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At least 289 records · Page 16Linked to original sources
PubMed2005

A kinetic model and its parameter estimation for the process of binding copper to human serum albumin by a voltammetric method.

Linear sweep anodic stripping voltammetry was applied to determine the concentration of free copper ions in the process of binding copper to human serum albumin (HSA) on the mercaptoethane sulfonate modified gold electrode surface. A kinetic model of two consecutive steps for the process of binding copper to HSA was first proposed on the basis of the electrochemical results and compared with a parallel kinetic response model by using residual analysis. The experimental data of the stripping peak currents with time was fitted according to the model and the kinetic parameters, binding rate constants, k1 and k2, were estimated to be 0.411 and 0.055 min(-1), respectively.

Copper↗
PubMed2005

Kinetic model for step flow growth of [100] steps.

A kinetic model for the step flow growth of [100] steps is derived. This model extends the implicit close-to-equilibrium assumption in the classical Burton-Cabrera-Frank theory to out-of-equilibrium growth regimes common in molecular beam epitaxy. In equilibrium, the kink density coincides with Burton, Cabrera, and Frank [Philos. Trans. R. Soc. London, Ser. A 243, 299 (1951)] but in a planar steady state solution for a periodic sequence of steps the kink density derivates and we analyze its scaling behavior with the step Peclet number. Furthermore, we observe a discontinuity of adatoms on the steps that might give a new explaination for step bunching.

Journal Article↗
PubMed2006

A kinetic model of calcium mass balance during dialysis therapy.

A kinetic model of Ca mass balance during dialysis has been developed. It is a single-compartment, variable-volume model to compute Ca mass balance during dialysis in its volume of distribution, the extracellular fluid. The model was used to analyze literature data which were suitable for the assessment of Ca mass balance over the course of dialysis. The modeled analyses predicted the serial plasma Ca concentrations very well. The mass balance analyses revealed a pool of rapidly diffusible Ca beyond the extracellular fluid distribution volume where Ca could be mobilized (M+(Ca)) or sequestered (M-(Ca)) very rapidly at rate equal but opposite in sign to dialyzer flux and thus effectively maintain near constant plasma Ca in the face of dialyzer Ca concentration gradients. This pool is likely the large pool of diffusible (miscible) Ca in connective tissue and on bone surfaces. Analysis of net Ca flux during dialysis with Cdi(Ca) = 2.50 mEq/l suggests that 80% of patients are in positive Ca balance during dialysis. Further studies are required to verify the model and to develop a model of interdialytic Ca mass balance.

Calcium↗
PubMed2006

Structural kinetic modeling of metabolic networks.

To develop and investigate detailed mathematical models of metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, kinetic modeling is still often severely hampered by inadequate knowledge of the enzyme-kinetic rate laws and their associated parameter values. Here we propose a method that aims to give a quantitative account of the dynamical capabilities of a metabolic system, without requiring any explicit information about the functional form of the rate equations. Our approach is based on constructing a local linear model at each point in parameter space, such that each element of the model is either directly experimentally accessible or amenable to a straightforward biochemical interpretation. This ensemble of local linear models, encompassing all possible explicit kinetic models, then allows for a statistical exploration of the comprehensive parameter space. The method is exemplified on two paradigmatic metabolic systems: the glycolytic pathway of yeast and a realistic-scale representation of the photosynthetic Calvin cycle.

Computer Simulation↗
PubMed1998

Physiological red blood cell kinetic model to explain the apparent discrepancy between adenosine breakdown inhibition and nucleoside transporter occupancy of draflazine.

A physiological red blood cell (RBC) kinetic model is proposed for the adenosine (ADO) transport into erythrocytes and its subsequent intracellular deamination into inactive inosine (INO) and further breakdown into hypoxanthine (HYPO). The model and its parameters were based on previous studies investigating the kinetics of the biochemical mechanism of uptake and metabolism of ADO in human erythrocytes. Application of the model for simulations of the breakdown of ADO in a RBC suspension revealed that the predicted adenosine breakdown inhibition (ABI) of draflazine corresponded well with the ABI measured ex vivo. The model definitely explained the apparent discrepancy between the ex vivo measured ABI and the nucleoside transporter occupancy of draflazine. Intracellular deamination of ADO rather than its transport by the nucleoside transporter is the rate-limiting step in the overall catabolism of ADO. Consequently, at least 90% occupancy of the transporter by draflazine is required to inhibit adenosine breakdown ex vivo substantially. Simulations on basis of the validated model were performed to evaluate the ABI for different experimental conditions and to mimic the clinical situation. The latter may be very helpful for the design of optimal dosing schemes of draflazine. It was demonstrated that the short half-life of released ADO was prolonged substantially in a dose-related manner after a continuous infusion of draflazine. Finally, the previously found different sigmoidal Emax relationships between the measured ABI and the concentrations of draflazine in plasma and whole blood could be explained by the ADO transport and breakdown RBC kinetic model and the capacity-limited specific RBC binding characteristics of draflazine.

