the combustion of an increased range of fuels. Focus is given to the formation of a large number of hazardous minor pollutants and the inability of current combustion models to predict the  formation of minor products such as alkenes, dienes, aromatics, aldehydes and soot nano-particles which have a deleterious impact on both the environment and on human health. Cleaner Combustion describes, at a fundamental level, the reactive chemistry of min

  14. Kinetic modelling of molecular hydrogen transport in microporous carbon materials.

    Hankel, Marlies; Zhang, Hong; Nguyen, Thanh X; Bhatia, Suresh K; Gray, Stephen K; Smith, Sean C


    The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H(2)/D(2) and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D(2) transport is dramatically favored over H(2). However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients-implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H(2)/D(2) in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage through the pore mouth, is also

  15. Agent dynamics in kinetic models of wealth exchange

    Chatterjee, Arnab


    We study the dynamics of individual agents in some kinetic models of wealth exchange, particularly, the models with savings. For the model with uniform savings, agents perform simple random walks in the `"wealth space". On the other hand, we observe ballistic diffusion in the model with distributed savings. There is an associated skewness in the gain-loss distribution which explains the steady state behavior in such models. We find that in general an agent gains while interacting with an agent with a larger saving propensity.

  16. Extraction of lycopene from tomato processing waste: kinetics and modelling.

    Poojary, Mahesha M; Passamonti, Paolo


    Lycopene, a nutraceutical compound, was extracted from tomato processing waste, an abundantly available food industry by-product in Italy. The extraction kinetics was mathematically described using the first order kinetic model, the mass transfer model and Peleg's model to understand the physicochemical behaviour of the extraction. Samples were extracted using acetone/n-hexane mixtures at different ratios (1:3, 2:2 and 3:1, v/v) and at different temperatures (30, 40 and 50 °C) and simultaneously analysed using UV-VIS spectrophotometry. The lycopene yield was in the range 3.47-4.03 mg/100g, which corresponds to a percentage recovery of 65.22-75.75. All kinetic models gave a good fit to the experimental data, but the best one was Peleg's model, having the highest RAdj(2) and the lowest RMSE, MBE and χ(2) values. All the models confirmed that a temperature of 30 °C and solvent mixture of acetone/n-hexane 1:3 (v/v) provided optimal conditions for extraction of lycopene.

  17. Construction of reduced transport model by gyro-kinetic simulation with kinetic electrons in helical plasmas

    Toda, S.; Nakata, M.; Nunami, M.; Ishizawa, A.; Watanabe, T.-H.; Sugama, H.


    A reduced model of the turbulent ion heat diffusivity is proposed by the gyrokinetic simulation code (GKV-X) with the adiabatic electrons for the high-Ti Large Helical Device discharge. The plasma parameter region of the short poloidal wavelength is studied, where the ion temperature gradient mode becomes unstable. The ion heat diffusivity by the nonlinear simulation with the kinetic electrons is found to be several times larger than the simulation results using the adiabatic electrons in the radial region 0.46 ion energy flux. The model of the turbulent diffusivity is derived as the function of the squared electrostatic potential fluctuation and the squared zonal flow potential. Next, the squared electrostatic potential fluctuation is approximated with the mixing length estimate. The squared zonal flow potential fluctuation is shown as the linear zonal flow response function. The reduced model of the turbulent diffusivity is derived as the function of the physical parameters by the linear GKV-X simulation with the kinetic electrons. This reduced model is applied to the transport code with the same procedure as.

  18. Kinetic Model of Biodiesel Processing Using Ultrasound

    Bambang Susilo


    Full Text Available Ultrasound is predicted to be able to accelerate the chemical reaction, to increase the conversion of plant oil into biodiesel, and to decrease the need of catalyst and energy input. The application of ultrasound for processing of biodiesel and the mathematical model were conducted in this research. The result of the experiments showed that the ultrasound increased reaction rate and the conversion of palm oil into biodiesel up to 100%. It was better than the process with mechanical stirrer that the conversion was just 96%. The duration to complete the process using ultrasound was 1 minute. It was 30 to 120 times faster than that with mechanical stirrer. Ultrasound transforms mechanical energy into inner energy of the fluids and causes an increasing of temperature. Simultaneously, natural mixing process undergo because of acoustic circulation. Simulation with experiment data showed that the acceleration of transesterification with ultrasound was affected not only by natural mixing and increasing temperature. The cavitation, surface tension of micro bubble, and hot spot accelerate chemical reaction. In fact, transesterification of palm oil with ultrasound still needs catalyst. It needs only about 20% of catalyst compared to the process with mechanical stirrer.

  19. Kinetic model of induced codeposition of Ni-Mo alloys

    ZENG, Yue; MA, Ming; XIAO, Xiao-Ming; LI, Ze-Lin; LIAN, Shi-Xun; ZHOU, Shao-Min


    The kinetic model of induced codeposition of nickel-molybdenum alloys from ammoniun citrate solution was studied on rotating disk electrodes to predict the behavior of the electrodeposition. Ihe molybdate (MoO42-) could be firstly electrochemically reduced to MoO2, and subsequently undergoes a chemical reduction with atomic hydrogen previously adsorbed on the inducing metal nickel to form molybdenum in alloys.The kinetic equations were derived, and the kinetic parameters were obtained from a comparison of experimental results and the kinetic equations. The electrochemical rate constants for discharge of nickel, molybdenum and water could been expressed as k1 ( E ) = 1. 23 × 10-9 CNexp( - 0. 198FE/ RT )mol/(dm2. s), k2 (E) = 3.28 × 10-10 CMoexp ( - 0.208FE/RT) mol/(dm2·s) and k3(E) = 1.27 × 10-6exp( - 0.062FE/RT) mol/(dm2 ·s), where CN and CMo are the concentrations of the nickel ion and molybdate, respectively, and E is the applied potential vs, saturated calornel electrode (SCE).The codeposition process could be well simulated by this model.

  20. A Generalized Michaelis-Menten Equation in Protein Synthesis: Effects of Mis-Charged Cognate tRNA and Mis-Reading of Codon.

    Dutta, Annwesha; Chowdhury, Debashish


    The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.

  1. Kinetic model of the Buyers’ market

    Zhykharsky, Alexander V.


    In this work the following results are received. The closed mathematical apparatus describing the process of interaction of the Buyers’ market with retail Shop is created. The “statistical analogy” between the vacuum electrostatic diode and the Buyers’ market co-operating with retail Shop is considered. On the basis of the spent analysis the closed mathematical apparatus describing process of interaction of the Buyers’ market with retail Shop is created. The analytical expressions connecting a stream of Buyers, come to Shop, and a stream of the gain of Shop, with parameters of the Buyers’ market are received. For check of adequacy of the received model it is solved of some real “market” problems. On the basis of the spent researches principles of construction of Information-analytical Systems of new type which provide direct measurements of parameters of the Buyers’ market are developed. Actually these Systems are devices for measurement of parameters of this market. In this work it is shown that by means of the device developed for measurement of parameters of the Buyers’ market, creation of a new science-“demandodynamics” the Buyers’ market, is possible. Here the term “demandodynamics the Buyers’ market” is accepted by analogy to the term “thermodynamics” in physics. (In this work it is shown that for the Buyers’ market concept “demand” is similar to concept “temperature” in physics.) The construction methodology “demandodynamics” the Buyers’ market is defined and is shown that within the limits of this science working out of a technique of a direct control by a condition of the Buyers’ market is possible.

  2. Kinetic models for historical processes of fast invasion and aggression

    Aristov, Vladimir V.; Ilyin, Oleg V.


    In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.

  3. Kinetic Modeling of Paraffin Aromatization over Zeolites: A Design Perspective

    Bhan, Aditya; Katare, Santhoji; Caruthers, James; Lauterbach, Jochen; Venkatasubramanian, Venkat; Delgass, Nicholas


    A generic framework for catalyst design involving the solution of a forward predictive problem using hybrid models and the inverse problem using evolutionary algorithms has been proposed. In that context, we investigate the aromatization of light paraffins over HZSM-5 to obtain the catalyst descriptors and associated kinetic parameters that predict performance. A detailed kinetic model that can fundamentally quantify the catalytic properties of acid sites in terms of intrinsic parameters such as rate constants and activation energies of elementary steps is developed on the basis of the following types of reactions: adsorption/desorption, oligomerization/ beta-scission, hydride transfer, protolysis and aromatization. The reaction network so generated has been grouped under various reaction families taking into account the different stabilities and reactivities of the adsorbed carbenium/carbonium ions. The detailed parameterization of each reaction type, optimizing fits to data, linking catalyst descriptors to performance, and means of improving the robustness of the model will be presented.

  4. 5-Lump kinetic model for gas oil catalytic cracking

    Ancheyta-Juarez, Jorge; Aguilar-Rodriguez, Enrique [Instituto Mexicano del Petroleo, Eje Central Lazaro Cardenas 152, Mexico 07730 DF (Mexico); Lopez-Isunza, Felipe [Universidad Autonoma Metropolitana-Iztapalapa, Mexico 09340 DF (Mexico)


    A new 5-lump kinetic model is proposed to describe the gas oil catalytic cracking (FCC) process. The model contains eight kinetic constants, including one for catalyst deactivation, taking into account LPG (combined C{sub 3}-C{sub 4}), dry gas (C{sub 2} and lighter) and coke yields separately from other lumps (unconverted gas oil and gasoline). Apparent activation energies were determined from experiments obtained in a microactivity reactor (MAT) at temperatures: 480C, 500C and 520C; for a catalyst-to-oil ratio of 5 using vacuum gas oil and equilibrium catalyst, both recovered from an industrial FCC unit. Product yields predicted by this model show good agreement with experimental data

  5. Pre-reheating magnetogenesis in the kinetic coupling model

    Fujita, Tomohiro; Namba, Ryo


    Recent blazar observations provide growing evidence for the presence of magnetic fields in the extragalactic regions. While natural speculation is to associate the production with inflationary physics, it is known that magnetogenesis solely from inflation is quite challenging. We therefore study a model in which a noninflaton field χ coupled to the electromagnetic field through its kinetic term, -I2(χ )F2/4 , continues to move after inflation until the completion of reheating. This leads to a postinflationary amplification of the electromagnetic field. We compute all the relevant contributions to the curvature perturbation, including gravitational interactions, and impose the constraints from the CMB scalar fluctuations on the strength of magnetic fields. We, for the first time, explicitly verify both the backreaction and CMB constraints in a simple yet successful magnetogenesis scenario without invoking a dedicated low-scale inflationary model in the weak-coupling regime of the kinetic coupling model.

  6. Modelling of an ASR countercurrent pyrolysis reactor with nonlinear kinetics

    Chiarioni, A.; Reverberi, A.P.; Dovi, V.G. [Universita degli Studi di Genova (Italy). Dipartimento di Ingegneria Chimica e di Processo ' G.B. Bonino' ; El-Shaarawi, A.H. [National Water Research Institute, Burlington, Ont. (Canada)


    The main objective of this work is focused on the modelling of a steady-state reactor where an automotive shredder residue (ASR) is subject to pyrolysis. The gas and solid temperature inside the reactor and the relevant density profiles of both phases are simulated for fixed values of the geometry of the apparatus and a lumped kinetic model is adopted to take into account the high heterogeneity of the ASR material. The key elements for the simulation are the inlet solid temperature and the outlet gas temperature. The problem is modelled by a system of first-order boundary-value ordinary differential equations and it is solved by means of a relaxation technique owing to the nonlinearities contained in the chemical kinetic expression. (author)

  7. Reproducing Phenomenology of Peroxidation Kinetics via Model Optimization

    Ruslanov, Anatole D.; Bashylau, Anton V.


    We studied mathematical modeling of lipid peroxidation using a biochemical model system of iron (II)-ascorbate-dependent lipid peroxidation of rat hepatocyte mitochondrial fractions. We found that antioxidants extracted from plants demonstrate a high intensity of peroxidation inhibition. We simplified the system of differential equations that describes the kinetics of the mathematical model to a first order equation, which can be solved analytically. Moreover, we endeavor to algorithmically and heuristically recreate the processes and construct an environment that closely resembles the corresponding natural system. Our results demonstrate that it is possible to theoretically predict both the kinetics of oxidation and the intensity of inhibition without resorting to analytical and biochemical research, which is important for cost-effective discovery and development of medical agents with antioxidant action from the medicinal plants.

  8. Kinetic modeling of the Townsend breakdown in argon

    Macheret, S. O.; Shneider, M. N. [Department of Mechanical and Aerospace Engineering, Princeton University, D-414 Engineering Quadrangle, Princeton, New Jersey 08544 (United States)


    Kinetic modeling of the Townsend breakdown in argon was performed in the “forward-back” approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.

  9. Stochastic effects in a discretized kinetic model of economic exchange

    Bertotti, M. L.; Chattopadhyay, A. K.; Modanese, G.


    Linear stochastic models and discretized kinetic theory are two complementary analytical techniques used for the investigation of complex systems of economic interactions. The former employ Langevin equations, with an emphasis on stock trade; the latter is based on systems of ordinary differential equations and is better suited for the description of binary interactions, taxation and welfare redistribution. We propose a new framework which establishes a connection between the two approaches by introducing random fluctuations into the kinetic model based on Langevin and Fokker-Planck formalisms. Numerical simulations of the resulting model indicate positive correlations between the Gini index and the total wealth, that suggest a growing inequality with increasing income. Further analysis shows, in the presence of a conserved total wealth, a simultaneous decrease in inequality as social mobility increases, in conformity with economic data.

  10. Kinetic modelling of enzyme inactivation Kinetics of heat inactivation of the extracellular proteinase from Pseudomonas fluorescens 22F.

    Schokker, E.P.


    The kinetics of heat inactivation of the extracellular proteinase from Pseudomonas fluorescens 22F was studied. It was established, by making use of kinetic modelling, that heat inactivation in the temperature range 35 - 70 °C was most likely caused by intermolecular autoproteolysis, where unfolded

  11. Ordering kinetics in model systems with inhibited interfacial adsorption

    Willart, J.-F.; Mouritsen, Ole G.; Naudts, J.


    The ordering kinetics in two-dimensional Ising-like spin moels with inhibited interfacial adsorption are studied by computer-simulation calculations. The inhibited interfacial adsorption is modeled by a particular interfacial adsorption condition on the structure of the domain wall between...... neighboring domains. This condition can be either hard, as modeled by a singularity in the domain-boundary potential, or soft, as modeled by a version of the Blume-Capel model. The results show that the effect of the steric hindrance, be it hard or soft, is only manifested in the amplitude, A...

  12. An autocatalytic kinetic model for describing microbial growth during fermentation.

    Ibarz, Albert; Augusto, Pedro E D


    The mathematical modelling of the behaviour of microbial growth is widely desired in order to control, predict and design food and bioproduct processing, stability and safety. This work develops and proposes a new semi-empirical mathematical model, based on an autocatalytic kinetic, to describe the microbial growth through its biomass concentration. The proposed model was successfully validated using 15 microbial growth patterns, covering the three most important types of microorganisms in food and biotechnological processing (bacteria, yeasts and moulds). Its main advantages and limitations are discussed, as well as the interpretation of its parameters. It is shown that the new model can be used to describe the behaviour of microbial growth.

  13. Modelling on corrosion inhibitor kinetics in carbon steel pipe used in oil industry

    Hasmi, A. N.; Nuraini, N.; Wahyuningrum, D.; Sumarti, N.; Bunjali, B.


    A model to explain the kinetics of corrosion inhibitor is proposed here. The model is based on Transition State Theory. Our model has many similarities with Michelis-Menten Kinetics. The kinetics difference between uninhibited corrosion and inhibited corrosion is presented. Our model showed the inhibitor could suppress the corrosion rate.

  14. Stepwise kinetic equilibrium models of quantitative polymerase chain reaction

    Cobbs Gary


    Full Text Available Abstract Background 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. Results 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

  15. Kinetic models of gene expression including non-coding RNAs

    Zhdanov, Vladimir P.


    In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

  16. Modeling organic micro pollutant degradation kinetics during sewage sludge composting.

    Sadef, Yumna; Poulsen, Tjalfe Gorm; Bester, Kai


    Degradation of 13 different organic micro-pollutants in sewage sludge during aerobic composting at 5 different temperatures over a 52 day period was investigated. Adequacy of two kinetic models: a single first order, and a dual first order expression (using an early (first 7 days) and a late-time (last 45 days) degradation coefficient), for describing micro-pollutant degradation, and kinetic constant dependency on composting temperature were evaluated. The results showed that both models provide relatively good descriptions of the degradation process, with the dual first order model being most accurate. The single first order degradation coefficient was 0.025 d(-1) on average across all compounds and temperatures. At early times, degradation was about three times faster than at later times. Average values of the early and late time degradation coefficients for the dual first order model were 0.066 d(-1) and 0.022 d(-1), respectively. On average 30% of the initial micro-pollutant mass present in the compost was degraded rapidly during the early stages of the composting process. Single first order and late time dual first order kinetic constants were strongly dependent on composting temperature with maximum values at temperatures of 35-65°C. In contrast the early time degradation coefficients were relatively independent of composting temperature.

  17. A robust methodology for kinetic model parameter estimation for biocatalytic reactions

    Al-Haque, Naweed; Andrade Santacoloma, Paloma de Gracia; Lima Afonso Neto, Watson;


    Effective estimation of parameters in biocatalytic reaction kinetic expressions are very important when building process models to enable evaluation of process technology options and alternative biocatalysts. The kinetic models used to describe enzyme-catalyzed reactions generally include several...

  18. A kinetic model for the first stage of pygas upgrading

    J. L. de Medeiros


    Full Text Available Pyrolysis gasoline - PYGAS - is an intermediate boiling product of naphtha steam cracking with a high octane number and high aromatic/unsaturated contents. Due to stabilization concerns, PYGAS must be hydrotreated in two stages. The first stage uses a mild trickle-bed conversion for removing extremely reactive species (styrene, dienes and olefins prior to the more severe second stage where sulfured and remaining olefins are hydrogenated in gas phase. This work addresses the reaction network and two-phase kinetic model for the first stage of PYGAS upgrading. Nonlinear estimation was used for model tuning with kinetic data obtained in bench-scale trickle-bed hydrogenation with a commercial Pd/Al2O3 catalyst. On-line sampling experiments were designed to study the influence of variables - temperature and spatial velocity - on the conversion of styrene, dienes and olefins.

  19. Stochastic kinetic models: Dynamic independence, modularity and graphs

    Bowsher, Clive G


    The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition $[A,D,B]$ of the vertices, the graphical separation $A\\perp B|D$ in the undirected KIG has an intuitive chemical interpretation and implies that $A$ is locally independent of $B$ given $A\\cup D$. It is proved that this separation also results in global independence of the internal histories of $A$ and $B$ conditional on a history of the jumps in $D$ which, under conditions we derive, corresponds to the internal history of $D$. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Gra...

  20. Kinetics approach to modeling of polymer additive degradation in lubricants

    llyaI.KUDISH; RubenG.AIRAPETYAN; Michael; J.; COVITCH


    A kinetics problem for a degrading polymer additive dissolved in a base stock is studied.The polymer degradation may be caused by the combination of such lubricant flow parameters aspressure, elongational strain rate, and temperature as well as lubricant viscosity and the polymercharacteristics (dissociation energy, bead radius, bond length, etc.). A fundamental approach tothe problem of modeling mechanically induced polymer degradation is proposed. The polymerdegradation is modeled on the basis of a kinetic equation for the density of the statistical distribu-tion of polymer molecules as a function of their molecular weight. The integrodifferential kineticequation for polymer degradation is solved numerically. The effects of pressure, elongational strainrate, temperature, and lubricant viscosity on the process of lubricant degradation are considered.The increase of pressure promotes fast degradation while the increase of temperature delaysdegradation. A comparison of a numerically calculated molecular weight distribution with an ex-perimental one obtained in bench tests showed that they are in excellent agreement with eachother.

  1. Kinetic model of metabolic network for xiamenmycin biosynthetic optimisation.

    Xu, Min-juan; Chen, Yong-cong; Xu, Jun; Ao, Ping; Zhu, Xiao-mei


    Xiamenmycins, a series of prenylated benzopyran compounds with anti-fibrotic bioactivities, were isolated from a mangrove-derived Streptomyces xiamenensis. To fulfil the requirements of pharmaceutical investigations, a high production of xiamenmycin is needed. In this study, the authors present a kinetic metabolic model to evaluate fluxes in an engineered Streptomyces lividans with xiamenmycin-oriented genetic modification based on generic enzymatic rate equations and stability constraints. Lyapunov function was used for a viability optimisation. From their kinetic model, the flux distributions for the engineered S. lividans fed on glucose and glycerol as carbon sources were calculated. They found that if the bacterium can utilise glucose simultaneously with glycerol, xiamenmycin production can be enhanced by 40% theoretically, while maintaining the same growth rate. Glycerol may increase the flux for phosphoenolpyruvate synthesis without interfering citric acid cycle. They therefore believe this study demonstrates a possible new direction for bioengineering of S. lividans.

  2. Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

    Nag Ambarish


    Full Text Available Abstract Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to

  3. Controllability in hybrid kinetic equations modeling nonequilibrium multicellular systems.

    Bianca, Carlo


    This paper is concerned with the derivation of hybrid kinetic partial integrodifferential equations that can be proposed for the mathematical modeling of multicellular systems subjected to external force fields and characterized by nonconservative interactions. In order to prevent an uncontrolled time evolution of the moments of the solution, a control operator is introduced which is based on the Gaussian thermostat. Specifically, the analysis shows that the moments are solution of a Riccati-type differential equation.

  4. A model for recovery kinetics of aluminum after large strain

    Yu, Tianbo; Hansen, Niels


    A model is suggested to analyze recovery kinetics of heavily deformed aluminum. The model is based on the hardness of isothermal annealed samples before recrystallization takes place, and it can be extrapolated to longer annealing times to factor out the recrystallization component of the hardness...... for conditions where recovery and recrystallization overlap. The model is applied to the isothermal recovery at temperatures between 140 and 220°C of commercial purity aluminum deformed to true strain 5.5. EBSD measurements have been carried out to detect the onset of discontinuous recrystallization. Furthermore...

  5. Computation Molecular Kinetics Model of HZE Induced Cell Cycle Arrest

    Cucinotta, Francis A.; Ren, Lei


    Cell culture models play an important role in understanding the biological effectiveness of space radiation. High energy and charge (HZE) ions produce prolonged cell cycle arrests at the G1/S and G2/M transition points in the cell cycle. A detailed description of these phenomena is needed to integrate knowledge of the expression of DNA damage in surviving cells, including the determination of relative effectiveness factors between different types of radiation that produce differential types of DNA damage and arrest durations. We have developed a hierarchical kinetics model that tracks the distribution of cells in various cell phase compartments (early G1, late G1, S, G2, and M), however with transition rates that are controlled by rate-limiting steps in the kinetics of cyclin-cdk's interactions with their families of transcription factors and inhibitor molecules. The coupling of damaged DNA molecules to the downstream cyclin-cdk inhibitors is achieved through a description of the DNA-PK and ATM signaling pathways. For HZE irradiations we describe preliminary results, which introduce simulation of the stochastic nature of the number of direct particle traversals per cell in the modulation of cyclin-cdk and cell cycle population kinetics. Comparison of the model to data for fibroblast cells irradiated photons or HZE ions are described.

  6. Kinetics and specificity of nickel hypersensitivity in the murine model.

    Siller, G M; Seymour, G J


    Nickel contact dermatitis appears to be almost exclusively a disease of females despite the increasing exposure of males to nickel. Successful murine models of nickel allergic contact dermatitis have been described. The purpose of this study is to investigate the kinetics and specificity of the response in this model and to examine if any differences exist between male and female. Mice were sensitised epicutaneously with nickel sulphate in aqueous solution of varying concentration, volume and duration of application. Following intradermal challenge, dose dependent response kinetics which approximated linearity were demonstrated upto the point of toxicity. Sensitised mice were challenged with Cobaltous chloride, Chromic chloride and Cupric sulphate and demonstrated no evidence of cross sensitivity to cobalt or chrome. Copper produced an irritant response making interpretation difficult. Earlier and stronger responses were observed in female mice, however these differences fell short of statistical significance. The results of the present study therefore establishes a reliable model for nickel hypersensitivity, that demonstrates both specificity and dose dependent kinetics without significant sex differences.

  7. Kinetic model on coke oven gas with steam reforming

    ZHANG Jia-yuan; ZHOU Jie-min; YAN Hong-jie


    The effects of factors such as the molar ratio of H2O to CH4 (n(H2O)/n(CH4)), methane conversion temperature and time on methane conversion rate were investigated to build kinetic model for reforming of coke-oven gas with steam. The results of experiments show that the optimal conditions for methane conversion are that the molar ratio of H2O to CH4 varies from 1.1 to 1.3and the conversion temperature varies from 1 223 to 1 273 K. The methane conversion rate is more than 95% when the molar ratio ofH2O to CH4 is 1.2, the conversion temperature is above 1 223 K and the conversion time is longer than 0.75 s. Kinetic model of methane conversion was proposed. All results demonstrate that the calculated values by the kinetic model accord with the experimental data well, and the error is less than 1.5%.

  8. Simulation of DME synthesis from coal syngas by kinetics model

    Shim, H.M.; Lee, S.J.; Yoo, Y.D.; Yun, Y.S.; Kim, H.T. [Ajou University, Suwon (Republic of Korea)


    DME (Dimethyl Ether) has emerged as a clean alternative fuel for diesel. In this study it is developed a simulation model through a kinetics model of the ASPEN plus simulator, performed to detect operating characteristics of DME direct synthesis. An overall DME synthesis process is referenced by experimental data of 3 ton/day (TPD) coal gasification pilot plant located at IAE in Korea. Supplying condition of DME synthesis model is equivalently set to 80 N/m{sup 3} of syngas which is derived from a coal gasification plant. In the simulation it is assumed that the overall DME synthesis process proceeds with steady state, vapor-solid reaction with DME catalyst. The physical properties of reactants are governed by Soave-Redlich-Kwong (SRK) EOS in this model. A reaction model of DME synthesis is considered that is applied with the LHHW (Langmuir-Hinshelwood Hougen Watson) equation as an adsorption-desorption model on the surface of the DME catalyst. After adjusting the kinetics of the DME synthesis reaction among reactants with experimental data, the kinetics of the governing reactions inner DME reactor are modified and coupled with the entire DME synthesis reaction. For validating simulation results of the DME synthesis model, the obtained simulation results are compared with experimental results: conversion ratio, DME yield and DME production rate. Then, a sensitivity analysis is performed by effects of operating variables such as pressure, temperature of the reactor, void fraction of catalyst and H{sub 2}/CO ratio of supplied syngas with modified model. According to simulation results, optimum operating conditions of DME reactor are obtained in the range of 265-275{sup o}C and 60 kg/cm{sup 2}. And DME production rate has a maximum value in the range of 1-1.5 of H{sub 2}/CO ratio in the syngas composition.

  9. Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis

    Durruty, Ignacio; Aguirrezábal, Luis A. N.; Echarte, María M.


    Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ′) while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809

  10. Kinetic models for fermentative hydrogen production: A review

    Wang, Jianlong; Wan, Wei [Laboratory of Environmental Technology, INET, Tsinghua University, Beijing 100084 (China)


    The kinetic models were developed and applied for fermentative hydrogen production. They were used to describe the progress of a batch fermentative hydrogen production process, to investigate the effects of substrate concentration, inhibitor concentration, temperatures, pH, and dilution rates on the process of fermentative hydrogen production, and to establish the relationship among the substrate degradation rate, the hydrogen-producing bacteria growth rate and the product formation rate. This review showed that the modified Gompertz model was widely used to describe the progress of a batch fermentative hydrogen production process, while the Monod model was widely used to describe the effects of substrate concentration on the rates of substrate degradation, hydrogen-producing bacteria growth and hydrogen production. Arrhenius model was used a lot to describe the effects of temperature on fermentative hydrogen production, while modified Han-Levenspiel model was used to describe the effects of inhibitor concentration on fermentative hydrogen production. The Andrew model was used to describe the effects of H{sup +} concentration on the specific hydrogen production rate, while the Luedeking-Piret model and its modified form were widely used to describe the relationship between the hydrogen-producing bacteria growth rate and the product formation rate. Finally, some suggestions for future work with these kinetic models were proposed. (author)

  11. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

    Zheng, Weihua; Andrec, Michael; Gallicchio, Emilio; Levy, Ronald M


    We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate.

  12. Multiensemble Markov models of molecular thermodynamics and kinetics.

    Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank


    We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model.

  13. Kinetic models for nucleocytoplasmic transport of messenger RNA.

    Schröder, H C; Müller, W E; Agutter, P S


    Much is known about the mechanism by which mRNAs cross the nuclear envelope (the translocation stage of nucleocytoplasmic transport), but far less is known about the preceding (intranuclear migration/release) and succeeding (cytoplasmic binding) stages. Therefore, existing information suffices for articulating detailed kinetic models of translocation, but not models for the overall mRNA transport process. In this paper, we show that simple kinetic models of translocation can (i) accommodate data about nucleocytoplasmic distributions of endogenous transcripts; (ii) predict the overall effects on these distributions of effectors such as insulin and epidermal growth factor; (iii) throw some light on the mechanism(s) of action of the HIV-1 protein Rev and produce experimentally testable predictions about this mechanism; and (iv) account for the action of influenza virus NS1 protein. However, the simplest forms of translocation models apparently fail to account for some properties of viral regulators such as HIV Rev and adenovirus E1B-E4 complex. To elucidate these topics, less narrowly focused models of mRNA transport are required, describing intranuclear binding/release as well as translocation. On the basis of our examination of translocation models, we suggest some criteria that the requisite broadly based models must satisfy.

  14. Study on kinetic model of microwave thermocatalytic treatment of biomass tar model compound.

    Anis, Samsudin; Zainal, Z A


    Kinetic model parameters for toluene conversion under microwave thermocatalytic treatment were evaluated. The kinetic rate constants were determined using integral method based on experimental data and coupled with Arrhenius equation for obtaining the activation energies and pre-exponential factors. The model provides a good agreement with the experimental data. The kinetic model was also validated with standard error of 3% on average. The extrapolation of the model showed a reasonable trend to predict toluene conversion and product yield both in thermal and catalytic treatments. Under microwave irradiation, activation energy of toluene conversion was lower in the range of 3-27 kJ mol(-1) compared to those of conventional heating reported in the literatures. The overall reaction rate was six times higher compared to conventional heating. As a whole, the kinetic model works better for tar model removal in the absence of gas reforming within a level of reliability demonstrated in this study.

  15. Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

    Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P


    The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis.

  16. Alkaline Hydrolysis Kinetics Modeling of Bagasse Pentosan Dissolution

    Yuxin Liu


    Full Text Available The main pentosan components of sugarcane bagasse, which can be subjected to alkaline hydrolysis, are xylose, arabinose, glucose, and galactose. The pentosan reaction mechanism was considered for alkali-treated bagasse with variation of temperature and time. The kinetics of pentosan degradation were studied concurrently at temperatures of 50 °C, 70 °C, and 90 °C, with a solid-liquid mass ratio of 1:15, a stirring speed of 500 revolutions/min, and different holding times for bagasse alkali pre-extraction. With respect to residual pentosan content and the losses of raw material, the hydrolysis rates of alkali pre-extraction and pentosan degradation reactions of bagasse all followed pseudo-first-order kinetic models. Finally, the main degradation activation energy was determined to be 20.86 KJ/mol, and the residual degradation activation energy was 28.75 KJ/mol according to the Arrhenius equation.

  17. Kinetic modeling of ethylbenzene dehydrogenation over hydrotalcite catalysts

    Atanda, Luqman


    Kinetics of ethylbenzene dehydrogenation to styrene was investigated over a series of quaternary mixed oxides of Mg3Fe0.25Me0.25Al0.5 (Me=Co, Mn and Ni) catalysts prepared by calcination of hydrotalcite-like compounds and compared with commercial catalyst. The study was carried out in the absence of steam using a riser simulator at 400, 450, 500 and 550°C for reaction times of 5, 10, 15 and 20s. Mg3Fe0.25Mn0.25Al0.5 afforded the highest ethylbenzene conversion of 19.7% at 550°C. Kinetic parameters for the dehydrogenation process were determined using the catalyst deactivation function based on reactant conversion model. The apparent activation energies for styrene production were found to decrease as follows: E1-Ni>E1-Co>E1-Mn. © 2011 Elsevier B.V.

  18. Kinetic modelling and mechanism of dye adsorption on unburned carbon

    Wang, S.B.; Li, H.T. [Curtin University of Technology, Perth, WA (Australia). Dept. of Chemical Engineering


    Textile dyeing processes are among the most environmentally unfriendly industrial processes by producing coloured wastewaters. The adsorption method using unburned carbon from coal combustion residue was studied for the decolourisation of typical acidic and basic dyes. It was discovered that the unburned carbon showed high adsorption capacity at 1.97 x 10{sup -4} and 5.27 x 10{sup -4} mol/g for Basic Violet 3 and Acid Black 1, respectively. The solution pH, particle size and temperature significantly influenced the adsorption capacity. Higher solution pH favoured the adsorption of basic dye while reduced the adsorption of acid dye. The adsorption of dye increased with increasing temperature but decreased with increasing particle size. Sorption kinetic data indicated that the adsorption kinetics followed the pseudo-second-order model. The adsorption mechanism consisted of two processes, external diffusion and intraparticle diffusion, and the external diffusion was the dominating process.

  19. An enhanced Brinson model with modified kinetics for martensite transformation

    Kim, Young-Jin; Lee, Jung Ju [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of); Jeong, Ju-Won [Korea Aerospace Research Institute, Daejeon (Korea, Republic of); Lim, Jae Hyuk [Chonbuk National University, Jeonju (Korea, Republic of)


    We propose an enhanced Brinson model with modified kinetics for martensite transformation. Two additional material constants are considered to follow the stress-temperature diagram above austenite start temperature (As) along with treatment to keep the continuity of the martensite volume fraction and the path dependency of the phase transformation. To demonstrate the performance of the proposed model, we implement this algorithm into ABAQUS user subroutine, then conduct several numerical simulations and compare their results with SMA wire experiments as well as those of three-dimensional SMA constitutive models. From the results, it turns out that the proposed model is as accurate as the three-dimensional models and shows better accuracy over original Brinson model in terms of recovery stress.

  20. Modeling the turbulent kinetic energy equation for compressible, homogeneous turbulence

    Aupoix, B.; Blaisdell, G. A.; Reynolds, William C.; Zeman, Otto


    The turbulent kinetic energy transport equation, which is the basis of turbulence models, is investigated for homogeneous, compressible turbulence using direct numerical simulations performed at CTR. It is shown that the partition between dilatational and solenoidal modes is very sensitive to initial conditions for isotropic decaying turbulence but not for sheared flows. The importance of the dilatational dissipation and of the pressure-dilatation term is evidenced from simulations and a transport equation is proposed to evaluate the pressure-dilatation term evolution. This transport equation seems to work well for sheared flows but does not account for initial condition sensitivity in isotropic decay. An improved model is proposed.

  1. Web-based kinetic modelling using JWS Online.

    Olivier, Brett G; Snoep, Jacky L


    JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet. It is implemented using a client-server strategy where the clients, in the form of web browser based Java applets, act as a graphical interface to the model servers, which perform the required numerical computations. The JWS Online website is publicly accessible at with mirrors at and

  2. Kinetic model for microbial growth and desulphurisation with Enterobacter sp.

    Liu, Long; Guo, Zhiguo; Lu, Jianjiang; Xu, Xiaolin


    Biodesulphurisation was investigated by using Enterobacter sp. D4, which can selectively desulphurise and convert dibenzothiophene into 2-hydroxybiphenyl (2-HBP). The experimental values of growth, substrate consumption and product generation were obtained at 95 % confidence level of the fitted values using three models: Hinshelwood equation, Luedeking-Piret and Luedeking-Piret-like equations. The average error values between experimental values and fitted values were less than 10 %. These kinetic models describe all the experimental data with good statistical parameters. The production of 2-HBP in Enterobacter sp. was by "coupled growth".

