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PubMed2026

GENKI: A generative framework for scalable and robust metabolic kinetic modeling.

GENKI (Generative ENsemble KPI-Informed) is a variational autoencoder-based framework for large-scale kinetic modeling of metabolism. Developed for metabolic engineering applications, GENKI is designed to improve the recovery of kinetically feasible models that reproduce experimentally observed phenotypes under genetic and environmental perturbations. The framework is trained on feasible kinetic model ensembles and uses phenotype-based key performance indicators (KPIs), derived from multi-omics and bioprocess data, to label and enrich models according to their agreement with mutant and condition-specific observations. This enables targeted generation of biologically relevant parameter sets with improved predictive performance. Crucially, GENKI recovers kinetic parameter sets that jointly reproduce wild-type and multiple perturbed physiologies within a single model. We apply GENKI to large-scale kinetic models of Escherichia coli and Saccharomyces cerevisiae under enzyme perturbations and oxygen shifts. In both systems, GENKI enriches kinetic ensembles with models that more accurately reproduce experimentally observed physiologies across multiple perturbations and conditions. GENKI therefore provides a practical framework for perturbation-aware kinetic model refinement within iterative Design-Build-Test-Learn workflows.

DBTL↗
PubMed2001

Receptor measurements via Tc-GSA kinetic modeling are proportional to functional hepatocellular mass.

UNLABELLED: Kinetic modeling of 99mTc-diethylenetriaminepentaacetic acid galactosyl human serum albumin (Tc-GSA) measures the total amount of asialoglycoprotein receptor within a subject's liver. This study tested the hypothesis that the amount of asialoglycoprotein receptor measured by Tc-GSA modeling provides a valid index of functional liver mass. METHODS: Twenty-two patients with cirrhosis, 18 patients with chronic hepatitis, and 9 patients with normal liver parenchyma were studied with Tc-GSA using a 30-min dynamic imaging protocol. The total amount of hepatic receptor was measured by kinetic modeling of the Tc-GSA time-activity data. The total number of viable hepatocytes was calculated using standard morphometric measurements of liver biopsy samples and liver volume measurements through CT. RESULTS: The total receptor amount strongly correlated with the total hepatocyte number (r = 0.803; P < 0.0001). CONCLUSION: Tc-GSA measurement of the total receptor amount is proportional to the number of viable hepatocytes and therefore provides a valid assessment of functional liver mass.

Asialoglycoprotein Receptor↗
PubMed1999

A Kinetic Model of Protein Adsorption/Surface-Induced Transition Kinetics Evaluated by the Scaled Particle Theory.

The adsorption of proteins and other large molecules at the liquid-solid interface often involves a surface-induced transition in either internal conformation or molecular orientation. Recently, Van Tassel et al. modeled this adsorption/transition process as the sequential surface placement of spreading disks. In this work, we employ the scaled particle theory (SPT) to derive approximate analytical expressions for the probability functions appearing in the kinetic equations for this model system. Specifically, the probability functions governing the adsorption and spreading events are calculated in terms of the reversible work required to create cavities in a binary system of spread and unspread disks. Compared to those derived earlier via a density expansion theory (DET), the SPT approximated probability functions are simpler and more accurate (compared to simulation), and are applicable over a wider set of parameter values. Copyright 1999 Academic Press.

Journal Article↗
PubMed2005

[Microbial growth kinetics model of specific spoilage organisms and shelf life prediction for tilapia at fluctuating temperatures].

It was studied on the growth kinetics model of specific spoilage organisms Pseudomonas spp. for cultured tilapia during aerobic storage at fluctuating temperatures from 0degreesC to 15degreesC and the applicability of the model in predicting the remaining shelf life. The mathematical model based on the effect of temperature on Pseudomonas spp. growth kinetics was developed by a Belehradek type equation. Bias and accuracy factors range from 0.906 to 0.942 and from 1.13 to 1.19, respectively, by comparing predicted value using Pseudomonas spp. growth kinetics model with observed value of Pseudomonas spp. growth for cultured tilapia stored at fluctuating temperatures under two kinds of fluctuating temperature designed . Relative errors by comparing remaining shelf life predicted based on growth model of Pseudomonas spp. with remaining shelf life experimentally determined by analyzing organoleptic, VBN and the number of Pseudomonas spp. on tilapia are 5.9 % and - 9.1%, respectively. It shows that the growth kinetics model of Pseudomonas spp. is valuable for rapid and realistic remaining shelf life prediction of cultured tilapia stored aerobically at fluctuating temperatures from 0- 15 degrees C.

