Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Kinetic modeling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12Linked to original sources

A kinetic model for binding protein-mediated arabinose transport.

A kinetic model is presented based on the simplest plausible mechanism for bacterial binding protein-dependent transport. The transport phenotypes of the 18 variant arabinose-binding proteins analyzed by Kehres and Hogg (1992, Protein Sci. 1, 1652-1660) (wild type and 17 mutants) are interpreted to mean that in wild-type arabinose uptake the forward transport rate (k(for)) greatly exceeds the dissociation rate (kund) of a binding protein docked with the AraG:AraH membrane complex, and that k(for) dominance is preserved in all of the binding protein surface mutants. The assumptions and predictions of the model are consistent with existing data from other periplasmic transport systems.

Arabinose↗

[A diffusion kinetics model of the growth of a cancerous tumor].

Diffusion kinetics model of development of solid tumor has been proposed. This model allows qualitative description of a number of experimental effects, e.g. formation of necrosis zones, change of exponential growth to linear one. Critical parameters for transfer from tumor stabilization mode to its growth have been obtained. Methods of calculation have been elaborated and model calculations have been carried out.

Animals↗

A kinetic model of human thyroid hormones and their conversion products.

We have examined the in vivo distribution and metabolism of radiolabeled T4 and T3 in 14 normal subjects using a kinetic model. Tracer amounts of [131I]T4 and [125I]T3 were injected simultaneously, and plasma samples were obtained for up to 7 days thereafter. Separation of these samples by thin layer chromatography yielded kinetic curves for 131I- and 125I-labeled T4, T3, iodide, and iodoprotein, which were then used to develop a kinetic model. The model includes several features. 1) Submodels were developed for T4, T3, iodide, and iodoprotein which simultaneously fit the observed data. 2) Two other submodels were needed for data fit, the first representing rT3, the other representing other intermediates, including the various diiodothyronines. The latter submodel was patterned initially after 3,3'-diiodothyronine kinetics. It was required to account for the delay in appearance of labeled iodide produced from the degradation of T4, and rT3 and proved to be essential for the successful fit of the data. 3) The model accounts for the conversion of T4 to T3 and rT3. Even though rT3 is quantitatively significant as a degradation pathway for T4, its presence does not contribute significantly to total plasma radioactivity after T4 administration because of its rapid turnover in comparison with T4. 4) The small amount of iodoprotein formed is a major contributor to total plasma radioactivity within 3 days after T3 administration. 5) The model permits the elimination of two methodological errors: that due to the presence of labeled iodide, T3, or T4 contaminants in the administered labeled hormones, and that due to the small amount of cross-over between thin layer chromatography peaks. The model provides a concise description of our current understanding of thyroid hormone metabolism and suggests areas where further information is required.

Adult↗

Estimating glucose metabolism using glucose analogs and two tracer kinetic models in isolated rabbit heart.

The purpose of this investigation was to 1) evaluate the relative accuracy of the Sokoloff and Patlak tracer kinetic models in estimating glucose metabolic rate (GMR) in the presence and absence of insulin; 2) evaluate the effect of nutritional state on the lumped constant (LC); and 3) compare the kinetics of 2-fluoro-2-deoxy-D-[14C]glucose (FDG) and 2-deoxy-D-[3H]glucose (DG) membrane transport and phosphorylation. The experimental preparation was the isolated, red blood cell-albumin-perfused rabbit heart. Our results showed that both tracer kinetic models provided GMR estimates that correlated well with the Fick method (for FDG, R = 0. 84 and 0.91 for the Sokoloff and Patlak models, respectively); nutritional state did not affect the LC; and FDG and DG have different transport and/or phosphorylation parameters. We also observed that 1) the addition of a fourth compartment to the Sokoloff model reduced the mean squared error between measured and modeled data by a factor of 7.4; 2) a longer time (21.8 min) was required to obtain a linear phase of the Patlak plot than is allowed in clinical studies; and 3) accurate GMR estimates were obtained only by using different LCs reflecting insulin's presence or absence. Our results indicate potential sources of error in the use of FDG and positron emission tomography to quantify GMR in patients.

Animals↗

Kinetic modeling of the polymer-derived ceramics route: investigation of the thermal decomposition kinetics of poly[B-(methylamino)borazine] precursors into boron nitride.