  3. Small velocity and finite temperature variations in kinetic relaxation models

    Markowich, Peter


    A small Knuden number analysis of a kinetic equation in the diffusive scaling is performed. The collision kernel is of BGK type with a general local Gibbs state. Assuming that the flow velocity is of the order of the Knudsen number, a Hilbert expansion yields a macroscopic model with finite temperature variations, whose complexity lies in between the hydrodynamic and the energy-transport equations. Its mathematical structure is explored and macroscopic models for specific examples of the global Gibbs state are presented. © American Institute of Mathematical Sciences.

  4. The permeability of red blood cells to chloride, urea and water

    Brahm, Jesper


    -1000 mmol l(-1), Michaelis-Menten-like kinetics; K½=127, 173 and 345 mmol l(-1)), and values at [urea]=1 mmol l(-1) are 29.5×10(-6), 467×10(-6) and 260×10(-6) cm s(-1), respectively. Diffusional water permeability, Pd, was 0.84×10(-3) (chick), 5.95×10(-3) (duck), 0.39×10(-3) (Amphiuma), 3.13×10(-3) (dog...

  5. Numerical Comparison of Solutions of Kinetic Model Equations

    A. A. Frolova


    Full Text Available The collision integral approximation by different model equations has created a whole new trend in the theory of rarefied gas. One widely used model is the Shakhov model (S-model obtained by expansion of inverse collisions integral in a series of Hermite polynomials up to the third order. Using the same expansion with another value of free parameters leads to a linearized ellipsoidal statistical model (ESL.Both model equations (S and ESL have the same properties, as they give the correct relaxation of non-equilibrium stress tensor components and heat flux vector, the correct Prandtl number at the transition to the hydrodynamic regime and do not guarantee the positivity of the distribution function.The article presents numerical comparison of solutions of Shakhov equation, ESL- model and full Boltzmann equation in the four Riemann problems for molecules of hard spheres.We have considered the expansion of two gas flows, contact discontinuity, the problem of the gas counter-flows and the problem of the shock wave structure. For the numerical solution of the kinetic equations the method of discrete ordinates is used.The comparison shows that solution has a weak sensitivity to the form of collision operator in the problem of expansions of two gas flows and results obtained by the model and the kinetic Boltzmann equations coincide.In the problem of the contact discontinuity the solution of model equations differs from full kinetic solutions at the point of the initial discontinuity. The non-equilibrium stress tensor has the maximum errors, the error of the heat flux is much smaller, and the ESL - model gives the exact value of the extremum of heat flux.In the problems of gas counter-flows and shock wave structure the model equations give significant distortion profiles of heat flux and non-equilibrium stress tensor components in front of the shock waves. This behavior is due to fact that in the models under consideration there is no dependency of the

  6. Modeling Heavy Metal Sorption Kinetics Using Fractional Calculus

    V. C. Friesen


    Full Text Available Heavy metals are commonly regarded as environmentally aggressive and hazardous to human health. Among the different metals, lead plays an important economic role due to its large use in the automotive industry, being an essential component of batteries. Different approaches have been reported in the literature aimed at lead removal, and among them a very successful one considers the use of water hyacinths for sorption-based operation. The modeling of the metal sorption kinetics is a fundamental step towards in-depth studies and proper separation equipment design and optimization. Fractional calculus represents a novel approach and a growing research field for process modeling, which is based on the successful use of derivatives of arbitrary order. This paper reports the modeling of the kinetics of lead sorption by water hyacinths (Eichhornia crassipes using a fractional calculus. A general procedure on error analysis is also employed to prove the actual fractional nature of the proposed model by the use of parametric variance analysis, which was carried out using two different approaches (with the complete Hessian matrix and with a simplified Hessian matrix. The joint parameter confidence regions were generated, allowing to successfully show the fractional nature of the model and the sorption process.

  7. Kinetic model of ductile iron solidification with experimental verification

    W. Kapturkiewicz


    Full Text Available A solidification model for ductile iron, including Weibull formula for nodule count has been presented. From this model, the following can be determined: cooling curves, kinetics of austenite and eutectic nucleation, austenite and eutectic growth velocity, volume fraction, distribution of Si and P both in austenite and eutectic grain with distribution in casting section.In the developed model of nodular graphite iron casting solidification, the correctness of the mathematical model has been experimentally verified in the range of the most significant factors, which include temperature field, the value of maximum undercooling, and the graphite nodule count interrelated with the casting cross-section. Literature offers practically no data on so confronted process model and simulation program.

  8. Langrangian model of nitrogen kinetics in the Chattahoochee river

    Jobson, H.E.


    A Lagrangian reference frame is used to solve the convection-dispersion equation and interpret water-quality obtained from the Chattahoochee River. The model was calibrated using unsteady concentrations of organic nitrogen, ammonia, and nitrite plus nitrate obtained during June 1977 and verified using data obtained during August 1976. Reaction kinetics of the cascade type are shown to provide a reasonable description of the nitrogen-species processes in the Chattahoochee River. The conceptual model is easy to visualize in the physical sense and the output includes information that is not easily determined from an Eulerian approach, but which is very helpful in model calibration and data interpretation. For example, the model output allows one to determine which data are of most value in model calibration or verification.

  9. Simulation of styrene polymerization reactors: kinetic and thermodynamic modeling

    A. S. Almeida


    Full Text Available A mathematical model for the free radical polymerization of styrene is developed to predict the steady-state and dynamic behavior of a continuous process. Special emphasis is given for the kinetic and thermodynamic models, where the most sensitive parameters were estimated using data from an industrial plant. The thermodynamic model is based on a cubic equation of state and a mixing rule applied to the low-pressure vapor-liquid equilibrium of polymeric solutions, suitable for modeling the auto-refrigerated polymerization reactors, which use the vaporization rate to remove the reaction heat from the exothermic reactions. The simulation results show the high predictive capability of the proposed model when compared with plant data for conversion, average molecular weights, polydispersity, melt flow index, and thermal properties for different polymer grades.

  10. Kinetic equations modelling wealth redistribution: a comparison of approaches.

    Düring, Bertram; Matthes, Daniel; Toscani, Giuseppe


    Kinetic equations modelling the redistribution of wealth in simple market economies is one of the major topics in the field of econophysics. We present a unifying approach to the qualitative study for a large variety of such models, which is based on a moment analysis in the related homogeneous Boltzmann equation, and on the use of suitable metrics for probability measures. In consequence, we are able to classify the most important feature of the steady wealth distribution, namely the fatness of the Pareto tail, and the dynamical stability of the latter in terms of the model parameters. Our results apply, e.g., to the market model with risky investments [S. Cordier, L. Pareschi, and G. Toscani, J. Stat. Phys. 120, 253 (2005)], and to the model with quenched saving propensities [A. Chatterjee, B. K. Chakrabarti, and S. S. Manna, Physica A 335, 155 (2004)]. Also, we present results from numerical experiments that confirm the theoretical predictions.

  11. 7-lump kinetic model for residual oil catalytic cracking

    XU Ou-guan; SU Hong-ye; MU Sheng-jing; CHU Jian


    In this paper a novel 7-lump kinetic model is proposed to describe residual oil catalytic cracking, in which coke is lumped separately for accurate prediction. The reactor block is modeled as a combination of an ideal pipe flow reactor (PFR)and a continuously stirred tank reactor (CSTR). Unit factors are designed to correct the deviation between model predictions and practical plant data and tuned by modified Levenberg-Marquardt algorithm. The parameters estimated are reliable and good agreement between the model predictions and plant observations is observed. The model helps us get good insight into the performance of an industrial riser reactor that would be useful for optimization of residual oil catalytic cracking.

  12. Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

    Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.


    Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

  13. Kinetic modelling of cadmium and lead removal by aquatic mosses

    R. J. E. Martins


    Full Text Available Because biosorption is a low cost and effective method for treating metal-bearing wastewaters, understanding the process kinetics is relevant for design purposes. In the present study, the performance of the aquatic moss Fontinalis antipyretica for removing cadmium and lead from simulated wastewaters has been evaluated. Five kinetic models (first-order, pseudo-first-order, Elovich, modified Ritchie second-order and pseudo-second-order were fitted to the experimental data and compared. Previously, the effect of parameters such as the initial solution pH, contact time, and initial metal ion concentration on biosorption was investigated. The initial pH of the solution was found to have an optimum value in the range of 4.0-6.0. The equilibrium sorption capacity of cadmium and lead by Fontinalis antipyretica increased with the initial metal concentration. For an initial metal concentration of 10 mg L-1, the uptake capacity of the moss, at equilibrium, is the same for both metals (4.8 mg g-1. Nevertheless, when the initial concentration increases up to 100 mg L-1, the uptake of Pb(II was higher than 78%. The pseudo-second order biosorption kinetics provided the better correlation with the experimental data (R² ≥ 0.999.

  14. Kinetic model for astaxanthin aggregation in water-methanol mixtures

    Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo


    The aggregation of astaxanthin in hydrated methanol was kinetically studied in the temperature range from 10 °C to 50 °C, at different astaxanthin concentrations and solvent composition. A kinetic model for the formation and transformation of astaxanthin aggregated has been proposed. Spectrophotometric studies showed that monomeric astaxanthin decayed to H-aggregates that after-wards formed J-aggregates when water content was 50% and the temperature lower than 20 °C; at higher temperatures, very stable J-aggregates were formed directly. Monomer formed very stable H-aggregates when the water content was greater than 60%; in these conditions H-aggregates decayed into J-aggregates only when the temperature was at least 50 °C. Through these findings it was possible to establish that the aggregation reactions took place through a two steps consecutive reaction with first order kinetic constants and that the values of these depended on the solvent composition and temperature.

  15. Kinetic Model for 1D aggregation of yeast ``prions''

    Kunes, Kay; Cox, Daniel; Singh, Rajiv


    Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeast have proteins which can undergo similar reconformation and aggregation processes to PrP; yeast forms are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein(1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics(2). The model assumes reconformation only upon aggregation, and includes aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates. We will compare to a more realistic stochastic kinetics model and present prelimary attempts to describe recent experiments on SUP35 strains. *-Supported by U.S. Army Congressionally Mandated Research Fund. 1) P. Chien and J.S. Weissman, Nature 410, 223 (2001); 2) J. Masel, V.A.> Jansen, M.A. Nowak, Biophys. Chem. 77, 139 (1999).

  16. Kinetic models for the VASIMR thruster helicon plasma source

    Batishchev, Oleg; Molvig, Kim


    Helicon gas discharge [1] is widely used by industry because of its remarkable efficiency [2]. High energy and fuel efficiencies make it very attractive for space electrical propulsion applications. For example, helicon plasma source is used in the high specific impulse VASIMR [3] plasma thruster, including experimental prototypes VX-3 and upgraded VX-10 [4] configurations, which operate with hydrogen (deuterium) and helium plasmas. We have developed a set of models for the VASIMR helicon discharge. Firstly, we use zero-dimensional energy and mass balance equations to characterize partially ionized gas condition/composition. Next, we couple it to one-dimensional hybrid model [6] for gas flow in the quartz tube of the helicon. We compare hybrid model results to a purely kinetic simulation of propellant flow in gas feed + helicon source subsystem. Some of the experimental data [3-4] are explained. Lastly, we discuss full-scale kinetic modeling of coupled gas and plasmas [5-6] in the helicon discharge. [1] M.A.Lieberman, A.J.Lihtenberg, 'Principles of ..', Wiley, 1994; [2] F.F.Chen, Plas. Phys. Contr. Fus. 33, 339, 1991; [3] F.Chang-Diaz et al, Bull. APS 45 (7) 129, 2000; [4] J.Squire et al., Bull. APS 45 (7) 130, 2000; [5] O.Batishchev et al, J. Plasma Phys. 61, part II, 347, 1999; [6] O.Batishchev, K.Molvig, AIAA technical paper 2000-3754, -14p, 2001.

  17. Economic inequality and mobility in kinetic models for social sciences

    Letizia Bertotti, Maria; Modanese, Giovanni


    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.

  18. Kinetic modelling of cytochrome c adsorption on SBA-15.

    Yokogawa, Yoshiyuki; Yamauchi, Rie; Saito, Akira; Yamato, Yuta; Toma, Takeshi


    The adsorption capacity of mesoporous silicate (MPS) materials as an adsorbent for protein adsorption from the aqueous phase and the mechanism of the adsorption processes by comparative analyses of the applicability of five kinetic transfer models, pseudo-first-order model, pseudo-second-order model, Elovich kinetic model, Bangham's equation model, and intraparticle diffusion model, were investigated. A mixture of tetraethyl orthosilicate (TEOS) and triblock copolymer as a template was stirred, hydrothermally treated to form the mesoporous SBA-15 structure, and heat-treated at 550°C to form the MPS material, SBA-15. The synthesized SBA-15 was immersed in a phosphate buffered saline (PBS) solution containing cytochrome c for 2, 48, and 120 hours at 4°C. The TEM observations of proteins on/in mesoporous SBA-15 revealed the protein behaviors. The holes of the MPS materials were observed to overlap those of the stained proteins for the first 2 hours of immersion. The stained proteins were observed between primary particles and partly inside the mesoporous channels in the MPS material when it had been immersed for 48 hours. For MPS when it had been immersed for 120 hours, stained proteins were observed in almost all meso-scale channels of MPS. The time profiles for adsorption of proteins can be described well by Bangham's equation model and the intraparticle diffusion model. The Bangham's equation model is based on the assumption that pore diffusion was the only rate controlling step during adsorption, whose contribution to the overall mechanism of cytochrome c adsorption on SBA-15 should not be neglected. The kinetic curves obtained from the experiment for cytochrome c adsorption on SBA-15 could show the three steps: the initial rapid increase of the adsorbed amount of cytochrome c, the second gradual increase, and the final equilibrium stage. These three adsorption steps can be interpreted well by the multi-linearity of the intraparticle diffusion model

  19. Investigation of kinetics model of dc reactive sputtering

    朱圣龙; 王福会; 吴维叓


    A novel physical sputtering kinetics model for reactive sputtering is presented.Reactive gas gettering effects and interactions among the characteristic parameters have been taken into account in the model.The data derived from the model accorded fairly well with experimental results.The relationship between the values of initial oxide coverage on the target and the ready states was depicted in the model.This relationship gives reasons for the difference of the threshold of reactive gas fluxes (Q) from the metal sputtering region to the oxide sputtering region and in reverse direction.The discontinuities in oxide coverage on the target surface (θ) versus reactive gas fluxes (Q) are referred to as the effects of reactive gas partial pressure (p) upon the forming rates of oxide on the surfaces of target (V0).The diversity of the oxygen flux threshold results from the variance of the initial values of oxide coverage on target.

  20. Study on Lumped Kinetic Model for FDFCC II. Validation and Prediction of Model

    Wu Feiyue; Weng Huixin; Luo Shixian


    On the basis of formulating the 9-lump kinetic model for gasoline catalytic upgrading and the 12-lump kinetic model for heavy oil FCC, this paper is aimed at development of a combined kinetic model for a typical FDFCC process after analyzing the coupled relationship and combination of these two models. The model is also verified by using commercial data, the results of which showed that the model can better predict the product yields and their quality, with the relative errors between the main products of the unit and commercial data being less than five percent. Furthermore, the combined model is used to predict and optimize the operating conditions for gasoline riser and heavy oil riser in FDFCC. So this paper can offer some guidance for the processing of FDFCC and is instructive to model research and development of such multi-reactor process and combined process.

  1. Adequacy indices for dialysis in acute renal failure: kinetic modeling.

    Debowska, Malgorzata; Lindholm, Bengt; Waniewski, Jacek


    Many aspects of the management of renal replacement therapy in acute renal failure (ARF), including the appropriate assessment of dialysis adequacy, remain unresolved, because ARF patients often are not in a metabolic steady state. The aim of this study was to evaluate a system of adequacy indices for dialysis in ARF patients using urea and creatinine kinetic modeling. Kinetic modeling was performed for two different fictitious patients (A and B) with characteristics described by the average parameters for two patient groups and for two blood purification treatments: sustained low efficiency daily dialysis (SLEDD) in Patient A and continuous venovenous hemofiltration (CVVH) in Patient B, based on data from a clinical report. Urea and creatinine generation rates were estimated according to the clinical data on the solute concentrations in blood. Then, using estimated generation rates, two hypothetical treatments were simulated, CVVH in Patient A and SLEDD in Patient B. KT/V, fractional solute removal (FSR) and equivalent renal clearance (EKR) were calculated according to the definitions developed for metabolically unstable patients. CVVH appeared as being more effective than SLEDD because KT/V, FSR, and EKR were higher for CVVH than SLEDD in Patients A and B. Creatinine KT/V, FSR, and EKR were lower and well correlated to the respective indices for urea. Urea and creatinine generation rates were overestimated more than twice in Patient A and by 30-40% in Patient B if calculated assuming the metabolically stable state than if estimated by kinetic modeling. Adequacy indices and solute generation rates for ARF patients should be estimated using the definition for unsteady metabolic state. EKR and FSR were higher for urea and creatinine with CVVH than with SLEDD, because of higher K.T and minimized compartmental effects for CVVH.

  2. Kinetics of solid state phase transformations: Measurement and modelling of some basic issues

    S Raju; E Mohandas


    A brief review of the issues involved in modelling of the solid state transformation kinetics is presented. The fact that apart from the standard thermodynamic parameters, certain path variables like heating or cooling rate can also exert a crucial influence on the kinetic outcome is stressed. The kinetic specialties that are intrinsic to phase changes proceeding under varying thermal history are enumerated. A simple and general modelling methodology for understanding the kinetics of non-isothermal transformations is outlined.

  3. Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability

    Sourbron, S. P.; Buckley, D. L.


    The tracer-kinetic models developed in the early 1990s for dynamic contrast-enhanced MRI (DCE-MRI) have since become a standard in numerous applications. At the same time, the development of MRI hardware has led to increases in image quality and temporal resolution that reveal the limitations of the early models. This in turn has stimulated an interest in the development and application of a second generation of modelling approaches. They are designed to overcome these limitations and produce additional and more accurate information on tissue status. In particular, models of the second generation enable separate estimates of perfusion and capillary permeability rather than a single parameter Ktrans that represents a combination of the two. A variety of such models has been proposed in the literature, and development in the field has been constrained by a lack of transparency regarding terminology, notations and physiological assumptions. In this review, we provide an overview of these models in a manner that is both physically intuitive and mathematically rigourous. All are derived from common first principles, using concepts and notations from general tracer-kinetic theory. Explicit links to their historical origins are included to allow for a transfer of experience obtained in other fields (PET, SPECT, CT). A classification is presented that reveals the links between all models, and with the models of the first generation. Detailed formulae for all solutions are provided to facilitate implementation. Our aim is to encourage the application of these tools to DCE-MRI by offering researchers a clearer understanding of their assumptions and requirements.

  4. A Photochemical Kinetic Model for Solid Dosage Forms.

    Carvalho, Thiago C; La Cruz, Thomas E; Tabora, Jose E


    Photochemical kinetics models for pharmaceutical compounds in solution have been extensively investigated, but not in solid phase upon exposure to different light sources. The objective of this study was to develop a mathematical model to describe the solid state photodegradation of pharmaceutical powder materials under different area/volumetric scales and light exposure conditions. The model considered the previous formalism presented for photodegradation kinetics in solution phase with important elements applied to static powder material being irradiated with a polychromatic light source. The model also included the influence of optical phenomena (i.e. reflectance, scattering factors, etc.) by applying Beer-Lambert law to light attenuation, including effects of powder density. Drug substance and drug product intermediates (blends and tablet cores) were exposed to different light sources and intensities. The model reasonably predicted the photodegradation levels of powder beds of drug substance and drug product intermediates under white and yellow lights with intensities around 5 to 11 kLux. Importantly, the model estimates demonstrated that the reciprocity law for photoreactions was held. Further model evaluation showed that, due to light attenuation, the powder bed is in virtual darkness at cake depths greater than 500 μm. At 100 μm, the photodegradation of the investigated compound is expected to be close to 100% in 10 days under white fluorescent halophosphate light at 9.5 kLux. For tablets, defining the volume over exposed surface area ratio is more challenging. Nevertheless, the model can consider a bracket between worst and best cases to provide a reasonable photodegradation estimate. This tool can be significantly leveraged to simulate different light exposure scenarios while assessing photostability risk in order to define appropriate Control Strategy in manufacturing. Copyright © 2017. Published by Elsevier B.V.

  5. Model-free kinetics applied to sugarcane bagasse combustion

    Ramajo-Escalera, B.; Espina, A.; Garcia, J.R. [Department of Organic and Inorganic Chemistry, University of Oviedo, 33006 Oviedo (Spain); Sosa-Arnao, J.H. [Mechanical Engineering Faculty, State University of Campinas (UNICAMP), P.O. Box 6122, 13083-970 Campinas, SP (Brazil); Nebra, S.A. [Interdisciplinary Center of Energy Planning, State University of Campinas (UNICAMP), R. Shigeo Mori 2013, 13083-770 Campinas, SP (Brazil)


    Vyazovkin's model-free kinetic algorithms were applied to determine conversion, isoconversion and apparent activation energy to both dehydration and combustion of sugarcane bagasse. Three different steps were detected with apparent activation energies of 76.1+/-1.7, 333.3+/-15.0 and 220.1+/-4.0kJ/mol in the conversion range of 2-5%, 15-60% and 70-90%, respectively. The first step is associated with the endothermic process of drying and release of water. The others correspond to the combustion (and carbonization) of organic matter (mainly cellulose, hemicellulose and lignin) and the combustion of the products of pyrolysis. (author)

  6. Fluctuation dissipation ratio in the one dimensional kinetic Ising model

    Lippiello, E.; Zannetti, M.


    The exact relation between the response function $R(t,t^{\\prime})$ and the two time correlation function $C(t,t^{\\prime})$ is derived analytically in the one dimensional kinetic Ising model subjected to a temperature quench. The fluctuation dissipation ratio $X(t,t^{\\prime})$ is found to depend on time through $C(t,t^{\\prime})$ in the time region where scaling $C(t,t^{\\prime}) = f(t/t^{\\prime})$ holds. The crossover from the nontrivial form $X(C(t,t^{\\prime}))$ to $X(t,t^{\\prime}) \\equiv 1$ t...

  7. Large Scale Simulations of the Kinetic Ising Model

    Münkel, Christian

    We present Monte Carlo simulation results for the dynamical critical exponent z of the two- and three-dimensional kinetic Ising model. The z-values were calculated from the magnetization relaxation from an ordered state into the equilibrium state at Tc for very large systems with up to (169984)2 and (3072)3 spins. To our knowledge, these are the largest Ising-systems simulated todate. We also report the successful simulation of very large lattices on a massively parallel MIMD computer with high speedups of approximately 1000 and an efficiency of about 0.93.

  8. Kinetic Relations for a Lattice Model of Phase Transitions

    Schwetlick, Hartmut; Zimmer, Johannes


    The aim of this article is to analyse travelling waves for a lattice model of phase transitions, specifically the Fermi-Pasta-Ulam chain with piecewise quadratic interaction potential. First, for fixed, sufficiently large subsonic wave speeds, we rigorously prove the existence of a family of travelling wave solutions. Second, it is shown that this family of solutions gives rise to a kinetic relation which depends on the jump in the oscillatory energy in the solution tails. Third, our constructive approach provides a very good approximate travelling wave solution.

  9. A generic 3D kinetic model of gene expression

    Zhdanov, Vladimir


    Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.

  10. Kinetic mixing effect in the 3 -3 -1 -1 model

    Dong, P. V.; Si, D. T.


    We show that the mixing effect of the neutral gauge bosons in the 3 -3 -1 -1 model comes from two sources. The first one is due to the 3 -3 -1 -1 gauge symmetry breaking as usual, whereas the second one results from the kinetic mixing between the gauge bosons of U (1 )X and U (1 )N groups, which are used to determine the electric charge and baryon minus lepton numbers, respectively. Such mixings modify the ρ -parameter and the known couplings of Z with fermions. The constraints that arise from flavor-changing neutral currents due to the gauge boson mixings and nonuniversal fermion generations are also given.

  11. Warped Higgsless Models with IR-Brane Kinetic Terms

    Davoudiasl, H; Lillie, Benjamin Huntington; Rizzo, T G


    We examine a warped Higgsless $SU(2)_L\\times SU(2)_R\\times U(1)_{B-L}$ model in 5--$d$ with IR(TeV)--brane kinetic terms. It is shown that adding a brane term for the $U(1)_{B-L}$ gauge field does not affect the scale ($\\sim 2-3$ TeV) where perturbative unitarity in $W_L^+ W_L^- \\to W_L^+ W_L^-$ is violated. This term could, however, enhance the agreement of the model with the precision electroweak data. In contrast, the inclusion of a kinetic term corresponding to the $SU(2)_D$ custodial symmetry of the theory delays the unitarity violation in $W_L^\\pm$ scattering to energy scales of $\\sim 6-7$ TeV for a significant fraction of the parameter space. This is about a factor of 4 improvement compared to the corresponding scale of unitarity violation in the Standard Model without a Higgs. We also show that null searches for extra gauge bosons at the Tevatron and for contact interactions at LEP II place non-trivial bounds on the size of the IR-brane terms.

  12. Kinetic modeling of 3D equilibria in a tokamak

    Albert, C. G.; Heyn, M. F.; Kasilov, S. V.; Kernbichler, W.; Martitsch, A. F.; Runov, A. M.


    External resonant magnetic perturbations (RMPs) can modify the magnetic topology in a tokamak. In this case the magnetic field cannot generally be described by ideal MHD equilibrium equations in the vicinity of resonant magnetic surfaces where parallel and perpendicular relaxation timescales are comparable. Usually, resistive MHD models are used to describe these regions. In the present work, a kinetic model is used for this purpose. Within this model, plasma response, current and charge density are computed with help of a Monte Carlo method, where guiding center orbit equations are solved using a semianalytical geometrical integrator. Besides its higher efficiency in comparison to usual integrators this method is not sensitive to noise in field quantities. The computed charges and currents are used to calculate the electromagnetic field with help of a finite element solver. A preconditioned iterative scheme is applied to search for a self-consistent solution. The discussed method is aimed at the nonlinear kinetic description of RMPs in experiments on Edge Localized Mode (ELM) mitigation by external perturbation coil systems without simplification of the device geometry.

  13. Kinetic modeling of ethane pyrolysis at high conversion.

    Xu, Chen; Al Shoaibi, Ahmed Sultan; Wang, Chenguang; Carstensen, Hans-Heinrich; Dean, Anthony M


    The primary objective of this study is to develop an improved first-principle-based mechanism that describes the molecular weight growth kinetics observed during ethane pyrolysis. A proper characterization of the kinetics of ethane pyrolysis is a prerequisite for any analysis of hydrocarbon pyrolysis and oxidation. Flow reactor experiments were performed with ~50/50 ethane/nitrogen mixtures with temperatures ranging from 550 to 850 °C at an absolute pressure of ~0.8 atm and a residence time of ~5 s. These conditions result in ethane conversions ranging from virtually no reaction to ~90%. Comparisons of predictions using our original mechanism to these data yielded very satisfactory results in terms of the temperature dependence of ethane conversion and prediction of the major products ethylene and hydrogen. However, there were discrepancies in some of the minor species concentrations that are involved in the molecular weight growth kinetics. We performed a series of CBS-QB3 analyses for the C(3)H(7), C(4)H(7), and C(4)H(9) potential energy surfaces to better characterize the radical addition reactions that lead to molecular weight growth. We also extended a published C(6)H(9) PES to include addition of vinyl to butadiene. The results were then used to calculate pressure-dependent rate constants for the multiple reaction pathways of these addition reactions. Inclusion of the unadjusted rate constants resulting from these analyses in the mechanism significantly improved the description of several of the species involved in molecular weight growth kinetics. We compare the predictions of this improved model to those obtained with a consensus model recently published as well as to ethane steam cracking data. We find that a particularly important reaction is that of vinyl addition to butadiene. Another important observation is that several radical addition reactions are partially equilibrated. Not only does this mean that reliable thermodynamic parameters are essential

  14. Kinetic and Stochastic Models of 1D yeast ``prions"

    Kunes, Kay


    Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP; yeast ``prions" are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein (1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics along with our own stochastic approach (2). Both models assume reconformation only upon aggregation, and include aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates.

  15. The Origin of the RNA World a Kinetic Model

    Wattis, J A D; Wattis, Jonathan A. D.; Coveney, Peter V.


    The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar but more general chemical assumptions to those of Eigen, namely that catalytic replication can lead to a large population of long chains. In particular, our models incorporate the possibility of (i) direct chain growth, (ii) template-assisted synthesis and (iii) catalysis by RNA replicase ribozymes, all with varying degrees of efficiency. However, in our models the reaction mechanisms are kept `open'; we do not assume the existence of closed hypercycles which sustain a population of long chains. Rather it is the feasibility of the initial emergence of a self-sustaining set of RNA chains from monomeric nucleotides which is our prime concern. We confront directly the central nonlinear features of the problem, which have often been overlooked in previous studies. Our detailed m...

  16. Upper D region chemical kinetic modeling of LORE relaxation times

    Gordillo-Vázquez, F. J.; Luque, A.; Haldoupis, C.


    The recovery times of upper D region electron density elevations, caused by lightning-induced electromagnetic pulses (EMP), are modeled. The work was motivated from the need to understand a recently identified narrowband VLF perturbation named LOREs, an acronym for LOng Recovery Early VLF events. LOREs associate with long-living electron density perturbations in the upper D region ionosphere; they are generated by strong EMP radiated from large peak current intensities of ±CG (cloud to ground) lightning discharges, known also to be capable of producing elves. Relaxation model scenarios are considered first for a weak enhancement in electron density and then for a much stronger one caused by an intense lightning EMP acting as an impulsive ionization source. The full nonequilibrium kinetic modeling of the perturbed mesosphere in the 76 to 92 km range during LORE-occurring conditions predicts that the electron density relaxation time is controlled by electron attachment at lower altitudes, whereas above 79 km attachment is balanced totally by associative electron detachment so that electron loss at these higher altitudes is controlled mainly by electron recombination with hydrated positive clusters H+(H2O)n and secondarily by dissociative recombination with NO+ ions, a process which gradually dominates at altitudes >88 km. The calculated recovery times agree fairly well with LORE observations. In addition, a simplified (quasi-analytic) model build for the key charged species and chemical reactions is applied, which arrives at similar results with those of the full kinetic model. Finally, the modeled recovery estimates for lower altitudes, that is <79 km, are in good agreement with the observed short recovery times of typical early VLF events, which are known to be associated with sprites.

  17. Kinetic model of sucrose accumulation in maturing sugarcane culm tissue.

    Uys, Lafras; Botha, Frederik C; Hofmeyr, Jan-Hendrik S; Rohwer, Johann M


    Biochemically, it is not completely understood why or how commercial varieties of sugarcane (Saccharum officinarum) are able to accumulate sucrose in high concentrations. Such concentrations are obtained despite the presence of sucrose synthesis/breakdown cycles (futile cycling) in the culm of the storage parenchyma. Given the complexity of the process, kinetic modelling may help to elucidate the factors governing sucrose accumulation or direct the design of experimental optimisation strategies. This paper describes the extension of an existing model of sucrose accumulation (Rohwer, J.M., Botha, F.C., 2001. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445) to account for isoforms of sucrose synthase and fructokinase, carbon partitioning towards fibre formation, and the glycolytic enzymes phosphofructokinase (PFK), pyrophosphate-dependent PFK and aldolase. Moreover, by including data on the maximal activity of the enzymes as measured in different internodes, a growth model was constructed that describes the metabolic behaviour as sugarcane parenchymal tissue matures from internodes 3-10. While there was some discrepancy between modelled and experimentally determined steady-state sucrose concentrations in the cytoplasm, steady-state fluxes showed a better fit. The model supports a hypothesis of vacuolar sucrose accumulation against a concentration gradient. A detailed metabolic control analysis of sucrose synthase showed that each isoform has a unique control profile. Fructose uptake by the cell and sucrose uptake by the vacuole had a negative control on the futile cycling of sucrose and a positive control on sucrose accumulation, while the control profile for neutral invertase was reversed. When the activities of these three enzymes were changed from their reference values, the effects on futile cycling and sucrose accumulation were amplified. The model can be run online at the JWS Online

  18. Reduced Models in Chemical Kinetics via Nonlinear Data-Mining

    Eliodoro Chiavazzo


    Full Text Available The adoption of detailed mechanisms for chemical kinetics often poses two types of severe challenges: First, the number of degrees of freedom is large; and second, the dynamics is characterized by widely disparate time scales. As a result, reactive flow solvers with detailed chemistry often become intractable even for large clusters of CPUs, especially when dealing with direct numerical simulation (DNS of turbulent combustion problems. This has motivated the development of several techniques for reducing the complexity of such kinetics models, where, eventually, only a few variables are considered in the development of the simplified model. Unfortunately, no generally applicable a priori recipe for selecting suitable parameterizations of the reduced model is available, and the choice of slow variables often relies upon intuition and experience. We present an automated approach to this task, consisting of three main steps. First, the low dimensional manifold of slow motions is (approximately sampled by brief simulations of the detailed model, starting from a rich enough ensemble of admissible initial conditions. Second, a global parametrization of the manifold is obtained through the Diffusion Map (DMAP approach, which has recently emerged as a powerful tool in data analysis/machine learning. Finally, a simplified model is constructed and solved on the fly in terms of the above reduced (slow variables. Clearly, closing this latter model requires nontrivial interpolation calculations, enabling restriction (mapping from the full ambient space to the reduced one and lifting (mapping from the reduced space to the ambient one. This is a key step in our approach, and a variety of interpolation schemes are reported and compared. The scope of the proposed procedure is presented and discussed by means of an illustrative combustion example.

  19. Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica.

    Saavedra, Emma; Marín-Hernández, Alvaro; Encalada, Rusely; Olivos, Alfonso; Mendoza-Hernández, Guillermo; Moreno-Sánchez, Rafael


    Glycolysis in the human parasite Entamoeba histolytica is characterized by the absence of cooperative modulation and the prevalence of pyrophosphate-dependent (over ATP-dependent) enzymes. To determine the flux-control distribution of glycolysis and understand its underlying control mechanisms, a kinetic model of the pathway was constructed by using the software gepasi. The model was based on the kinetic parameters determined in the purified recombinant enzymes, and the enzyme activities, and steady-state fluxes and metabolite concentrations determined in amoebal trophozoites. The model predicted, with a high degree of accuracy, the flux and metabolite concentrations found in trophozoites, but only when the pyrophosphate concentration was held constant; at variable pyrophosphate, the model was not able to completely account for the ATP production/consumption balance, indicating the importance of the pyrophosphate homeostasis for amoebal glycolysis. Control analysis by the model revealed that hexokinase exerted the highest flux control (73%), as a result of its low cellular activity and strong AMP inhibition. 3-Phosphoglycerate mutase also exhibited significant flux control (65%) whereas the other pathway enzymes showed little or no control. The control of the ATP concentration was also mainly exerted by ATP consuming processes and 3-phosphoglycerate mutase and hexokinase (in the producing block). The model also indicated that, in order to diminish the amoebal glycolytic flux by 50%, it was required to decrease hexokinase or 3-phosphoglycerate mutase by 24% and 55%, respectively, or by 18% for both enzymes. By contrast, to attain the same reduction in flux by inhibiting the pyrophosphate-dependent enzymes pyrophosphate-phosphofructokinase and pyruvate phosphate dikinase, they should be decreased > 70%. On the basis of metabolic control analysis, steps whose inhibition would have stronger negative effects on the energy metabolism of this parasite were identified


    Bowsher, Clive G


    The dynamic properties and independence structure of stochastic kinetic models (SKMs) are analyzed. An SKM is a highly multivariate jump process used to model chemical reaction networks, particularly those in biochemical and cellular systems. We identify SKM subprocesses with the corresponding counting processes and propose a directed, cyclic graph (the kinetic independence graph or KIG) that encodes the local independence structure of their conditional intensities. Given a partition [A, D, B] of the vertices, the graphical separation A ⊥ B|D in the undirected KIG has an intuitive chemical interpretation and implies that A is locally independent of B given A ∪ D. It is proved that this separation also results in global independence of the internal histories of A and B conditional on a history of the jumps in D which, under conditions we derive, corresponds to the internal history of D. The results enable mathematical definition of a modularization of an SKM using its implied dynamics. Graphical decomposition methods are developed for the identification and efficient computation of nested modularizations. Application to an SKM of the red blood cell advances understanding of this biochemical system.

