Kinetic Modeling Approach Research Articles

Computational models of the JAK1/2-STAT1 signaling

Despite a conceptually simple mechanism of signaling, the JAK-STAT pathway exhibits considerable behavioral complexity. Computational pathway models are tools to investigate in detail signaling process. They integrate well with experimental studies, helping to explain molecular dynamics and to state new hypotheses, most often about the structure of interactions.A relatively small amount of experimental data is available for a JAK1/2-STAT1 variant of the pathway, hence, only several computational models were developed. Here we review a dominant approach of kinetic modeling of the JAK1/2-STAT1 pathway, based on ordinary differential equations. We also give a brief overview of attempts to computationally infer topology of this pathway.

Bimodality in the firm size distributions: a kinetic exchange model approach

Firm growth process in the developing economies is known to produce divergence in their growth path giving rise to bimodality in the size distribution. Similar bimodality has been observed in wealth distribution as well. Here, we introduce a modified kinetic exchange model which can reproduce such features. In particular, we will show numerically that a nonlinear retention rate (or savings propensity) causes this bimodality. This model can accommodate binary trading as well as the whole system-side trading thus making it more suitable to explain the non-standard features of wealth distribution as well as firm size distribution.

Electron attachment to CF3 and CF3Br at temperatures up to 890 K: Experimental test of the kinetic modeling approach

Thermal rate constants and product branching fractions for electron attachment to CF3Br and the CF3 radical have been measured over the temperature range 300-890 K, the upper limit being restricted by thermal decomposition of CF3Br. Both measurements were made in Flowing Afterglow Langmuir Probe apparatuses; the CF3Br measurement was made using standard techniques, and the CF3 measurement using the Variable Electron and Neutral Density Attachment Mass Spectrometry technique. Attachment to CF3Br proceeds exclusively by the dissociative channel yielding Br(-), with a rate constant increasing from 1.1 × 10(-8) cm(3) s(-1) at 300 K to 5.3 × 10(-8) cm(3) s(-1) at 890 K, somewhat lower than previous data at temperatures up to 777 K. CF3 attachment proceeds through competition between associative attachment yielding CF3 (-) and dissociative attachment yielding F(-). Prior data up to 600 K showed the rate constant monotonically increasing, with the partial rate constant of the dissociative channel following Arrhenius behavior; however, extrapolation of the data using a recently proposed kinetic modeling approach predicted the rate constant to turn over at higher temperatures, despite being only ~5% of the collision rate. The current data agree well with the previous kinetic modeling extrapolation, providing a demonstration of the predictive capabilities of the approach.

A General Approach for Kinetic Modeling of Solid-Gas Reactions at Reactor Scale: Application to Kaolinite Dehydroxylation

Understanding the industrial reactors behavior is a difficult task in the case of solid state reactions such as solid-gas reactions. Indeed the solid phase is a granular medium through which circulate gaseous reactants and products. The properties of such a medium are modified in space and time due to reactions occurring at a microscopic scale. The thermodynamic conditions are driven not only by the operating conditions but also by the heat and mass transfers in the reactor. We propose to numerically resolve the thermohydraulic equations combined with kinetic laws which describe the heterogeneous reactions. The major advantage of this approach is due to the large variety of kinetic models of grains transformation (~40) compared to the usual approach, especially in the case of surface nucleation and growth processes which need to quantitatively describe the grain conversion kinetics at a microscopic scale due to nucleation frequency and growth rate laws obtained in separate isothermal and isobaric experiments. The heat and mass transfers terms entering in the balance equations at a macroscopic scale depend on the kinetics evaluated at the microscopic scale. These equations give the temperature and partial pressure in the reactor, which in turn influence the microscopic kinetic behavior.

IR Spectroscopy Analysis and Kinetic Modeling Study for NH3 Adsorption and Desorption on H- and Fe-BEA Catalysts

Among different types of Fe-exchanged zeolites, Fe-BEA exhibits very promising surface properties for developing efficient urea or NH3-SCR systems. In this work, dedicated experimental and kinetic modeling studies were performed in order to elucidate mechanistic aspects related to NH3 storage and release on these catalysts. A series of NH3 adsorption and desorption experiments were performed over both H- and Fe-exchanged BEA zeolites, taking into account a broad range of operating conditions. Coupling FTIR spectroscopy, surface NH3 adspecies were characterized. NH3 gaseous concentration profiles were subsequently simulated by means of a detailed multisite kinetic model, being able to account for low-temperature adsorption phenomena. Finally, correlations between surface acidity and model sites were enabled by comparing IR spectroscopy and model predicted results, leading to the development of a phenomenological semidetailed, multisite kinetic modeling approach.