A complete kinetic modeling of the polymer-derived ceramics (PDCs) route is achieved for the first time through the investigation of the solid-state decomposition of a typical melt-spinnable poly[B-(methylamino)borazine] into boron nitride fibers at various heating rates. Through the use of the Lorentz fitting approach, it is shown that the two-step weight loss associated with the polymer-to-ceramic conversion is governed by a complex interplay of five diffusion-type transport mechanisms that are independent of the applied heating schedule. The application of the Friedman method to dynamic thermogravimetry data yields Ea and ln A values that are seen to increase with the extent of the ceramic conversion from region one (Ea = 38.73 kJ mol(-1)) to region five (Ea = 146.64 kJ mol(-1)). This fact indicates that both the mechanisms within those regions are parallel routes to the formation of the final solid-state material and their complexity increases with the conversion progress. The cross-linking process (first weight loss) of the polymer is governed by three dependent poorly energetic mechanisms. The first weight loss is activated by ammonolysis reactions that provide a modified polymer capable of undergoing condensation reactions in regions two and three to yield a highly cross-linked polymer. A large evolution of methylamine is identified during this process. Mineralization (region four) and ceramization (region five) steps are represented by two highly energetic multistep mechanisms. The mineralization step is associated with a large evolution of methylamine and occurs during the transition between the cross-linking and ceramization processes through the cleavage of the inter-ring B-N bonds. Ceramization represents the end of the polymer-to-ceramic conversion in which the planar consolidation of BN hexagons occurs through complex structural rearrangements of the borazine units (cleavage of the intraring B-N bonds) accompanied with an ammonia evolution. Finally, the simulation of the polymer-to-ceramic conversion was demonstrated through a simplified model that appropriately predicted experimental data.

Journal Article↗

The kinetic model and simulation of blood coagulation--the kinetic influence of activated protein C.

The paper described a limited part of the coagulation pathway, and in particular the inhibitory effects of activated protein C in the context of thrombin production. This is a computational modeling study with various assumption made of kinetic rates laws and their summation. The level of complexity and assumed parameters makes conclusions uncertain. However, an interesting outcome is that kinetic reaction rates may show oscillation behavior under particular, high levels of protein C feedback inhibition. The model would defy quantitative practical use, but could have predictive value as a qualitative descriptor of coagulation.

Biological Clocks↗

Construction of kinetic models to understand metabolism in vivo.

This review describes increasingly complex kinetic models that simulate carbohydrate metabolism in a simple eucaryotic system which undergoes differentiation. Dynamic models of complex metabolic networks serve to organize and analyze the many interdependent variables involves and to define the rate-limiting events controlling metabolism in vivo. Since the ultimate justification for and test of any model are its predictive values, a series of predictions and related experiments will be described.

Carbohydrate Metabolism↗

Best method for estimating urea volume of distribution: comparison of single pool variable volume kinetic modeling measurements with bioimpedance and anthropometric methods.

The urea volume of distribution (Vurea) is a key component of the Kt/V parameter calculated during urea kinetic modeling. The Vurea parameter has been approximated empirically using total body water (TBW) estimates derived from anthropometric formulas or measured by bioelectric impedance analysis (BIA). The author compared TBW values derived using various anthropometric formulas (Watson, Hume, Randall, Tzamaloukas, Chertow) and BIA to the Vurea parameter calculated using three point variable volume single pool urea kinetic modeling. A total of 127 chronic hemodialysis patients were studied (mean age 66 +/- 13 years; 42% female; 37% black; 47% diabetic). Agreement between anthropometric formulas, BIA, and Vurea values was assessed by linear regression and Bland Altman analyses. The closest correlations were obtained with the BIA (r = 0.972), Chertow (r = 0.917), and Tzamaloukas (r = 0.905) methods. When compared with Vurea, 95% confidence intervals by Bland Altman analysis were lowest with BIA (4L) and highest with the Watson method (8L). These results indicate that BIA best approximates Vurea in dialysis patients.

Aged↗

Optimization of sodium removal in paired filtration dialysis by single pool sodium and conductivity kinetic models.

Sodium removal is one of the main factors affecting intradialytic cardiovascular stability and interdialytic hypertension, and its removal should therefore be individualized. The aims of this study were: (1) to test the ability of a single-pool variable volume (SPVV) sodium kinetic model (NaKM) to optimize sodium removal in paired filtration dialysis (PFD), and (2) to test a SPVV conductivity kinetic model (CKM) in order to verify whether CKM can be used as an alternative for NaKM in estimating sodium balance. The mean difference between the NaKM-predicted and measured end-PFD plasma water ionized sodium concentrations was 0.00 +/- 0.55 mEq/l, which means that the model has an imprecision of < or = 1.1 mEq/ l. The mean difference between predicted and measured sodium removal was 0.21 +/- 16.86 mEq/session, which means a model overestimate of 0.21 mEq/session. The mean difference between the CKM-predicted and measured end-PFD ultrafiltrate conductivity was 0.01 +/- 0.05 mS/cm, which means an inaccuracy of the model of 0.01 mS/cm and an imprecision of < or = 0.1 mS/cm. The regression in the ionized sodium concentration measured in plasma or blood on the conductive values of the ultrafiltrate shows an error of < or = 2 mEq/l in the prediction of the ionized sodium concentration in blood by means of ultrafiltrate conductivity measurements. These results demonstrate that both models make it possible to obtain a level of dialytic sodium removal that is almost equivalent to interdialytic sodium loading. Moreover, given that it does not require blood sampling and the possibility of making repeated and inexpensive ultrafiltrate conductivity measurements, the CKM allows online monitoring of programmed sodium removal.