  1. Modeling the kinetics of carbon coagulation in explosives detonation

    Ree, F. H.; Viecelli, J. A.; Glosli, J. N.


    A typical insensitive high explosive such as LX-17 has a large carbon content. The detonation behavior of these explosives is affected by a slow coagulation of carbon atoms by diffusion and their possible transformation from one chemical bonding type to another. We have used the Brenner bond order potential to compute the melting line of diamond at high pressure and high temperature by molecular dynamics and Monte Carlo simulations, with the goal to refine the potential for the study of the kinetics of the graphite diamond transition. The slow diffusion-controlled kinetics of carbon clusters has been examined by including a time-dependent surface correction to the Gibbs free energy of these clusters in the nonequilibrium CHEQ code. We also propose a new explosive burn model which incorporates a partial release of the heat of detonation in a fast reaction zone, followed by a diffusion-limited release of the remaining energy. Hydrodynamic applications of the new burn model to LX-17 show that computed expansion and compression results both agree closely with experimental data.

  2. Rotational and divergent kinetic energy in the mesoscale model ALADIN

    V. Blažica


    Full Text Available Kinetic energy spectra from the mesoscale numerical weather prediction (NWP model ALADIN with horizontal resolution 4.4 km are split into divergent and rotational components which are then compared at horizontal scales below 300 km and various vertical levels. It is shown that about 50% of kinetic energy in the free troposphere in ALADIN is divergent energy. The percentage increases towards 70% near the surface and in the upper troposphere towards 100 hPa. The maximal percentage of divergent energy is found at stratospheric levels around 100 hPa and at scales below 100 km which are not represented by the global models. At all levels, the divergent energy spectra are characterised by shallower slopes than the rotational energy spectra, and the difference increases as horizontal scales become larger. A very similar vertical distribution of divergent energy is obtained by using the standard ALADIN approach for the computation of spectra based on the extension zone and by applying detrending approach commonly used in mesoscale NWP community.

  3. Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.

    Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun


    To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.

  4. A study of the kinetic energy generation with general circulation models

    Chen, T.-C.; Lee, Y.-H.


    The history data of winter simulation by the GLAS climate model and the NCAR community climate model are used to examine the generation of atmospheric kinetic energy. The contrast between the geographic distributions of the generation of kinetic energy and divergence of kinetic energy flux shows that kinetic energy is generated in the upstream side of jets, transported to the downstream side and destroyed there. The contributions from the time-mean and transient modes to the counterbalance between generation of kinetic energy and divergence of kinetic energy flux are also investigated. It is observed that the kinetic energy generated by the time-mean mode is essentially redistributed by the time-mean flow, while that generated by the transient flow is mainly responsible for the maintenance of the kinetic energy of the entire atmospheric flow.

  5. Study on Lumped Kinetic Model for FDFCC I. Establishment of Model

    Wu Feiyue; Weng Huixin; Luo Shixian


    According to the process features and the reaction mechanism of FDFCC technology, its two reaction subsystems, one for heavy oil riser reactor, the other for gasoline riser reactor, were respectively studied. Correspondingly, a 12-lump kinetic model for heavy oil FCC and a 9-lump kinetic model for gasoline catalytic upgrading were presented. Based on this work, mathematical correlation of the lumps in the feeds and products involved in the reaction subsystems and those of the overall reaction system were analyzed in detail. Then, a combined kinetic model for FDFCC, which was based on the data recovered from a commercial unit, was put forward. The reaction performance embodied by the kinetic constants for the combined model of FDFCC was in accordance with catalytic cracking reaction mechanism. The model-calculated values were close to the data obtained in commercial scale. The model was easy to be applied in practice and could also provide some theoretical groundwork for further research on kinetic model for FDFCC.

  6. Quantum kinetics and thermalization in a particle bath model.

    Alamoudi, S M; Boyanovsky, D; de Vega, H J


    We study the dynamics of relaxation and thermalization in an exactly solvable model of a particle interacting with a harmonic oscillator bath. Our goal is to understand the effects of non-Markovian processes on the relaxational dynamics and to compare the exact evolution of the distribution function with approximate Markovian and non-Markovian quantum kinetics. There are two different cases that are studied in detail: (i) a quasiparticle (resonance) when the renormalized frequency of the particle is above the frequency threshold of the bath and (ii) a stable renormalized "particle" state below this threshold. The time evolution of the occupation number for the particle is evaluated exactly using different approaches that yield to complementary insights. The exact solution allows us to investigate the concept of the formation time of a quasiparticle and to study the difference between the relaxation of the distribution of bare particles and that of quasiparticles. For the case of quasiparticles, the exact occupation number asymptotically tends to a statistical equilibrium distribution that differs from a simple Bose-Einstein form as a result of off-shell processes whereas in the stable particle case, the distribution of particles does not thermalize with the bath. We derive a non-Markovian quantum kinetic equation which resums the perturbative series and includes off-shell effects. A Markovian approximation that includes off-shell contributions and the usual Boltzmann equation (energy conserving) are obtained from the quantum kinetic equation in the limit of wide separation of time scales upon different coarse-graining assumptions. The relaxational dynamics predicted by the non-Markovian, Markovian, and Boltzmann approximations are compared to the exact result. The Boltzmann approach is seen to fail in the case of wide resonances and when threshold and renormalization effects are important.

  7. Developing a computational model of human hand kinetics using AVS

    Abramowitz, Mark S. [State Univ. of New York, Binghamton, NY (United States)


    As part of an ongoing effort to develop a finite element model of the human hand at the Institute for Scientific Computing Research (ISCR), this project extended existing computational tools for analyzing and visualizing hand kinetics. These tools employ a commercial, scientific visualization package called AVS. FORTRAN and C code, originally written by David Giurintano of the Gillis W. Long Hansen`s Disease Center, was ported to a different computing platform, debugged, and documented. Usability features were added and the code was made more modular and readable. When the code is used to visualize bone movement and tendon paths for the thumb, graphical output is consistent with expected results. However, numerical values for forces and moments at the thumb joints do not yet appear to be accurate enough to be included in ISCR`s finite element model. Future work includes debugging the parts of the code that calculate forces and moments and verifying the correctness of these values.

  8. A Global Modeling Framework for Plasma Kinetics: Development and Applications

    Parsey, Guy Morland

    The modern study of plasmas, and applications thereof, has developed synchronously with com- puter capabilities since the mid-1950s. Complexities inherent to these charged-particle, many- body, systems have resulted in the development of multiple simulation methods (particle-in-cell, fluid, global modeling, etc.) in order to both explain observed phenomena and predict outcomes of plasma applications. Recognizing that different algorithms are chosen to best address specific topics of interest, this thesis centers around the development of an open-source global model frame- work for the focused study of non-equilibrium plasma kinetics. After verification and validation of the framework, it was used to study two physical phenomena: plasma-assisted combustion and the recently proposed optically-pumped rare gas metastable laser. Global models permeate chemistry and plasma science, relying on spatial averaging to focus attention on the dynamics of reaction networks. Defined by a set of species continuity and energy conservation equations, the required data and constructed systems are conceptually similar across most applications, providing a light platform for exploratory and result-search parameter scan- ning. Unfortunately, it is common practice for custom code to be developed for each application-- an enormous duplication of effort which negatively affects the quality of the software produced. Presented herein, the Python-based Kinetic Global Modeling framework (KGMf) was designed to support all modeling phases: collection and analysis of reaction data, construction of an exportable system of model ODEs, and a platform for interactive evaluation and post-processing analysis. A symbolic ODE system is constructed for interactive manipulation and generation of a Jacobian, both of which are compiled as operation-optimized C-code. Plasma-assisted combustion and ignition (PAC/PAI) embody the modernization of burning fuel by opening up new avenues of control and optimization

  9. Ab initio determination of kinetics for atomic layer deposition modeling

    Remmers, Elizabeth M.

    A first principles model is developed to describe the kinetics of atomic layer deposition (ALD) systems. This model requires no fitting parameters, as it is based on the reaction pathways, structures, and energetics obtained from quantum-chemical studies. Using transition state theory and partition functions from statistical mechanics, equilibrium constants and reaction rates can be calculated. Several tools were created in Python to aid in the calculation of these quantities, and this procedure was applied to two systems- zinc oxide deposition from diethyl zinc (DEZ) and water, and alumina deposition from trimethyl aluminum (TMA) and water. A Gauss-Jordan factorization is used to decompose the system dynamics, and the resulting systems of equations are solved numerically to obtain the temporal concentration profiles of these two deposition systems.

  10. Kinetic modelling of runaway electrons in dynamic scenarios

    Stahl, A; Papp, G; Landreman, M; Fülöp, T


    Improved understanding of runaway-electron formation and decay processes are of prime interest for the safe operation of large tokamaks, and the dynamics of the runaway electrons during dynamical scenarios such as disruptions are of particular concern. In this paper, we present kinetic modelling of scenarios with time-dependent plasma parameters; in particular, we investigate hot-tail runaway generation during a rapid drop in plasma temperature. With the goal of studying runaway-electron generation with a self-consistent electric-field evolution, we also discuss the implementation of a conservative collision operator and demonstrate its properties. An operator for avalanche runaway-electron generation, which takes the energy dependence of the scattering cross section and the runaway distribution into account, is investigated. We show that the simpler avalanche model of Rosenbluth & Putvinskii [Nucl. Fusion 37, 1355 (1997)] can give very inaccurate results for the avalanche growth rate (either lower or hig...

  11. High Temperature Chemical Kinetic Combustion Modeling of Lightly Methylated Alkanes

    Sarathy, S M; Westbrook, C K; Pitz, W J; Mehl, M


    Conventional petroleum jet and diesel fuels, as well as alternative Fischer-Tropsch (FT) fuels and hydrotreated renewable jet (HRJ) fuels, contain high molecular weight lightly branched alkanes (i.e., methylalkanes) and straight chain alkanes (n-alkanes). Improving the combustion of these fuels in practical applications requires a fundamental understanding of large hydrocarbon combustion chemistry. This research project presents a detailed high temperature chemical kinetic mechanism for n-octane and three lightly branched isomers octane (i.e., 2-methylheptane, 3-methylheptane, and 2,5-dimethylhexane). The model is validated against experimental data from a variety of fundamental combustion devices. This new model is used to show how the location and number of methyl branches affects fuel reactivity including laminar flame speed and species formation.

  12. Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics

    Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL; Mayes, Melanie [ORNL; Frerichs, Joshua T [ORNL; Jagadamma, Sindhu [ORNL


    While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.

  13. Kinetic modelling of central carbon metabolism in Escherichia coli.

    Peskov, Kirill; Mogilevskaya, Ekaterina; Demin, Oleg


    In the present study, we developed a detailed kinetic model of Escherichia coli central carbon metabolism. The main model assumptions were based on the results of metabolic and regulatory reconstruction of the system and thorough model verification with experimental data. The development and verification of the model included several stages, which allowed us to take into account both in vitro and in vivo experimental data and avoid the ambiguity that frequently occurs in detailed models of biochemical pathways. The choice of the level of detail for the mathematical description of enzymatic reaction rates and the evaluation of parameter values were based on available published data. Validation of the complete model of the metabolic pathway describing specific physiological states was based on fluxomics and metabolomics data. In particular, we developed a model that describes aerobic growth of E. coli in continuous culture with a limiting concentration of glucose. Such modification of the model was used to integrate experimental metabolomics data obtained in steady-state conditions for wild-type E. coli and genetically modified strains, e.g. knockout of the pyruvate kinase gene (pykA). Following analysis of the model behaviour, and comparison of the coincidence between predicted and experimental data, it was possible to investigate the functional and regulatory properties of E. coli central carbon metabolism. For example, a novel metabolic regulatory mechanism for 6-phosphogluconate dehydrogenase inhibition by phosphoenolpyruvate was hypothesized, and the flux ratios between the reactions catalysed by enzyme isoforms were predicted. The mathematical model described here has been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at © 2012 The Authors Journal compilation © 2012 FEBS.

  14. Elementary Processes and Kinetic Modeling for Hydrogen and Helium Plasmas

    Roberto Celiberto


    Full Text Available We report cross-sections and rate coefficients for excited states colliding with electrons, heavy particles and walls useful for the description of H 2 /He plasma kinetics under different conditions. In particular, the role of the rotational states in resonant vibrational excitations of the H 2 molecule by electron impact and the calculation of the related cross-sections are illustrated. The theoretical determination of the cross-section for the rovibrational energy exchange and dissociation of H 2 molecule, induced by He atom impact, by using the quasi-classical trajectory method is discussed. Recombination probabilities of H atoms on tungsten and graphite, relevant for the determination of the nascent vibrational distribution, are also presented. An example of a state-to-state plasma kinetic model for the description of shock waves operating in H 2 and He-H 2 mixtures is presented, emphasizing also the role of electronically-excited states in affecting the electron energy distribution function of free electrons. Finally, the thermodynamic properties and the electrical conductivity of non-ideal, high-density hydrogen plasma are finally discussed, in particular focusing on the pressure ionization phenomenon in high-pressure high-temperature plasmas.

  15. Pyrolysis Kinetic Modelling of Wheat Straw from the Pannonian Region

    Ivan Pešenjanski


    Full Text Available The pyrolysis/devolatilization is a basic step of thermochemical processes and requires fundamental characterization. In this paper, the kinetic model of pyrolysis is specified as a one-step global reaction. This type of reaction is used to describe the thermal degradation of wheat straw samples by measuring rates of mass loss of solid matter at a linear increase in temperature. The mentioned experiments were carried out using a derivatograph in an open-air environment. The influence of different factors was investigated, such as particle size, humidity levels, and the heating rate in the kinetics of devolatilization. As the measured values of mass loss and temperature functions transform in Arrhenius coordinates, the results are shown in the form of saddle curves. Such characteristics cannot be approximated with one equation in the form of Arrhenius law. For use in numerical applications, transformed functions can be approximated by linear regression for three separate intervals. Analysis of measurement resulting in granulation and moisture content variations shows that these factors have no significant influence. Tests of heating rate variations confirm the significance of this impact, especially in warmer regions. The influence of this factor should be more precisely investigated as a general variable, which should be the topic of further experiments.

  16. Integration Strategies for Efficient Multizone Chemical Kinetics Models

    McNenly, M J; Havstad, M A; Aceves, S M; Pitz, W J


    Three integration strategies are developed and tested for the stiff, ordinary differential equation (ODE) integrators used to solve the fully coupled multizone chemical kinetics model. Two of the strategies tested are found to provide more than an order of magnitude of improvement over the original, basic level of usage for the stiff ODE solver. One of the faster strategies uses a decoupled, or segregated, multizone model to generate an approximate Jacobian. This approach yields a 35-fold reduction in the computational cost for a 20 zone model. Using the same approximate Jacobian as a preconditioner for an iterative Krylov-type linear system solver, the second improved strategy achieves a 75-fold reduction in the computational cost for a 20 zone model. The faster strategies achieve their cost savings with no significant loss of accuracy. The pressure, temperature and major species mass fractions agree with the solution from the original integration approach to within six significant digits; and the radical mass fractions agree with the original solution to within four significant digits. The faster strategies effectively change the cost scaling of the multizone model from cubic to quadratic, with respect to the number of zones. As a consequence of the improved scaling, the 40 zone model offers more than a 250-fold cost savings over the basic calculation.

  17. Kinetic Model of Biogas Yield Production from Vinasse at Various Initial pH: Comparison between Modified Gompertz Model and First Order Kinetic Model



    Full Text Available Anaerobic treatment using anaerobic digestion can convert organic materials of vinasse into biogas. The purpose of this study was modeling kinetic of biogas production using modified Gompertz model and first order kinetic model at variation of initial pH. Substrates were consisted of two kinds of compositions, which were vinasse+rumen (VR and vinasse+rumen+urea (VRU. Initial pH in each substrate was 6, 7 and 8. Degradation process was done in 30 days using batch anaerobic digesters at room temperature. Both, at VR and VRU, initial pH of 7 generated the more total biogas than the others two (initial pH of 6 and 8. Biogas formed at substrate of VRU was more than that at substrate of VR. The best condition was substrate of VRU and initial pH of 7. At best condition, kinetic constants of biogas production model using modified Gompertz were ym (biogas production potential = 6.49 mL/g VS; U (maximum biogas production rate = 1.24 mL/g VS. day; &lambda (minimum time to produce biogas = 1.79 days. Whereas kinetic constants of biogas production model using first order kinetic were ym (biogas production potential = 6.78 mL/g VS; k (biogas production rate = 0.176 /day. The difference between the predicted and measured biogas yield (fitting error was higher with the first-order kinetic model (1.54-7.50% than with the modified Gompertz model (0.76-3.14%.

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

    Togai, Kuninori

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

  19. Kinetic Modeling of Incremental Ambulatory Peritoneal Dialysis Exchanges.

    Guest, Steven; Leypoldt, John K; Cassin, Michelle; Schreiber, Martin


    ♦ BACKGROUND: Incremental peritoneal dialysis (PD), the gradual introduction of dialysate exchanges at less than full-dose therapy, has been infrequently described in clinical reports. One concern with less than full-dose dialysis is whether urea clearance targets are achievable with an incremental regimen. In this report, we used a large database of PD patients, across all membrane transport types, and performed urea kinetic modeling determinations of possible incremental regimens for an individual membrane type. ♦ METHODS: Using a modified 3-pore model of peritoneal transport, various incremental manual continuous ambulatory PD (CAPD) exchanges employing glucose and/or icodextrin were evaluated. Peritoneal urea clearances from those simulations were added to residual kidney urea clearance for patients with various glomerular filtration rates (GFRs), and the total weekly urea clearance was then compared to the total weekly urea Kt/V target of 1.7. All 4 peritoneal membrane types were modeled. For each simulated prescription, net ultrafiltration and carbohydrate absorption were also calculated. ♦ RESULTS: Incremental CAPD regimens of 2 exchanges a day met adequacy targets if the GFR was 6 mL/min/1.73 m(2) in all membrane types. For regimens employing 3 exchanges a day, Kt/V targets were achieved at GFR levels of 4 to 5 mL/min/1.73 m(2) in high transporters to low transporters but higher tonicity 2.5% glucose solutions or icodextrin were required in some regimens. ♦ CONCLUSIONS: This work demonstrates that with incremental CAPD regimens, urea kinetic targets are achievable in most new starts to PD with residual kidney function. Incremental PD may be a less intrusive, better accepted initial treatment regime and a cost-effective way to initiate chronic dialysis in the incident patient. The key role of intrinsic kidney function in incremental regimens is highlighted in this analysis and would warrant conscientious monitoring. Copyright © 2017 International

  20. Adaptation of the microdosimetric kinetic model to hypoxia

    Bopp, C.; Hirayama, R.; Inaniwa, T.; Kitagawa, A.; Matsufuji, N.; Noda, K.


    Ion beams present a potential advantage in terms of treatment of lesions with hypoxic regions. In order to use this potential, it is important to accurately model the cell survival of oxic as well as hypoxic cells. In this work, an adaptation of the microdosimetric kinetic (MK) model making it possible to account for cell hypoxia is presented. The adaptation relies on the modification of damage quantity (double strand breaks and more complex lesions) due to the radiation. Model parameters such as domain size and nucleus size are then adapted through a fitting procedure. We applied this approach to two cell lines, HSG and V79 for helium, carbon and neon ions. A similar behaviour of the parameters was found for the two cell lines, namely a reduction of the domain size and an increase in the sensitive nuclear volume of hypoxic cells compared to those of oxic cells. In terms of oxygen enhancement ratio (OER), the experimental data behaviour can be reproduced, including dependence on particle type at the same linear energy transfer (LET). Errors on the cell survival prediction are of the same order of magnitude than for the original MK model. Our adaptation makes it possible to account for hypoxia without modelling the OER as a function of the LET of the particles, but directly accounting for hypoxic cell survival data.

  1. Kinetic effects of adriamycin and bleomycin on two osteosarcoma models.

    Bell, D F; Bell, R S; Mankin, H J; Gebhardt, M C; Weltie, F; O'Brien, T


    Although chemotherapeutic drugs are frequently administered to patients with osteosarcoma, there has been little research into the effect of cytotoxic drugs on osteosarcoma cell biology. The effect of two drugs (Adriamycin and bleomycin) on cell cycle kinetics was investigated in vitro in an established line of human osteosarcoma cells and in vivo using the Dunn osteosarcoma model. The cell cycle changes were consistent with G2 arrest for both drugs in vivo and in vitro. The alteration in cell cycle distribution was correlated with inhibition of 3H-thymidine incorporation in vitro. In vivo, the greater change in cell cycle distribution caused by Adriamycin was reflected in the increased inhibition of tumor growth found with this drug.

  2. Formulation and kinetic modeling of curcumin loaded intranasal mucoadhesive microemulsion

    B Mikesh Patel


    Full Text Available It is a challenge to develop the optimum dosage form of poorly water-soluble drugs and to target them due to limited bioavailability, intra and inter subject variability. In this investigation, mucoadhesive microemulsion of curcumin was developed by water titration method taking biocompatible components for intranasal delivery and was characterized. Nasal ciliotoxicity studies were carried out using excised sheep nasal mucosa. in vitro release studies of formulations and PDS were performed. Labrafil M 1944 CS based microemulsion was transparent, stable and nasal non-ciliotoxic having particle size 12.32±0.81nm (PdI=0.223 and from kinetic modeling, the release was found to be Fickian diffusion for mucoadhesive microemulsion.

  3. An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion

    Sarathy, S M; Thomson, M J; Pitz, W J; Lu, T


    Biodiesel is typically a mixture of long chain fatty acid methyl esters for use in compression ignition engines. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This research study presents new combustion data for methyl decanoate in an opposed-flow diffusion flame. An improved detailed chemical kinetic model for methyl decanoate combustion is developed, which serves as the basis for deriving a skeletal mechanism via the direct relation graph method. The novel skeletal mechanism consists of 648 species and 2998 reactions. This mechanism well predicts the methyl decanoate opposed-flow diffusion flame data. The results from the flame simulations indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene.

  4. Testing a dissipative kinetic k-essence model

    Cardenas, V H; Villanueva, J R


    In this work, we present a study of a purely kinetic k-essence model, characterized basically by a parameter $\\alpha$ in presence of a bulk dissipative term, whose relationship between viscous pressure $\\Pi$ and energy density $\\rho$ of the background follows a polytropic type law $\\Pi \\propto \\rho^{\\lambda+1/2}$, where $\\lambda$, in principle, is a parameter without restrictions. Analytical solutions for the energy density of the k-essence field are found in two specific cases: $\\lambda=1/2$ and $\\lambda=(1-\\alpha)/2\\alpha$, and then we show that these solutions posses the same functional form than the non-viscous counterpart. Finally, both approach are contrasted with observational data from type Ia supernova, and the most recent Hubble parameter measurements, and therefore, the best values for the parameters of the theory are founds.

  5. Testing a dissipative kinetic k-essence model

    Cardenas, Victor H.; Villanueva, J.R. [Universidad de Valparaiso, Instituto de Fisica y Astronomia, Valparaiso (Chile); Centro de Astrofisica de Valparaiso, Valparaiso (Chile); Cruz, Norman [Universidad de Santiago de Chile, Departamento de Fisica, Santiago (Chile)


    In thiswork,we present a study of a purely kinetic k-essence model, characterized basically by a parameter α in presence of a bulk dissipative term, whose relationship between viscous pressure Π and energy density ρ of the background follows a polytropic type law, Π ∝ ρ{sup λ+1/2}, where λ, in principle, is a parameter without restrictions. Analytical solutions for the energy density of the k-essence field are found in two specific cases: λ = 1/2 and λ = (1 - α)/2α, and then we show that these solutions possess the same functional form as the non-viscous counterpart. Finally, both approaches are contrasted with observational data from type Ia supernova, and the most recent Hubble parameter measurements, and therefore, the best values for the parameters of the theory are found. (orig.)

  6. Phase transition in kinetic exchange opinion models with independence

    Crokidakis, Nuno


    In this work we study the critical behavior of a three-state ($+1$, $-1$, $0$) opinion model with independence. Each agent has a probability $q$ to act as independent, i.e., he/she can choose his/her opinion independently of the opinions of the other agents. On the other hand, with the complementary probability $1-q$ the agent interacts with a randomly chosen individual through a kinetic exchange. Our analytical and numerical results show that the independence mechanism acts as a noise that induce an order-disorder transition at critical points $q_{c}$ that depend on the individuals' flexibility. For a special value of this flexibility the system undergoes a transition to an absorbing state with all opinions $0$.

  7. Thermal stability of n-dodecane : experiments and kinetic modelling

    Herbinet, Olivier; Battin-Leclerc, Frédérique; Fournet, René


    The thermal decomposition of n-dodecane, a component of some jet fuels, has been studied in a jet-stirred reactor at temperatures from 793 to 1093 K, for residence times between 1 and 5 s and at atmospheric pressure. Thermal decomposition of hydrocarbon fuel prior the entrance in the combustion chamber is an envisaged way to cool the wall of hypersonic vehicles. The products of the reaction are mainly hydrogen, methane, ethane, 1,3-butadiene and 1-alkenes from ethylene to 1-undecene. For higher temperatures and residence times acetylene, allene, propyne, cyclopentene, 1,3-cyclopentadiene and aromatic compounds from benzene to pyrene through naphthalene have also been observed. A previous detailed kinetic model of the thermal decomposition of n-dodecane generated using EXGAS software has been improved and completed by a sub-mechanism explaining the formation and the consumption of aromatic compounds.

  8. Kinetic Model for a Spherical Rolling Robot with Soft Shell in a Beeline Motion

    Sheng Zhang


    Full Text Available A simplified kinetic model called Spring Pendulum is developed for a spherical rolling robot with soft shell in order to meet the needs of attitude stabilization and controlling for the robot. The elasticity and plasticity of soft shell is represented by some uniform springs connected to the bracket in this model. The expression of the kinetic model is deduced from Newtonian mechanics principles. Testing data of the driving angle acquired from a prototype built by authors indicate that testing data curve accords to the theoretic kinetic characteristic curve, so the kinetic model is validated

  9. Critical Analysis of Underground Coal Gasification Models. Part II: Kinetic and Computational Fluid Dynamics Models

    Alina Żogała


    Originality/value: This paper presents state of art in the field of coal gasification modeling using kinetic and computational fluid dynamics approach. The paper also presents own comparative analysis (concerned with mathematical formulation, input data and parameters, basic assumptions, obtained results etc. of the most important models of underground coal gasification.

  10. Generic phase coexistence in the totally asymmetric kinetic Ising model

    Godrèche, Claude; Luck, Jean-Marc


    The physical analysis of generic phase coexistence in the North-East-Center Toom model was originally given by Bennett and Grinstein. The gist of their argument relies on the dynamics of interfaces and droplets. We revisit the same question for a specific totally asymmetric kinetic Ising model on the square lattice. This nonequilibrium model possesses the remarkable property that its stationary-state measure in the absence of a magnetic field coincides with that of the usual ferromagnetic Ising model. We use both analytical arguments and numerical simulations in order to make progress in the quantitative understanding of the phenomenon of generic phase coexistence. At zero temperature a mapping onto the TASEP allows an exact determination of the time-dependent shape of the ballistic interface sweeping a large square minority droplet of up or down spins. At finite temperature, measuring the mean lifetime of such a droplet allows an accurate measurement of its shrinking velocity v, which depends on temperature T and magnetic field h. In the absence of a magnetic field, v vanishes with an exponent Δ_v≈2.5+/-0.2 as the critical temperature T c is approached. At fixed temperature in the ordered phase, v vanishes at the phase-boundary fields +/- h_b(T) which mark the limits of the coexistence region. The latter fields vanish with an exponent Δ_h≈3.2+/-0.3 as T c is approached.

  11. Detailed kinetic modeling study of n-pentanol oxidation

    Heufer, Karl Alexander


    To help overcome the world\\'s dependence upon fossil fuels, suitable biofuels are promising alternatives that can be used in the transportation sector. Recent research on internal combustion engines shows that short alcoholic fuels (e.g., ethanol or n-butanol) have reduced pollutant emissions and increased knock resistance compared to fossil fuels. Although higher molecular weight alcohols (e.g., n-pentanol and n-hexanol) exhibit higher reactivity that lowers their knock resistance, they are suitable for diesel engines or advanced engine concepts, such as homogeneous charge compression ignition (HCCI), where higher reactivity at lower temperatures is necessary for engine operation. The present study presents a detailed kinetic model for n-pentanol based on modeling rules previously presented for n-butanol. This approach was initially validated using quantum chemistry calculations to verify the most stable n-pentanol conformation and to obtain C-H and C-C bond dissociation energies. The proposed model has been validated against ignition delay time data, speciation data from a jet-stirred reactor, and laminar flame velocity measurements. Overall, the model shows good agreement with the experiments and permits a detailed discussion of the differences between alcohols and alkanes. © 2012 American Chemical Society.

  12. Scale-up and kinetic modeling for bioethanol production.

    Imamoglu, Esra; Sukan, Fazilet Vardar


    Bioethanol was produced from acidic hydrolysate of rice hulls using recombinant Escherichia coli KO11. Two different issues (scale-up and kinetic modeling) were evaluated simultaneously and concomitantly for bioethanol production. During the step-wise scale-up process from 100 mL shaken flask to 10 L stirred-tank bioreactor, the constant Reynolds number and the constant impeller tip speed were evaluated as scale-up methodologies under laboratory conditions. It was determined that the volumetric bioethanol productivity was 88% higher in 10 L bioreactor in comparison to the value of 0.21 g L(-1) h(-1) in shaken flask. The modified Monod and Luedeking-Piret models provided an accurate approach for the modeling of the experimental data. Ethanol concentration reached the maximum level of 29.03 g/L, which was 5% higher than the value of model prediction in 10 L bioreactor. The findings of this research could contribute to the industrial scale productions especially from lignocellulosic raw materials.

  13. Gompertz kinetics model of fast chemical neurotransmission currents.

    Easton, Dexter M


    At a chemical synapse, transmitter molecules ejected from presynaptic terminal(s) bind reversibly with postsynaptic receptors and trigger an increase in channel conductance to specific ions. This paper describes a simple but accurate predictive model for the time course of the synaptic conductance transient, based on Gompertz kinetics. In the model, two simple exponential decay terms set the rates of development and decline of transmitter action. The first, r, triggering conductance activation, is surrogate for the decelerated rate of growth of conductance, G. The second, r', responsible for Y, deactivation of the conductance, is surrogate for the decelerated rate of decline of transmitter action. Therefore, the differential equation for the net conductance change, g, triggered by the transmitter is dg/dt=g(r-r'). The solution of that equation yields the product of G(t), representing activation, and Y(t), which defines the proportional decline (deactivation) of the current. The model fits, over their full-time course, published records of macroscopic ionic current associated with fast chemical transmission. The Gompertz model is a convenient and accurate method for routine analysis and comparison of records of synaptic current and putative transmitter time course. A Gompertz fit requiring only three independent rate constants plus initial current appears indistinguishable from a Markov fit using seven rate constants.

  14. Construction of the simplest model to explain complex receptor activation kinetics

    Bywater, RP; Sorensen, A; Røgen, Peter;


    We study the mathematical solutions to the kinetic equations arising from various simple ligand-reactor models. Focusing on the prediction of the various models for the activity vs. concentration curve, we find that solutions to the kinetic equations arising from the so-called dimer model exibit...

  15. Understanding the Pulsar High Energy Emission: Macroscopic and Kinetic Models

    Kalapotharakos, Constantinos; Brambilla, Gabriele; Timokhin, Andrey; Kust Harding, Alice; Kazanas, Demos


    Pulsars are extraordinary objects powered by the rotation of magnetic fields of order 10^8, 10^12G anchored onto neutron stars and rotating with periods 10^(-3)-10s. These fields mediate the conversion of their rotational energy into MHD winds and at the same time accelerate particles to energies sufficiently high to produce GeV photons. Fermi, since its launch in 2008, has established several trends among the observed gamma-ray pulsar properties playing a catalytic role in the current modeling of the high energy emission in pulsar magnetospheres. We judiciously use the guidance provided by the Fermi data to yield meaningful constraints on the macroscopic parameters of our global dissipative pulsar magnetosphere models. Our FIDO (Force-Free Inside, Dissipative Outside) models indicate that the dissipative regions lie outside the light cylinder near the equatorial current sheet. Our models reproduce the light-curve phenomenology while a detailed comparison of the model spectral properties with those observed by Fermi reveals the dependence of the macroscopic conductivity parameter on the spin-down rate providing a unique insight into the understanding of the physical mechanisms behind the high-energy emission in pulsar magnetospheres. Finally, we further exploit these important results by building self-consistent 3D global kinetic particle-in-cell (PIC) models which, eventually, provide the dependence of the macroscopic parameter behavior (e.g. conductivity) on the microphysical properties (e.g. particle multiplicities, particle injection rates). Our PIC models provide field structures and particle distributions that are not only consistent with each other but also able to reproduce a broad range of the observed gamma-ray phenomenology (light curves and spectral properties) of both young and millisecond pulsars.

  16. Hopping electron model with geometrical frustration: kinetic Monte Carlo simulations

    Terao, Takamichi


    The hopping electron model on the Kagome lattice was investigated by kinetic Monte Carlo simulations, and the non-equilibrium nature of the system was studied. We have numerically confirmed that aging phenomena are present in the autocorrelation function C ({t,tW )} of the electron system on the Kagome lattice, which is a geometrically frustrated lattice without any disorder. The waiting-time distributions p(τ ) of hopping electrons of the system on Kagome lattice has been also studied. It is confirmed that the profile of p (τ ) obtained at lower temperatures obeys the power-law behavior, which is a characteristic feature of continuous time random walk of electrons. These features were also compared with the characteristics of the Coulomb glass model, used as a model of disordered thin films and doped semiconductors. This work represents an advance in the understanding of the dynamics of geometrically frustrated systems and will serve as a basis for further studies of these physical systems.

  17. Kinetic modelling of runaway electrons in dynamic scenarios

    Stahl, A.; Embréus, O.; Papp, G.; Landreman, M.; Fülöp, T.


    Improved understanding of runaway-electron formation and decay processes are of prime interest for the safe operation of large tokamaks, and the dynamics of the runaway electrons during dynamical scenarios such as disruptions are of particular concern. In this paper, we present kinetic modelling of scenarios with time-dependent plasma parameters; in particular, we investigate hot-tail runaway generation during a rapid drop in plasma temperature. With the goal of studying runaway-electron generation with a self-consistent electric-field evolution, we also discuss the implementation of a collision operator that conserves momentum and energy and demonstrate its properties. An operator for avalanche runaway-electron generation, which takes the energy dependence of the scattering cross section and the runaway distribution into account, is investigated. We show that the simplified avalanche model of Rosenbluth and Putvinskii (1997 Nucl. Fusion 37 1355) can give inaccurate results for the avalanche growth rate (either lower or higher) for many parameters, especially when the average runaway energy is modest, such as during the initial phase of the avalanche multiplication. The developments presented pave the way for improved modelling of runaway-electron dynamics during disruptions or other dynamic events.