Adenosine↗
PubMed2005

Kinetic modeling and thermodynamic study to remove Pb(II), Cd(II), Ni(II) and Zn(II) from aqueous solution using dead and living Azolla filiculoides.

Dead Azolla filiculoides can remove Pb(2+),Cd(2+), Ni(2+) and Zn(2+) corresponding to second-order kinetic model. The maximum adsorption capacity (Q(max)) to remove these metal ions by the alkali and CaCl(2)/MgCl(2)/NaCl (2:1:1, molar ratio) activated Azolla from 283 to 313K was 1.431-1.272, 1.173-0.990, 1.365-1.198 and 1.291-0.981mmol/g dry biomass, respectively. Q(max) to remove these heavy metals by the non-activated Azolla at the mentioned temperature range was obtained 1.131-0.977, 1.092-0.921, 1.212-0.931 and 1.103-0.923mmol/g dry biomass, respectively. In order to remove these metal ions by the activated Azolla, the enthalpy change (DeltaH) was -4.403, -4.495, -4.557 and -4.365kcal/mol and the entropy change (DeltaS) was 2.290, 1.268, 1.745 and 1.006cal/molK, respectively. While, to remove these metal ions by the non-activated Azolla, DeltaH was -3.685, -3.766, -3.967 and -3.731kcal/mol and DeltaS was 2.440, 1.265, 1.036 and 0.933cal/molK, respectively. On the other hand, the living Azolla removed these heavy metals corresponding to first-order kinetic model. It was also shown that pH, temperature and photoperiod were effective both on the rate of Azolla growth and the rate of heavy metals uptake during 10 days. It was appeared the use of Ca(NO(3))(2) increased both Azolla growth rate and the rate of heavy metals uptake while the using KNO(3) although increased Azolla growth rate but decreased the rate of heavy metals uptake.

Adsorption↗
PubMed1990

Folding of ribonuclease T1. 2. Kinetic models for the folding and unfolding reactions.

The slow refolding of ribonuclease T1 was investigated by different probes. Structural intermediates with secondary structure are formed early during refolding, as indicated by the rapid regain of a native-like circular dichroism spectrum in the amide region. This extensive structure formation is much faster than the slow steps of refolding, which are limited in rate by the reisomerization of incorrect proline isomers. The transient folding intermediates were also detected by unfolding assays, which make use of the reduced stability of folding intermediates relative to that of the native protein. The results of this and the preceding paper [Kiefhaber et al. (1990) Biochemistry (preceding paper in this issue)] were used to propose kinetic models for the unfolding and refolding of ribonuclease T1. The unfolding mechanism is based on the assumption that, after the structural unfolding step, the slow isomerizations of two X-Pro peptide bonds occur independently of each other in the denatured protein. At equilibrium a small amount of fast-folding species coexists with three slow-folding species: two with one incorrect proline isomer each and another, dominant species with both these prolines in the incorrect isomeric state. In the mechanism for refolding we assume that all slow-folding molecules can rapidly regain most of the secondary and part of the tertiary structure early in folding. Reisomerizations of incorrect proline peptide bonds constitute the slow, rate-limiting steps of refolding. A peculiar feature of the kinetic model for refolding is that the major unfolded species with two incorrect proline isomers can enter two alternative folding pathways, depending on which of the two reisomerizes first. The relative rates of reisomerization of the respective proline peptide bonds at the stage of the rapidly formed intermediate determine the choice of pathway. It is changed in the presence of prolyl isomerase, because this enzyme catalyzes these two isomerizations with different efficiency and consequently leads to a shift from the very slow to the intermediate refolding pathway.

Circular Dichroism↗
PubMed2006

Studies on a kinetic model for butyric acid bioproduction by Clostridium butyricum.