Animals↗
PubMed2006

Pharmacodynamics of moxifloxacin and levofloxacin against Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli: simulation of human plasma concentrations after intravenous dosage in an in vitro kinetic model.

OBJECTIVES: To compare in an in vitro kinetic model the pharmacodynamics of moxifloxacin and levofloxacin with a concentration-time profile simulating the human free non-protein bound concentrations of 400 mg moxifloxacin intravenous (iv) once daily, 500 mg levofloxacin iv once daily and 750 mg levofloxacin iv once daily against strains of Streptococcus pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli with variable susceptibility to fluoroquinolones. METHODS: The strains used in the study included S. pneumoniae ATCC 6306 (native strain), S. pneumoniae 19397 (double mutation; gyrA and parC), S. pneumoniae 4241 (single mutation; parC), S. aureus ATCC 13709 (native strain), S. aureus MB5 (single mutation; gyrA), E. coli M12 (single mutation; gyrA), E. coli ATCC 25922 (native strain) and K. pneumoniae ATCC 29655 (native strain). The strains were exposed to moxifloxacin and levofloxacin in an in vitro kinetic model simulating the free human serum concentration-time profile of moxifloxacin 400 mg once daily, levofloxacin 500 mg once daily and 750 mg once daily. Repeated samples were taken regularly during 24 h and viable counts were carried out. RESULTS AND CONCLUSIONS: A correlation was seen between both the area under the serum concentration curve and MIC (AUC/MIC) and the peak concentration/MIC (Cmax/MIC) versus area under the bactericidal killing curve (AUBKC) or Deltalog0-24 cfu/mL. Compiling all data, an AUC/MIC of approximately 100 and a Cmax/MIC of 10 gave a maximal bactericidal effect for both levofloxacin and moxifloxacin. In accordance with the results from others, our study indicated that a lower AUC/MIC was needed for S. pneumoniae in comparison with the Gram-negative bacteria studied. Moxifloxacin yielded higher AUC/MIC and Cmax/MIC against the investigated Gram-positive bacteria in comparison with levofloxacin 500 mg once daily and 750 mg once daily.

Animals↗
PubMed2004

The role of urea kinetic modeling in assessing the adequacy of dialysis.

The adequacy of dialysis based on urea kinetic modeling has more than 20 years of history. Its methodological approach has demonstrated a strong capacity to improve the outcomes of the dialysis therapy. However, recent results of clinical interventional studies and necessary advances in new models of dialysis schemes, particularly daily and nocturnal hemodialysis, have led to the question if whether that methodology is suitable to address current challenges. This work tries to reach an answer to that question. The major conclusion is that urea kinetic modeling provides an extraordinary starting point to both keeping the clinical support to physicians and building new pharmacokinetic and physiological models that throw light on the understanding of the basic mechanisms that underlie the chronic renal disease, in a synergetic manner. Despite this promising expectation, misuse and improper extensions of urea kinetic modeling may jeopardize its credibility to nephrologists. Our concern about this issue emerges mainly from the analysis of recent attempts to extend this methodology to more frequent renal replacement therapies.

Computer Simulation↗
PubMed1996

Clinical evaluation of a peritoneal dialysis kinetic modeling set.

A closed system kinetic modeling set (KMS) has been fabricated which permits collection of a small 100-mL aliquot from each exchange. The KMS was used to collect aliquots from 65 exchanges in 13 patients. The concentrations of urea nitrogen (UN), creatinine (Cr), glucose (G), and total protein (TP) were measured in each individual aliquot (Cka) and drain bag (Cba), and all aliquots for each dialysis treatment were used to calculate the concentrations expected in total batched dialysate (BaC) for the treatment and were compared to the measured concentrations (BaM) in mixed total dialysate. The ratios Cka/Cba [mean+/- two times coefficient of variation (mean +/- 2CV)] were 1.00 +/- 5%, 1.00 +/- 5%, 1.01 +/- 10%, and 1.00 +/- 6%, respectively, for UN, Cr, G, and TP (each, n = 61). The ratios BaC/BaM (mean +/- 2CV) were 1.00 +/- 2%, 1.00 +/- 5%, 1.01 +/- 3%, and 0.99 +/- 5%, respectively, for UN, Cr, G, and TP (each, n = 15). We concluded that the KMS aliquots can be reliably used for kinetic and total clearance calculations without mixing and transporting large volumes of dialysate.