  18. Kinetic Model of Hypophosphite Oxidation on a Nickel Electrode in D2O Solution


    Kinetic model of hypophosphite oxidation on a nickel electrode was studied in D2Osolution in order to reach a better understanding of the oxidation mechanism. In the model the electrooxidation of hypophosphite undergo a H abstraction of hypophosphite from the P-H bond to form the phosphorus-centered radical PHO2-, which subsequently is electrochemically reacted with water to form the final product, phosphite. The kinetic equations were derived, and the kinetic parameters were obtained from a comparison of experimental results and the kinetic equations. The process of hypophosphite electrooxidation could be well simulated by this model

  19. Applicaiton of a Kinetic Multireaction Model for Studying Metolachlor Adsorption in Soil



    Metolachlor retention on a Sharkey clay soil was quantified using a kinetic batch method for different initial solution concentrations.Time-dependent adsorption was carried out by monitoring solution concentration at different reaction times.Adsorption was kinetic multireaction model which includes reverible and irreversible retention processes of the equilibrium and kinetic types,The predictive capability of the model for the dexcription of experimental results for metolachlor retention was examined and proved to be adequate。

  20. Modeling turbulence structure. Chemical kinetics interaction in turbulent reactive flows

    Magnussen, B.F. [The Norwegian Univ. of Science and Technology, Trondheim (Norway)


    The challenge of the mathematical modelling is to transfer basic physical knowledge into a mathematical formulation such that this knowledge can be utilized in computational simulation of practical problems. The combustion phenomena can be subdivided into a large set of interconnected phenomena like flow, turbulence, thermodynamics, chemical kinetics, radiation, extinction, ignition etc. Combustion in one application differs from combustion in another area by the relative importance of the various phenomena. The difference in fuel, geometry and operational conditions often causes the differences. The computer offers the opportunity to treat the individual phenomena and their interactions by models with wide operational domains. The relative magnitude of the various phenomena therefore becomes the consequence of operational conditions and geometry and need not to be specified on the basis of experience for the given problem. In mathematical modelling of turbulent combustion, one of the big challenges is how to treat the interaction between the chemical reactions and the fluid flow i.e. the turbulence. Different scientists adhere to different concepts like the laminar flamelet approach, the pdf approach of the Eddy Dissipation Concept. Each of these approaches offers different opportunities and problems. All these models are based on a sound physical basis, however none of these have general validity in taking into consideration all detail of the physical chemical interaction. The merits of the models can only be judged by their ability to reproduce physical reality and consequences of operational and geometric conditions in a combustion system. The presentation demonstrates and discusses the development of a coherent combustion technology for energy conversion and safety based on the Eddy Dissipation Concept by Magnussen. (author) 30 refs.

  1. Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins

    Al-Sabawi, Mustafa N.

    catalytic conversions respectively, are reported. Using these data, heterogeneous kinetic models accounting for intracrystallite molecular transport, adsorption and thermal and catalytic cracking of both cycloparaffin reactants are established. Results show that undesirable hydrogen transfer reactions are more pronounced and selectively favoured against other reactions at lower reaction temperatures, while the desirable ring-opening and cracking reactions predominate at the higher reaction temperatures. Moreover, results of the present work show that while crystallite size may have an effect on the overall conversion in some situations, there is a definite effect on the selectivity of products obtained during the cracking of MCH and decalin and the cracking of MCH in a mixture with co-reactants such as 1,3,5-triisopropylbenzene. Keywords. cycloparaffins, naphthenes, fluid catalytic cracking, kinetic modeling, Y-zeolites, diffusion, adsorption, ring-opening, hydrogen transfer, catalyst selectivity.

  2. Micellization kinetics in block copolymer solutions : Scaling model

    Dormidontova, EE


    The kinetics of micelle evolution of diblock copolymers from unimers toward the equilibrium state is studied analytically on the basis of consideration of the kinetic equations. The association/dissociation rate constants for unimer insertion/expulsion and micelle fusion/fission are calculated by

  3. Micellization kinetics in block copolymer solutions : Scaling model

    Dormidontova, EE


    The kinetics of micelle evolution of diblock copolymers from unimers toward the equilibrium state is studied analytically on the basis of consideration of the kinetic equations. The association/dissociation rate constants for unimer insertion/expulsion and micelle fusion/fission are calculated by ap

  4. Kinetic modeling of water sorption by roasted and ground coffee

    Fernanda Machado Baptestini


    Full Text Available The objective of this study was to model the kinetics of water sorption in roasted and ground coffee. Crude Arabica coffee beans with an initial moisture content of 0.1234 kgwkgdm-1 were used. These beans were roasted to a medium roast level (SCCA # 55 and ground at three particle sizes: coarse (1.19 mm, medium (0.84 mm and fine (0.59 mm. To obtain the water sorption isotherms and the isosteric heat, different conditions of temperature and relative humidity were analyzed using the dynamic method at 25ºC (0.50, 0.60, 0.70, and 0.80 of RH and 30°C (0.30, 0.40, 0.50, 0.60, 0.70, and 0.80 of RH and using the static method at 25ºC (0.332 and 0.438 of RH. The GAB model best represented the hygroscopic equilibrium of roasted coffee at every particle size. Isosteric heat of sorption for the fine particle size increased with increments of equilibrium moisture content, indicating a strong bond energy between water molecules and the product components. The Gibbs free energy decreased with the increase in equilibrium moisture content and with temperature.

  5. Fluctuation theorems for discrete kinetic models of molecular motors

    Faggionato, Alessandra; Silvestri, Vittoria


    Motivated by discrete kinetic models for non-cooperative molecular motors on periodic tracks, we consider random walks (also not Markov) on quasi one dimensional (1d) lattices, obtained by gluing several copies of a fundamental graph in a linear fashion. We show that, for a suitable class of quasi-1d lattices, the large deviation rate function associated to the position of the walker satisfies a Gallavotti-Cohen symmetry for any choice of the dynamical parameters defining the stochastic walk. This class includes the linear model considered in Lacoste et al (2008 Phys. Rev. E 78 011915). We also derive fluctuation theorems for the time-integrated cycle currents and discuss how the matrix approach of Lacoste et al (2008 Phys. Rev. E 78 011915) can be extended to derive the above Gallavotti-Cohen symmetry for any Markov random walk on {Z} with periodic jump rates. Finally, we review in the present context some large deviation results of Faggionato and Silvestri (2017 Ann. Inst. Henri Poincaré 53 46-78) and give some specific examples with explicit computations.

  6. Python framework for kinetic modeling of electronically excited reaction pathways

    Verboncoeur, John; Parsey, Guy; Guclu, Yaman; Christlieb, Andrew


    The use of plasma energy to enhance and control the chemical reactions during combustion, a technology referred to as ``plasma assisted combustion'' (PAC), can result in a variety of beneficial effects: e.g. stable lean operation, pollution reduction, and wider range of p-T operating conditions. While experimental evidence abounds, theoretical understanding of PAC is at best incomplete, and numerical tools still lack in reliable predictive capabilities. In the context of a joint experimental-numerical effort at Michigan State University, we present here an open-source modular Python framework dedicated to the dynamic optimization of non-equilibrium PAC systems. Multiple sources of experimental reaction data, e.g. reaction rates, cross-sections and oscillator strengths, are used in order to quantify the effect of data uncertainty and limiting assumptions. A collisional-radiative model (CRM) is implemented to organize reactions by importance and as a potential means of measuring a non-Maxwellian electron energy distribution function (EEDF), when coupled to optical emission spectroscopy data. Finally, we explore scaling laws in PAC parameter space using a kinetic global model (KGM) accelerated with CRM optimized reaction sequences and sparse stiff integrators.

  7. Modeling battery cells under discharge using kinetic and stochastic battery models

    Kaj, Ingemar; Konane, Victorien


    In this paper we review several approaches to mathematical modeling of simple battery cells and develop these ideas further with emphasis on charge recovery and the response behavior of batteries to given external load. We focus on models which use few parameters and basic battery data, rather than detailed reaction and material characteristics of a specific battery cell chemistry, starting with the coupled ODE linear dynamics of the kinetic battery model. We show that a related system of PDE...

  8. Kinetic theories for spin models for cooperative relaxation dynamics

    Pitts, Steven Jerome

    The facilitated kinetic Ising models with asymmetric spin flip constraints introduced by Jackle and co-workers [J. Jackle, S. Eisinger, Z. Phys. B 84, 115 (1991); J. Reiter, F. Mauch, J. Jackle, Physica A 184, 458 (1992)] exhibit complex relaxation behavior in their associated spin density time correlation functions. This includes the growth of relaxation times over many orders of magnitude when the thermodynamic control parameter is varied, and, in some cases, ergodic-nonergodic transitions. Relaxation equations for the time dependence of the spin density autocorrelation function for a set of these models are developed that relate this autocorrelation function to the irreducible memory function of Kawasaki [K. Kawasaki, Physica A 215, 61 (1995)] using a novel diagrammatic series approach. It is shown that the irreducible memory function in a theory of the relaxation of an autocorrelation function in a Markov model with detailed balance plays the same role as the part of the memory function approximated by a polynomial function of the autocorrelation function with positive coefficients in schematic simple mode coupling theories for supercooled liquids [W. Gotze, in Liquids, Freezing and the Glass Transition, D. Levesque, J. P. Hansen, J. Zinn-Justin eds., 287 (North Holland, New York, 1991)]. Sets of diagrams in the series for the irreducible memory function are summed which lead to approximations of this type. The behavior of these approximations is compared with known results from previous analytical calculations and from numerical simulations. For the simplest one dimensional model, relaxation equations that are closely related to schematic extended mode coupling theories [W. Gotze, ibid] are also derived using the diagrammatic series. Comparison of the results of these approximate theories with simulation data shows that these theories improve significantly on the results of the theories of the simple schematic mode coupling theory type. The potential

  9. Disposition of smoked cannabis with high [Delta]9-tetrahydrocannabinol content: A kinetic model.

    Hunault, C.C.; van Eijkeren, J.C.; Mensinga, T.T.; de Vries, I.; Leenders, M.E.C.; Meulenbelt, J.


    Introduction No model exists to describe the disposition and kinetics of inhaled cannabis containing a high THC dose. We aimed to develop a kinetic model providing estimates of the THC serum concentrations after smoking cannabis cigarettes containing high THC doses (up to 69 mg THC).Methods

  10. Disposition of smoked cannabis with high [Delta]9-tetrahydrocannabinol content: A kinetic model.

    Hunault, C.C.; van Eijkeren, J.C.; Mensinga, T.T.; de Vries, I.; Leenders, M.E.C.; Meulenbelt, J.


    Introduction No model exists to describe the disposition and kinetics of inhaled cannabis containing a high THC dose. We aimed to develop a kinetic model providing estimates of the THC serum concentrations after smoking cannabis cigarettes containing high THC doses (up to 69 mg THC).Methods Twenty-f

  11. A kinetic model for the glucose/glycine Maillard reaction pathways

    Martins, S.I.F.S.; Boekel, van M.A.J.S.


    A comprehensive kinetic model for the glucose/glycine Maillard reaction is proposed based on an approach called multiresponse kinetic modelling. Special attention was paid to reactants, intermediates and end products: -fructose, N-(1-deoxy--fructos-1-yl)-glycine (DFG), 1-deoxy-2,3-hexodiulose and

  12. Predicting individual responses to pravastatin using a physiologically based kinetic model for plasma cholesterol concentrations

    Pas, N.C.A. van de; Rullmann, J.A.C.; Woutersen, R.A.; Ommen, B. van; Rietjens, I.M.C.M.; Graaf, A.A. de


    We used a previously developed physiologically based kinetic (PBK) model to analyze the effect of individual variations in metabolism and transport of cholesterol on pravastatin response. The PBK model is based on kinetic expressions for 21 reactions that interconnect eight different body

  13. A kinetic model for runaway electrons in the ionosphere

    G. Garcia


    Full Text Available Electrodynamic models and measurements with satellites and incoherent scatter radars predict large field aligned current densities on one side of the auroral arcs. Different authors and different kinds of studies (experimental or modeling agree that the current density can reach up to hundreds of µA/m2. This large current density could be the cause of many phenomena such as tall red rays or triggering of unstable ion acoustic waves. In the present paper, we consider the issue of electrons moving through an ionospheric gas of positive ions and neutrals under the influence of a static electric field. We develop a kinetic model of collisions including electrons/electrons, electrons/ions and electrons/neutrals collisions. We use a Fokker-Planck approach to describe binary collisions between charged particles with a long-range interaction. We present the essential elements of this collision operator: the Langevin equation for electrons/ions and electrons/electrons collisions and the Monte-Carlo and null collision methods for electrons/neutrals collisions. A computational example is given illustrating the approach to equilibrium and the impact of the different terms (electrons/electrons and electrons/ions collisions on the one hand and electrons/neutrals collisions on the other hand. Then, a parallel electric field is applied in a new sample run. In this run, the electrons move in the z direction parallel to the electric field. The first results show that all the electron distribution functions are non-Maxwellian. Furthermore, runaway electrons can carry a significant part of the total current density, up to 20% of the total current density.


    AbdulMunem A. Karim


    Full Text Available    This study deals with  kinetics of hydrodesulphurization (HDS reaction of vacuum gas oil (611-833 K which was distillated from Kirkuk crude oil and which was obtained by blending the fractions, light vacuum gas oil (611 - 650 K, medium vacuum gas oil (650-690 K, heavy vacuum gas oil (690-727 K and very heavy vacuum gas oil (727-833 K.   The vacuum gas oil was hydrotreated on a commercial cobalt-molybdenum alumina catalyst presulfied at specified conditions in a laboratory trickle bed reactor. The reaction temperature range (583-643 K,liquid hourly space velocity range (1.5-3.75 h-1 and hydrogen pressure was kept constant at 3.5 MPa with hydrogen to oil ratio about 250 lt/lt.           The conversion results for desulphurization reaction appeared to obey the second order reaction. According to this model, the rate constants for desulphurization reaction were determined. Finally, the apparent activation energy (Ea, enthalpy of activation ( H* and entropy ( S* were calculated based on the values of rate constant (k2 and were equal 80.3792 KJ/mole, 75.2974 KJ/mole and 197.493 J/mole, respectively.

  15. Freed by interaction kinetic states in the Harper model

    Frahm, Klaus M.; Shepelyansky, Dima L.


    We study the problem of two interacting particles in a one-dimensional quasiperiodic lattice of the Harper model. We show that a short or long range interaction between particles leads to emergence of delocalized pairs in the non-interacting localized phase. The properties of these freed by interaction kinetic states (FIKS) are analyzed numerically including the advanced Arnoldi method. We find that the number of sites populated by FIKS pairs grows algebraically with the system size with the maximal exponent b = 1, up to a largest lattice size N = 10 946 reached in our numerical simulations, thus corresponding to a complete delocalization of pairs. For delocalized FIKS pairs the spectral properties of such quasiperiodic operators represent a deep mathematical problem. We argue that FIKS pairs can be detected in the framework of recent cold atom experiments [M. Schreiber et al., Science 349, 842 (2015)] by a simple setup modification. We also discuss possible implications of FIKS pairs for electron transport in the regime of charge-density wave and high T c superconductivity.

  16. Kinetic modeling for chemiluminescent radicals in acetylene combustion

    Marques Carla S. T.


    Full Text Available Kinetic modeling to reproduce the experimental chemiluminescence of OH*, CHO*, CH* and C2* excited radicals formed in C2H2/O2 combustion in a closed chamber was evaluated. A reaction mechanism with 37 species and 106 elementary reactions for C2H2/O2 combustion at phi=1.00 and phi=1.62 was validated through chemiluminescence measurements, where formation and decay reactions of excited radicals are included. KINAL package was used for simulations. Ordinary differential equations were solved by the DIFF program and production rate analysis were acquired by the ROPA program. There was good agreement between experimental and simulated chemiluminescence profiles of all radicals for both combustions. The results showed CH has a meaningful role in the production of excited radicals. Reactions: H + O2 = OH* + O; CH + O = CHO*; C2H + O2 = CH* + CO2 and CH2 + C = C2* + H2 were the main reactions paths used to reproduce the experimental profiles.

  17. Oil cracking to gases: Kinetic modeling and geological significance

    TIAN Hui; WANG Zhaoming; XIAO Zhongyao; LI Xianqing; XIAO Xianming


    ATriassic oil sample from LN14 of Tarim Basin was pyrolyzed using the sealed gold tubes at 200-620℃ under a constant pressure of 50 MPa.The gaseous and residual soluble hydrocarbons were analyzed. The results show that the cracking of oil to gas can be divided into two distinct stages: the primary generation of total C1-5 gases from liquid oil characterized by the dominance of C2-5 hydrocarbons and the secondary or further cracking of C2-5gases to methane and carbon-rich matters leading to the progressive dryness of gases. Based on the experimental data, the kinetic parameters were determined for the primary generation and secondary cracking of oil cracking gases and extrapolated to geological conditions to predict the thermal stability and cracking extent of crude oil. Finally, an evolution model for the thermal destruction of crude oil was proposed and its implications to the migration and accumulation of oil cracking gases were discussed.

  18. Kinetic model of the bichromatic dark trap for atoms

    Krasnov, I. V.


    A kinetic model of atom confinement in a bichromatic dark trap (BDT) is developed with the goal of describing its dissipative properties. The operating principle of the deep BDT is based on using the combination of multiple bichromatic cosine-Gaussian optical beams (CGBs) for creating high-potential barriers, which is described in our previous work (Krasnov 2016 Laser Phys. 26 105501). In the indicated work, particle motion in the BDT is described in terms of classical trajectories. In the present study, particle motion is analyzed by means of the Wigner function (phase-space distribution function (DF)), which allows one to properly take into account the quantum fluctuations of optical forces. Besides, we consider an improved scheme of the BDT, where CGBs create, apart from plane potential barriers, a narrow cooling layer. We find an asymptotic solution of the Fokker-Planck equation for the DF and show that the DF of particles deeply trapped in a BDT with a cooling layer is the Tsallis distribution with the effective temperature, which can be considerably lower than in a BDT without a cooling layer. Moreover, it can be adjusted by slightly changing the CGBs’ radii. We also study the effect of particle escape from the trap due to the scattering of resonant photons and show that the particle lifetime in a BDT can exceed several tens of hours when it is limited by photon scattering.

  19. A physiologically based in silico kinetic model predicting plasma cholesterol concentrations in humans

    Pas, van de N.C.A.; Woutersen, R.A.; Ommen, van B.; Rietjens, I.M.C.M.; Graaf, de A.A.


    Increased plasma cholesterol concentration is associated with increased risk of cardiovascular disease. This study describes the development, validation, and analysis of a physiologically based kinetic (PBK) model for the prediction of plasma cholesterol concentrations in humans. This model was dire

  20. Review of reactive kinetic models describing reductive dechlorination of chlorinated ethenes in soil and groundwater

    Chambon, Julie Claire Claudia; Bjerg, Poul Løgstrup; Scheutz, Charlotte;


    Reductive dechlorination is a major degradation pathway of chlorinated ethenes in anaerobic subsurface environments, and reactive kinetic models describing the degradation process are needed in fate and transport models of these contaminants. However, reductive dechlorination is a complex biologi...

  1. A physiologically based in silico kinetic model predicting plasma cholesterol concentrations in humans

    Pas, N.C.A. van de; Woutersen, R.A.; Ommen, B. van; Rietjens, I.M.C.M.; Graaf, A.A. de


    Increased plasma cholesterol concentration is associated with increased risk of cardiovascular disease. This study describes the development, validation, and analysis of a physiologically based kinetic (PBK) model for the prediction of plasma cholesterol concentrations in humans. This model was

  2. Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling

    Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan


    Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.

  3. Analysis of a kinetic multi-segment foot model. Part I: Model repeatability and kinematic validity.

    Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L


    Kinematic multi-segment foot models are still evolving, but have seen increased use in clinical and research settings. The addition of kinetics may increase knowledge of foot and ankle function as well as influence multi-segment foot model evolution; however, previous kinetic models are too complex for clinical use. In this study we present a three-segment kinetic foot model and thorough evaluation of model performance during normal gait. In this first of two companion papers, model reference frames and joint centers are analyzed for repeatability, joint translations are measured, segment rigidity characterized, and sample joint angles presented. Within-tester and between-tester repeatability were first assessed using 10 healthy pediatric participants, while kinematic parameters were subsequently measured on 17 additional healthy pediatric participants. Repeatability errors were generally low for all sagittal plane measures as well as transverse plane Hindfoot and Forefoot segments (mediansegment rigidity analysis suggested rigid body behavior for the Shank and Hindfoot, with the Forefoot violating the rigid body assumptions in terminal stance/pre-swing. Joint excursions were consistent with previously published studies.

  4. Validation of the point kinetic neutronic model of the PBMR / Deon Marais

    Marais, Deon


    This study introduces a new method for the validation of the point kinetic neutronic model of the PBMR. In this study the diffusion equation solution, as implemented in the TlNTE PBMR 268 MW reactor model, replaces the point kinetic model, as implemented in the Flownex V502 PBMR plant model. An indirect coupling method is devised and implemented in an external program called Flownex-Tinte-Interface (FTI) to facilitate the data exchange between these two codes. The validation...

  5. A detailed chemical kinetic model for pyrolysis of the lignin model compound chroman

    James Bland


    Full Text Available The pyrolysis of woody biomass, including the lignin component, is emerging as a potential technology for the production of renewable fuels and commodity chemicals. Here we describe the construction and implementation of an elementary chemical kinetic model for pyrolysis of the lignin model compound chroman and its reaction intermediate ortho-quinone methide (o-QM. The model is developed using both experimental and theoretical data, and represents a hybrid approach to kinetic modeling that has the potential to provide molecular level insight into reaction pathways and intermediates while accurately describing reaction rates and product formation. The kinetic model developed here can replicate all known aspects of chroman pyrolysis, and provides new information on elementary reaction steps. Chroman pyrolysis is found to proceed via an initial retro-Diels–Alder reaction to form o-QM + ethene (C2H4, followed by dissociation of o-QM to the C6H6 isomers benzene and fulvene (+ CO. At temperatures of around 1000–1200 K and above fulvene rapidly isomerizes to benzene, where an activation energy of around 270 kJ mol-1 is required to reproduce experimental observations. A new G3SX level energy surface for the isomerization of fulvene to benzene supports this result. Our modeling also suggests that thermal decomposition of fulvene may be important at around 950 K and above. This study demonstrates that theoretical protocols can provide a significant contribution to the development of kinetic models for biomass pyrolysis by elucidating reaction mechanisms, intermediates, and products, and also by supplying realistic rate coefficients and thermochemical properties.

  6. Modeling of hydrogen production methods: Single particle model and kinetics assessment

    Miller, R.S.; Bellan, J. [California Institute of Technology, Pasadena, CA (United States)


    The investigation carried out by the Jet Propulsion Laboratory (JPL) is devoted to the modeling of biomass pyrolysis reactors producing an oil vapor (tar) which is a precursor to hydrogen. This is an informal collaboration with NREL whereby JPL uses the experimentally-generated NREL data both as initial and boundary conditions for the calculations, and as a benchmark for model validation. The goal of this investigation is to find drivers of biomass fast-pyrolysis in the low temperature regime. The rationale is that experimental observations produce sparse discrete conditions for model validation, and that numerical simulations produced with a validated model are an economic way to find control parameters and an optimal operation regime, thereby circumventing costly changes in hardware and tests. During this first year of the investigation, a detailed mathematical model has been formulated for the temporal and spatial accurate modeling of solid-fluid reactions in biomass particles. These are porous particles for which volumetric reaction rate data is known a priori and both the porosity and the permeability of the particle are large enough to allow for continuous gas phase flow. The methodology has been applied to the pyrolysis of spherically symmetric biomass particles by considering previously published kinetics schemes for both cellulose and wood. The results show that models which neglect the thermal and species boundary layers exterior to the particle will generally over predict both the pyrolysis rates and experimentally obtainable tar yields. An evaluation of the simulation results through comparisons with experimental data indicates that while the cellulose kinetics is reasonably accurate, the wood pyrolysis kinetics is not accurate; particularly at high reactor temperatures. Current effort in collaboration with NREL is aimed at finding accurate wood kinetics.

  7. Mathematical modeling taking into account of intrinsic kinetic properties of cylinder-type vanadium catalyst

    陈振兴; 李洪桂; 王零森


    The method to calculate internal surface effective factor of cylinder-type vanadium catalyst Ls-9 was given. Based on hypothesis of subjunctive one dimension diffusion and combined shape adjustment factor with threestep catalytic mechanism model, the macroscopic kinetic model equation about SO2 oxidation on Ls-9 was deduced.With fixed-bed integral reactor and under the conditions of temperature 350 - 410 ℃, space velocity 1 800 - 5 000h-1, SO2 inlet content 7 %- 12%, the macroscopic kinetic data were detected. Through model parameter estimation,the macroscopic kinetic model equation was obtained.

  8. A model for the occurrence and analysis of ionic thermocurrent spectrum involving different orders of kinetics

    Jai Prakash


    Ionic thermocurrent (ITC) spectrum is much similar to a thermoluminescence (TL) glow curve involving monomolecular kinetics. It has already been reported that different orders of kinetics are involved in TL processes, which depend specifically on the extent of recombination and simultaneous retrapping. It is found that the involvement of different orders of kinetics in ITC spectrum depends on the experimental conditions of polarization and rate of rapid cooling. Consequently, order of kinetics involved in the ITC spectrum does not represent any specific feature of the system under investigation. An equation is developed which explains the occurrence of ITC spectrum involving any order of kinetics. Dielectric relaxation parameters, order of kinetics and approximate number of dipoles per unit volume are evaluated conveniently and easily following the proposed model.

  9. Symmetrical kinematics does not imply symmetrical kinetics in people with transtibial amputation using cycling model.

    Childers, W Lee; Kogler, Géza F


    People with amputation move asymmetrically with regard to kinematics (joint angles) and kinetics (joint forces and moments). Clinicians have traditionally sought to minimize kinematic asymmetries, assuming kinetic asymmetries would also be minimized. A cycling model evaluated locomotor asymmetries. Eight individuals with unilateral transtibial amputation pedaled with 172 mm-length crank arms on both sides (control condition) and with the crank arm length shortened to 162 mm on the amputated side (CRANK condition). Pedaling kinetics and limb kinematics were recorded. Joint kinetics, joint angles (mean and range of motion [ROM]), and pedaling asymmetries were calculated from force pedals and with a motion capture system. A one-way analysis of variance with tukey post hoc compared kinetics and kinematics across limbs. Statistical significance was set to p kinetic asymmetries as clinically assumed. We propose that future research should concentrate on defining acceptable asymmetry.

  10. Kinetic modelling of RDF pyrolysis: Model-fitting and model-free approaches.

    Çepelioğullar, Özge; Haykırı-Açma, Hanzade; Yaman, Serdar


    In this study, refuse derived fuel (RDF) was selected as solid fuel and it was pyrolyzed in a thermal analyzer from room temperature to 900°C at heating rates of 5, 10, 20, and 50°C/min in N2 atmosphere. The obtained thermal data was used to calculate the kinetic parameters using Coats-Redfern, Friedman, Flylnn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) methods. As a result of Coats-Redfern model, decomposition process was assumed to be four independent reactions with different reaction orders. On the other hand, model free methods demonstrated that activation energy trend had similarities for the reaction progresses of 0.1, 0.2-0.7 and 0.8-0.9. The average activation energies were found between 73-161kJ/mol and it is possible to say that FWO and KAS models produced closer results to the average activation energies compared to Friedman model. Experimental studies showed that RDF may be a sustainable and promising feedstock for alternative processes in terms of waste management strategies.

  11. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    Grossman, Max; Willacy, Karen; Allen, Mark


    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  12. Application of Uncertainty and Sensitivity Analysis to a Kinetic Model for Enzymatic Biodiesel Production

    Price, Jason Anthony; Nordblad, Mathias; Woodley, John


    This paper demonstrates the added benefits of using uncertainty and sensitivity analysis in the kinetics of enzymatic biodiesel production. For this study, a kinetic model by Fedosov and co-workers is used. For the uncertainty analysis the Monte Carlo procedure was used to statistically quantify...

  13. Modelling fungal solid-state fermentation: The role of inactivation kinetics

    Smits, J.P.; Sonsbeek, H.M. van; Knol, W.; Tramper, J.; Geelhoed, W.; Peeters, M.; Rinzema, A.


    The theoretical mathematical models described in this paper are used to evaluate the effects of fungal biomass inactivation kinetics on a non- isothermal tray solid-state fermentation (SSF). The inactivation kinetics, derived from previously reported experiments done under isothermal conditions and

  14. A calculation of internal kinetic energy and polarizability of compressed argon from the statistical atom model

    Seldam, C.A. ten; Groot, S.R. de

    From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of

  15. Acceleration of the KINETICS Integrated Dynamical/Chemical Computational Model Using MPI

    Grossman, Max; Willacy, Karen; Allen, Mark


    Understanding the evolution of a planet's atmosphere not only provides a better theoretical understanding of planetary physics and the formation of planets, but also grants useful insight into Earth's own atmosphere. One of the tools used at JPL for the modeling of planetary atmospheres and protostellar disks is KINETICS. KINETICS can simulate years of complex dynamics and chemistry.

  16. Detailed Chemical Kinetic Modeling of Diesel Combustion with Oxygenated Fuels

    Curran, H J; Fisher, E M; Glaude, P-A; Marinov, N M; Pitz, W J; Westbrook, C K; Flynn, P F; Durrett, R P; zur Loye, A O; Akinyemi, O C; Dryer, F L


    mixing model to study the premixed, rich ignition process. Using n-heptane as a representative diesel fuel, they showed that addition of an oxygenated additive, methanol, to the fuel reduced the concentrations of a number of hydrocarbon species in the products of the rich ignition. Specifically, methanol addition reduced the total concentrations of acetylene, ethylene and 1,3-butadiene, as well as propargyl and vinyl radicals, in the ignition products. These are the same species shown in a number of studies [4-6] to be responsible for formation of aromatic and polycyclic aromatic species in flames, species which lead eventually to production of soot. Flynn et al. did not, however, examine the kinetic processes responsible for the computed reduction in production of soot precursor species. At least two hypotheses have been advanced to explain the role that oxygenated species play in diesel ignition and the reduction in the concentrations of these species. The first is that the additive, methanol in the case of Flynn et al., does not contain any C-C bonds and cannot then produce significant levels of the species such as acetylene, ethylene or the unsaturated radicals which are known to lead to aromatic species. The second hypothesis is that the product distribution changes very naturally as oxygen is added and the overall equivalence ratio is reduced. In the present study, we repeat the ignition calculations of Flynn et al. and include a number of other oxygenated species to determine which of these theories is more applicable to this model.

  17. Comparative evaluation of kinetic, equilibrium and semi-equilibrium models for biomass gasification

    Buragohain, Buljit [Center for Energy, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India); Chakma, Sankar; Kumar, Peeush [Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India); Mahanta, Pinakeswar [Center for Energy, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India); Department of Mechanical Engineering, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India); Moholkar, Vijayanand S. [Center for Energy, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India); Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati – 781 039, Assam (India)


    Modeling of biomass gasification has been an active area of research for past two decades. In the published literature, three approaches have been adopted for the modeling of this process, viz. thermodynamic equilibrium, semi-equilibrium and kinetic. In this paper, we have attempted to present a comparative assessment of these three types of models for predicting outcome of the gasification process in a circulating fluidized bed gasifier. Two model biomass, viz. rice husk and wood particles, have been chosen for analysis, with gasification medium being air. Although the trends in molar composition, net yield and LHV of the producer gas predicted by three models are in concurrence, significant quantitative difference is seen in the results. Due to rather slow kinetics of char gasification and tar oxidation, carbon conversion achieved in single pass of biomass through the gasifier, calculated using kinetic model, is quite low, which adversely affects the yield and LHV of the producer gas. Although equilibrium and semi-equilibrium models reveal relative insensitivity of producer gas characteristics towards temperature, the kinetic model shows significant effect of temperature on LHV of the gas at low air ratios. Kinetic models also reveal volume of the gasifier to be an insignificant parameter, as the net yield and LHV of the gas resulting from 6 m and 10 m riser is same. On a whole, the analysis presented in this paper indicates that thermodynamic models are useful tools for quantitative assessment of the gasification process, while kinetic models provide physically more realistic picture.

  18. Comparative evaluation of kinetic, equilibrium and semi-equilibrium models for biomass gasification

    Buljit Buragohain, Sankar Chakma, Peeush Kumar, Pinakeswar Mahanta, Vijayanand S. Moholkar


    Full Text Available Modeling of biomass gasification has been an active area of research for past two decades. In the published literature, three approaches have been adopted for the modeling of this process, viz. thermodynamic equilibrium, semi-equilibrium and kinetic. In this paper, we have attempted to present a comparative assessment of these three types of models for predicting outcome of the gasification process in a circulating fluidized bed gasifier. Two model biomass, viz. rice husk and wood particles, have been chosen for analysis, with gasification medium being air. Although the trends in molar composition, net yield and LHV of the producer gas predicted by three models are in concurrence, significant quantitative difference is seen in the results. Due to rather slow kinetics of char gasification and tar oxidation, carbon conversion achieved in single pass of biomass through the gasifier, calculated using kinetic model, is quite low, which adversely affects the yield and LHV of the producer gas. Although equilibrium and semi-equilibrium models reveal relative insensitivity of producer gas characteristics towards temperature, the kinetic model shows significant effect of temperature on LHV of the gas at low air ratios. Kinetic models also reveal volume of the gasifier to be an insignificant parameter, as the net yield and LHV of the gas resulting from 6 m and 10 m riser is same. On a whole, the analysis presented in this paper indicates that thermodynamic models are useful tools for quantitative assessment of the gasification process, while kinetic models provide physically more realistic picture.

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

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


    The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  20. Empirical and physics based mathematical models of uranium hydride decomposition kinetics with quantified uncertainties.

    Salloum, Maher N.; Gharagozloo, Patricia E.


    Metal particle beds have recently become a major technique for hydrogen storage. In order to extract hydrogen from such beds, it is crucial to understand the decomposition kinetics of the metal hydride. We are interested in obtaining a a better understanding of the uranium hydride (UH3) decomposition kinetics. We first developed an empirical model by fitting data compiled from different experimental studies in the literature and quantified the uncertainty resulting from the scattered data. We found that the decomposition time range predicted by the obtained kinetics was in a good agreement with published experimental results. Secondly, we developed a physics based mathematical model to simulate the rate of hydrogen diffusion in a hydride particle during the decomposition. We used this model to simulate the decomposition of the particles for temperatures ranging from 300K to 1000K while propagating parametric uncertainty and evaluated the kinetics from the results. We compared the kinetics parameters derived from the empirical and physics based models and found that the uncertainty in the kinetics predicted by the physics based model covers the scattered experimental data. Finally, we used the physics-based kinetics parameters to simulate the effects of boundary resistances and powder morphological changes during decomposition in a continuum level model. We found that the species change within the bed occurring during the decomposition accelerates the hydrogen flow by increasing the bed permeability, while the pressure buildup and the thermal barrier forming at the wall significantly impede the hydrogen extraction.