Convection↗

Investigations of different kinetic models for zinc ions uptake by a natural zeolitic tuff.

The kinetics of uptake of zinc ions from aqueous solutions by natural zeolitic tuff has been investigated. Batch experiments at constant temperature and hydrodynamic conditions have been performed. A decrease in the initial zinc concentration in aqueous solutions prolongs the time needed for equilibrium. Various kinetic models including the film-diffusion model, the surface diffusion model and the heterogeneous diffusion model have been tested for the description of the experimental results of zinc concentration in the solution over time. Diffusion through the film and diffusion through the surface of the particle could be the rate limiting steps at the initial reaction time. However, the heterogeneous diffusion model seems to be the best model providing a satisfactory fitting of the experimental results from the beginning of the process to the point of equilibrium, particularly at lower initial zinc concentrations.

Kinetics↗

Kinetic modelling of Amadori N-(1-deoxy-D-fructos-1-yl)-glycine degradation pathways. Part II--kinetic analysis.

A kinetic model for N-(1-deoxy-D-fructos-1-yl)-glycine (DFG) thermal decomposition was proposed. Two temperatures (100 and 120 degrees C) and two pHs (5.5 and 6.8) were studied. The measured responses were DFG, 3-deoxyosone, 1-deoxyosone, methylglyoxal, acetic acid, formic acid, glucose, fructose, mannose and melanoidins. For each system the model parameters, the rate constants, were estimated by non-linear regression, via multiresponse modelling. The determinant criterion was used as the statistical fit criterion. Model discrimination was performed by both chemical insight and statistical tests (Posterior Probability and Akaike criterion). Kinetic analysis showed that at lower pH DFG 1,2-enolization is favoured whereas with increasing pH 2,3-enolization becomes a more relevant degradation pathway. The lower amount observed of 1-DG is related with its high reactivity. It was shown that acetic acid, a main degradation product from DFG, was mainly formed through 1-DG degradation. Also from the estimated parameters 3-DG was found to be the main precursor in carbohydrate fragments formation, responsible for colour formation. Some indication was given that as the reaction proceeded other compounds besides DFG become reactants themselves with the formation among others of methylglyoxal. The multiresponse kinetic analysis was shown to be both helpful in deriving relevant kinetic parameters as well as in obtaining insight into the reaction mechanism.

Acetic Acid↗

A kinetic model of cooperativity in aspartate transcarbamylase.

A relatively simple kinetic model is proposed to account simultaneously for data on the binding of carbamyl phosphate and succinate to aspartate trans carbamylase (ATCase), and for the relaxation spectrum associated with this binding. The model also accounts for measurements of the initial velocity of the reaction of ATCase with respect to aspartate and carbamyl phosphate. The principal assumption made is that ATCase consists of three identical noninteracting cooperative dimers. Ordered binding and both sequential and concerted conformational changes in the dimers are needed to account for the properties of ATCase. The values of the parameters of this model can be determined by fitting to existing experimental evidence. Various new quantitative predictions are made that can serve as additional tests of the proposed theory.

Adenosine Triphosphate↗

Development and validation of a kinetic model for enzymatic saccharification of lignocellulosic biomass.

A multireaction kinetic model was developed for closed-system enzymatic hydrolysis of lignocellulosic biomass such as corn stover. Three hydrolysis reactions were modeled, two heterogeneous reactions for cellulose breakdown to cellobiose and glucose and one homogeneous reaction for hydrolyzing cellobiose to glucose. Cellulase adsorption onto pretreated lignocellulose was modeled via a Langmuir-type isotherm. The sugar products of cellulose hydrolysis, cellobiose and glucose, as well as xylose, the dominant sugar prevalent in most hemicellulose hydrolyzates, were assumed to competitively inhibit the enzymatic hydrolysis reactions. Model parameters were estimated from experimental data generated using dilute acid pretreated corn stover as the substrate. The model performed well in predicting cellulose hydrolysis trends at experimental conditions both inside and outside the design space used for parameter estimation and can be used for in silico process optimization.

Carbohydrates↗

Second-order kinetic model for the sorption of cadmium onto tree fern: a comparison of linear and non-linear methods.