Blood Glucose↗
PubMed2000

Kinetic modeling of lactose hydrolysis with an immobilized beta-galactosidase from Kluyveromyces fragilis.

The kinetic model of the hydrolysis of lactose with a beta-galactosidase from Kluyveromyces fragilis immobilized on a commercial silica-alumina (KA-3, from Südchemie) has been determined. A wide experimental range of the main variables has been employed: temperature, concentrations of substrate, and products and concentration of enzyme. The runs were performed in a complex buffer with the salt composition of milk. The effect of pH and temperature on the stability and the activity of the enzyme have been studied. The optimum pH for the enzyme activity was, approximately, seven. The immobilized enzyme was more stable than the free one at acidic pH, but more instable at basic pH. The maximum temperature used for the hydrolysis runs performed to select the kinetic model was 40 degrees C, so inactivation of the enzyme during the kinetic runs has been avoided. Agitation, concentration of enzyme in the solid and particle size were selected to ensure that the overall rate was that of the chemical reaction. Eleven kinetic models were proposed to fit experimental data, from first order to more complex ones, such as those taking into account inhibition by one of the compounds involved in the hydrolysis reaction. Applying statistical and physical criteria, a Michaelis-Menten model with a competitive inhibition by galactose has been selected. The model is able to fit the experimental data correctly in the wide experimental range studied. Finally, the model obtained is compared to the one selected in a previous work for the hydrolysis of lactose with the free enzyme.

Journal Article↗
PubMed2005

Sonochemical degradation of azo dyes in aqueous solution: a new heterogeneous kinetics model taking into account the local concentration of OH radicals and azo dyes.

The sonochemical decolorization and decomposition of azo dyes, such as C. I. Reactive Red 22 and methyl orange, were performed from the viewpoints of wastewater treatment and to determine the reaction kinetics. A low concentration of the azo dye solution was irradiated with a 200 kHz and 1.25 W/cm2 ultrasound in a homogeneous aqueous solution. The azo dye solutions were readily decolorized by the irradiation. The sonochemical decolorization was also depressed by the addition of the t-butyl alcohol radical scavenger. These results indicated that azo dye molecules were mainly decomposed by OH radicals formed from the water sonolysis. In this paper, we propose a new kinetics model taking into account the heterogeneous reaction kinetics similar to a Langmuir-Hinshelwood mechanism or an Eley-Rideal mechanism. The proposed kinetics model is based on the local reaction site at the interface region of the cavitation bubbles, where azo dye molecules are quickly decomposed because an extremely high concentration of OH radicals exists in this region. To confirm the proposed kinetics model, the effects of the initial concentration of azo dyes, irradiated atmosphere and pH on the decomposition rates were investigated. The obtained results were in good agreement with the proposed kinetics model.

Journal Article↗
PubMed1988

Discrimination of kinetic models in heteroscedastic parametric estimation of bentazepam following multiple dosing.

The aim of the present study was to attempt to discriminate between single- and two-compartment kinetic models used for calculating the pharmacokinetic parameters of bentazepam when the plasma concentrations of different administrations are used as initial data during multiple dosage regimes. Determination of the best estimated pharmacokinetic parameters was performed using non-linear regression analysis, weighting the data as a function of the error of the analytical technique. Bentazepam was administered at a dose of 25 mg orally at intervals of 8, 12 or 24 h to a total of 9 patients. The mean values of the parameters established for the single-compartment model were Ka = 2.024 h-1; Vd = 2.198 l/kg and Ke = 0.130 h-1. For the two-compartment model these values were: Ka = 2.134 h-1, Vc = 2.049 l/kg, K10 = 0.154 h-1, K12 = 0.042 h-1 and K21 = 0.103 h-1. By application of the MAICE test mean AIC values of 41.62 and 42.52 were obtained for the single- and two-compartment models, respectively. The most suitable kinetic model was determined for each patient according to the predictive nature of the individual parameters of the two kinetic models and by analysis of the residuals of the non-linear regressions of the parametric estimation.

Azepines↗
PubMed2005

[Kinetics model of spherical immobilized cellulase].