  1. Kinetic modelling of nitrogen and organics removal in vertical and horizontal flow wetlands.

    Saeed, Tanveer; Sun, Guangzhi


    This paper provides a comparative evaluation of the kinetic models that were developed to describe the biodegradation of nitrogen and organics removal in wetland systems. Reaction kinetics that were considered in the model development included first order kinetics, Monod and multiple Monod kinetics; these kinetics were combined with continuous-stirred tank reactor (CSTR) or plug flow pattern to produce equations to link inlet and outlet concentrations of each key pollutants across a single wetland. Using three statistical parameters, a critical evaluation of five potential models was made for vertical and horizontal flow wetlands. The results recommended the models that were developed based on Monod models, for predicting the removal of nitrogen and organics in a vertical and horizontal flow wetland system. No clear correlation was observed between influent BOD/COD values and kinetic coefficients of BOD(5) in VF and HF wetlands, illustrating that the removal of biodegradable organics was insensitive to the nature of organic matter. Higher effluent COD/TN values coincided with greater denitrification kinetic coefficients, signifying the dependency of denitrification on the availability of COD in VF wetland systems. In contrast, the trend was opposite in HF wetlands, indicating that availability of NO(3)-N was the main limiting step for nitrogen removal. Overall, the results suggested the possible application of the developed alternative predictive models, for understanding the complex biodegradation routes of nitrogen and organics removal in VF and HF wetland systems.

  2. Kinetic Potential Model of the Cloud-to-Drizzle Transition

    McGraw, Robert; Liu, Yangang; Luke, Edward; Senum, Gunnar


    It has been nearly a decade since the kinetic potential theory of drizzle formation in warm clouds was introduced [McGraw and Liu, Phys. Rev. Letts. 90, 018501 (2003)], and much progress in understanding the cloud-drizzle transition, especially regarding the role of turbulence, has been achieved within its framework. This poster will begin with an introduction to the kinetic potential idea, working up to the method it provides for predicting drizzle threshold conditions and rates, and concludes with an analysis this year of DOE/ARM cloud parcel vertical velocity measurements - discussing their implications for assessing turbulence fluctuations in water vapor saturation ratio and cloud droplet size.

  3. Fuzzy Logic as a Computational Tool for Quantitative Modelling of Biological Systems with Uncertain Kinetic Data.

    Bordon, Jure; Moskon, Miha; Zimic, Nikolaj; Mraz, Miha


    Quantitative modelling of biological systems has become an indispensable computational approach in the design of novel and analysis of existing biological systems. However, kinetic data that describe the system's dynamics need to be known in order to obtain relevant results with the conventional modelling techniques. These data are often hard or even impossible to obtain. Here, we present a quantitative fuzzy logic modelling approach that is able to cope with unknown kinetic data and thus produce relevant results even though kinetic data are incomplete or only vaguely defined. Moreover, the approach can be used in the combination with the existing state-of-the-art quantitative modelling techniques only in certain parts of the system, i.e., where kinetic data are missing. The case study of the approach proposed here is performed on the model of three-gene repressilator.

  4. Optimization of a Reduced Chemical Kinetic Model for HCCI Engine Simulations by Micro-Genetic Algorithm


    A reduced chemical kinetic model (44 species and 72 reactions) for the homogeneous charge compression ignition (HCCI) combustion of n-heptane was optimized to improve its autoignition predictions under different engine operating conditions. The seven kinetic parameters of the optimized model were determined by using the combination of a micro-genetic algorithm optimization methodology and the SENKIN program of CHEMKIN chemical kinetics software package. The optimization was performed within the range of equivalence ratios 0.2-1.2, initial temperature 310-375 K and initial pressure 0.1-0.3 MPa. The engine simulations show that the optimized model agrees better with the detailed chemical kinetic model (544 species and 2 446 reactions) than the original model does.

  5. Modeling the kinetics of the nitriding and nitrocarburizing of iron

    Somers, Marcel A. J.; Mittemeijer, Eric J.


    The growth kinetics of the iron-nitride compound layer during nitriding and nitrocarburizing of pure iron has been investigated for various temperatures and various combinations of imposed nitrogen and carbon activities. The results indicate that no local equilibrium occurs at the gas/solid inter...

  6. Calcite growth kinetics: Modeling the effect of solution stoichiometry

    Wolthers, M.; Nehrke, G.; Gustafsson, J.P.; Van Cappellen, P.


    Until recently the influence of solution stoichiometry on calcite crystal growth kinetics has attracted little attention, despite the fact that in most aqueous environments calcite precipitates from non-stoichiometric solution. In order to account for the dependence of the calcite crystal growth rat

  7. Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca

    Eremeeva, Elena V.; Bartsev, Sergey I.; Berkel, van Willem J.H.; Vysotski, Eugene S.


    Upon binding their metal ion cofactors, Ca2+-regulated photoproteins display a rapid increase of light signal, which reaches its peak within milliseconds. In the present study, we investigate bioluminescence kinetics of the entire photoprotein family. All five recombinant hydromedusan Ca2+-regulated

  8. [Study on simplification of extraction kinetics model and adaptability of total flavonoids model of Scutellariae radix].

    Chen, Yang; Zhang, Jin; Ni, Jian; Dong, Xiao-Xu; Xu, Meng-Jie; Dou, Hao-Ran; Shen, Ming-Rui; Yang, Bo-Di; Fu, Jing


    Because of irregular shapes of Chinese herbal pieces, we simplified the previously deduced general extraction kinetic model for TCMs, and integrated particle diameters of Chinese herbs that had been hard to be determined in the final parameter "a". The reduction of the direct determination of particle diameters of Chinese herbs was conducive to increase the accuracy of the model, expand the application scope of the model, and get closer to the actual production conditions. Finally, a simplified model was established, with its corresponding experimental methods and data processing methods determined. With total flavonoids in Scutellariae Radix as the determination index, we conducted a study on the adaptability of total flavonoids extracted from Scutellariae Radix with the water decoction method in the model. The results showed a good linear correlation among the natural logarithm value of the mass concentration of total flavonoids in Scutellariae Radix, the time and the changes in the natural logarithm of solvent multiple. Through calculating and fitting, efforts were made to establish the kinetic model of extracting total flavonoids from Scutellariae Radix with the water decoction method, and verify the model, with a good degree of fitting and deviation within the range of the industrial production requirements. This indicated that the model established by the method has a good adaptability.

  9. Isotope exchange kinetics in metal hydrides I : TPLUG model.

    Larson, Rich; James, Scott Carlton; Nilson, Robert H.


    A one-dimensional isobaric reactor model is used to simulate hydrogen isotope exchange processes taking place during flow through a powdered palladium bed. This simple model is designed to serve primarily as a platform for the initial development of detailed chemical mechanisms that can then be refined with the aid of more complex reactor descriptions. The one-dimensional model is based on the Sandia in-house code TPLUG, which solves a transient set of governing equations including an overall mass balance for the gas phase, material balances for all of the gas-phase and surface species, and an ideal gas equation of state. An energy equation can also be solved if thermodynamic properties for all of the species involved are known. The code is coupled with the Chemkin package to facilitate the incorporation of arbitrary multistep reaction mechanisms into the simulations. This capability is used here to test and optimize a basic mechanism describing the surface chemistry at or near the interface between the gas phase and a palladium particle. The mechanism includes reversible dissociative adsorptions of the three gas-phase species on the particle surface as well as atomic migrations between the surface and the bulk. The migration steps are more general than those used previously in that they do not require simultaneous movement of two atoms in opposite directions; this makes possible the creation and destruction of bulk vacancies and thus allows the model to account for variations in the bulk stoichiometry with isotopic composition. The optimization code APPSPACK is used to adjust the mass-action rate constants so as to achieve the best possible fit to a given set of experimental data, subject to a set of rigorous thermodynamic constraints. When data for nearly isothermal and isobaric deuterium-to-hydrogen (D {yields} H) and hydrogen-to-deuterium (H {yields} D) exchanges are fitted simultaneously, results for the former are excellent, while those for the latter show

  10. Isotope exchange kinetics in metal hydrides I : TPLUG model.

    Larson, Rich; James, Scott Carlton; Nilson, Robert H.


    A one-dimensional isobaric reactor model is used to simulate hydrogen isotope exchange processes taking place during flow through a powdered palladium bed. This simple model is designed to serve primarily as a platform for the initial development of detailed chemical mechanisms that can then be refined with the aid of more complex reactor descriptions. The one-dimensional model is based on the Sandia in-house code TPLUG, which solves a transient set of governing equations including an overall mass balance for the gas phase, material balances for all of the gas-phase and surface species, and an ideal gas equation of state. An energy equation can also be solved if thermodynamic properties for all of the species involved are known. The code is coupled with the Chemkin package to facilitate the incorporation of arbitrary multistep reaction mechanisms into the simulations. This capability is used here to test and optimize a basic mechanism describing the surface chemistry at or near the interface between the gas phase and a palladium particle. The mechanism includes reversible dissociative adsorptions of the three gas-phase species on the particle surface as well as atomic migrations between the surface and the bulk. The migration steps are more general than those used previously in that they do not require simultaneous movement of two atoms in opposite directions; this makes possible the creation and destruction of bulk vacancies and thus allows the model to account for variations in the bulk stoichiometry with isotopic composition. The optimization code APPSPACK is used to adjust the mass-action rate constants so as to achieve the best possible fit to a given set of experimental data, subject to a set of rigorous thermodynamic constraints. When data for nearly isothermal and isobaric deuterium-to-hydrogen (D {yields} H) and hydrogen-to-deuterium (H {yields} D) exchanges are fitted simultaneously, results for the former are excellent, while those for the latter show

  11. A simple kinetic model for growth and biosynthesis of polyhydroxyalkanoate in Bacillus flexus.

    Divyashree, M Somashekara; Rastogi, Navin K; Shamala, T Ramachandriah


    Polyhydroxyalkanoate (PHA), which is produced by several bacteria, is a biodegradable polymer that has many industrial and medical applications. This study deals with development of a simple kinetic model and modification of the logistic equation that can provide an adequate description of PHA formation process by Bacillus flexus. The parameters studied were kinetics of microbial growth, substrate consumption, and product formation. The microbial growth was described by simplification of Monod's model. A simplified Luedeking-Piret type model could be employed to represent the product kinetics. The kinetic constants were evaluated on the basis of non-linear regression and the differential equations were solved using Runge-Kutta algorithm and MATLAB software. A good agreement was found between the experimental and predicted values, which indicated that the model differential equations could describe the PHA formation and fermentation process. In this study, a modification of the logistic equation has also been attempted for describing the growth of B. flexus.

  12. The models of cosmological inflation in the context of kinetic approximation

    Fomin, I.


    In this work the building of models of cosmological inflation with approximate linear dependence of the scalar field kinetic energy on the state parameter is considered. The key parameters of cosmological perturbations are also calculated.

  13. Analysis of Stability for Gas-Kinetic Non-Local Traffic Model

    SUN Xi-Ming; DONG Yu-Jie


    @@ The gas-kinetic non-local traffic model is improved by taking into account the relative velocity of the correlated vehicles. The stability of different relaxation time modes is analytically investigated with the perturbation method.

  14. Energetic and exergetic performance analysis and modeling of drying kinetics of kiwi slices

    Darvishi, Hosain; Zarein, Mohammad; Farhudi, Zanyar


    This work focused on the effects of the moisture content, slices thickness and microwave power on aspects of energy and exergy, drying kinetics, moisture diffusivity, activation energy, and modeling...

  15. Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

    Bordbar, Aarash; McCloskey, Douglas; Zielinski, Daniel C


    challenge. Here, we constructed multi-omic, data-driven, personalized whole-cell kinetic models of erythrocyte metabolism for 24 healthy individuals based on fasting-state plasma and erythrocyte metabolomics and whole-genome genotyping. We show that personalized kinetic rate constants, rather than......-induced anemia) and how genetic variation (inosine triphosphatase deficiency) may protect against this side effect. This study demonstrates the feasibility of personalized kinetic models, and we anticipate their use will accelerate discoveries in characterizing individual metabolic variation....

  16. Oxygen reduction kinetics on mixed conducting SOFC model cathodes

    Baumann, F.S.


    The kinetics of the oxygen reduction reaction at the surface of mixed conducting solid oxide fuel cell (SOFC) cathodes is one of the main limiting factors to the performance of these promising systems. For ''realistic'' porous electrodes, however, it is usually very difficult to separate the influence of different resistive processes. Therefore, a suitable, geometrically well-defined model system was used in this work to enable an unambiguous distinction of individual electrochemical processes by means of impedance spectroscopy. The electrochemical measurements were performed on dense thin film microelectrodes, prepared by PLD and photolithography, of mixed conducting perovskite-type materials. The first part of the thesis consists of an extensive impedance spectroscopic investigation of La0.6Sr0.4Co0.8Fe0.2O3 (LSCF) microelectrodes. An equivalent circuit was identified that describes the electrochemical properties of the model electrodes appropriately and enables an unambiguous interpretation of the measured impedance spectra. Hence, the dependencies of individual electrochemical processes such as the surface exchange reaction on a wide range of experimental parameters including temperature, dc bias and oxygen partial pressure could be studied. As a result, a comprehensive set of experimental data has been obtained, which was previously not available for a mixed conducting model system. In the course of the experiments on the dc bias dependence of the electrochemical processes a new and surprising effect was discovered: It could be shown that a short but strong dc polarisation of a LSCF microelectrode at high temperature improves its electrochemical performance with respect to the oxygen reduction reaction drastically. The electrochemical resistance associated with the oxygen surface exchange reaction, initially the dominant contribution to the total electrode resistance, can be reduced by two orders of magnitude. This &apos

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

    Safta, Cosmin [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Najm, Habib N. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Knio, Omar [Johns Hopkins Univ., Baltimore, MD (United States)


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

  18. [Kinetic model of enhanced biological phosphorus removal with mixed acetic and propionic acids as carbon sources. (I): Model constitution].

    Zhang, Chao; Chen, Yin-Guang


    Based on activated sludge model No. 2 (ASM2), the anaerobic/aerobic kinetic model of phosphorus-accumulating organisms (PAO) was established with mixed short-chain fatty acids (SCFAs) as the base substance in enhanced biological phosphorus removal process. The characteristic of the PAO model was that the anaerobic metabolism rates of glycogen degradation, poly-beta-hydroxyalkanoates synthesis and polyphosphate hydrolysis were expressed by SCFAs uptake equation, and the effects of anaerobic maintenance on kinetics and stoichiometry were considered. The PAO kinetic model was composed of 3 soluble components, 4 particulate components and a pH parameter, which constituted the matrix of stoichiometric coefficients. On the basis of PAO model, the GAO kinetic model was established, which included 7 processes, and phosphorus content influenced the aerobic metabolism only.

  19. Application of a hybrid kinetic-continuum solver to the near wall modelling

    Rovenskaya, O.; Croce, G.


    A hybrid method dynamically coupling the direct numerical solution of the S-model kinetic equation and Navier-Stokes equations is applied to a numerical simulation of the flow through the channel of a finite length due to arbitrarily pressure ratios and for a wide range of Knudsen number. The decomposition of the physical domain into kinetic and hydrodynamic sub-domains is updated at each time step. The solution is advanced in time simultaneously in both kinetic and hydrodynamic domains: the coupling is achieved by matching half fluxes at the interface of the kinetic and Navier-Stokes domains, thus taking care of the conservation of momentum, energy and mass through the interface. Solver efficiency is increased via MPI (Message Passing Interface) parallelization. Accuracy and reliability of the method, for different decomposition criteria, are assessed via comparison with a pure kinetic solution.

  20. Application of micro-genetic algorithm for calibration of kinetic parameters in HCCI engine combustion model

    Haozhong HUANG; Wanhua SU


    The micro-genetic algorithm (μGA) as a highly effective optimization method, is applied to calibrate to a newly developed reduced chemical kinetic model (40 species and 62 reactions) for the homogeneous charge compression ignition (HCCI) combustion of n-heptane to improve its autoignition predictions for different engine operating conditions. The seven kinetic parameters of the calibrated model are determined using a combination of the Micro-Genetic Algorithm and the SENKIN program of CHEMKIN chemical kinetics software package. Simulation results show that the autoignition predictions of the calibrated model agree better with those of the detailed chemical kinetic model (544 species and 2 446 reactions) than the original model over the range of equivalence ratios from 0.1-1.3 and temperature from 300-3 000 K. The results of this study have demonstrated that the μGA is an effective tool to facilitate the calibration of a large number of kinetic parameters in a reduced kinetic model.

  1. Kinetic model for DT ignition and burn in ICF targets

    Anisimov, S.I.; Oparin, A.M.; Meyer-ter-Vehn, J. [Max-Planck-Institut fuer Quantenoptik, D-85748 Garching (Germany)]|[L.D. Landau Institute for Theoretical Physics, 117940 Moscow (Russia)


    Ignition and burn of DT targets is studied taking into account kinetic effects. Kinetic equations describing the interaction of the high-energy reaction products with target plasma are solved using the particle-in-cell (PIC) code for collisional plasma. Volume and spark ignition configurations are simulated for initial temperatures and {l_angle}{rho}{ital R}{r_angle} values of practical interest and target masses between 0.1 and 10 mg. Optically thick configurations igniting at temperatures below 5 keV are considered. Burn of the targets with reduced tritium content is simulated. It was shown that, for 25{percent} tritium concentration, the energy output is reduced only by 15{percent}. {copyright} {ital 1996 American Institute of Physics.}

  2. Chemical kinetic modeling of H{sub 2} applications

    Westbrook, C.K.; Marinov, N.; Pitz, W.J.; Curran, H. [Lawrence Livermore National Lab., CA (United States)


    This project is intended to develop detailed and simplified kinetic reaction mechanisms for the combustion of practical systems fueled by hydrogen, and then to use those mechanisms to examine the performance, efficiency, pollutant emissions, and other characteristics of those systems. During the last year, a H2/NOx mechanism has been developed that gives much improved predictions of NOx emissions compared to experimental data. Preliminary chemical kinetic and equilibrium calculations have been performed in support of Br2-H2O experiments to be conducted at NREL. Hydrogen, hydrogen/methane and hydrogen/natural gas mixtures have been investigated in a knock-rating engine to assess their automotive knock characteristics. The authors are currently developing the simplified analog reaction mechanisms that are computationally simple, yet still reproduce many of the macroscopic features of flame propagation.

  3. Kinetic modelling in food science : a case study on chlorophyll degradation in olives

    Boekel, van M.A.J.S.


    This paper critically reviews the use of kinetics in modelling (bio)chemical changes in foods. Multiresponse modelling (taking more reactants and products of the reaction under study into consideration in the modelling process) is advocated as opposed to uniresponse modelling (in which only one



    l introductionGlycerol production by fermentation has beenwidely investigated to meet the great commercialdemand in last decades and osmotolerant yeast wasthe microorganism studied most. To analyze thefermentation process more efficiently, a kinetic modelshould be established but little works about it werereported because of its complicated metabolism ofglycerol [1-3]. Batch fermentation experiment showedthat low glucose concentration in the latterfermentation stage resulted in decrease in both glucoseconsu...

  5. Cell kinetic modelling and the chemotherapy of cancer

    Knolle, Helmut


    During the last 30 years, many chemical compounds that are active against tumors have been discovered or developed. At the same time, new methods of testing drugs for cancer therapy have evolved. nefore 1964, drug testing on animal tumors was directed to observation of the incfease in life span of the host after a single dose. A new approach, in which the effects of multiple doses on the proliferation kinetics of the tumor in vivo as well as of cell lines in vitro are investigated, has been outlined by Skipper and his co-workers in a series of papers beginning in 1964 (Skipper, Schabel and Wilcox, 1964 and 1965). They also investigated the influence of the time schedule in the treatment of experimental tumors. Since the publication of those studies, cell population kinetics cannot be left out of any discussion of the rational basis of chemotherapy. When clinical oncologists began to apply cell kinetic concepts in practice about 15 years ago, the theoretical basis was still very poor, in spite of Skipper's pro...

  6. Application of Discrete Lumped Kinetic Modeling on Vacuum Gas Oil Hydrocracking

    Han Longnian; Fang Xiangchen; Peng Chong; Zhao Tao


    The kinetic model of vacuum gas oil (VGO) hydrocracking based on discrete lumped approach was investigated, and some improvement was put forward at the same time in this article. A parallel reaction scheme to describe the conver-sion of VGO into products (gases, gasoline, and diesel) proposed by Orochko was used. The different experimental data were analyzed statistically and then the product distribution and kinetic parameters were simulated by available data. Fur-thermore, the kinetic parameters were correlated based on the feed property, reaction temperature, and catalyst activity. An optimization code in Matlab 2011b was written to ifne-tune these parameters. The model had a favorable ability to predict the product distribution and there was a good agreement between the model predictions and experiment data. Hence, the ki-netic parameters indeed had something to do with feed properties, reaction temperature and catalyst activity.

  7. Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

    Morin, José A.; Ibarra, Borja; Cao, Francisco J.


    Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

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

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


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

  9. 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

    İsmail Tosun


    Full Text Available 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.

  10. 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.

    Tosun, Ismail


    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.

  11. Modeling the oxygen uptake kinetics during exercise testing of patients with chronic obstructive pulmonary diseases using nonlinear mixed models

    Baty, Florent; Ritz, Christian; van Gestel, Arnoldus


    regression. Simultaneous modeling of multiple kinetics requires nonlinear mixed models methodology. To the best of our knowledge, no such curve-fitting approach has been used to analyze multiple [Formula: see text]O2 kinetics in both research and clinical practice so far. METHODS: In the present study, we...... describe functionality of the R package medrc that extends the framework of the commonly used packages drc and nlme and allows fitting nonlinear mixed effects models for automated nonlinear regression modeling. The methodology was applied to a data set including 6MWT [Formula: see text]O2 kinetics from 61...... patients with chronic obstructive pulmonary disease (disease severity stage II to IV). The mixed effects approach was compared to a traditional curve-by-curve approach. RESULTS: A six-parameter nonlinear regression model was jointly fitted to the set of [Formula: see text]O2 kinetics. Significant...

  12. Modeling the oxygen uptake kinetics during exercise testing of patients with chronic obstructive pulmonary diseases using nonlinear mixed models

    Baty, Florent; Ritz, Christian; van Gestel, Arnoldus;


    regression. Simultaneous modeling of multiple kinetics requires nonlinear mixed models methodology. To the best of our knowledge, no such curve-fitting approach has been used to analyze multiple [Formula: see text]O2 kinetics in both research and clinical practice so far. METHODS: In the present study, we...... describe functionality of the R package medrc that extends the framework of the commonly used packages drc and nlme and allows fitting nonlinear mixed effects models for automated nonlinear regression modeling. The methodology was applied to a data set including 6MWT [Formula: see text]O2 kinetics from 61...... patients with chronic obstructive pulmonary disease (disease severity stage II to IV). The mixed effects approach was compared to a traditional curve-by-curve approach. RESULTS: A six-parameter nonlinear regression model was jointly fitted to the set of [Formula: see text]O2 kinetics. Significant...

  13. Systematic construction of kinetic models from genome-scale metabolic networks.

    Natalie J Stanford

    Full Text Available The quantitative effects of environmental and genetic perturbations on metabolism can be studied in silico using kinetic models. We present a strategy for large-scale model construction based on a logical layering of data such as reaction fluxes, metabolite concentrations, and kinetic constants. The resulting models contain realistic standard rate laws and plausible parameters, adhere to the laws of thermodynamics, and reproduce a predefined steady state. These features have not been simultaneously achieved by previous workflows. We demonstrate the advantages and limitations of the workflow by translating the yeast consensus metabolic network into a kinetic model. Despite crudely selected data, the model shows realistic control behaviour, a stable dynamic, and realistic response to perturbations in extracellular glucose concentrations. The paper concludes by outlining how new data can continuously be fed into the workflow and how iterative model building can assist in directing experiments.

  14. A kinetic model for the transport of electrons in a graphene layer

    Fermanian Kammerer, Clotilde; Méhats, Florian


    In this article, we propose a new numerical scheme for the computation of the transport of electrons in a graphene device. The underlying quantum model for graphene is a massless Dirac equation, whose eigenvalues display a conical singularity responsible for non-adiabatic transitions between the two modes. We first derive a kinetic model which takes the form of two Boltzmann equations coupled by a collision operator modeling the non-adiabatic transitions. This collision term includes a Landau-Zener transfer term and a jump operator whose presence is essential in order to ensure a good energy conservation during the transitions. We propose an algorithmic realization of the semi-group solving the kinetic model, by a particle method. We give analytic justification of the model and propose a series of numerical experiments studying the influences of the various sources of errors between the quantum and the kinetic models.

  15. Product sampling during transient continuous countercurrent hydrolysis of canola oil and development of a kinetic model

    Wang, Weicheng


    A chemical kinetic model has been developed for the transient stage of the continuous countercurrent hydrolysis of triglycerides to free fatty acids and glycerol. Departure functions and group contribution methods were applied to determine the equilibrium constants of the four reversible reactions in the kinetic model. Continuous countercurrent hydrolysis of canola oil in subcritical water was conducted experimentally in a lab-scale reactor over a range of temperatures and the concentrations of all neutral components were quantified. Several of the rate constants in the model were obtained by modeling this experimental data, with the remaining determined from calculated equilibrium constants. Some reactions not included in the present, or previous, hydrolysis modeling efforts were identified from glycerolysis kinetic studies and may explain the slight discrepancy between model and experiment. The rate constants determined in this paper indicate that diglycerides in the feedstock accelerate the transition from "emulsive hydrolysis" to "rapid hydrolysis". © 2013 Elsevier Ltd.

  16. A kinetics modeling study on the inhibition of glucose on cellulosome of Clostridium thermocellum.

    Zhang, Pengcheng; Wang, Buyun; Xiao, Qunfang; Wu, Shan


    A simplified kinetics model was built to study the inhibition of glucose on cellulosome of Clostridium thermocellum. Suitable reaction conditions were adopted to evaluate the model. The model was evaluated at different temperatures and further with various activated carbon additions as adsorbent for glucose. Investigation results revealed that the model could describe the hydrolysis kinetics of cellulose by cellulosome quite well. Glucose was found to be an inhibitor for cellulosome based on the kinetics analysis. Inhibition increased with the increase in temperature. Activated carbon as adsorbent could lower the inhibition. Parameters in the model were further discussed based on the experiment. The model might also be used to describe the strong inhibition of cellobiose on cellulosome. Saccharification of cellulose by both cellulosome and C. thermocellum could be enhanced efficiently by activated carbon addition.

  17. Reactive molecular dynamics simulation and chemical kinetic modeling of pyrolysis and combustion of n-dodecane

    Wang, Quan-De [College of Chemistry, Sichuan University, Chengdu (China); Wang, Jing-Bo; Li, Juan-Qin; Tan, Ning-Xin; Li, Xiang-Yuan [College of Chemical Engineering, Sichuan University, Chengdu (China)


    The initiation mechanisms and kinetics of pyrolysis and combustion of n-dodecane are investigated by using the reactive molecular dynamics (ReaxFF MD) simulation and chemical kinetic modeling. From ReaxFF MD simulations, we find the initiation mechanisms of pyrolysis of n-dodecane are mainly through two pathways, (1) the cleavage of C-C bond to form smaller hydrocarbon radicals, and (2) the dehydrogenation reaction to form an H radical and the corresponding n-C{sub 12}H{sub 25} radical. Another pathway is the H-abstraction reactions by small radicals including H, CH{sub 3}, and C{sub 2}H{sub 5}, which are the products after the initiation reaction of n-dodecane pyrolysis. ReaxFF MD simulations lead to reasonable Arrhenius parameters compared with experimental results based on first-order kinetic analysis of n-dodecane pyrolysis. The density/pressure effects on the pyrolysis of n-dodecane are also analyzed. By appropriate mapping of the length and time from macroscopic kinetic modeling to ReaxFF MD, a simple comparison of the conversion of n-dodecane from ReaxFF MD simulations and that from kinetic modeling is performed. In addition, the oxidation of n-dodecane is studied by ReaxFF MD simulations. We find that formaldehyde molecule is an important intermediate in the oxidation of n-dodecane, which has been confirmed by kinetic modeling, and ReaxFF leads to reasonable reaction pathways for the oxidation of n-dodecane. These results indicate that ReaxFF MD simulations can give an atomistic description of the initiation mechanism and product distributions of pyrolysis and combustion for hydrocarbon fuels, and can be further used to provide molecular based robust kinetic reaction mechanism for chemical kinetic modeling of hydrocarbon fuels. (author)

  18. Experimental and Chemical Kinetic Modeling Study of Dimethylcyclohexane Oxidation and Pyrolysis

    Eldeeb, Mazen A.


    A combined experimental and chemical kinetic modeling study of the high-temperature ignition and pyrolysis of 1,3-dimethylcyclohexane (13DMCH) is presented. Ignition delay times are measured behind reflected shock waves over a temperature range of 1049–1544 K and pressures of 3.0–12 atm. Pyrolysis is investigated at average pressures of 4.0 atm at temperatures of 1238, 1302, and 1406 K. By means of mid-infrared direct laser absorption at 3.39 μm, fuel concentration time histories are measured under ignition and pyrolytic conditions. A detailed chemical kinetic model for 13DMCH combustion is developed. Ignition measurements show that the ignition delay times of 13DMCH are longer than those of its isomer, ethylcyclohexane. The proposed chemical kinetic model predicts reasonably well the effects of equivalence ratio and pressure, with overall good agreement between predicted and measured ignition delay times, except at low dilution levels and high pressures. Simulated fuel concentration profiles agree reasonably well with the measured profiles, and both highlight the influence of pyrolysis on the overall ignition kinetics at high temperatures. Sensitivity and reaction pathway analyses provide further insight into the kinetic processes controlling ignition and pyrolysis. The work contributes toward improved understanding and modeling of the oxidation and pyrolysis kinetics of cycloalkanes.

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

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


    The objectives of this work were the classification of dynamic metabolic biomarker candidates and the modeling and characterization of kinetic regulatory mechanisms in human metabolism with response to external perturbations by physical activity. Longitudinal metabolic concentration data of 47 individuals from 4 different groups were examined, obtained from a cycle ergometry cohort study. In total, 110 metabolites (within the classes of acylcarnitines, amino acids, and sugars) were measured through a targeted metabolomics approach, combining tandem mass spectrometry (MS/MS) with the concept of stable isotope dilution (SID) for metabolite quantitation. Biomarker candidates were selected by combined analysis of maximum fold changes (MFCs) in concentrations and P-values resulting from statistical hypothesis testing. Characteristic kinetic signatures were identified through a mathematical modeling approach utilizing polynomial fitting. Modeled kinetic signatures were analyzed for groups with similar behavior by applying hierarchical cluster analysis. Kinetic shape templates were characterized, defining different forms of basic kinetic response patterns, such as sustained, early, late, and other forms, that can be used for metabolite classification. Acetylcarnitine (C2), showing a late response pattern and having the highest values in MFC and statistical significance, was classified as late marker and ranked as strong predictor (MFC = 1.97, P modeling approach demonstrates high potential for dynamic biomarker identification and the investigation of kinetic mechanisms in disease or pharmacodynamics studies using MS data from longitudinal cohort studies.

  20. Modeling Oxidation Kinetics of SiC-Containing Refractory Diborides


    K. E. Spear, R. E. Tressler, and C. F. Ram- berg, “Passive-Oxidation Kinetics of High - Purity Silicon Carbide from 800 to 1100 C,” J. Am. Ceram. Soc...investigations47–53 in pure oxygen; there is a large scatter in the data. Figure 2 includes data collected on high purity SiC by Ramberg et al.,47 and...mechanism. Data reported for pure SiC in air/oxygen, for ZrB2 containing varying volume fractions of SiC , and for SiC –HfB2 ultra- high temperature

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

    Gering, Kevin L.


    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.

  2. Towards Kinetic Modeling of Global Metabolic Networks Methylobacterium extorquens AM1 Growth as Validation

    Ping Ao; Lik Wee Lee; Mary E. Lidstrom; Lan Yin; Xiaomei Zhu


    Here we report a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium. Its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, ghiconeogensis, PHB synthesis and acetyl-CoA conversion pathway, respiration and energy metabolism. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. Our method consists of the following major steps: 1) using a generic enzymatic rate equation to reduce the number of enzymatic parameters to a minimum set while still preserving their characteristics; 2) using a set of steady state fluxes and metabolite concenwations in the physiological range as the expected output steady state fluxes and metabolite concentrations for the kinetic model to restrict the parametric space of enzymatic reactions; 3) choosing enzyme constants K's and K'eqs optimized for reactions under physiological concentrations, if their experimental values are unknown; 4) for models which do not cover the entire metabolic network of the organisms, designing a dynamical exchange for the coupling between the metabolism represented in the model and the rest not included.

  3. Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model

    Raganati, Francesca; Procentese, Alessandra; Olivieri, Giuseppe; Götz, Peter; Salatino, Piero; Marzocchella, Antonio


    This paper presents a kinetic dynamic model of acetone-butanol-ethanol production by Clostridium acetobutylicum DSM 792 developed with the biochemical networks simulator COPASI. This model is an evolution of previous models described in the literature, updated by including various mono-, di-,

  4. Computational model, method, and system for kinetically-tailoring multi-drug chemotherapy for individuals

    Gardner, Shea Nicole


    A method and system for tailoring treatment regimens to individual patients with diseased cells exhibiting evolution of resistance to such treatments. A mathematical model is provided which models rates of population change of proliferating and quiescent diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith. A treatment regimen may then be selected from the plurlaity of treatment options based on the efficacy value.

  5. First-principle based modeling of urea decomposition kinetics in aqueous solutions

    Nicolle, André; Cagnina, Stefania; de Bruin, Theodorus


    This study aims at validating a multi-scale modeling methodology based on an implicit solvent model for urea thermal decomposition pathways in aqueous solutions. The influence of the number of cooperative water molecules on kinetics was highlighted. The obtained kinetic model is able to accurately reproduce urea decomposition in aqueous phase under a variety of experimental conditions from different research groups. The model also highlights the competition between HNCO desorption to gas phase and hydrolysis in aqueous phase, which may influence SCR depollution process operation.

  6. The adsorptive-kinetic model of in-situ phosphorus doped film polysilicon deposition process

    Nalivaiko O. Yu.


    Full Text Available The investigation of deposition kinetics of in-situ phosphorus doped polysilicon films has been performed. The adsorptive-kinetic model of in-situ phosphorus doped polysilicon deposition has been developed. The values of heterogeneous reaction constants and constants, which describe the desorption process for monosilane and phosphine, have been defined. The optimal process conditions, which provide the acceptable deposition rate, thickness uniformity, high doping level and conformal step coverage, have been founded.

  7. A Model for the Interfacial Kinetics of Phospholipase D Activity on Long-Chain Lipids


    outer vesicle layer scooting mode hydrolysis to analyze the interfacial kinetics, inhibition, and substrate preferences of bee venom phospholipase A2...California ABSTRACT The membrane -active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a...Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial

  8. Modeling physiological processes in plankton on enzyme kinetic principles

    Ted Packard


    Full Text Available Many ecologically important chemical transformations in the ocean are controlled by biochemical enzyme reactions in plankton. Nitrogenase regulates the transformation of N2 to ammonium in some cyanobacteria and serves as the entryway for N2 into the ocean biosphere. Nitrate reductase controls the reduction of NO3 to NO2 and hence new production in phytoplankton. The respiratory electron transfer system in all organisms links the carbon oxidation reactions of intermediary metabolism with the reduction of oxygen in respiration. Rubisco controls the fixation of CO2 into organic matter in phytoplankton and thus is the major entry point of carbon into the oceanic biosphere. In addition to these, there are the enzymes that control CO2 production, NH4 excretion and the fluxes of phosphate. Some of these enzymes have been recognized and researched by marine scientists in the last thirty years. However, until recently the kinetic principles of enzyme control have not been exploited to formulate accurate mathematical equations of the controlling physiological expressions. Were such expressions available they would increase our power to predict the rates of chemical transformations in the extracellular environment of microbial populations whether this extracellular environment is culture media or the ocean. Here we formulate from the principles of bisubstrate enzyme kinetics, mathematical expressions for the processes of NO3 reduction, O2 consumption, N2 fixation, total nitrogen uptake.