A generalized kinetic model for the formation and growth of single-walled metal oxide nanotubes

We demonstrate a generalized kinetic modeling and experimental approach to describe the formation and growth of single-walled metal oxide nanotubes. These materials can now be synthesized using solution-based methods at temperatures as low as 95°C. Ultimately, it is desired to produce nanotubes on a larger scale (e.g., kilogram or ton) for technological applications. However, a quantitative multiscale understanding of nanotube growth, via a detailed growth model, is critical in order to predict and control key properties such as the length distribution and concentration of the nanotubes. Such a model can then be used to design liquid-phase reactors for scale-up of nanotube synthesis. The present model considers three types of species present in the synthesis solution: molecular precursors, amorphous nanoparticles, and nanotubes. The nucleation of a nanotube embryo is due to the rearrangement of an amorphous nanoparticle into an ordered tubular structure, as revealed by recent works. The nanotube growth model is represented by up to 800 population-balance differential equations. Parameterization, validation, and predictive evaluation of the model is carried out via detailed statistical TEM measurements of nanotube length distributions throughout the synthesis. This model is capable of explaining and predicting the evolution of nanotube populations as a function of kinetic parameters. It also allows insight into mesoscale and microscale nanotube growth processes. For example, it shows that two different mechanisms operate during nanotube growth: (1) growth by precursor addition, and (2) oriented attachment of nanotubes to each other.

Electron attachment to fluorocarbon radicals

Thermal electron attachment rate constants for a series of small fluorocarbon radicals (CF(2), C(2)F(3), 1-C(3)F(7), 2-C(3)F(7), C(3)F(5), CF(3)O) were measured from 300 to 600 K using the variable electron and neutral density attachment mass spectrometry method. With the exception of CF(2), for which no attachment was observed, all species exclusively underwent dissociative attachment to yield F(-). The magnitude and temperature dependences of the rate constants varied significantly between species; however, attachment was in all cases inefficient, never exceeding 2% of the calculated collisional value. The data are interpreted and extrapolated to conditions inaccessible to the experiment using a kinetic modeling approach to the electron attachment process.

Mapping Human Brain Fatty Acid Amide Hydrolase Activity with PET

Endocannabinoid tone has recently been implicated in a number of prevalent neuropsychiatric conditions. [(11)C]CURB is the first available positron emission tomography (PET) radiotracer for imaging fatty acid amide hydrolase (FAAH), the enzyme which metabolizes the prominent endocannabinoid anandamide. Here, we sought to determine the most suitable kinetic modeling approach for quantifying [(11)C]CURB that binds selectively to FAAH. Six healthy volunteers were scanned with arterial blood sampling for 90 minutes. Kinetic parameters were estimated regionally using a one-tissue compartment model (TCM), a 2-TCM with and without irreversible trapping, and an irreversible 3-TCM. The 2-TCM with irreversible trapping provided the best identifiability of PET outcome measures among the approaches studied (coefficient of variation (COV) of the net influx constant K(i) and the composite parameter λk(3) (λ=K(1)/k(2)) <5%, and COV(k(3))<10%). Reducing scan time to 60 minutes did not compromise the identifiability of rate constants. Arterial spin labeling measures of regional cerebral blood flow were only slightly correlated with K(i), but not with k(3) or λk(3). Our data suggest that λk(3) is sensitive to changes in FAAH activity, therefore, optimal for PET quantification of FAAH activities with [(11)C]CURB. Simulations showed that [(11)C]CURB binding in healthy subjects is far from a flow-limited uptake.

Electron attachment to 14 halogenated alkenes and alkanes, 300-600 K

Thermal electron attachment to 14 alkenes and alkanes with bromine, fluorine, and iodine substituents has been studied over the temperature range 300-600 K using a flowing-afterglow Langmuir-probe apparatus. Rate coefficients and anion products are reported, most for the first time. Among these were 3 isomers of C(3)F(5)Br and the 2 isomers of C(3)F(7)I. Four dibromide compounds were studied, all of which yield Br(2)(-) product in addition to Br(-) product. The results are analyzed using a statistical kinetic modeling approach, which is able to reproduce both attachment rate coefficients and product branching ratios within experimental uncertainty. The kinetic modeling indicates that factor of 2 differences in attachment rate coefficients to the isomeric species can be explained by subtle variations in the potential surfaces.