A comparison was made of the linear least-squares method and a trial-and-error non-linear method of the widely used pseudo-second-order kinetic model for the sorption of cadmium onto ground-up tree fern. Four pseudo-second-order kinetic linear equations are discussed. Kinetic parameters obtained from the four kinetic linear equations using the linear method differed but they were the same when using the non-linear method. A type 1 pseudo-second-order linear kinetic model has the highest coefficient of determination. Results show that the non-linear method may be a better way to obtain the desired parameters.

Absorption↗

Kinetic modeling of the radiolytic degradation of Acid Orange 7 in aqueous solutions.

The degradation of Acid Orange 7 (AO7) in aqueous solutions induced by gamma-ray irradiation was investigated in terms of both the disappearance of parent molecule (decoloration) and the degree of mineralization. The disappearance of AO7 followed pseudo first-order kinetics, whereas its mineralization could be described by zero-order kinetics. The pseudo first-order degradation rate constants were found to be proportional to irradiation dose rates and the reciprocals of initial AO7 concentrations. Based on the experimental results and a reaction analysis on the steady-state radiolysis of aerated aqueous solutions, a kinetic model was developed for describing the radiolytic degradation of AO7. Moreover, with this kinetic model, the reaction rate constants of e(aq)(-) and H. with AO7 were estimated as 3.0 x 10(9) and 8.4 x 10(9) x L mol(-1) s(-1), respectively. Taking the relative contributions of oxidative and reductive species to AO7 degradation into account, oxidative radiolysis proved to be a better approach for the degradation of AO7.

Azo Compounds↗

A kinetic model of phosphofructokinase from Plasmodium berghei. Influence of ATP and fructose-6-phosphate.

Phosphofructokinase (PFK) from the malarial parasite Plasmodium berghei shows the following kinetic features: the more the pH is decreased, the more the enzyme is inhibited by ATP; in contrast to PFK from erythrocytes, this inhibition is less potent by two orders of magnitude; as in the red cell, fructose-6-phosphate (F6P) is a positive effector. Kinetic modelling of PFK from P. berghei has been performed by taking the pH-dependence of activity into regard, implicitly by the estimation of pH-dependent kinetic parameters for the inhibition by ATP and the activation by F6P and explicitly by the assumption of protonation-steps involved in allosteric regulation. By means of a novel procedure of model discrimination [D. Buckwitz and H.-G. Holzhütter: A new method to discriminate between enzyme-kinetic models. In: Application of Computational Methods in Medicine (Györi, I., ed.), Akademai, Budapest, in press] we have selected among several kinetic models the best rate equation which provides an adequate quantitative description of the kinetic behaviour of the enzyme in the relevant ranges of substrate concentrations and pH (5.8-7.6). It thus becomes clear how the highly increased glycolytic flux in malaria-infected cells could be affected through PFK.

Adenosine Triphosphate↗

Kinetic models suggest bimolecular reaction steps in axonal Na+-channel gating.

Abstract kinetic models that can successfully simulate the ion-permeability features of axonal Na+ channels suggest the presence of bimolecular reaction steps in the activation of the channels. A chemically plausible interpretation of minimum complexity is described. The implied chemical formalism is highly suggestive of an activator-controlled gating system with strong similarities to the acetylcholine-regulated system. Conformational changes that underlie the ion-conductance changes are suggested to possess a greater sensitivity to the membrane field in axonal parts of excitable membranes than at synaptic parts. This would allow axonal permeability changes to be energetically regulated more conservatively than is observed for synaptic ion channels. Axonal K+ channels with delayed activation kinetics would serve to reverse the increase in membrane permeability to Na+ with a minimum of chemical dissipation.

Axons↗

Kinetic studies of Heck coupling reactions using palladacycle catalysts: experimental and kinetic modeling of the role of dimer species.

Experimental kinetic studies of the coupling of p-bromobenzaldehyde (1) with butyl acrylate (2) using the dimeric palladacycles complex (4) with chelating nitrogen ligands were carried out together with kinetic modeling using a reaction rate expression based on the mechanism shown in Scheme 2. The oxidative addition product of 1 was found to be the resting state within the catalytic cycle. The formation of dimeric Pd species external to the catalytic cycle helped to rationalize a non-first-order rate dependence on catalyst concentration. Theoretical modeling showed how the relative concentrations of the different intermediate species within the catalystic cycle can influence the observed rate dependence on Pd concentration. It was shown how conventional kinetic studies may give reaction orders in substrates which differ from those which would be observed under practical synthetic conditions. Comparison between phosphine- and nonphosphine-based palladacycles suggests that they follow the same reaction mechanism. The role of water in accelerating the initial formation of the active catalyst species is noted.

Journal Article↗