  9. Adsorption rate of phenol from aqueous solution onto organobentonite: surface diffusion and kinetic models.

    Ocampo-Perez, Raul; Leyva-Ramos, Roberto; Mendoza-Barron, Jovita; Guerrero-Coronado, Rosa M


    The concentration decay curves for the adsorption of phenol on organobentonite were obtained in an agitated tank batch adsorber. The experimental adsorption rate data were interpreted with diffusional models as well as first-order, second-order and Langmuir kinetic models. The surface diffusion model adjusted the data quite well, revealing that the overall rate of adsorption was controlled by surface diffusion. Furthermore, the surface diffusion coefficient increased raising the mass of phenol adsorbed at equilibrium and was independent of the particle diameter in the range 0.042-0.0126 cm. It was demonstrated that the overall rate of adsorption was essentially not affected by the external mass transfer. The second-order and the Langmuir kinetic models fitted the experimental data quite well; however, the kinetic constants of both models varied without any physical meaning while increasing the particle size and the mass of phenol adsorbed at equilibrium. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. A new class of enhanced kinetic sampling methods for building Markov state models

    Bhoutekar, Arti; Ghosh, Susmita; Bhattacharya, Swati; Chatterjee, Abhijit


    Markov state models (MSMs) and other related kinetic network models are frequently used to study the long-timescale dynamical behavior of biomolecular and materials systems. MSMs are often constructed bottom-up using brute-force molecular dynamics (MD) simulations when the model contains a large number of states and kinetic pathways that are not known a priori. However, the resulting network generally encompasses only parts of the configurational space, and regardless of any additional MD performed, several states and pathways will still remain missing. This implies that the duration for which the MSM can faithfully capture the true dynamics, which we term as the validity time for the MSM, is always finite and unfortunately much shorter than the MD time invested to construct the model. A general framework that relates the kinetic uncertainty in the model to the validity time, missing states and pathways, network topology, and statistical sampling is presented. Performing additional calculations for frequently-sampled states/pathways may not alter the MSM validity time. A new class of enhanced kinetic sampling techniques is introduced that aims at targeting rare states/pathways that contribute most to the uncertainty so that the validity time is boosted in an effective manner. Examples including straightforward 1D energy landscapes, lattice models, and biomolecular systems are provided to illustrate the application of the method. Developments presented here will be of interest to the kinetic Monte Carlo community as well.

  11. Development, validation and application of multi-point kinetics model in RELAP5 for analysis of asymmetric nuclear transients

    Pradhan, Santosh K., E-mail: [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India); Obaidurrahman, K. [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India); Iyer, Kannan N. [Department of Mechanical Engineering, IIT Bombay, Mumbai 400076 (India); Gaikwad, Avinash J. [Nuclear Safety Analysis Division, Atomic Energy Regulatory Board, Mumbai 400094 (India)


    Highlights: • A multi-point kinetics model is developed for RELAP5 system thermal hydraulics code. • Model is validated against extensive 3D kinetics code. • RELAP5 multi-point kinetics formulation is used to investigate critical break for LOCA in PHWR. - Abstract: Point kinetics approach in system code RELAP5 limits its use for many of the reactivity induced transients, which involve asymmetric core behaviour. Development of fully coupled 3D core kinetics code with system thermal-hydraulics is the ultimate requirement in this regard; however coupling and validation of 3D kinetics module with system code is cumbersome and it also requires access to source code. An intermediate approach with multi-point kinetics is appropriate and relatively easy to implement for analysis of several asymmetric transients for large cores. Multi-point kinetics formulation is based on dividing the entire core into several regions and solving ODEs describing kinetics in each region. These regions are interconnected by spatial coupling coefficients which are estimated from diffusion theory approximation. This model offers an advantage that associated ordinary differential equations (ODEs) governing multi-point kinetics formulation can be solved using numerical methods to the desired level of accuracy and thus allows formulation based on user defined control variables, i.e., without disturbing the source code and hence also avoiding associated coupling issues. Euler's method has been used in the present formulation to solve several coupled ODEs internally at each time step. The results have been verified against inbuilt point-kinetics models of RELAP5 and validated against 3D kinetics code TRIKIN. The model was used to identify the critical break in RIH of a typical large PHWR core. The neutronic asymmetry produced in the core due to the system induced transient was effectively handled by the multi-point kinetics model overcoming the limitation of in-built point kinetics model

  12. Equivalent Models and Exact Linearization by the Optimal Control of Monod Kinetics Models

    Krassimira Ljakova


    Full Text Available The well-known global biotechnological models are non-linear and nonstationary. In addition the process variables are difficult to measure, the model parameters are time varying, the measurement noise and measurement delay increase the control problems, etc. One possible way to solve some of these problems is to determine the most simple and easy for use equivalent models. The differential geometric approach [DGA] and especially the exact linearization permit an easy application of the optimal control. The approach and its application in the control of the biotechnological process are discussed in the paper. The optimization technique is used for fed-batch and continuos biotechnological processes when the specific growth rate is described by the Monod kinetics.

  13. Determination of Model Kinetics for Forced Unsteady State Operation of Catalytic CH4 Oxidation

    Effendy Mohammad


    Full Text Available The catalytic oxidation of methane for abating the emission vented from coal mine or natural gas transportation has been known as most reliable method. A reverse flow reactor operation has been widely used to oxidize this methane emission due to its capability for autothermal operation and heat production. The design of the reverse flow reactor requires a proper kinetic rate expression, which should be developed based on the operating condition. The kinetic rate obtained in the steady state condition cannot be applied for designing the reactor operated under unsteady state condition. Therefore, new approach to develop the dynamic kinetic rate expression becomes indispensable, particularly for periodic operation such as reverse flow reactor. This paper presents a novel method to develop the kinetic rate expression applied for unsteady state operation. The model reaction of the catalytic methane oxidation over Pt/-Al2O3 catalyst was used with kinetic parameter determined from laboratory experiments. The reactor used was a fixed bed, once-through operation, with a composition modulation in the feed gas. The switching time was set at 3 min by varying the feed concentration, feed flow rate, and reaction temperature. The concentrations of methane in the feed and product were measured and analysed using gas chromatography. The steady state condition for obtaining the kinetic rate expression was taken as a base case and as a way to judge its appropriateness to be applied for dynamic system. A Langmuir-Hinshelwood reaction rate model was developed. The time period during one cycle was divided into some segments, depending on the ratio of CH4/O2. The experimental result shows that there were kinetic regimes occur during one cycle: kinetic regime controlled by intrinsic surface reaction and kinetic regime controlled by external diffusion. The kinetic rate obtained in the steady state operation was not appropriate when applied for unsteady state operation

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

    Kumar, B Shiva; Venkateswarlu, Ch


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

  15. An efficient approach to bioconversion kinetic model generation based on automated microscale experimentation integrated with model driven experimental design

    Chen, B. H.; Micheletti, M.; Baganz, F.;


    design. It incorporates a model driven approach to the experimental design that minimises the number of experiments to be performed, while still generating accurate values of kinetic parameters. The approach has been illustrated with the transketolase mediated asymmetric synthesis of L...... experimental design.]it comparison with conventional methodology, the modelling approach enabled a nearly 4-fold decrease in the number of experiments while the microwell experimentation enabled a 45-fold decrease in material requirements and a significant increase in experimental throughput. The approach......Reliable models of enzyme kinetics are required for the effective design of bioconversion processes. Kinetic expressions of the enzyme-catalysed reaction rate however, are frequently complex and establishing accurate values of kinetic parameters normally requires a large number of experiments...

  16. Optimization and kinetic modeling of cadmium desorption from citrus peels: A process for biosorbent regeneration

    Njikam, Eloh, E-mail: [Department of Civil and Environmental Engineering, University of Alaska Fairbanks, P.O. Box 755900, Fairbanks, AK 99775 (United States); Schiewer, Silke, E-mail: [Department of Civil and Environmental Engineering, University of Alaska Fairbanks, P.O. Box 755900, Fairbanks, AK 99775 (United States)


    Graphical abstract: Cadmium was completely and quickly desorbed from grapefruit peels using 0.01 M HNO{sub 3}. The kinetics followed a novel 1st or 2nd order kinetic model, related to the remaining metal bound as the rate-determining reactant concentration. For 0.001 M HNO{sub 3}, desorption was incomplete and the model fit less perfect. Highlights: Black-Right-Pointing-Pointer Metal desorption was over 90% complete within 50 min for most desorbents. Black-Right-Pointing-Pointer Models for biosorbent desorption kinetics were developed. Black-Right-Pointing-Pointer Desorption kinetics best fit a novel first-order model related to remaining metal bound. Black-Right-Pointing-Pointer Cd uptake after desorption by HNO{sub 3} was similar to the original uptake. Black-Right-Pointing-Pointer The optimal desorbent was 0.1 or 0.01 M acid, being fast, efficient and cheap. - Abstract: Citrus peel biosorbents are efficient in removing heavy metals from wastewater. Heavy metal recovery and sorbent regeneration are important for the financial competitiveness of biosorption with other processes. The desorbing agents HNO{sub 3}, NaNO{sub 3}, Ca(NO{sub 3}){sub 2}, EDTA, S, S-EDDS, and Na-Citrate were studied at different concentrations to optimize cadmium elution from orange or grapefruit peels. In most cases, desorption was fast, being over 90% complete within 50 min. However sodium nitrate and 0.001 M nitric acid were less efficient. Several new models for desorption kinetics were developed. While zero-, first- and second-order kinetics are commonly applied for modeling adsorption kinetics, the present study adapts these models to describe desorption kinetics. The proposed models relate to the number of metal-filled binding sites as the rate-determining reactant concentration. A model based on first order kinetics with respect to the remaining metal bound performed best. Cd bound in subsequent adsorption after desorption was similar to the original amount bound for desorption by

  17. C. botulinum inactivation kinetics implemented in a computational model of a high-pressure sterilization process.

    Juliano, Pablo; Knoerzer, Kai; Fryer, Peter J; Versteeg, Cornelis


    High-pressure, high-temperature (HPHT) processing is effective for microbial spore inactivation using mild preheating, followed by rapid volumetric compression heating and cooling on pressure release, enabling much shorter processing times than conventional thermal processing for many food products. A computational thermal fluid dynamic (CTFD) model has been developed to model all processing steps, including the vertical pressure vessel, an internal polymeric carrier, and food packages in an axis-symmetric geometry. Heat transfer and fluid dynamic equations were coupled to four selected kinetic models for the inactivation of C. botulinum; the traditional first-order kinetic model, the Weibull model, an nth-order model, and a combined discrete log-linear nth-order model. The models were solved to compare the resulting microbial inactivation distributions. The initial temperature of the system was set to 90 degrees C and pressure was selected at 600 MPa, holding for 220 s, with a target temperature of 121 degrees C. A representation of the extent of microbial inactivation throughout all processing steps was obtained for each microbial model. Comparison of the models showed that the conventional thermal processing kinetics (not accounting for pressure) required shorter holding times to achieve a 12D reduction of C. botulinum spores than the other models. The temperature distribution inside the vessel resulted in a more uniform inactivation distribution when using a Weibull or an nth-order kinetics model than when using log-linear kinetics. The CTFD platform could illustrate the inactivation extent and uniformity provided by the microbial models. The platform is expected to be useful to evaluate models fitted into new C. botulinum inactivation data at varying conditions of pressure and temperature, as an aid for regulatory filing of the technology as well as in process and equipment design.

  18. Explicit equilibria in a kinetic model of gambling

    Bassetti, F.; Toscani, G.


    We introduce and discuss a nonlinear kinetic equation of Boltzmann type which describes the evolution of wealth in a pure gambling process, where the entire sum of wealths of two agents is up for gambling, and randomly shared between the agents. For this equation the analytical form of the steady states is found for various realizations of the random fraction of the sum which is shared to the agents. Among others, the exponential distribution appears as steady state in case of a uniformly distributed random fraction, while Gamma distribution appears for a random fraction which is Beta distributed. The case in which the gambling game is only conservative-in-the-mean is shown to lead to an explicit heavy tailed distribution.

  19. Kinetic Modeling of Plasma Methane Conversion Using Gliding Arc

    Antonius Indarto; Jae-Wook Choi; Hwaung Lee; Hyung Keun Song


    Plasma methane (CH4) conversion in gliding arc discharge was examined. The result data of experiments regarding the performance of gliding arc discharge were presented in this paper. A simulation which is consisted some chemical kinetic mechanisms has been provided to analyze and describe the plasma process. The effect of total gas flow rate and input frequency refers to power consumption have been studied to evaluate the performance of gliding arc plasma system and the reaction mechanism of decomposition.Experiment results indicated that the maximum conversion of CH4 reached 50% at the total gas flow rate of 1 L/min. The plasma reaction was occurred at the atmospheric pressure and the main products were C (solid), hydrogen, and acetylene (C2H2). The plasma reaction of methane conversion was exothermic reaction which increased the product stream temperature around 30-50 ℃.

  20. Kinetic Monte Carlo modelling of neutron irradiation damage in iron

    Gamez, L. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Departamento de Fisica Aplicada, ETSII, UPM, Madrid (Spain)], E-mail:; Martinez, E. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Lawrence Livermore National Laboratory, LLNL, CA 94550 (United States); Perlado, J.M.; Cepas, P. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Caturla, M.J. [Departamento de Fisica Aplicada, Universidad de Alicante, Alicante (Spain); Victoria, M. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Marian, J. [Lawrence Livermore National Laboratory, LLNL, CA 94550 (United States); Arevalo, C. [Instituto de Fusion Nuclear, UPM, Madrid (Spain); Hernandez, M.; Gomez, D. [CIEMAT, Madrid (Spain)


    Ferritic steels (FeCr based alloys) are key materials needed to fulfill the requirements expected in future nuclear fusion facilities, both for magnetic and inertial confinement, and advanced fission reactors (GIV) and transmutation systems. Research in such field is actually a critical aspect in the European research program and abroad. Experimental and multiscale simulation methodologies are going hand by hand in increasing the knowledge of materials performance. At DENIM, it is progressing in some specific part of the well-linked simulation methodology both for defects energetics and diffusion, and for dislocation dynamics. In this study, results obtained from kinetic Monte Carlo simulations of neutron irradiated Fe under different conditions are presented, using modified ad hoc parameters. A significant agreement with experimental measurements has been found for some of the parameterization and mechanisms considered. The results of these simulations are discussed and compared with previous calculations.

  1. Effect of wall growth on the kinetic modeling of nitrite oxidation in a CSTR.

    Dokianakis, Spiros N; Kornaros, Michael; Lyberatos, Gerasimos


    A simple kinetic model was developed for describing nitrite oxidation by autotrophic aerobic nitrifiers in a continuous stirred tank reactor (CSTR), in which mixed (suspended and attached) growth conditions prevail. The CSTR system was operated under conditions of constant nitrite feed concentration and varying volumetric flow rates. Experimental data from steady-state conditions in the CSTR system and from batch experiments were used for the determination of the model's kinetic parameters. Model predictions were verified against experimental data obtained under transient operating conditions, when volumetric flow rate and nitrite feed concentration disturbances were imposed on the CSTR. The presented kinetic modeling procedure is quite simple and general and therefore can also be applied to other mixed growth biological systems.

  2. Mathematical Model of Sorption Kinetics of Crude Oil by Rubber Particles from Scrap Tyres

    Felix A. AISIEN


    Full Text Available This paper present an insight into how rubber particles from scrap tyres can be utilized to clean up oil spillages as well as how the process of sorption of crude oil by rubber particles can be stimulated based on sorption kinetics. Crude oil sorption tests using recycled rubber particles (a model absorbent were designed for investigating crude oil concentration profiles. The model based on a linear driving force (LDF was developed using a set of experimental data and multiple regression analysis. The crude oil sorption performance tests were conducted under various operating conditions by varying parameters such as rubber particle size and absorption temperature. The predictive capacity of the kinetic model was evaluated under conditions significantly different from those that have already been measured. The experimental results obtained previously were correlated with the first order sorption kinetics model developed. The results showed that the first order kinetics model accurately correlate the experimental data generated. Also, satisfactory results were obtained from simulation of other operating conditions; hence the crude oil sorption kinetics is first order.

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

    García-Gen, Santiago [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Sousbie, Philippe; Rangaraj, Ganesh [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France); Lema, Juan M. [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Rodríguez, Jorge, E-mail: [Department of Chemical Engineering, Institute of Technology, University of Santiago de Compostela, 15782 Santiago de Compostela (Spain); Institute Centre for Water and Environment (iWater), Masdar Institute of Science and Technology, PO Box 54224 Abu Dhabi (United Arab Emirates); Steyer, Jean-Philippe; Torrijos, Michel [INRA, UR50, Laboratoire de Biotechnologie de l’Environnement, Avenue des Etangs, Narbonne F-11100 (France)


    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 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 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.

  4. A Numerical Procedure for Model Identifiability Analysis Applied to Enzyme Kinetics

    Daele, Timothy, Van; Van Hoey, Stijn; Gernaey, Krist;


    exercise, thereby bypassing the challenging task of model structure determination and identification. Parameter identification problems can thus lead to ill-calibrated models with low predictive power and large model uncertainty. Every calibration exercise should therefore be precededby a proper model...... and Pronzato (1997) and which can be easily set up for any type of model. In this paper the proposed approach is applied to the forward reaction rate of the enzyme kinetics proposed by Shin and Kim(1998). Structural identifiability analysis showed that no local structural model problems were occurring......The proper calibration of models describing enzyme kinetics can be quite challenging. In the literature, different procedures are available to calibrate these enzymatic models in an efficient way. However, in most cases the model structure is already decided on prior to the actual calibration...

  5. Systematic identification of crystallization kinetics within a generic modelling framework

    Abdul Samad, Noor Asma Fazli Bin; Meisler, Kresten Troelstrup; Gernaey, Krist


    A systematic development of constitutive models within a generic modelling framework has been developed for use in design, analysis and simulation of crystallization operations. The framework contains a tool for model identification connected with a generic crystallizer modelling tool-box, a tool...

  6. Analysis of kinetic Langmuir model. Part I: Integrated kinetic Langmuir equation (IKL): a new complete analytical solution of the Langmuir rate equation.

    Marczewski, Adam W


    In the article, a new integrated kinetic Langmuir equation (IKL) is derived. The IKL equation is a simple and easy to analyze but complete analytical solution of the kinetic Langmuir model. The IKL is compared with the nth-order, mixed 1,2-order, and multiexponential kinetic equations. The impact of both equilibrium coverage θ(eq) and relative equilibrium uptake u(eq) on kinetics is explained. A newly introduced Langmuir batch equilibrium factor f(eq) that is the product of both parameters θ(eq)u(eq) is used to determine the general kinetic behavior. The analysis of the IKL equation allows us to understand fully the Langmuir kinetics and explains its relation with respect to the empirical pseudo-first-order (PFO, i.e., Lagergren), pseudo-second-order (PSO), and mixed 1,2-order kinetic equations, and it shows the conditions of their possible application based on the Langmuir model. The dependence of the initial adsorption rate on the system properties is analyzed and compared to the earlier published approximate equations.

  7. Global fully kinetic models of planetary magnetospheres with iPic3D

    Gonzalez, D.; Sanna, L.; Amaya, J.; Zitz, A.; Lembege, B.; Markidis, S.; Schriver, D.; Walker, R. J.; Berchem, J.; Peng, I. B.; Travnicek, P. M.; Lapenta, G.


    We report on the latest developments of our approach to model planetary magnetospheres, mini magnetospheres and the Earth's magnetosphere with the fully kinetic, electromagnetic particle in cell code iPic3D. The code treats electrons and multiple species of ions as full kinetic particles. We review: 1) Why a fully kinetic model and in particular why kinetic electrons are needed for capturing some of the most important aspects of the physics processes of planetary magnetospheres. 2) Why the energy conserving implicit method (ECIM) in its newest implementation [1] is the right approach to reach this goal. We consider the different electron scales and study how the new IECIM can be tuned to resolve only the electron scales of interest while averaging over the unresolved scales preserving their contribution to the evolution. 3) How with modern computing planetary magnetospheres, mini magnetosphere and eventually Earth's magnetosphere can be modeled with fully kinetic electrons. The path from petascale to exascale for iPiC3D is outlined based on the DEEP-ER project [2], using dynamic allocation of different processor architectures (Xeon and Xeon Phi) and innovative I/O technologies.Specifically results from models of Mercury are presented and compared with MESSENGER observations and with previous hybrid (fluid electrons and kinetic ions) simulations. The plasma convection around the planets includes the development of hydrodynamic instabilities at the flanks, the presence of the collisionless shocks, the magnetosheath, the magnetopause, reconnection zones, the formation of the plasma sheet and the magnetotail, and the variation of ion/electron plasma flows when crossing these frontiers. Given the full kinetic nature of our approach we focus on detailed particle dynamics and distribution at locations that can be used for comparison with satellite data. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint ar

  8. Insulin kinetics and the Neonatal Intensive Care Insulin-Nutrition-Glucose (NICING) model.

    Dickson, J L; Pretty, C G; Alsweiler, J; Lynn, A; Chase, J G


    Models of human glucose-insulin physiology have been developed for a range of uses, with similarly different levels of complexity and accuracy. STAR (Stochastic Targeted) is a model-based approach to glycaemic control. Elevated blood glucose concentrations (hyperglycaemia) are a common complication of stress and prematurity in very premature infants, and have been associated with worsened outcomes and higher mortality. This research identifies and validates the model parameters for model-based glycaemic control in neonatal intensive care. C-peptide, plasma insulin, and BG from a cohort of 41 extremely pre-term (median age 27.2 [26.2-28.7] weeks) and very low birth weight infants (median birth weight 839 [735-1000] g) are used alongside C-peptide kinetic models to identify model parameters associated with insulin kinetics in the NICING (Neonatal Intensive Care Insulin-Nutrition-Glucose) model. A literature analysis is used to determine models of kidney clearance and body fluid compartment volumes. The full, final NICING model is validated by fitting the model to a cohort of 160 glucose, insulin, and nutrition data records from extremely premature infants from two different NICUs (neonatal intensive care units). Six model parameters related to insulin kinetics were identified. The resulting NICING model is more physiologically descriptive than prior model iterations, including clearance pathways of insulin via the liver and kidney, rather than a lumped parameter. In addition, insulin diffusion between plasma and interstitial spaces is evaluated, with differences in distribution volume taken into consideration for each of these spaces. The NICING model was shown to fit clinical data well, with a low model fit error similar to that of previous model iterations. Insulin kinetic parameters have been identified, and the NICING model is presented for glycaemic control neonatal intensive care. The resulting NICING model is more complex and physiologically relevant, with no

  9. Development and Sensitivity Analysis of a Fully Kinetic Model of Sequential Reductive Dechlorination in Groundwater

    Malaguerra, Flavio; Chambon, Julie Claire Claudia; Bjerg, Poul Løgstrup


    been modeled using modified Michaelis–Menten kinetics and has been implemented in the geochemical code PHREEQC. The model have been calibrated using a Shuffled Complex Evolution Metropolis algorithm to observations of chlorinated solvents, organic acids, and H2 concentrations in laboratory batch...

  10. Kinetic Modeling of Next-Generation High-Energy, High-Intensity Laser-Ion Accelerators

    Albright, Brian James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Yin, Lin [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Stark, David James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    One of the long-standing problems in the community is the question of how we can model “next-generation” laser-ion acceleration in a computationally tractable way. A new particle tracking capability in the LANL VPIC kinetic plasma modeling code has enabled us to solve this long-standing problem

  11. High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells

    Altintas, Ali; Davidsen, Kristian; Garde, Christian


    - and intra-cellular peroxide we have developed a mathematical model that describes two distinct kinetic processes, an initial rapid degradation in the first 10–20 min followed by a slower process. Using this model, a qualitative comparison allowed us to assign the dependence of temporal events to genetic...

  12. A kinetic type extended model for dense gases and macromolecular fluids

    M. Cristina Carrisi


    Full Text Available Extended thermodynamics is an important theory which is appreciated from mathematicians and physicists. Following its ideas and considering the macroscopic approach with suggestions from the kinetic one, we find in this paper, the solution of an interesting model: the model for dense gases and macromolecular fluids.

  13. Kinetic Models for Adiabatic Reversible Expansion of a Monatomic Ideal Gas.

    Chang, On-Kok


    A fixed amount of an ideal gas is confined in an adiabatic cylinder and piston device. The relation between temperature and volume in initial/final phases can be derived from the first law of thermodynamics. However, the relation can also be derived based on kinetic models. Several of these models are discussed. (JN)

  14. The evaluation of benzene and phenol biodegradation kinetics by applying non-structured models.

    Trigueros, D E G; Módenes, A N; Espinoza-Quiñones, F R; Kroumov, A D


    The biodegradation kinetics of the aromatic hydrocarbons benzene and phenol as single substrates and as a mixture were investigated through non-structured model analysis. The material balance equations involving the models of Monod and Andrews and representing the biodegradation kinetics of individual substrates in batch mode were numerically solved. Further, utilization of a benzene-phenol mixture was described by applying more sophisticated mathematical forms of competitive, noncompetitive and uncompetitive inhibition models as well as the sum kinetic interactions parameters (SKIP) model. In order to improve the performance of the studied models, some modifications were also proposed. The Particle Swarm Global Optimization method, coded in Maple, was applied to the parameter identification procedure of each model, where the least square method was used as a search statistical criterion. The description of the biodegradation kinetics of a benzene-phenol mixture by the competitive inhibition model was based on the information that the compounds could be catabolized via one metabolic pathway of Pseudomonas putida F1. Simulation results were in good agreement with the experimental data and proved the robustness of the applied methods and models. The developed knowledge database could be very useful in the optimization of the biodegradation processes of different bioreactor types and operational conditions.

  15. Solvatochromic and Kinetic Response Models in (Ethyl Acetate + Chloroform or Methanol Solvent Mixtures

    L. R. Vottero


    Full Text Available The present work analyzes the solvent effects upon the solvatochromic response models for a set of chemical probes and the kinetic response models for an aromatic nucleophilic substitution reaction, in binary mixtures in which both pure components are able to form intersolvent complexes by hydrogen bonding.

  16. Modelling of pretreatment and saccharification with different feedstocks and kinetic modeling of sorghum saccharification.

    Prathyusha, N; Kamesh, Reddi; Rani, K Yamuna; Sumana, C; Sridhar, S; Prakasham, R S; Yashwanth, V V N; Sheelu, G; Kumar, M Pradeep


    Experiments have been performed for pretreatment of sorghum, wheat straw and bamboo through high temperature alkali pretreatment with different alkaline loading and temperatures, and the data on extent of delignification in terms of the final compositions of cellulose, hemicellulose and lignin have been generated. Further, enzymatic saccharification has been carried out in all the cases to find the extent of conversion possible after 72h. The effect of different operating parameters on the extent of delignification and cellulose conversion are evaluated. This data is employed to develop a generalized multi-feedstock and individual feedstock based models which can be used to determine the extent of delignification and cellulose conversion for any and specific biomass respectively with alkaline pretreatment and similar enzyme conditions as considered in the present study. Also, a kinetic model is developed and validated for sorghum for cellulosic conversion.

  17. Evaluation of rate law approximations in bottom-up kinetic models of metabolism

    Du, Bin; Zielinski, Daniel C.; Kavvas, Erol S.


    . These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction......Background: The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws...... with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. Results: In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation...

  18. Kinetics and mathematical modeling of homoacetic fermentation of lactate by Clostridium formicoaceticum.

    Yang, S T; Tang, I C; Okos, M R


    Fermentation kinetics of Clostridium formicoaceticum grown on lactate at pH 7.0 and 35 degrees C was studied. Acetate was the only fermentation product and its production was growth associated. The growth of this bacterium was insensitive to the lactate concentrations studied, but was inhibited by acetic acid. A Monod-type expression with product inhibition similar to the noncompetitive inhibition of enzyme kinetics was used to model the batch fermentation. An integrated equation was developed and used to help estimating the kinetic parameters in the model. This mathematical model can be used to simulate the homoacetic fermentation of lactate by C. formicoaceticum at pH 7.0 and 35 degrees C.

  19. Enzymatic saccharification of acid pretreated corn stover: Empirical and fractal kinetic modelling.

    Wojtusik, Mateusz; Zurita, Mauricio; Villar, Juan C; Ladero, Miguel; Garcia-Ochoa, Felix


    Enzymatic hydrolysis of corn stover was studied at agitation speeds from 50 to 500rpm in a stirred tank bioreactor, at high solid concentrations (20% w/w dry solid/suspension), 50°C and 15.5mgprotein·gglucane(-1). Two empirical kinetic models have been fitted to empirical data, namely: a potential model and a fractal one. For the former case, the global order dramatically decreases from 13 to 2 as agitation speed increases, suggesting an increment in the access of enzymes to cellulose in terms of chemisorption followed by hydrolysis. For its part, the fractal kinetic model fits better to data, showing its kinetic constant a constant augmentation with increasing agitation speed up to a constant value at 250rpm and above, when mass transfer limitations are overcome. In contrast, the fractal exponent decreases with rising agitation speed till circa 0.19, suggesting higher accessibility of enzymes to the substrate.

  20. Phase transformations in low-carbon steels; modelling the kinetics in terms of the interface mobility

    Leeuwen, Y. van; Kop, T.A.; Sietsma, J.; Zwaag, S. van der [Technische Univ. Delft (Netherlands). Lab. of Materials Science


    The mechanical properties of steel are determined by the microstructure that develops during the production process and is a joint result of effects of chemical composition and of heat treatment. This paper deals with the kinetics of the phase transformation between the high temperature FCC-phase austenite and the low temperature BCC-phase ferrite as it occurs during controlled cooling. In order to predict the transformation kinetics, a physical model has been developed that considers both composition effects and the actual lattice transformation rate. The model is verified against experimental dilatometry data for three lean carbon-manganese steel grades. Notwithstanding the model having no adjustable parameters, it yields adequate simulations of the transformation kinetics. (orig.)

  1. Macroscopic dynamics of incoherent soliton ensembles: soliton-gas kinetics and direct numerical modeling

    Carbone, Francesco; El, Gennady


    We undertake a detailed comparison of the results of direct numerical simulations of the integrable soliton gas dynamics with the analytical predictions inferred from the exact solutions of the relevant kinetic equation for solitons. We use the KdV soliton gas as a simplest analytically accessible model yielding major insight into the general properties of soliton gases in integrable systems. Two model problems are considered: (i) the propagation of a `trial' soliton through a one-component `cold' soliton gas consisting of randomly distributed solitons of approximately the same amplitude; and (ii) collision of two cold soliton gases of different amplitudes (soliton gas shock tube problem) leading to the formation of an incoherend dispersive shock wave. In both cases excellent agreement is observed between the analytical predictions of the soliton gas kinetics and the direct numerical simulations. Our results confirm relevance of the kinetic equation for solitons as a quantitatively accurate model for macrosco...

  2. Fokker Planck kinetic modeling of suprathermal alpha-particles in a fusion plasma

    Peigney, Benjamin-Edouard; Tikhonchuk, Vladimir


    We present an ion kinetic model describing the ignition and burn of the deuterium-tritium fuel of inertial fusion targets. The analysis of the underlying physical model enables us to develop efficient numerical methods to simulate the creation, transport and collisional relaxation of fusion reaction products (alpha-particles) at a kinetic level. A two-energy-scale approach leads to a self-consistent modeling of the coupling between suprathermal alpha-particles and the thermal bulk of the imploding plasma. This method provides an accurate numerical treatment of energy deposition and transport processes involving suprathermal particles. The numerical tools presented here are validated against known analytical results. This enables us to investigate the potential role of ion kinetic effects on the physics of ignition and thermonuclear burn in inertial confinement fusion schemes.

  3. An optimization approach to kinetic model reduction for combustion chemistry

    Lebiedz, Dirk


    Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on optimization of trajectories and show its applicability to realistic combustion models. As most model reduction methods, it identifies points on a slow invariant manifold based on time scale separation in the dynamics of the reaction system. The numerical approximation of points on the manifold is achieved by solving a semi-infinite optimization problem, where the dynamics enter the problem as constraints. The proof of existence of a solution for an arbitrarily chosen dimension of the reduced model (slow manifold) is extended to the case of realistic combustion models including thermochemistry by considering the properties of proper maps. The model reduction approach is finally applied to three models based on realistic reaction mechanisms: 1. ozone decomposition as a small t...

  4. Kinetic modelling of runaway electron avalanches in tokamak plasmas

    Nilsson, E; Peysson, Y; Granetz, R S; Saint-Laurent, F; Vlainic, M


    Runaway electrons (REs) can be generated in tokamak plasmas if the accelerating force from the toroidal electric field exceeds the collisional drag force due to Coulomb collisions with the background plasma. In ITER, disruptions are expected to generate REs mainly through knock-on collisions, where enough momentum can be transferred from existing runaways to slow electrons to transport the latter beyond a critical momentum, setting off an avalanche of REs. Since knock-on runaways are usually scattered off with a significant perpendicular component of the momentum with respect to the local magnetic field direction, these particles are highly magnetized. Consequently, the momentum dynamics require a full 3-D kinetic description, since these electrons are highly sensitive to the magnetic non-uniformity of a toroidal configuration. A bounce-averaged knock-on source term is derived. The generation of REs from the combined effect of Dreicer mechanism and knock-on collision process is studied with the code LUKE, a s...

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

    Liu, Fei; Heiner, Monika; Yang, Ming


    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.

  6. Calibration of Chemical Kinetic Models Using Simulations of Small-Scale Cookoff Experiments

    Wemhoff, A P; Becker, R C; Burnham, A K


    Establishing safe handling limits for explosives in elevated temperature environments is a difficult problem that often requires extensive simulation. The largest influence on predicting thermal cookoff safety lies in the chemical kinetic model used in these simulations, and these kinetic model reaction sequences often contain multiple steps. Several small-scale cookoff experiments, notably Differential Scanning Calorimetry (DSC), Thermogravimetric Analysis (TGA), One-Dimensional Time-to-Explosion (ODTX), and the Scaled Thermal Explosion (STEX) have been performed on various explosives to aid in cookoff behavior determination. Past work has used a single test from this group to create a cookoff model, which does not guarantee agreement with the other experiments. In this study, we update the kinetic parameters of an existing model for the common explosive 2,4,6-Trinitrotoluene (TNT) using DSC and ODTX experimental data at the same time by minimizing a global Figure of Merit based on hydrodynamic simulated data. We then show that the new kinetic model maintains STEX agreement, reduces DSC agreement, and improves ODTX and TGA agreement when compared to the original model. In addition, we describe a means to use implicit hydrodynamic simulations of DSC experiments to develop a reaction model for TNT melting.

  7. Effects of different per translational kinetics on the dynamics of a core circadian clock model.

    Paula S Nieto

    Full Text Available Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

  8. Modelling drying kinetics of thyme (Thymus vulgaris L.): theoretical and empirical models, and neural networks.

    Rodríguez, J; Clemente, G; Sanjuán, N; Bon, J


    The drying kinetics of thyme was analyzed by considering different conditions: air temperature of between 40°C  and 70°C , and air velocity of 1 m/s. A theoretical diffusion model and eight different empirical models were fitted to the experimental data. From the theoretical model application, the effective diffusivity per unit area of the thyme was estimated (between 3.68 × 10(-5) and 2.12 × 10 (-4) s(-1)). The temperature dependence of the effective diffusivity was described by the Arrhenius relationship with activation energy of 49.42 kJ/mol. Eight different empirical models were fitted to the experimental data. Additionally, the dependence of the parameters of each model on the drying temperature was determined, obtaining equations that allow estimating the evolution of the moisture content at any temperature in the established range. Furthermore, artificial neural networks were developed and compared with the theoretical and empirical models using the percentage of the relative errors and the explained variance. The artificial neural networks were found to be more accurate predictors of moisture evolution with VAR ≥ 99.3% and ER ≤ 8.7%.