Electron Attachment to Fe(CO)n (n = 0–5)

The rate constants of thermal electron attachment at 300 and 400 K to Fe(CO)(n) (n = 0-5) have been measured using a flowing afterglow Langmuir probe apparatus. The stable species Fe(CO)(5) was studied using the traditional method of monitoring electron depletion as a function of reaction time, and the remaining short-lived species were studied using the variable electron and neutral density attachment mass spectrometry (VENDAMS) technique. Attachment to Fe(CO)(5) is purely dissociative and about 20% efficient with a rate constant of (7.9 ± 1.4) × 10(-8) cm(3) s(-1) at 300 K and (8.8 ± 2) × 10(-8) cm(3) s(-1) at 400 K. The attachment rate constants decrease significantly as each CO ligand is removed, with Fe(CO)(n) (n = 4 to 1) attaching with efficiencies on the order of 10%, 1%, 0.1%, and 0.01% respectively. Under the conditions here, attachment to Fe(CO)(4) and Fe(CO)(3) are likely entirely dissociative, whereas attachment to Fe(CO)(2) and Fe(CO) are almost entirely associative. A statistical kinetic modeling approach is used to explain the strong dependence of the attachment rate constant on the number of ligands present in the neutral species through a combination of increasing autodetachment rates and decreasing exothermicities to dissociative attachment. The VENDAMS data also define the 300 K mutual neutralization rate constant of Fe(CO)(4)(-) + Ar(+) to be (5.0 ± 0.8) × 10(-8) cm(3) s(-1) with an upper limit to branching fraction of 0.5 to yield Fe(CO)(4), indicating that significant fragmentation to smaller Fe(CO)(n) occurs.

Kinetic modeling of enzymatic hydrolysis of pretreated kitchen wastes for enhancing bioethanol production

It is well known that use of low cost and abundant waste materials in microbial fermentations can reduce product costs. Kitchen wastes disposed of in large amounts from cafeterias, restaurants, dining halls, food processing plants, and household kitchens contain high amounts of carbohydrate components such as glucose, starch, and cellulose. Efficient utilization of these sugars is another opportunity to reduce ethanol costs. In this study, the effect of pretreatment methods (hot water, acid solutions, and a control) on enzymatic hydrolysis of kitchen wastes was evaluated using a kinetic modeling approach. Fermentation experiments conducted with and without traditional fermentation nutrients were assessed at constant conditions of pH 4.5 and temperature of 30°C for 48h using commercial dry baker’s yeast, Saccharomyces cerevisiae. The control, which involved no treatment, and hot water treated samples gave close glucose concentrations after 6h. The highest and lowest rates of glucose production were found as 0.644 and 0.128 (h−1) for the control (or no-pretreated (NPT)) and 1% acid solutions, respectively. The fermentation results indicated that final ethanol concentrations are not significantly improved by adding nutrients (17.2–23.3g/L). Thus, it was concluded that product cost can be lowered to a large extent if (1) kitchen wastes are used as a substrate, (2) no fermentation nutrient is used, and (3) hydrolysis time is applied for about 6h. Further optimization study is needed to increase the yield to higher levels.

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

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

Kinetics of Cu(II) Reduction by Natural Organic Matter

The kinetics of Cu(II) reduction by Suwannee River fulvic acid (SRFA) at concentrations from 0.25 to 8 mg L(-1) have been investigated in 2 mM NaHCO(3) and 0.7 M NaCl at pH 8.0. In the absence of oxygen, SRFA reduced Cu(II) to Cu(I) in a biphasic manner, with initial rapid formation of Cu(I) followed by a much slower increase in Cu(I) concentration over time. When present, oxygen only had a noticeable effect on Cu(I) concentrations in the second phase of the reduction process and at high [SRFA]. In both the absence and presence of oxygen, the rate of Cu(I) generation increased with increasing [SRFA]. At 8 mg L(-1) [SRFA], nearly 75% of the 0.4 μM Cu(II) initially present was reduced to Cu(I) after 20 min, although the yield of Cu(I) relative to [SRFA] decreased at [SRFA] > 1 mg L(-1). Two plausible kinetic modeling approaches were found to satisfactorily describe the experimental data over a range of [SRFA]. Despite some uncertainty as to which approach is correct, common features of both approaches were complexation of Cu(II) by SRFA and reduction of Cu(II) by two different electron donor groups within SRFA: a relatively labile electron donor (with a concentration of 1.1 × 10(-4) equiv of e(-) (g of SRFA)(-1)) that reduced Cu(II) relatively rapidly and a less labile donor (with a concentration of 3.1 × 10(-4) equiv of e(-) (g of SRFA)(-1)) that reduced Cu(II) more slowly.