A kinetics model was developed for predicting and simulating immobilized cellulase performance, which follows Michaelis-Menten kinetics with competitive product inhibition. Taking into account the effects of competitive product inhibition, inner diffusional limitation, substrate concentration and carrier size, the substrate distribution and the product distribution in carriers were investigated, and the effectiveness factors were also calculated over a wide range of parameters. The effects of competitive product inhibition are shown to increase the substrate concentration in the carrier, and, additionally, to increase the effectiveness factors slightly. With the increase of inner diffusion coefficient, both the effectiveness factors and the substrate concentration in the carrier increase. As the carrier size increases, on the other hand, these values decrease. The effectiveness factors and the substrate concentration in the carrier are found to increase when substrate concentration in the reaction system increases.

Cellulase↗
PubMed2004

An experimental comparison of a kinetic model for the reaction of alpha-pinene and Delta(3)-carene with ozone and nitrogen oxides.

UNLABELLED: A kinetic model was compiled to simulate reactions of the monoterpenes, alpha-pinene and Delta(3)-carene, with O(3), NO(2) and NO. The influence of different initial settings of O(3), NO(2) and NO on the monoterpene reaction was evaluated. At initial levels of 75 p.p.b. of O(3), NO(2) and NO each, 1.5% of alpha-pinene and 1.1% of Delta(3)-carene were calculated to react after 215 s. The corresponding experimental results showed that 9.3-12.2% of alpha-pinene and 9.9-11.7% of Delta(3)-carene reacted. The calculated levels of O(3), NO(2) and NO were compared to experimental measurements and were shown to correspond well. However, comparison of the amount of monoterpene reacted between calculated and experimental results, demonstrated that the calculations underestimated the amount of monoterpene reacted in the experimental chamber. The difference between experimental and calculated results could, e.g., be the effect of surfaces and the presence of water, which are parameters not included in the kinetic model known to have influence on these reactions. PRACTICAL IMPLICATIONS: A compiled kinetic model could be used to predict concentrations of O(3), NO(2), NO and to predict the effects on the monoterpene reaction in a Teflon reaction chamber when changing the initial concentrations of O(3), NO(2). However, the results in the present work show that surface and moisture effects have to be settled and the effects included in future models.

Air Pollution, Indoor↗
PubMed1997

Kinetic model of excitatory synaptic transmission to cerebellar Purkinje cells.

We present a minimal kinetic model for excitatory synaptic transmission to cerebellar Purkinje cells. The main components are a kinetic model for a single glutamate receptor, which is calibrated with the help of patch clamp data, and a mean field approximation for the dynamics of a population of channels, which generate an EPSC. The resulting minimal model of the parallel fiber-Purkinje cell synapse is used to estimate the dynamics of glutamate in the synaptic cleft and to clarify the role of receptor desensitization in synaptic transmission. We also apply the model to different aspects of synaptic modulation, like long-term depression and potentiation by pharmacological application of ampakines. In the framework of the minimal model these effects can be understood as the result of modified receptor kinetics.

Animals↗
PubMed1998

Kinetic modeling for macromolecule loading into crosslinked polyacrylamide hydrogel matrix by swelling.

A kinetic model was proposed to characterize the swelling phenomenon of polyacrylamide hydrogel and to quantify and predict the loading of insulin into the hydrogel by swelling. Polyacrylamide hydrogel and porcine insulin were used in the study. During swelling, the insulin concentration in the hydrogel was found to be higher than that in the loading solution, which could be attributed to ionization of the ionic networks, Donnan exclusion, and the possible ionic interactions between the anionic carboxylic pendants and cationic insulin. The experimental results demonstrated that the proposed kinetic model was able to describe the swelling kinetics of polyacrylamide hydrogel and the loading kinetics of insulin by using only two constants [input rate (Kin) and output rate (Kout)]. The experimental values of Kin and Kout were found to highly depend on the concentration of HCl. As medium pH declined (because of the addition of HCl), the degree of swelling decreased and the insulin loading amount in the hydrogel was reduced. A linear log-log function was observed between Kin and the volume fraction of HCl. The Kout values also decreased with the addition of HCl, but remained constant after more than 1% (v/v) of HCl (0.01 N) was added. The proposed model was able to characterize the swelling kinetics of polyacrylamide and predict the loading dose of insulin in the polyacrylamide hydrogel by swelling.

Acrylic Resins↗
PubMed2000

Chemical kinetic modelling of PCDD formation from chlorophenol catalysed by incinerator fly ash.