  9. Modeling of hydrogenation kinetics from triglyceride compositional data.

    Holser, Ronald A; List, Gary R; King, Jerry W; Holliday, Russell L; Neff, William E


    A mathematical model was developed to describe the reduction of soybean oil triglycerides during hydrogenation. The model was derived from reaction and transport mechanisms and formulated into a system of first-order irreversible rate expressions that included terms for temperature, hydrogen pressure, and catalyst concentration. The model parameters were estimated from experimental data, and the model was used to simulate the results of hydrogenation performed over the pressure range of 0.069-6.9 MPa. The model could be extended to include geometrical isomers formed during hydrogenation.

  10. Modeling hepatitis C virus kinetics under therapy using pharmacokinetic and pharmacodynamic information

    Perelson, Alan S [Los Alamos National Laboratory; Shudo, Emi [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory


    Mathematical models have proven helpful in analyzing the virological response to antiviral therapy in hepatitis C virus (HCY) infected subjects. Objective: To summarize the uses and limitations of different models for analyzing HCY kinetic data under pegylated interferon therapy. Methods: We formulate mathematical models and fit them by nonlinear least square regression to patient data in order estimate model parameters. We compare the goodness of fit and parameter values estimated by different models statistically. Results/Conclusion: The best model for parameter estimation depends on the availability and the quality of data as well as the therapy used. We also discuss the mathematical models that will be needed to analyze HCV kinetic data from clinical trials with new antiviral drugs.

  11. A hydrodynamics-reaction kinetics coupled model for evaluating bioreactors derived from CFD simulation.

    Wang, Xu; Ding, Jie; Guo, Wan-Qian; Ren, Nan-Qi


    Investigating how a bioreactor functions is a necessary precursor for successful reactor design and operation. Traditional methods used to investigate flow-field cannot meet this challenge accurately and economically. Hydrodynamics model can solve this problem, but to understand a bioreactor in sufficient depth, it is often insufficient. In this paper, a coupled hydrodynamics-reaction kinetics model was formulated from computational fluid dynamics (CFD) code to simulate a gas-liquid-solid three-phase biotreatment system for the first time. The hydrodynamics model is used to formulate prediction of the flow field and the reaction kinetics model then portrays the reaction conversion process. The coupled model is verified and used to simulate the behavior of an expanded granular sludge bed (EGSB) reactor for biohydrogen production. The flow patterns were visualized and analyzed. The coupled model also demonstrates a qualitative relationship between hydrodynamics and biohydrogen production. The advantages and limitations of applying this coupled model are discussed.

  12. Development of chemical kinetic models for lean NOx traps.

    Larson, Richard S.


    Overall project goal: Obtain the fundamental surface chemistry knowledge needed for the design and optimal utilization of NOx trap catalysts, thereby helping to speed the widespread adoption of this technology. Relevance to VT Program goals: Effective, durable advanced aftertreatment systems for lean-burn engines must be available if the fuel economy advantages of these engines are to be realized. Specific current year objective: Identify and correct any deficiencies in the previously developed reaction mechanism describing normal storage/regeneration cycles, and complete development of a supplementary mechanism accounting for the effects of sulfation. A fundamental understanding of LNT chemistry is needed to realize the full potential of this aftertreatment technology, which could lead to greater use of fuel-efficient lean-burn engines. We have used a multi-tiered approach to developing an elementary chemical mechanism benchmarked against experimental data: (1) Simulate a set of steady flow experiments, with storage effects minimized, to infer a tentative mechanism for chemistry on precious metal sites (completed). (2) Simulate a set of long cycle experiments to infer a mechanism for NOx and oxygen storage sites while simultaneously finalizing precious metal chemistry (completed). (3) Simulate a simplified sulfation/desulfation protocol to obtain a supplementary set of reactions involving sulfur on all three kinds of sites (nearly completed). (4) Investigate the potential role of reductants other than CO and H{sub 2}. While simulation of isothermal experiments is the preferred way to extract kinetic parameters, simulation of realistic storage/regeneration cycles requires that exotherms be considered. Our ultimate goal is to facilitate improved designs for LNT-based aftertreatment systems and to assist in the development of improved catalysts.

  13. A kinetic model for molecular diffusion through pores.

    D'Agostino, Tommaso; Salis, Samuele; Ceccarelli, Matteo


    The number of pathogens developing multiple drug resistance is ever increasing. The impact on healthcare systems is huge and the need for novel antibiotics as well a new way to develop them is urgent, especially against Gram-negative bacteria. The first defense of these bacteria is the outer membrane, where unspecific protein channels (porins) modulate nutrients passive diffusion. Also polar antibiotics enter through this path and down-regulation and/or mutation of porins are very common in drug resistant strains. Our inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features enabling better penetration through porins. Molecular dynamics simulations offer an extraordinary tool in the study of the dynamics of biological systems; however, one of the major drawbacks of this method is that its use is currently restricted to study time scales of the order of microsecond. Enhanced sampling methods like Metadynamics have been recently used to investigate the diffusion of antibiotics through bacterial porins. The main limitation is that dynamical properties cannot be estimated because of the different potential that the systems under study are experiencing. Recently, the scope of Metadynamics has been extended. By applying an a posteriori analysis one can obtain rates of transitions and rate-limiting steps of the process under study, directly comparable with kinetic data extracted from electrophysiology experiments. In this work, we apply this method to the study of the permeability of Escherichia coli's OmpF with respect to Meropenem, finding good agreement with the residence time obtained analyzing experimental current noise. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  14. A simple model for complex dissolution kinetics: a case study of norfloxacin.

    Skrdla, Peter J


    A new semi-empirical model, particularly useful for studying complex dissolution kinetics, is presented here. It uses only two 'fit parameters', each possessing physically relevant units (in the time domain). The model is based on the idea that dispersion (variation) in the activation energy barrier may arise in certain cases, as a result of (quantized) molecular kinetic energies affecting the speed of the rate-determining step (r.d.s.) of the dissolution event. For such 'dispersive dissolutions', the r.d.s. is assumed to involve 2D denucleation. The author's dispersive kinetic model is shown to be applicable to the dissolution of various formulations of norfloxacin which produce very asymmetric, sigmoidal concentration versus time (C-t) profiles. It is derived by assuming an activation energy distribution having the functional form of the Maxwell-Boltzmann (M-B) distribution, coupled with a first-order rate expression. However, this model can also be reduced to give the same functional form as the classical Noyes-Whitney equation, in order to accurately fit/describe dissolution profiles which appear logarithmic (such profiles are due to dissolution phenomena that are not dispersive; i.e. for cases where the activation energy is essentially single-valued). Thus, the kinetic model presented in this work may potentially find broad applicability to the modeling of various dissolution trends observed in the literature.

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

    Cotten Cameron


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

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

    Cotten, Cameron; Reed, Jennifer L


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

  17. An experimental and kinetic modeling study of combustion of isomers of butanol

    Grana, Roberto; Frassoldati, Alessio; Faravelli, Tiziano; Ranzi, Eliseo [Dipartimento di Chimica, Materiali e Ingegneria Chimica, Politecnico di Milano, Milano (Italy); Niemann, Ulrich; Seiser, Reinhard; Cattolica, Robert; Seshadri, Kalyanasundaram [Department of Mechanical and Aerospace Engineering, University of California at San Diego, La Jolla, CA 92093-0411 (United States)


    A kinetic model is developed to describe combustion of isomers of butanol - n-butanol (n-C{sub 4}H{sub 9}OH), sec-butanol (sec-C{sub 4}H{sub 9}OH), iso-butanol (iso-C{sub 4}H{sub 9}OH), and tert-butanol (tert-C{sub 4}H{sub 9}OH). A hierarchical approach is employed here. This approach was previously found to be useful for developing detailed and semi-detailed mechanism of oxidation of various hydrocarbon fuels. This method starts from lower molecular weight compounds of a family of species and proceeds to higher molecular weight compounds. The pyrolysis and oxidation mechanisms of butanol isomers are similar to those for hydrocarbon fuels. Here, the development of the complete set of the primary propagation reactions for butanol isomers proceeds from the extension of the kinetic parameters for similar reactions already studied and recently revised for ethanol, n-propanol and iso-propanol. A detailed description leading to evaluation of rate constants for initiation reactions, metathesis reactions, decomposition reactions of alkoxy radicals, isomerization reactions, and four-center molecular dehydration reactions are given. Decomposition and oxidation of primary intermediate products are described using a previously developed semi-detailed kinetic model for hydrocarbon fuels. The kinetic mechanism is made up of more than 7000 reactions among 300 species. The model is validated by comparing predictions made using this kinetic model with previous and new experimental data on counterflow non-premixed flames of n-butanol and iso-butanol. The structures of these flames were measured by removing gas samples from the flame and analyzing them using a gas chromatograph. Temperature profiles were measured using coated thermocouples. The flame structures were measured under similar conditions for both fuels to elucidate the similarities and differences in combustion characteristics of the two isomers. The profiles measured include those of butanol, oxygen, carbon dioxide

  18. Experimental and Modeling Study of Kinetics for Methane Hydrate Formation with Tetrahydrofuran as Promoter

    Ning Zhengfu; Zhang Shixi; Zhang Qin; Zhen Shuangyi; Chen Guangjin


    The kinetics behavior of methane hydrate formation in the presence of tetrahydrofuran (THF) as promoter was studied. A set of experimental equipment was designed and constructed. A series of kinetics data for the formation of methane hydrate in the presence of THF were measured with the isochoric method. The influences of temperature,pressure and liquid flow rate on the methane consumption rate were studied respectively. Based on the Chen-Guo hydrate formation mechanism,a kinetics model for the formation of methane hydrate in the presence of THF by using the dimensionless Gibbs free energy difference of quasi-chemical reaction of basic hydrate formation,,as the driving force was proposed. The model was used to calculate the rate of methane consumption and it was shown that the calculated results were in good agreement with the experimental results.

  19. Modeling of Scale-Dependent Bacterial Growth by Chemical Kinetics Approach

    Haydee Martínez


    Full Text Available We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli  JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

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

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


    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.

  1. Process Simulation for the Design and Scale Up of Heterogeneous Catalytic Process: Kinetic Modelling Issues

    Antonio Tripodi


    Full Text Available Process simulation represents an important tool for plant design and optimization, either applied to well established or to newly developed processes. Suitable thermodynamic packages should be selected in order to properly describe the behavior of reactors and unit operations and to precisely define phase equilibria. Moreover, a detailed and representative kinetic scheme should be available to predict correctly the dependence of the process on its main variables. This review points out some models and methods for kinetic analysis specifically applied to the simulation of catalytic processes, as a basis for process design and optimization. Attention is paid also to microkinetic modelling and to the methods based on first principles, to elucidate mechanisms and independently calculate thermodynamic and kinetic parameters. Different case studies support the discussion. At first, we have selected two basic examples from the industrial chemistry practice, e.g., ammonia and methanol synthesis, which may be described through a relatively simple reaction pathway and the relative available kinetic scheme. Then, a more complex reaction network is deeply discussed to define the conversion of bioethanol into syngas/hydrogen or into building blocks, such as ethylene. In this case, lumped kinetic schemes completely fail the description of process behavior. Thus, in this case, more detailed—e.g., microkinetic—schemes should be available to implement into the simulator. However, the correct definition of all the kinetic data when complex microkinetic mechanisms are used, often leads to unreliable, highly correlated parameters. In such cases, greater effort to independently estimate some relevant kinetic/thermodynamic data through Density Functional Theory (DFT/ab initio methods may be helpful to improve process description.

  2. Modelling kinetics of plant canopy architecture: concepts and applications

    Birch, C.J.; Andrieu, B.; Fournier, C.; Vos, J.; Room, P.


    Most crop models simulate the crop canopy as an homogeneous medium. This approach enables modelling of mass and energy transfer through relatively simple equations, and is useful for understanding crop production. However, schematisation of an homogeneous medium cannot address the heterogeneous natu

  3. Stydy on the Model of Ion Exchange Kinetics

    ChenFengrong; JiangZhixin


    In this paper, a macrokinetics model equation describing the characteristics of the solid-liquid mass transfer has been proposed.The qualitative analysis and experimental verification have been done for this mode equation.The model equation can explain the ion exchange process considerably well.

  4. Simplified kinetic models of methanol oxidation on silver

    Andreasen, Anders; Lynggaard, Hasse Harloff; Stegelmann, Carsten


    reaction intermediate (MARI) approximation and the irreversible step (IS) approximation. This leads to further reduction in model complexity and in number of parameters. Computations verify that the performance of the model is preserved despite the reduction of the vast amount of parameters....

  5. A methodology for modeling photocatalytic reactors for indoor pollution control using previously estimated kinetic parameters

    Passalia, Claudio; Alfano, Orlando M. [INTEC - Instituto de Desarrollo Tecnologico para la Industria Quimica, CONICET - UNL, Gueemes 3450, 3000 Santa Fe (Argentina); FICH - Departamento de Medio Ambiente, Facultad de Ingenieria y Ciencias Hidricas, Universidad Nacional del Litoral, Ciudad Universitaria, 3000 Santa Fe (Argentina); Brandi, Rodolfo J., E-mail: [INTEC - Instituto de Desarrollo Tecnologico para la Industria Quimica, CONICET - UNL, Gueemes 3450, 3000 Santa Fe (Argentina); FICH - Departamento de Medio Ambiente, Facultad de Ingenieria y Ciencias Hidricas, Universidad Nacional del Litoral, Ciudad Universitaria, 3000 Santa Fe (Argentina)


    Highlights: Black-Right-Pointing-Pointer Indoor pollution control via photocatalytic reactors. Black-Right-Pointing-Pointer Scaling-up methodology based on previously determined mechanistic kinetics. Black-Right-Pointing-Pointer Radiation interchange model between catalytic walls using configuration factors. Black-Right-Pointing-Pointer Modeling and experimental validation of a complex geometry photocatalytic reactor. - Abstract: A methodology for modeling photocatalytic reactors for their application in indoor air pollution control is carried out. The methodology implies, firstly, the determination of intrinsic reaction kinetics for the removal of formaldehyde. This is achieved by means of a simple geometry, continuous reactor operating under kinetic control regime and steady state. The kinetic parameters were estimated from experimental data by means of a nonlinear optimization algorithm. The second step was the application of the obtained kinetic parameters to a very different photoreactor configuration. In this case, the reactor is a corrugated wall type using nanosize TiO{sub 2} as catalyst irradiated by UV lamps that provided a spatially uniform radiation field. The radiative transfer within the reactor was modeled through a superficial emission model for the lamps, the ray tracing method and the computation of view factors. The velocity and concentration fields were evaluated by means of a commercial CFD tool (Fluent 12) where the radiation model was introduced externally. The results of the model were compared experimentally in a corrugated wall, bench scale reactor constructed in the laboratory. The overall pollutant conversion showed good agreement between model predictions and experiments, with a root mean square error less than 4%.

  6. Succinate overproduction: A case study of computational strain design using a comprehensive Escherichia coli kinetic model

    Ali eKhodayari


    Full Text Available Computational strain design prediction accuracy has been the focus for many recent efforts through the selective integration of kinetic information into metabolic models. In general, kinetic model prediction quality is determined by the range and scope of genetic and/or environmental perturbations used during parameterization. In this effort, we apply the k-OptForce procedure on a kinetic model of E. coli core metabolism constructed using the Ensemble Modeling (EM method and parameterized using multiple mutant strains data under aerobic respiration with glucose as the carbon source. Minimal interventions are identified that improve succinate yield under both aerobic and anaerobic conditions to test the fidelity of model predictions under both genetic and environmental perturbations. Under aerobic condition, k-OptForce identifies interventions that match existing experimental strategies pointing at a number of unexplored flux redirections such as routing glyoxylate flux through the glycerate metabolism to improve succinate yield. Many of the identified interventions rely on the kinetic descriptions and would not be discoverable by a purely stoichiometric description. In contrast, under fermentative (anaerobic conditions, k-OptForce fails to identify key interventions including up-regulation of anaplerotic reactions and elimination of competitive fermentative products. This is due to the fact that the pathways activated under anaerobic conditions were not properly parameterized as only aerobic flux data were used in the model construction. This study shed light on the importance of condition-specific model parameterization and provides insight onto how to augment kinetic models so as to correctly respond to multiple environmental perturbations.

  7. Succinate Overproduction: A Case Study of Computational Strain Design Using a Comprehensive Escherichia coli Kinetic Model.

    Khodayari, Ali; Chowdhury, Anupam; Maranas, Costas D


    Computational strain-design prediction accuracy has been the focus for many recent efforts through the selective integration of kinetic information into metabolic models. In general, kinetic model prediction quality is determined by the range and scope of genetic and/or environmental perturbations used during parameterization. In this effort, we apply the k-OptForce procedure on a kinetic model of E. coli core metabolism constructed using the Ensemble Modeling (EM) method and parameterized using multiple mutant strains data under aerobic respiration with glucose as the carbon source. Minimal interventions are identified that improve succinate yield under both aerobic and anaerobic conditions to test the fidelity of model predictions under both genetic and environmental perturbations. Under aerobic condition, k-OptForce identifies interventions that match existing experimental strategies while pointing at a number of unexplored flux re-directions such as routing glyoxylate flux through the glycerate metabolism to improve succinate yield. Many of the identified interventions rely on the kinetic descriptions that would not be discoverable by a purely stoichiometric description. In contrast, under fermentative (anaerobic) condition, k-OptForce fails to identify key interventions including up-regulation of anaplerotic reactions and elimination of competitive fermentative products. This is due to the fact that the pathways activated under anaerobic condition were not properly parameterized as only aerobic flux data were used in the model construction. This study shed light on the importance of condition-specific model parameterization and provides insight on how to augment kinetic models so as to correctly respond to multiple environmental perturbations.

  8. A Kinetic Ladle Furnace Process Simulation Model: Effective Equilibrium Reaction Zone Model Using FactSage Macro Processing

    Van Ende, Marie-Aline; Jung, In-Ho


    The ladle furnace (LF) is widely used in the secondary steelmaking process in particular for the de-sulfurization, alloying, and reheating of liquid steel prior to the casting process. The Effective Equilibrium Reaction Zone model using the FactSage macro processing code was applied to develop a kinetic LF process model. The slag/metal interactions, flux additions to slag, various metallic additions to steel, and arcing in the LF process were taken into account to describe the variations of chemistry and temperature of steel and slag. The LF operation data for several steel grades from different plants were accurately described using the present kinetic model.

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

    Marc Breit


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

  10. Modeling on the Effect of Coal Loads on Kinetic Energy of Balls for Ball Mills

    Yan Bai


    Full Text Available This paper presents a solution for the detection and control of coal loads that is more accurate and convenient than those currently used. To date, no research has addressed the use of a grinding medium as the controlled parameter. To improve the accuracy of the coal load detection based on the kinetic energy of balls in a tubular ball mill, a Discrete Element Method (DEM model for ball kinematics based on coal loads is proposed. The operating process for a ball mill and the ball motion, as influenced by the coal quality and the coal load, was analyzed carefully. The relationship between the operating efficiency of a coal pulverizing system, coal loads, and the balls’ kinetic energy was obtained. Origin and Matlab were utilized to draw the variation of parameters with increasing coal loads in the projectile and cascading motion states. The parameters include the balls’ real-time kinetic energy, the friction energy consumption, and the mill’s total work. Meanwhile, a method of balanced adjacent degree and a physical experiment were proposed to verify the considerable effect of the balls’ kinetic energy on coal loads. The model and experiment results indicate that a coal load control method based on the balls’ kinetic energy is therefore feasible for the optimized operation of a coal pulverizing system.

  11. Kinetic modeling and fitting software for interconnected reaction schemes: VisKin.

    Zhang, Xuan; Andrews, Jared N; Pedersen, Steen E


    Reaction kinetics for complex, highly interconnected kinetic schemes are modeled using analytical solutions to a system of ordinary differential equations. The algorithm employs standard linear algebra methods that are implemented using MatLab functions in a Visual Basic interface. A graphical user interface for simple entry of reaction schemes facilitates comparison of a variety of reaction schemes. To ensure microscopic balance, graph theory algorithms are used to determine violations of thermodynamic cycle constraints. Analytical solutions based on linear differential equations result in fast comparisons of first order kinetic rates and amplitudes as a function of changing ligand concentrations. For analysis of higher order kinetics, we also implemented a solution using numerical integration. To determine rate constants from experimental data, fitting algorithms that adjust rate constants to fit the model to imported data were implemented using the Levenberg-Marquardt algorithm or using Broyden-Fletcher-Goldfarb-Shanno methods. We have included the ability to carry out global fitting of data sets obtained at varying ligand concentrations. These tools are combined in a single package, which we have dubbed VisKin, to guide and analyze kinetic experiments. The software is available online for use on PCs.

  12. Modeling the high pressure inactivation kinetics of Listeria monocytogenes on RTE cooked meat products

    Hereu, A.; Dalgaard, Paw; Garriga, M.;


    provided the best fit to the HP-inactivation kinetics. The relationships between the primary kinetic parameters (log kmax and log Nres) and pressure treatments were described by a polynomial secondary model. To estimate HP-inactivation of L. monocytogenes in log (N/N0) over time, a one-step global fitting...... procedure was applied. The secondary model was integrated into the primary model and the combined equation was fitted to the entire data-set to readjust parameter values. Validation of the developed models both under dynamic conditions and using external independent data supported their suitability...... for predictive purposes, e.g., to set the process criteria required to meet food safety objectives. Industrial relevanceQuantitative mathematical models for predicting inactivation of pathogens by HPP provide useful tools for a process optimization and real time control of a unit operation. The developed models...

  13. Brief report on thermodynamics of chromium slags and kinetic modelling of chromite reduction (1995-96)

    Xiao Yamping; Holappa, L. [Helsinki Univ. of Technology, Otaniemi (Finland). Lab. of Metallurgy


    This article summaries the research work on thermodynamics of chromium slags and kinetic modelling of chromite reduction. The thermodynamic properties of FeCr slag systems were calculated with the regular solution model. The effects of CaO/MgO ratio, Al{sub 2}0{sub 3} amount as well as the slag basicity on the activities of chromium oxides and the oxidation state of chromium were examined. The calculated results were compared to the experimental data in the literature. In the kinetic modelling of the chromite reduction, the reduction possibilities and tendencies of the chromite constitutes with CO were analysed based on the thermodynamic calculation. Two reaction models, a structural grain model and a multi-layers reaction model, were constructed and applied to simulate the chromite pellet reduction and chromite lumpy ore reduction, respectively. The calculated reduction rates were compared with the experimental measurements and the reaction mechanisms were discussed. (orig.) SULA 2 Research Programme; 4 refs.

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

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


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

  15. Inverse and direct modeling applied in the estimation of kinetic parameters of BSA adsorption

    David Curbelo Rodríguez


    Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} The kinetic modeling applied in the parameters estimation of chromatographic adsorption processes is an important tool in the understanding and improvement of these separation systems. In this work, two kinetic models were utilized in the parameters estimation of BSA adsorption. The correlations between the irreversible kinetic model and the reversible kinetic model with the experimental data were carried out using the Linear Driving Force and the Random Restricted Window (R2W method, respectively. From both models was possible to achieve a good fit with the experimental data, obtaining parameters with higher accuracy due to the low residues of the cost function.

  16. Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum.

    Penkler, Gerald; du Toit, Francois; Adams, Waldo; Rautenbach, Marina; Palm, Daniel C; van Niekerk, David D; Snoep, Jacky L


    The enzymes in the Embden-Meyerhof-Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation of the model, we compared model predictions for steady-state fluxes and metabolite concentrations of the hexose phosphates with experimental values for intact parasites. The model, which is completely based on kinetic parameters that were measured for the individual enzymes, gives an accurate prediction of the steady-state fluxes and intermediate concentrations. This is the first detailed kinetic model for glucose metabolism in P. falciparum, one of the most prolific malaria-causing protozoa, and the high predictive power of the model makes it a strong tool for future drug target identification studies. The modelling workflow is transparent and reproducible, and completely documented in the SEEK platform, where all experimental data and model files are available for download. The mathematical models described in the present study have been submitted to the JWS Online Cellular Systems Modelling Database ( The investigation and complete experimental data set is available on SEEK (10.15490/seek.1. 56). © 2015 FEBS.

  17. Spectral Problems for the Orientation-Free Discrete Kinetic Models

    朱光华; 金燕芳; 方竞


    We present computations using orientation-free discrete velocity models for the dispersion relationship of ultrasound propagation in monatomic hard-sphere gases (or a type of gas composed of a system of vortices).Comparisons with previous verified fixed-orientation results for the propagation of the sound mode in rarefied gases show that, if collective excitations are considered, an orientation-free eight-velocity model can capture more physical insights. We also demonstrate the symmetry property of the spectra using the orientation-free eight-velocity model.

  18. A kinetic model for citric acid productionfrom apple pomac by ...



    Oct 6, 2008 ... the analysis, design and operation of a fermenter. Fer- ... model of the process. MATERIALS AND ... Chemical treatments included potassium ferrocyanide .... production from synthesis gas via fermentation processes using.

  19. Modeling biodegradation and kinetics of glyphosate by artificial neural network.

    Nourouzi, Mohsen M; Chuah, Teong G; Choong, Thomas S Y; Rabiei, F


    An artificial neural network (ANN) model was developed to simulate the biodegradation of herbicide glyphosate [2-(Phosphonomethylamino) acetic acid] in a solution with varying parameters pH, inoculum size and initial glyphosate concentration. The predictive ability of ANN model was also compared with Monod model. The result showed that ANN model was able to accurately predict the experimental results. A low ratio of self-inhibition and half saturation constants of Haldane equations (glyphosate on bacteria growth. The value of K(i)/K(s) increased when the mixed inoculum size was increased from 10(4) to 10(6) bacteria/mL. It was found that the percentage of glyphosate degradation reached a maximum value of 99% at an optimum pH 6-7 while for pH values higher than 9 or lower than 4, no degradation was observed.

  20. Kinetic models of cell growth, substrate utilization and bio ...



    May 2, 2008 ... A simple model was proposed using the Logistic Equation for the growth,. Leudeking-Piret ... (melanoidin) which may create many problems and also .... Where, the constant µ is defined as the specific growth rate. Equation 1 ...

  1. Inequality measures in kinetic exchange models of wealth distributions

    Ghosh, Asim; Chatterjee, Arnab; Inoue, Jun-ichi; Chakrabarti, Bikas K.


    In this paper, we study the inequality indices for some models of wealth exchange. We calculated Gini index and newly introduced k-index and compare the results with reported empirical data available for different countries. We have found lower and upper bounds for the indices and discuss the efficiencies of the models. Some exact analytical calculations are given for a few cases. We also exactly compute the quantities for Gamma and double Gamma distributions.

  2. Inequality measures in kinetic exchange models of wealth distributions

    Ghosh, Asim; Inoue, Jun-ichi; Chakrabarti, Bikas K


    In this paper, we study the inequality indices for some models of wealth exchange. We calculated Gini index and newly introduced k-index and compare the results with reported empirical data available for different countries. We have found lower and upper bounds for the indices and discuss the efficiencies of the models. Some exact analytical calculations are given for a few cases. We also exactly compute the quantities for Gamma and double Gamma distributions.

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

    Baker Syed; Poskar C; Junker Björn


    Abstract 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. Wh...

  4. Dynamic Model of Heat Inactivation Kinetics for Bacterial Adaptation▿

    Corradini, Maria G.; Peleg, Micha


    The Weibullian-log logistic (WeLL) inactivation model was modified to account for heat adaptation by introducing a logistic adaptation factor, which rendered its “rate parameter” a function of both temperature and heating rate. The resulting model is consistent with the observation that adaptation is primarily noticeable in slow heat processes in which the cells are exposed to sublethal temperatures for a sufficiently long time. Dynamic survival patterns generated with the proposed model were in general agreement with those of Escherichia coli and Listeria monocytogenes as reported in the literature. Although the modified model's rate equation has a cumbersome appearance, especially for thermal processes having a variable heating rate, it can be solved numerically with commercial mathematical software. The dynamic model has five survival/adaptation parameters whose determination will require a large experimental database. However, with assumed or estimated parameter values, the model can simulate survival patterns of adapting pathogens in cooked foods that can be used in risk assessment and the establishment of safe preparation conditions. PMID:19201963

  5. Kinetic model development for biogas production from cattle dung

    Ghatak, Manjula Das; Mahanta, P.


    Biogas is a mixture of methane, carbon dioxide and traces of numerous trace of elements. It is produced by anaerobic digestion of organic matters including cattle dung which depend upon various factors affecting the population and activity of microorganisms producing biogas. Among the various factors temperature is one of them which play a significant role in biogas production from cattle dung. Biogas production from cattle dung was studied at temperatures 35°C to 55°C at a step of 5°C to study the effect of temperature on biogas production from cattle dung. In this work a mathematical model is developed for evaluating the effect of temperature on the rate of biogas production from cattle dung. The new mathematical model is derived by adding the effect of temperature on the modified Gompertz model. The new model is found to be suitable for predicting the biogas production from cattle dung in the temperature range 35°C to 55°C. The results from the new model are found to be highly correlated to the experimental data of present study.

  6. A Three-Dimensional Scale-adaptive Turbulent Kinetic Energy Model in ARW-WRF Model

    Zhang, Xu; Bao, Jian-Wen; Chen, Baode


    A new three-dimensional (3D) turbulent kinetic energy (TKE) subgrid mixing model is developed to address the problem of simulating the convective boundary layer (CBL) across the terra incognita in the Advanced Research version of the Weather Research and Forecasting Model (ARW-WRF). The new model combines the horizontal and vertical subgrid turbulent mixing into a single energetically consistent framework, in contrast to the convectional one-dimensional (1D) planetary boundary layer (PBL) schemes. The transition between large-eddy simulation (LES) and mesoscale limit is accomplished in the new scale-adaptive model. A series of dry CBL and real-time simulations using the WRF model are carried out, in which the newly-developed, scale-adaptive, more general and energetically consistent TKE-based model is compared with the conventional 1D TKE-based PBL schemes for parameterizing vertical subgrid turbulent mixing against the WRF LES dataset and observations. The characteristics of the WRF-simulated results using the new and conventional schemes are compared. The importance of including the nonlocal component in the vertical buoyancy specification in the newly-developed general TKE-based scheme is illustrated. The improvements of the new scheme over convectional PBL schemes across the terra incognita can be seen in the partitioning of vertical flux profiles. Through comparing the results from the simulations against the WRF LES dataset and observations, we will show the feasibility of using the new scheme in the WRF model in the lieu of the conventional PBL parameterization schemes.

  7. Lifshitz-Allen-Cahn domain-growth kinetics of Ising models with conserved density

    Fogedby, Hans C.; Mouritsen, Ole G.


    The domain-growth kinetics of p=fourfold degenerate (2×1) ordering in two-dimensional Ising models with conserved density is studied as a function of temperature and range of Kawasaki spin exchange. It is found by computer simulations that the zero-temperature freezing-in behavior for nearest...

  8. Systems biology from micro-organisms to human metabolic diseases: the role of detailed kinetic models.

    Bakker, Barbara M; van Eunen, Karen; Jeneson, Jeroen A L; van Riel, Natal A W; Bruggeman, Frank J; Teusink, Bas


    Human metabolic diseases are typically network diseases. This holds not only for multifactorial diseases, such as metabolic syndrome or Type 2 diabetes, but even when a single gene defect is the primary cause, where the adaptive response of the entire network determines the severity of disease. The latter may differ between individuals carrying the same mutation. Understanding the adaptive responses of human metabolism naturally requires a systems biology approach. Modelling of metabolic pathways in micro-organisms and some mammalian tissues has yielded many insights, qualitative as well as quantitative, into their control and regulation. Yet, even for a well-known pathway such as glycolysis, precise predictions of metabolite dynamics from experimentally determined enzyme kinetics have been only moderately successful. In the present review, we compare kinetic models of glycolysis in three cell types (African trypanosomes, yeast and skeletal muscle), evaluate their predictive power and identify limitations in our understanding. Although each of these models has its own merits and shortcomings, they also share common features. For example, in each case independently measured enzyme kinetic parameters were used as input. Based on these 'lessons from glycolysis', we will discuss how to make best use of kinetic computer models to advance our understanding of human metabolic diseases.

  9. Experimental and Kinetic Modeling Study of C2H2Oxidation at High Pressure

    Lopez, Jorge Gimenez; Rasmussen, Christian Tihic; Hashemi, Hamid


    A detailed chemical kinetic model for oxidation of acetylene at intermediate temperatures and high pressure has been developed and evaluated experimentally. The rate coefficients for the reactions of C2H2 with HO2 and O2 were investigated, based on the recent analysis of the potential energy...

  10. Testing of kinetic models: usefulness of the multiresponse approach as applied to chlorophyll degradation in foods

    Boekel, van M.A.J.S.


    Cascades of reactions, in which several reactants and products take part, frequently occur in foods. This work shows that kinetic modelling of such reactions having parameters in common is much more powerful when using a multiresponse rather than a uniresponse approach (i.e. analysing more than one

  11. Kinetic model of biodiesel production using immobilized lipase Candida antarctica lipase B

    Fedosov, Sergey; Brask, Jesper; Pedersen, Anders K.


    We have designed a kinetic model of biodiesel production using Novozym 435 (Nz435) with immobilized Candida antarctica lipase B (CALB) as a catalyst. The scheme assumed reversibility of all reaction steps and imitated phase effects by introducing various molecular species of water and methanol...

  12. Toward a Kinetic Model for Acrylamide Formation in a Glucose-Asparagine Reaction System

    Knol, J.J.; Loon, W.A.M.; Linssen, J.P.H.; Ruck, A.L.; Boekel, van M.A.J.S.


    A kinetic model for the formation of acrylamide in a glucose-asparagine reaction system is pro-posed. Equimolar solutions (0.2 M) of glucose and asparagine were heated at different tempera-tures (120-200 C) at pH 6.8. Besides the reactants, acrylamide, fructose, and melanoidins were quantified after

  13. A kinetic model of the electron-beam-pumped XeCl laser active medium

    Boichenko, A.M.; Derzhiev, V.I.; Zhidkov, A.G.; Iakovlenko, S.I. (Institut Obshchei Fiziki, Moscow (USSR))


    Kinetic models are developed for XeCl laser active media in different buffer gases (helium, neon, and argon) pumped by an electron beam. In the calculations of the generation characteristics, allowance is made for the effect of the cavity field on the photoinduced transitions. The numerical results on the efficiency are in good agreement with experiments on electron beams. 17 refs.

  14. Magnetohydrodynamic Model for Plasma Instabilities in the Ion-Kinetic Regime

    Kuvshinov, B. N.


    A magnetized plasma is considered. It is shown that the MHD model provides an adequate description of plasma instabilities in the ion-kinetic regime, where the characteristic scales of the plasma motion fall below the ion Larmor radius. This conclusion is the consequence of the fact that the well kn

  15. Relationship between in situ degradation kinetics and in vitro gas production fermentation using different mathematical models

    Rodrigues, M.A.M.; Cone, J.W.; Ferreira, L.M.M.; Blok, M.C.; Guedes, C.