Integration of kinetic modeling and desirability function approach for multi-objective optimization of UASB reactor treating poultry manure wastewater

An integrated multi-objective optimization approach within the framework of nonlinear regression-based kinetic modeling and desirability function was proposed to optimize an up-flow anaerobic sludge blanket (UASB) reactor treating poultry manure wastewater (PMW). Chen–Hashimoto and modified Stover–Kincannon models were applied to the UASB reactor for determination of bio-kinetic coefficients. A new empirical formulation of volumetric organic loading rate was derived for the first time for PMW to estimate the dimensionless kinetic parameter (K) in the Chen–Hashimoto model. Maximum substrate utilization rate constant and saturation constant were predicted as 11.83gCOD/L/day and 13.02gCOD/L/day, respectively, for the modified Stover–Kincannon model. Based on four process-related variables, three objective functions including a detailed bio-economic model were derived and optimized by using a LOQO/AMPL algorithm, with a maximum overall desirability of 0.896. The proposed optimization scheme demonstrated a useful tool for the UASB reactor to optimize several responses simultaneously.

Role of Elongation and Secondary Pathways in S6 Amyloid Fibril Growth

The concerted action of a large number of individual molecular level events in the formation and growth of fibrillar protein structures creates a significant challenge for differentiating between the relative contributions of different self-assembly steps to the overall kinetics of this process. The characterization of the individual steps is, however, an important requirement for achieving a quantitative understanding of this general phenomenon which underlies many crucial functional and pathological pathways in living systems. In this study, we have applied a kinetic modeling approach to interpret experimental data obtained for the aggregation of a selection of site-directed mutants of the protein S6 from Thermus thermophilus. By studying a range of concentrations of both the seed structures, used to initiate the reaction, and of the soluble monomer, which is consumed during the growth reaction, we are able to separate unambiguously secondary pathways from primary nucleation and fibril elongation. In particular, our results show that the characteristic autocatalytic nature of the growth process originates from secondary processes rather than primary nucleation events, and enables us to derive a scaling law which relates the initial seed concentration to the onset of the growth phase.

Kinetic modelling of plant metabolic pathways

This paper provides a review of kinetic modelling of plant metabolic pathways as a tool for analysing their control and regulation. An overview of different modelling strategies is presented, starting with those approaches that only require a knowledge of the network stoichiometry; these are referred to as structural. Flux-balance analysis, metabolic flux analysis using isotope labelling, and elementary mode analysis are briefly mentioned as three representative examples. The main focus of this paper, however, is a discussion of kinetic modelling, which requires, in addition to the stoichiometry, a knowledge of the kinetic properties of the constituent pathway enzymes. The different types of kinetic modelling analysis, namely time-course simulation, steady-state analysis, and metabolic control analysis, are explained in some detail. An overview is presented of strategies for obtaining model parameters, as well as software tools available for simulation of such models. The kinetic modelling approach is exemplified with discussion of three models from the general plant physiology literature. With the aid of kinetic modelling it is possible to perform a control analysis of a plant metabolic system, to identify potential targets for biotechnological manipulation, as well as to ascertain the regulatory importance of different enzymes (including isoforms of the same enzyme) in a pathway. Finally, a framework is presented for extending metabolic models to the whole-plant scale by linking biochemical reactions with diffusion and advective flow through the phloem. Future challenges include explicit modelling of subcellular compartments, as well as the integration of kinetic models on the different levels of the cellular and organizational hierarchy.