A kinetic model is developed for PCDD formation from chlorophenol catalysed by incinerator fly ash. The key step in the model is a Langmuir-Hinshelwood type elementary step for the coupling of two adsorbed chlorophenol species to PCDD. Kinetic expression is derived which can relate PCDD formation rates with process variables including temperature, precursor concentration, fly ash loading and number of active sites in fly ash. Calculated PCDD formation rates based on this kinetic model are in good agreement with laboratory measurements reported in the literature. When the model is applied to industrial incinerator conditions, at maximum a PCDD yield of 10(-3) microg/N m3 is calculated.

Air Pollution↗
PubMed2005

Kinetic model for binary homogeneous nucleation in the H2O-H2SO4 system: comparison with experiments and classical theory of nucleation.

A kinetic model to predict nucleation rates in the sulfuric acid-water system is presented. It allows calculating steady-state nucleation rates and the corresponding time lag, using a direct solution of a system of kinetic equations that describe the populations of sub- and near-critical clusters. This kinetic model takes into account cluster-cluster collisions and decay of clusters into smaller clusters. The model results are compared with some predictions obtained with the classical nucleation theory (CNT) and also with available measurement data obtained in smog chambers or flow tubes. It is shown that in the case of slow nucleation processes, the kinetic model and the CNT as used by Shugard et al. [J. Chem. Phys. 75, 5298 (1974)] give the same results. However, in the case of intensive nucleation, a large part of the nucleation flux is due to cluster-cluster collisions and the CNT underestimates the nucleation rates.

Chemistry, Physical↗
PubMed2006

Process optimization of fenton oxidation using kinetic modeling.

In the remediation, water, and wastewater industries, an appropriate understanding of the chemical reactions governing the Fenton system allows the development of kinetic models to help design and optimize the performance and efficiency of treatment processes. In this work a rigorous kinetic model describing substrate oxidation by Fenton's reagent, following validation by comparison with experimental data, is extended and applied to provide insight and gain information regarding optimum initial conditions, solution environment, and operating regimes for the decomposition of a target contaminant. The effect of variables such as initial molar ratios of H202 to Fe(II), H202 dosing regimes, solution pH, and the presence or absence of oxygen on the rate and efficiency of contaminant degradation is presented and discussed in light of the reactions involved. Model simulations of the oxidation of various organic species demonstrate the significant role organic radicals and oxidation byproducts can have on treatment performance. An appropriate understanding of the oxidation pathway of the target organic and the reactions of degradation products is essential for the accurate application and use of the kinetic model for design and optimization purposes.

Ferrous Compounds↗
PubMed1992

Errors introduced by tissue heterogeneity in estimation of local cerebral glucose utilization with current kinetic models of the [18F]fluorodeoxyglucose method.

The effects of tissue heterogeneity on the estimation of regional cerebral glucose utilization (rCMRglc) in normal humans with [18F]2-fluoro-2-deoxy-D-glucose ([18F]FDG) and positron emission tomography (PET) were compared with respect to the various kinetic models of the [18F]FDG method. The kinetic models were conventional homogeneous tissue models of the [18F]FDG method, with (4K Model) and without (3K Model) a rate constant to account for an apparent loss of [18F]2-fluoro-2-deoxy-D-glucose-6-phosphate ([18F]FDG-6-P), and a tissue heterogeneity model (TH Model). When either of the kinetic models designed for homogeneous tissues was applied to heterogeneous tissues, estimates of the rate constant for efflux of [18F]FDG from the tissue (k2*) and of the rate constant for phosphorylation of [18F]FDG (k3*) decreased as the duration of the experimental period was increased. When the 4K Model was used, estimates of the rate constant for the apparent dephosphorylation of [18F]FDG-6-P (k4*) were significantly greater than zero and fell with increasing duration of the experimental period. Although the TH Model included no term to describe an apparent dephosphorylation of [18F]FDG-6-P, the fit of the TH Model to the time course of total tissue radioactivity was at least as good as and often better than the fit of the 4K Model in the 120-min period following the pulse of [18F]FDG. Hence, the high estimates of k4* found in PET studies of less than or equal to 120 min can be explained as the consequence of measuring radioactivity in a heterogeneous tissue and applying a model designed for a homogeneous tissue; there remains no evidence of significant dephosphorylation of [18F]FDG-6-P in this time period. Furthermore, use of the 4K Model led to an overestimation of rCMRglc; whole-brain glucose utilization calculated with the 4K Model was greater than 20% higher than values usually obtained in normal humans by the model-independent Kety-Schmidt technique. rCMRglc was accurately estimated by the TH Model and, in experimental periods sufficiently long to minimize the effects of tissue heterogeneity, also by the original 3K Model of the deoxyglucose method.

Adult↗