    In vitro and in situ studies were conducted to evaluate the influence of different mathematical models, used to fit gas production profiles of 15 feedstuffs, on estimates of nylon bag organic matter (OM) degradation kinetics. The gas production data were fitted to Exponential, Logistic, Gompertz and

  16. The modeling of carbon isotope kinetics and its application to the evaluation of natural gas

    Xianqing LI; Xianming XIAO; Yongchun TANG; Hui TIAN; Qiang ZHOU; Yunfeng YANG; Peng DONG; Yan WANG; Zhihong SONG


    The modeling of carbon isotope kinetics of natural gas is an issue driving pioneering research in the oil and gas geochemistry in China and internationally.Combined with the sedimentary burial history and basin geothermal history,the modeling of carbon isotope kinetics provides a new and effective means for the determination of the origin and accumulation history of natural gas pools.In this paper,we introduce the modeling of carbon isotope kinetics of natural gas formation and its applications to the assessment of natural gas maturity,the determination of the gas source,the history of gas accumulation,and the oil-gas ratio.It is shown that this approach is of great value for these applications.The carbon isotopic characteristics of natural gas are not only affected by the gas source and maturity of the source rock,but also are related to the accumulation condition and geothermal gradient in a basin.There are obvious differences in the characteristics of carbon isotope ratios between instantaneous gas and cumulative gas.Different basins have different kinetic models of carbon isotope fractionation,which depends on the gas source condition,the accumulation history and the sedimentary-tectonic history.Since the origin of natural gas in the superimposed basin in China is very complicated,and the natural gas pool is characterized by multiphase and variable gas-sources,this paper may provide a new perspective on the study and evaluation of natural gas.

  17. Comparison of Parameter Estimation Methods in Stochastic Chemical Kinetic Models: Examples in Systems Biology.

    Gupta, Ankur; Rawlings, James B


    Stochastic chemical kinetics has become a staple for mechanistically modeling various phenomena in systems biology. These models, even more so than their deterministic counterparts, pose a challenging problem in the estimation of kinetic parameters from experimental data. As a result of the inherent randomness involved in stochastic chemical kinetic models, the estimation methods tend to be statistical in nature. Three classes of estimation methods are implemented and compared in this paper. The first is the exact method, which uses the continuous-time Markov chain representation of stochastic chemical kinetics and is tractable only for a very restricted class of problems. The next class of methods is based on Markov chain Monte Carlo (MCMC) techniques. The third method, termed conditional density importance sampling (CDIS), is a new method introduced in this paper. The use of these methods is demonstrated on two examples taken from systems biology, one of which is a new model of single-cell viral infection. The applicability, strengths and weaknesses of the three classes of estimation methods are discussed. Using simulated data for the two examples, some guidelines are provided on experimental design to obtain more information from a limited number of measurements.

  18. Evaluation of the Kinetic Energy Approach for Modeling Turbulent Fluxes in Stratocumulus

    Lenderink, G.; Holtslag, A.A.M.


    The modeling of vertical mixing by a turbulence scheme on the basis of prognostic turbulent kinetic energy (E) and a diagnostic length scale (l ) is investigated with particular emphasis on the representation of entrainment. The behavior of this E–l scheme is evaluated for a stratocumulus case obser

  19. Kinetic model of II-VI(001) semiconductor surfaces : Growth rates in atomic layer epitaxy

    Volkmann, T; Ahr, M; Biehl, M


    We present a zinc-blende lattice gas model of II-VI(001) surfaces, which is investigated by means of kinetic Monte Carlo simulations. Anisotropic effective interactions between surface metal atoms allow for the description of, e.g., the sublimation of CdTe(001), including the reconstruction of Cd-te

  20. Impact of contamination with long-lived radionuclides on PET kinetics modelling in multitracer studies

    Jødal, Lars; Hansen, Søren Baarsgaard; Jensen, Svend B


    Introduction: An important issue in multitracer studies is the separation of signals from the different radiotracers. This is especially the case when an early tracer has a long physical half-life and kinetic modelling has to be performed, because the early tracer can confer a long-lived contamin...

  1. Kinetics modeling of delta-ferrite formation and retainment during casting of supermartensitic stainless steel

    Nießen, Frank; Tiedje, Niels Skat; Hald, John


    -ferrite originates from the incomplete transformation to austenite. The kinetics model predicted the measured amount of δ-ferrite and the partitioning of Cr and Ni reasonably well. Further, it showed that slower cooling for the investigated alloy leads to less retained δ-ferrite, which is in excellent agreement...

  2. Assessment of the kinetic-frictional model for dense granular flow

    Boon Ho Ng; Yulong Ding; Mojtaba Ghadiri


    This paper aims to quantitatively assess the application of kinetic-frictional model to simulate the motion of dry granular materials in dense condition, in particular, the annular shearing in Couette configuration. The weight of frictional stress was varied to study the contribution of the frictional stress in dense granular flows. The results show that the pure kinetic-theory-based computational fluid dynamics (CFD) model (without frictional stress) over-predicts the dominant solids motion of dense granular flow while adding frictional stress [Schaeffer, D. G. (1987). Instability in the evolution equations describing incompressible granular flow. Journal of Differential Equations, 66(1), 19-50] with the solids pressure of [Lun, C. KTK., Savage, S. B., Jeffrey, D. J., & Chepurniy, N. (1984). Kinetic theories for granular flow: Inelastic particles in Couette flow and slightly inelastic particles in a general flow field. Journal of Fluid Mechanics, 140, 223-256] in the CFD model improves the simulation to better conform available experimental results. The results also suggest that frictional stress transmission plays an important role in dense granular flow and should not be neglected in granular flow simulations. Compatible simulation results to the experimental data are seen by increasing the weight of frictional stress to a factor of 1.25-1.5. These improved simulation results suggest the current constitutive relations (kinetic-frictional model) need to be improved in order to better reflect the real dense granular flow.

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

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


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

  4. Modelling and simulation of a transketolase mediated reaction: Sensitivity analysis of kinetic parameters

    Sayar, N.A.; Chen, B.H.; Lye, G.J.


    In this paper we have used a proposed mathematical model, describing the carbon-carbon bond format ion reaction between beta-hydroxypyruvate and glycolaldehyde to synthesise L-erythrulose, catalysed by the enzyme transketolase, for the analysis of the sensitivity of the process to its kinetic par....... (C) 2009 Elsevier B.V. All rights reserved....

  5. Preliminary model and validation of molten carbonate fuel cell kinetics under sulphur poisoning

    Audasso, E.; Nam, S.; Arato, E.; Bosio, B.


    MCFC represents an effective technology to deal with CO2 capture and relative applications. If used for these purposes, due to the working conditions and the possible feeding, MCFC must cope with a different number of poisoning gases such as sulphur compounds. In literature, different works deal with the development of kinetic models to describe MCFC performance to help both industrial applications and laboratory simulations. However, in literature attempts to realize a proper model able to consider the effects of poisoning compounds are scarce. The first aim of the present work is to provide a semi-empirical kinetic formulation capable to take into account the effects that sulphur compounds (in particular SO2) have on the MCFC performance. The second aim is to provide a practical example of how to effectively include the poisoning effects in kinetic models to simulate fuel cells performances. To test the reliability of the proposed approach, the obtained formulation is implemented in the kinetic core of the SIMFC (SIMulation of Fuel Cells) code, an MCFC 3D model realized by the Process Engineering Research Team (PERT) of the University of Genova. Validation is performed through data collected at the Korea Institute of Science and Technology in Seoul.

  6. Model for reaction kinetics in pyrolysis of wood

    Ahuja, P.; Singh, P.C.; Upadhyay, S.N.; Kumar, S. [Banaras Hindu Univ., Varanasi (India)


    A reaction model for the pyrolysis of small and large particles of wood Is developed. The chemical reactions that take place when biomass is pyrolyzed are the devolatilization reactions (primary) and due to the vapour-solid interactions (secondary). In the case of small particles, when the volatiles are immediately removed by the purge gas, only primary reactions occur and the reaction model is described by weight loss and char forming reactions. The of heterogeneous secondary reactions occur in the case of large particles due to the interaction between the volatiles and the hot nascent primary char. A chain reaction mechanism of secondary char formation is proposed. The model takes both the volatiles retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. 7 refs., 3 figs., 2 tabs.

  7. Model for reaction kinetics in pyrolysis of wood

    Ahuja, P.; Singh, P.C.; Upadhyay, S.N.; Kuma, S. [Banaras Hindu Univ., Varanasi (India)


    A reaction model for the pyrolysis of small and large particles of wood is developed. The chemical reactions that take place when biomass is pyrolyzed are the devolatilization reactions (primary) and due to the vapour-solid interactions (secondary). In the case of small particles, when the volatiles are immediately removed by the purge gas, only primary reactions occur and the reaction model is described by weight loss and char forming reactions. The heterogeneous secondary reactions occur in the case of large particles due to the interaction between the volatiles and the hot nascent primary char. A chain reaction mechanism of secondary char formation is proposed. The model takes both the volatiles retention time and cracking and repolymerization reactions of the vapours with the decomposing solid as well as autocatalysis into consideration. 6 refs., 3 figs., 2 tabs.

  8. The development from kinetic coefficients of a predictive model for the growth of Eichhomia crassipes in the field. I. Generating kinetic coefficients for the model in greenhouse culture

    C. F. Musil


    Full Text Available The kinetics of N- and P- limited growth of Eichhornia crassipes (Mart . Solms were investigated in greenhouse culture with the object of developing a model for predicting population sizes, yields, growth rates and frequencies and amounts of harvest, under varying conditions of nutrient loading and climate, to control both nutrient inputs and excessive growth in eutrophied aquatic systems. The kinetic coefficients, maximum specific growth rate (Umax, half saturation coefficient (Ks and yield coefficient (Yc were measured under N and P limitation in replicated batch culture experiments. Umax values and Ks concentrations derived under N limitation ranged from 5,37 to 8,86% d + and from 400 to 1 506 µg  N ℓ1respectively. Those derived under P limitation ranged from 4,51 to 10,89% d 1 and from 41 to 162 fig P ℓ1 respectively. Yc values (fresh mass basis determined ranged from 1 660 to 1 981 (87 to 98 dry mass basis for N and from 16 431 to 18 671 (867 to 980 dry mass basis for P. The reciprocals of Yc values (dry mass basis, expressed as percentages, adequately estimated the minimum limiting concentrations of N and P {% dry mass in the plant tissues. Kinetic coefficients determined are compared with those reported for algae. The experimental method used and results obtained are critically assessed.

  9. A kinetic model for the burst phase of processive cellulases

    Præstgaard, Eigil; Olsen, Jens Elmerdahl; Murphy, Leigh;


    of the model, which can be solved analytically, shows that the burst and slowdown can be explained by the relative rates of the sequential reactions in the hydrolysis process and the occurrence of obstacles for the processive movement along the cellulose strand. More specifically, the maximum enzyme activity...... reflects a balance between a rapid processive movement, on the one hand, and a slow release of enzyme which is stalled by obstacles, on the other. This model only partially accounts for the experimental data, and we therefore also test a modified version that takes into account random enzyme inactivation...

  10. Effect of substrate competition in kinetic models of metabolic networks.

    Schäuble, Sascha; Stavrum, Anne Kristin; Puntervoll, Pål; Schuster, Stefan; Heiland, Ines


    Substrate competition can be found in many types of biological processes, ranging from gene expression to signal transduction and metabolic pathways. Although several experimental and in silico studies have shown the impact of substrate competition on these processes, it is still often neglected, especially in modelling approaches. Using toy models that exemplify different metabolic pathway scenarios, we show that substrate competition can influence the dynamics and the steady state concentrations of a metabolic pathway. We have additionally derived rate laws for substrate competition in reversible reactions and summarise existing rate laws for substrate competition in irreversible reactions.

  11. Improving the kinetics from molecular simulations using biased Markov state models

    Rudzinski, Joseph F.; Kremer, Kurt; Bereau, Tristan

    Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and experimentally-measured observables. This work presents a robust and systematic framework for reweighting the ensemble of dynamical paths sampled in a molecular simulation in order to ensure consistency with a set of given kinetic observables. The method employs the well-developed Markov state modeling framework in order to efficiently treat simulated dynamical paths. We demonstrate that, for two distinct coarse-grained peptide models, biasing the Markov state model to reproduce a small number of reference kinetic constraints significantly improves the dynamical properties of the model, while simultaneously refining the static equilibrium properties.

  12. Kinetic Model of Fixed Bed Reactor with Immobilized Microorganisms for Removing Low-Concentration SO2


    On the basis of the analysis of the process of treating low concentrations of sulfur dioxide (SO2) gas in a fixed bed reactor, a kinetic model is proposed for this process after taking into consideration the effects of internal diffusion, cell concentration, and production yield of microorganisms but ignoring the effect of external diffusion. The results obtained from the model simulation show that this model can indicate the influence of the process factors, Cin, η, μmax, Cx, A, h, Km, and Q, on the removal of SO2 and that the prediction of the results by this model is also satisfactory. This kinetic model can also provide some very important indications regarding the preparation of immobilized microorganisms, selection and domestication of proper species of microorganisms, as well as the design of bioreactors.

  13. A spatial kinetic model for simulating VVER-1000 start-up transient

    Kashi, Samira [Department of Nuclear Engineering, Shahid Beheshti University, Tehran (Iran, Islamic Republic of); Moghaddam, Nader Maleki, E-mail: [Department of Nuclear Engineering and Physics, Amir Kabir University of Technology, Tehran (Iran, Islamic Republic of); Shahriari, Majid [Department of Nuclear Engineering, Shahid Beheshti University, Tehran (Iran, Islamic Republic of)


    Research highlights: > A spatial kinetic model of a VVER-1000 reactor core is presented. > The reactor power is tracked using the point kinetic equations from 100 W to 612 kW. > The lamped parameter approximation is used for solving the energy balance equations. > The value of reactivity related to feedback effects of core elements is calculated. > The main neutronic parameters during the transient are calculated. - Abstract: An accurate prediction of reactor core behavior in transients depends on how much it could be possible to exactly determine the thermal feedbacks of the core elements such as fuel, clad and coolant. In short time transients, results of these feedbacks directly affect the reactor power and determine the reactor response. Such transients are commonly happened during the start-up process which makes it necessary to carefully evaluate the detail of process. Hence this research evaluates a short time transient occurring during the start up of VVER-1000 reactor. The reactor power was tracked using the point kinetic equations from HZP state (100 W) to 612 kW. Final power (612 kW) was achieved by withdrawing control rods and resultant excess reactivity was set into dynamic equations to calculate the reactor power. Since reactivity is the most important part in the point kinetic equations, using a Lumped Parameter (LP) approximation, energy balance equations were solved in different zones of the core. After determining temperature and total reactivity related to feedbacks in each time step, the exact value of reactivity is obtained and is inserted into point kinetic equations. In reactor core each zone has a specific temperature and its corresponding thermal feedback. To decrease the effects of point kinetic approximations, these partial feedbacks in different zones are superposed to show an accurate model of reactor core dynamics. In this manner the reactor point kinetic can be extended to the whole reactor core which means 'Reactor spatial

  14. Nonlinear kinetic modeling and simulations of Raman scattering in a two-dimensional geometry

    Bénisti Didier


    Full Text Available In this paper, we present our nonlinear kinetic modeling of stimulated Raman scattering (SRS by the means of envelope equations, whose coefficients have been derived using a mixture of perturbative and adiabatic calculations. First examples of the numerical resolution of these envelope equations in a two-dimensional homogeneous plasma are given, and the results are compared against those of particle-in-cell (PIC simulations. These preliminary comparisons are encouraging since our envelope code provides threshold intensities consistent with those of PIC simulations while requiring computational resources reduced by 4 to 5 orders of magnitude compared to full-kinetic codes.

  15. Kinetic Modeling of Food Quality: A Critical Review

    Boekel, van T.


    ABSTRACT: This article discusses the possibilities to study relevant quality aspects of food, such as color, nutrient content, and safety, in a quantitative way via mathematical models. These quality parameters are governed by chemical, biochemical, microbial, and physical changes. It is argued that

  16. Kinetic study and modeling of biosurfactant production using Bacillus sp.

    Hesty Heryani


    Conclusions: For further development and industrial applications, the modified Gompertz equation is proposed to predict the cell mass and biosurfactant production as a goodness of fit was obtained with this model. The modified Gompertz equation was also extended to enable the excellent prediction of the surface tension.

  17. Temperature in warm inflation in non minimal kinetic coupling model

    Goodarzi, Parviz


    Warm inflation in the non minimal derivative coupling model with a general dissipation coefficient is considered. We investigate conditions for the existence of the slow roll approximation and study cosmological perturbations. The spectral index, and the power spectrum are calculated and the temperature of the universe at the end of the slow roll warm inflation is obtained.

  18. Catalytic conversion of lignin pyrolysis model compound- guaiacol and its kinetic model including coke formation

    Zhang, Huiyan; Wang, Yun; Shao, Shanshan; Xiao, Rui


    Lignin is the most difficult to be converted and most easy coking component in biomass catalytic pyrolysis to high-value liquid fuels and chemicals. Catalytic conversion of guaiacol as a lignin model compound was conducted in a fixed-bed reactor over ZSM-5 to investigate its conversion and coking behaviors. The effects of temperature, weight hourly space velocity (WHSV) and partial pressure on product distribution were studied. The results show the maximum aromatic carbon yield of 28.55% was obtained at temperature of 650 °C, WHSV of 8 h‑1 and partial pressure of 2.38 kPa, while the coke carbon yield was 19.55%. The reaction pathway was speculated to be removing methoxy group to form phenols with further aromatization to form aromatics. The amount of coke increased with increasing reaction time. The surface area and acidity of catalysts declined as coke formed on the acid sites and blocked the pore channels, which led to the decrease of aromatic yields. Finally, a kinetic model of guaiacol catalytic conversion considering coke deposition was built based on the above reaction pathway to properly predict product distribution. The experimental and model predicting data agreed well. The correlation coefficient of all equations were all higher than 0.90.

  19. A feasible kinetic model for the hydrogen oxidation on ruthenium electrodes

    Rau, M.S.; Gennero de Chialvo, M.R. [Programa de Electroquimica Aplicada e Ingenieria Electroquimica (PRELINE), Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe (Argentina); Chialvo, A.C., E-mail: [Programa de Electroquimica Aplicada e Ingenieria Electroquimica (PRELINE), Facultad de Ingenieria Quimica, Universidad Nacional del Litoral, Santiago del Estero 2829, 3000 Santa Fe (Argentina)


    The hydrogen oxidation reaction (hor) was studied on a polycrystalline ruthenium electrode in H{sub 2}SO{sub 4} solution at different rotation rates ({omega}). The experimental polarization curves recorded on steady state show the existence of a maximum current with a non-linear dependence of the current density on {omega}{sup 1/2}. On the basis of the Tafel-Heyrovsky-Volmer kinetic mechanism, coupled with a process of inhibition of active sites by the reversible electroadsorption of hydroxyl species, it was possible to appropriately describe the origin of the maximum current. The corresponding set of kinetic parameters was also calculated from the correlation of the experimental results with the proposed kinetic model.

  20. A Minimal Model for Large-scale Epitaxial Growth Kinetics of Graphene

    Jiang, Huijun


    Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be $C_{1}$-attachment for concave growth front segments and $C_{5}$-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment.

  1. Kinetic modelling of the demineralization of shrimp exoskeleton using citric acid

    Alewo Opuada AMEH


    Full Text Available Citric acid was used in the demineralization of shrimp exoskeleton and the kinetics of the demineralization process was studied. Kinetic data was obtained by demineralisation using five acid concentrations (0.1, 0.2, 0.3, 0.4 and 0.5M. The obtained kinetic data were fitted to the shrinking core model for fluid particle reactions. The concentration of calcium was found to decrease with time. For all acid concentrations considered, the best predictive mechanism for the demineralization process was determined to be Ash Layer Diffusion Control Mechanism. This was indicated by the high R2 values obtained (0.965 with 150% excess of citric acid.

  2. The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria

    Serdenko, T. V.; Barabash, Y. M.; Knox, P. P.; Seifullina, N. Kh.


    The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one—to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism.

  3. New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.

    Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda


    Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms.

  4. A kinetic compartment model for evaluating salivary gland scintigraphies

    Afzelius, Pia; Fuglsang, Stefan


    through a syringe. Time activity curves were generated for each of the four major salivary glands (i.e. the right and left submandibular and right and left parotid glands). Excretion fractions (the fraction of mobilizable radioactivity after administering lemon juice) and the gland activity......-to-thyroid activity ratio were calculated. The data were fitted to both a one- and two-phase uptake model. RESULTS: The median uptake slope and maximal activity were significantly higher in the parotid glands than the submandibular glands (Pparotid glands than...... the submandibular glands (Pparotid glands (Pparotid and submandibular glands. CONCLUSIONS: Tracer accumulation can be represented by a one-phase simple uptake model. The background regions...

  5. A U-shaped bioartificial pancreas with rapid glucose-insulin kinetics. In vitro evaluation and kinetic modelling.

    Reach, G; Jaffrin, M Y; Desjeux, J F


    crossing the membranes. We present herein the kinetic modelling of glucose and insulin transfer in this "ultrafiltration chamber," whose functional characteristics are compatible with closed-loop insulin delivery.

  6. Production of furfural from palm oil empty fruit bunches: kinetic model comparation

    Panjaitan, J. R. H.; Monica, S.; Gozan, M.


    Furfural is a chemical compound that can be applied to pharmaceuticals, cosmetics, resins and cleaning compound which can be produced by acid hydrolysis of biomass. Indonesia’s demand for furfural in 2010 reached 790 tons that still imported mostly 72% from China. In this study, reaction kinetic models of furfural production from oil palm empty fruit bunches with submitting acid catalyst at the beginning of the experiment will be determine. Kinetic data will be obtained from hydrolysis of empty oil palm bunches using sulfuric acid catalyst 3% at temperature 170°C, 180°C and 190°C for 20 minutes. From this study, the kinetic model to describe the production of furfural is the kinetic model where generally hydrolysis reaction with an acid catalyst in hemicellulose and furfural will produce the same decomposition product which is formic acid with different reaction pathways. The activation energy obtained for the formation of furfural, the formation of decomposition products from furfural and the formation of decomposition products from hemicellulose is 8.240 kJ/mol, 19.912 kJ/mol and -39.267 kJ / mol.

  7. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB

    Ahsan Munir


    Full Text Available Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs. Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131.

  8. Effects of three heavy metals on the bacteria growth kinetics. A bivariate model for toxicological assessment

    Rial, Diego; Vazquez, Jose Antonio; Murado, Miguel Anxo [Instituto de Investigacions Marinas (CSIC), Vigo (ES). Grupo de Reciclado y Valorizacion de Materiales Residuales (REVAL)


    The effects of three heavy metals (Co, Ni and Cd) on the growth kinetics of five bacterial strains with different characteristics (Pseudomonas sp., Phaeobacter sp. strain 27-4, Listonella anguillarum, Carnobacterium piscicola and Leuconostoc mesenteroides subsp. lysis) were studied in a batch system. A bivariate model, function of time and dose, is proposed to describe simultaneously all the kinetic profiles obtained by incubating a microorganism at increasing concentrations of individual metals. This model combines the logistic equation for describing growth, with a modification of the cumulative Weibull's function for describing the dose-dependent variations of growth parameters. The comprehensive model thus obtained - which minimizes the effects of the experimental error - was statistically significant in all the studied cases, and it raises doubts about toxicological evaluations that are based on a single growth parameter, especially if it is not obtained from a kinetic equation. In lactic acid bacteria cultures (C. piscicola and L. mesenteroides), Cd induced remarkable differences in yield and time course of characteristic metabolites. A global parameter is defined (ED{sub 50,{tau}}: dose of toxic chemical that reduces the biomass of a culture by 50% compared to that produced by the control at the time corresponding to its semi maximum biomass) that allows comparing toxic effects on growth kinetics using a single value. (orig.)

  9. Kinetic characterization of the sole nonmuscle myosin-2 from the model organism Drosophila melanogaster.

    Heissler, Sarah M; Chinthalapudi, Krishna; Sellers, James R


    Nonmuscle myosin-2 is the primary enzyme complex powering contractility of the F-actin cytoskeleton in the model organism Drosophila. Despite myosin's essential function in fly development and homeostasis, its kinetic features remain elusive. The purpose of this in vitro study is a detailed steady-state and presteady-state kinetic characterization of the Drosophila nonmuscle myosin-2 motor domain. Kinetic features are a slow steady-state ATPase activity, high affinities for F-actin and ADP, and a low duty ratio. Comparative analysis of the overall enzymatic signatures across the nonmuscle myosin-2 complement from model organisms indicates that the Drosophila protein resembles nonmuscle myosin-2s from metazoa rather than protozoa, though modulatory aspects of myosin motor function are distinct. Drosophila nonmuscle myosin-2 is uniquely insensitive toward blebbistatin, a commonly used myosin-2 inhibitor. An in silico modeling approach together with kinetic studies indicate that the nonconsensus amino acid Met466 in the Drosophila nonmuscle myosin-2 active-site loop switch-2 acts as blebbistatin desensitizer. Introduction of the M466I mutation sensitized the protein for blebbistatin, resulting in a half-maximal inhibitory concentration of 36.3 ± 4.1 µM. Together, these data show that Drosophila nonmuscle myosin-2 is a bona fide molecular motor and establish an important link between switch-2 and blebbistatin sensitivity.

  10. Reaction kinetics and modeling of photoinitiated cationic polymerization of an alicyclic based diglycidyl ether

    Harikrishna, R., E-mail: [Polymer Science and Engineering Division, National Chemical Laboratory, Pune 411008 (India); Ponrathnam, S. [Polymer Science and Engineering Division, National Chemical Laboratory, Pune 411008 (India); Tambe, S.S. [Chemical Engineering and Process Development Division, National Chemical Laboratory, Pune 411008 (India)


    Highlights: • Photocationic polymerization of alicyclic based diglycidyl ether was carried out. • Kinetic parameters were influenced by gelation and diffusional restrictions. • Applicability of autocatalytic model was established by nonlinear regression. • System showed higher activation energy than cycloaliphatic and aromatic diepoxides. -- Abstract: Photoinitiated cationic polymerization of cycloaliphatic diepoxides had received tremendous attention, while studies with lesser polymerizable diglycidyl ethers are comparatively less reported. The present work deals with the photoinitiated cationic polymerization of cyclohexane dimethanol diglycidyl ether followed by estimation of kinetic parameters. The effects of concentration of photoinitiator and temperature on curing performance were studied using photo differential scanning calorimeter or photo DSC with polychromatic radiation. It was observed that the rate of polymerization as well as ultimate conversion increased with increasing concentration of photoinitiator and temperature. The influences of gelation as well as diffusional restrictions have remarkable effect on cure performance. The kinetic parameters as per autocatalytic kinetic model were studied by Levenberg–Marquardt nonlinear regression method instead of conventional linear method for obtaining more accurate values of apparent rate constant. It was observed that the model fits with data from initial stages to almost towards the end of the reaction. The activation energy was found to be higher than the values reported for more reactive cycloaliphatic diepoxides. The value of pre-exponential factor increased with increase in activation energy showing influence of gelation at early stages of reaction.

  11. Quantitative nucleation and growth kinetics of gold nanoparticles via model-assisted dynamic spectroscopic approach.

    Zhou, Yao; Wang, Huixuan; Lin, Wenshuang; Lin, Liqin; Gao, Yixian; Yang, Feng; Du, Mingming; Fang, Weiping; Huang, Jiale; Sun, Daohua; Li, Qingbiao


    Lacking of quantitative experimental data and/or kinetic models that could mathematically depict the redox chemistry and the crystallization issue, bottom-to-up formation kinetics of gold nanoparticles (GNPs) remains a challenge. We measured the dynamic regime of GNPs synthesized by l-ascorbic acid (representing a chemical approach) and/or foliar aqueous extract (a biogenic approach) via in situ spectroscopic characterization and established a redox-crystallization model which allows quantitative and separate parameterization of the nucleation and growth processes. The main results were simplified as the following aspects: (I) an efficient approach, i.e., the dynamic in situ spectroscopic characterization assisted with the redox-crystallization model, was established for quantitative analysis of the overall formation kinetics of GNPs in solution; (II) formation of GNPs by the chemical and the biogenic approaches experienced a slow nucleation stage followed by a growth stage which behaved as a mixed-order reaction, and different from the chemical approach, the biogenic method involved heterogeneous nucleation; (III) also, biosynthesis of flaky GNPs was a kinetic-controlled process favored by relatively slow redox chemistry; and (IV) though GNPs formation consists of two aspects, namely the redox chemistry and the crystallization issue, the latter was the rate-determining event that controls the dynamic regime of the whole physicochemical process.

  12. Modeling the homogenization kinetics of as-cast U-10wt% Mo alloys

    Xu, Zhijie; Joshi, Vineet; Hu, Shenyang; Paxton, Dean; Lavender, Curt; Burkes, Douglas


    Low-enriched U-22at% Mo (U-10Mo) alloy has been considered as an alternative material to replace the highly enriched fuels in research reactors. For the U-10Mo to work effectively and replace the existing fuel material, a thorough understanding of the microstructure development from as-cast to the final formed structure is required. The as-cast microstructure typically resembles an inhomogeneous microstructure with regions containing molybdenum-rich and -lean regions, which may affect the processing and possibly the in-reactor performance. This as-cast structure must be homogenized by thermal treatment to produce a uniform Mo distribution. The development of a modeling capability will improve the understanding of the effect of initial microstructures on the Mo homogenization kinetics. In the current work, we investigated the effect of as-cast microstructure on the homogenization kinetics. The kinetics of the homogenization was modeled based on a rigorous algorithm that relates the line scan data of Mo concentration to the gray scale in energy dispersive spectroscopy images, which was used to generate a reconstructed Mo concentration map. The map was then used as realistic microstructure input for physics-based homogenization models, where the entire homogenization kinetics can be simulated and validated against the available experiment data at different homogenization times and temperatures.

  13. Chemical kinetic modeling of a methane opposed flow diffusion flame and comparison to experiments

    Marinov, N.M., Pitz, W.J.; Westbrook, C.K. [Lawrence Livermore National Lab., CA (United States); Vincitore, A.M.; Senka, S.M. [Univ. of California, Los Angeles, CA (United States); Lutz, A.E. [Sandia National Labs., Livermore, CA (United States)


    The chemical structure of an opposed flow, methane diffusion flame is studied using a chemical kinetic model and the results are compared to experimental measurements. The chemical kinetic paths leading to aromatics and polycyclic aromatics hydrocarbons (PAHs) in the diffusion flame are identified. These paths all involve resonantly stabilized radicals which include propargyl, allyl, cyclopentadienyl, and benzyl radicals. The modeling results show reasonable agreement with the experimental measurements for the large hydrocarbon aliphatic compounds, aromatics, and PAHs. the benzene was predicted to be formed primarily by the reaction sequence of Allyl plus Propargyl equals Fulvene plus H plus H followed by fulvene isomerization to benzene. Naphthalene was modeled using the reaction of benzyl with propargyl, while the combination of cyclopentadienyl radicals were shown to be a minor contributor in the diffusion flame. The agreement between the model and experiment for the four-ring PAHs was poor.

  14. Network inference using asynchronously updated kinetic Ising Model

    Zeng, Hong-Li; Alava, Mikko; Mahmoudi, Hamed


    Network structures are reconstructed from dynamical data by respectively naive mean field (nMF) and Thouless-Anderson-Palmer (TAP) approximations. For TAP approximation, we use two methods to reconstruct the network: a) iteration method; b) casting the inference formula to a set of cubic equations and solving it directly. We investigate inference of the asymmetric Sherrington- Kirkpatrick (S-K) model using asynchronous update. The solutions of the sets cubic equation depend of temperature T in the S-K model, and a critical temperature Tc is found around 2.1. For T Tc there are three real roots. The iteration method is convergent only if the cubic equations have three real solutions. The two methods give same results when the iteration method is convergent. Compared to nMF, TAP is somewhat better at low temperatures, but approaches the same performance as temperature increase. Both methods behave better for longer data length, but for improvement arises, TAP is well pronounced.

  15. Modeling and kinetic characterization of wastewater disinfection using chlorine and UV irradiation.

    Mounaouer, Brahmi; Abdennaceur, Hassen


    Sewage disinfection has the primary objective of inactivating pathogenic organisms to prevent the dissemination of waterborne diseases. This study analyzed individual disinfection, with chlorine alone, ultraviolet radiation alone, and a combined disinfection process (chlorine-UV radiation). Pseudomonas aeruginosa ATCC 15442, Escherichia coli ATCC 11229, Salmonella typhi ATCC 14028, and Clostridium perfringens were selected to evaluate the efficiency of different disinfection processes. The aim of the present study was to characterize the kinetics of chlorine (as NaHOCl) consumption, to evaluate responses of these bacterial species to the chlorination, the ultraviolet (UV) radiation, and the chlorine/UV disinfection processes in secondary wastewater using a batch laboratory reactor. Another target of this work was to study the modeling of the kinetic of water disinfection by chlorination and/or UV irradiation. Two kinetic models (Chick-Watson and Hom) were tested as to ability to scale disinfection of these bacterial species by different ultraviolet and/or chlorine doses. The results of the kinetics of chlorine consumption showed that monochloramines and trichloramines were the most important forms of residual chlorine as compared to free chlorine and dichloramines. The kinetics of inactivation of all examined bacterial strains showed that the application of the model of Hom in its original form was not representative of this kinetics of inactivation. Modification of this model, considering an initial decline of bacteria during the contact of water with chlorine, improved the results of the model. By the same, results revealed that the involved processes of UV irradiation were too complex to be approached by a simplified formulation, even in the case of specific strains of microorganisms and the use of nearly constant UV radiation intensity. In fact, the results have pointed out that the application of the Chick-Watson law is known to be inadequate to describe

  16. A Study of the Optimal Model of the Flotation Kinetics of Copper Slag from Copper Mine BOR

    Stanojlović, Rodoljub D.; Sokolović, Jovica M.


    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.

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

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


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

  18. Two-site kinetic modeling of bacteriophages transport through columns of saturated dune sand.

    Schijven, Jack F; Hassanizadeh, S Majid; de Bruin, Ria H A M


    Breakthrough curves, on a semi-log scale, from tests in porous media with block-input of viruses, bacteria, protozoa and colloidal particles often exhibit a typical skewness: a rather slowly rising limb and a smooth transition of a declining limb to a very long tail. One-site kinetic models fail to fit the rising and declining limbs together with the tail satisfactorily. Inclusion of an equilibrium adsorption site does not seem to improve simulation results. This was encountered in the simulation of breakthrough curves from a recent field study on the removal of bacteriophages MS2 and PRD1 by passage through dune sand. In the present study, results of laboratory experiments for the study of this issue are presented. Breakthrough curves of salt and bacteriophages MS2, PRDI, and phiX174 in 1 D column experiments have been measured. One- and two-site kinetic models have been applied to fit and predict breakthrough curves from column experiments. The two-site model fitted all breakthrough curves very satisfactorily, accounting for the skewness of the rising limb as well as for the smooth transition of the declining limb to the tail of the breakthrough curve. The one-site model does not follow the curvature of the breakthrough tail, leading to an overestimation of the inactivation rate coefficient for attached viruses. Interaction with kinetic site 1 is characterized by relatively fast attachment and slow detachment, whereas attachment to and detachment from kinetic site 2 is fast. Inactivation of viruses and interaction with kinetic site 2 provide only a minor contribution to removal. Virus removal is mainly determined by the attachment to site 1. Bacteriophage phiX174 attached more than MS2 and PRD1, which can be explained by the greater electrostatic repulsion that MS2 and PRD1 experience compared to the less negatively charged phiX174.

  19. Collective learning modeling based on the kinetic theory of active particles

    Burini, D.; De Lillo, S.; Gibelli, L.


    This paper proposes a systems approach to the theory of perception and learning in populations composed of many living entities. Starting from a phenomenological description of these processes, a mathematical structure is derived which is deemed to incorporate their complexity features. The modeling is based on a generalization of kinetic theory methods where interactions are described by theoretical tools of game theory. As an application, the proposed approach is used to model the learning processes that take place in a classroom.

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

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


    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.