A comparative kinetic study on ultra-deep hydrodesulfurization of pre-treated gas oil over nanosized MoS2, CoMo-sulfide, and commercial CoMo/Al2O3 catalysts

Unsupported nanosized MoS2 and CoMo-sulfide catalysts were synthesized, and their catalytic performances for the deep hydrodesulfurization (HDS) of treated gas oil were investigated as compared with that of a CoMo/Al2O3 catalyst. The HDS reactions were carried out in a batch autoclave reactor at 340°C and 3MPa H2. The CoMo-sulfide catalyst shows the highest activity and can reduce the sulfur content to less than 10ppm. The decrease in total sulfur content as a function of reaction time was found to follow pseudo-second order kinetics (empirical form). The change in the concentration of some individual representative sulfur-containing species in gas oil as a function of time was found to follow pseudo-first-order kinetics. However, the change in combined concentration of these species in the gas oil during HDS with the reaction time was found to corroborate pseudo-second-order kinetics. A kinetic model approach was proposed from which an estimation of the intrinsic kinetic data can be achieved. The model fitted the obtained data reasonably well, suggesting its potential for better assessment of the catalytic activity in the HDS of real feedstock. The study reveals that ranking of catalyst activities using model refractory sulfur-containing compounds does not necessarily imply a typical rank in case of investigating the real feedstocks.

Enzyme inactivation kinetics: Coupled effects of temperature and moisture content

Enzymes are often dried for stability reasons and to facilitate handling. However, they are often susceptible to inactivation during drying. It is generally known that temperature and moisture content influence the enzyme inactivation kinetics. However, the coupled effect of both variables on enzyme inactivation over a broad temperature–moisture content range is still not well understood. Therefore, the inactivation of β-galactosidase in maltodextrin matrix is investigated using a newly developed method. An improved kinetic modelling approach is introduced, to predict the inactivation over a large range of temperature–moisture values. The model assumes a two-step inactivation mechanism involving reversible unfolding and irreversible inactivation. The model is able to describe the inactivation kinetics of β-galactosidase accurately, showing the temperature-dependent kinetic transition from reversible unfolding to irreversible inactivation limited. Application of this approach can provide immediate understanding of the effect of processing on enzyme inactivation and indicates the processes’ critical points, which offers the possibility for optimisation.

Selective epoxidation of natural triglycerides using acidic ion exchange resin as catalyst

ABSTRACTEpoxidation is a very useful reaction in organic synthesis. Due to the high reactivity of the epoxide group it can be used as an active intermediate for the synthesis of many high‐value products. Epoxides are commercial products and they have many industrial uses. Understanding the kinetics of epoxidation reactions can lead to production of value‐added products from locally available renewable natural resources. This research investigated the kinetics of epoxidation of cottonseed oil by peroxyacetic acid (PAA) generated in situ from hydrogen peroxide and glacial acetic acid (AA) in the presence of acidic ion exchange resin (AIER) catalysts, namely Amberlite IR‐120. The effect of several variables including temperature, stirring speed, catalyst loading, and particle size, concentration of hydrogen peroxide and AA on oxirane conversion was studied. A satisfactory level of oxirane conversion (greater than 65%) with high selectivity (greater than 90%) could be obtained if the epoxidation was carried out at optimum conditions, using in situ generated PAA. The Langmuir–Hinshelwood–Hougen–Watson (L–H–H–W) kinetic model approach has been adopted for the development of overall reaction rate equations, and the proposed kinetic model includes the major side reactions for the estimation of kinetic parameters. Kinetic parameters were estimated by fitting experimental data using a nonlinear regression method. From the estimated kinetic constants, the activation energy for the AIER catalysed epoxidation of cottonseed oil was found to be 10.1 kcal mol−1. Copyright © 2010 Curtin University of Technology and John Wiley &amp; Sons, Ltd.

Effect of organic exudates of Phaeodactylum tricornutum on the Fe(II) oxidation rate constant

Fe(II) oxidation kinetics were studied in seawater and in seawater enriched with exudates excreted by Phaeodactylum tricornutum as an organic ligand model. The exudates produced after 2, 4, and 8 days of culture at 6.21 × 107, 2.29 × 108, and 4.98 × 108 cell L–1 were selected. The effects of pH (7.2–8.2), temperature (5–35 ºC), and salinity (10–36.72) on the Fe(II) oxidation rate were studied. All the data were compared with the results for seawater without exudates (control). The Fe(II) rate constant decreased as a function of culture time and cell concentration in the culture at different pH, temperature, and salinity. All the experimental data obtained in this study were fitted to a polynomial function in order to quantify the fractional contribution of the organic exudates from the diatoms to the Fe(II) oxidation rate in natural seawater. Experimental results showed that the organic exudates excreted by P. tricornutum affect Fe(II) oxidation, increasing the lifetime of Fe(II) in seawater. A kinetic model approach was carried out to account for the speciation of each Fe(II) type together with its contribution to the overall rate.