AIMS: This paper discusses the establishment of a kinetic model for cell growth, butyric acid production and substrate consumption of Clostridium butyricum ZJUCB in batch cultivation. METHODS AND RESULTS: Mathematic simulations were proposed by the logistic equation for the cell growth, the Luedeking-Piret equation for butyric acid production and the Luedeking-Piret-like equation for glucose consumption. CONCLUSION: We compared the performance of our model against that obtained by the empirically experimental design. The experiment-validated model was found suitable for studying butyric acid fermentation kinetics in a complex dynamic behaviour of C. butyricum, especially for its singular growth phenomenon. SIGNIFICANCE AND IMPACT OF THE STUDY: The model parameters are estimated from the data fitting and evaluated for simulation of the time courses of the concentrations of cell biomass, butyric acid and glucose and the model appears to fit the experimental data well. The results may be useful for butyric acid production by microbial fermentation.

Biomass↗
PubMed2003

Kinetic modeling of the laser-induced breakdown spectroscopy plume from metallic lead.

We report initial results of a study aimed toward developing a computational fluid dynamics (CFD) model to simulate the laser-induced breakdown spectroscopy (LIBS) plume for the purpose of understanding the physical and chemical factors that control the LIBS signature. The kinetic model developed for modeling studies of the LIBS plume from metallic lead includes a set of air reactions and ion chemistry as well as the oxidization, excitation, and ionization of lead atoms. At total of 38 chemical species and 220 reactions are included in the model. Experimental measurements of the spatial and temporal dependence of a number of lead emission lines have been made of the LIBS plume from metallic lead. The mechanism of generation of excited Pb states in the LIBS plume is analyzed through kinetic modeling and sensitivity analysis. Initial CFD model results for the LIBS plume are presented.

Journal Article↗
PubMed2002

Correlates of urea kinetic modeling during hemodialysis in patients with acute renal failure.

The current guidelines on dialysis adequacy in acute renal failure (ARF) are loosely defined and have been extrapolated from patients with end-stage renal disease. The objectives of this study were (1) to compare three methods of urea kinetic modeling measurement in patients with ARF receiving intermittent hemodialysis, (2) to compare prescribed to delivered dose of dialysis, and (3) to explore the factors that are associated with dialysis delivery. 'Single-pool' urea kinetic modeling was assessed by the Ureakin) software and the second-generation equation which uses a logarithmic estimate of spKt/V. 'Equilibrated' Kt/V (eKt/V) was calculated using the rate adjustment equation. The prescribed dose was derived using the manufacturer's specifications of the dialyzer clearance, prescribed time, actual delivered blood and dialysate flow, and estimates of volume of urea distribution. A total of 78 consecutive spKt/V measurements were obtained in 24 patients. The mean urea reduction ratio was 51 +/- 1%. The delivered spKt/V was significantly lower than that prescribed (0.87 +/- 0.03 or 0.83 +/- 0.03 vs. 1.28 +/- 0.05; p = 0.0001). The equilibrated Kt/V was markedly lower than the delivered spKt/V (0.73 +/- 0.03 vs. 0.83 +/- 0.03; p = 0.0001). Univariate analyses demonstrated that female gender, low body mass index, low predialysis weight, use of cellulose acetate dialyzers, and increased prescribed time were associated with increased odds of prescribed spKt/V > or =1.2. Similarly, old age, increased delivered time, and high cytokine production were associated with increased odds of delivered spKt/V > or =1.2. In summary, while the impact of delivered intermittent hemodialysis on the survival of patients with ARF remains to be determined, these results indicate that dialysis delivery is suboptimal in ARF, and empiric dosing should strongly consider factors related to lean body mass, including age and gender.

Acute Kidney Injury↗
PubMed2005

Kinetic models for chemotaxis: hydrodynamic limits and spatio-temporal mechanisms.

We study kinetic models for chemotaxis, incorporating the ability of cells to assess temporal changes of the chemoattractant concentration as well as its spatial variations. For prescribed smooth chemoattractant density, the macroscopic limit is carried out rigorously. It leads to a drift equation with a chemotactic sensitivity depending on the time derivative of the chemoattractant density. As an application it is shown by numerical experiments that the new model can resolve the chemotactic wave paradox. For this purpose, the macroscopic equation is coupled to a simple activation-inhibition model for the chemoattractant which produces the chemoattractant waves typical for the slime mold Dictyostelium discoideum.

Animals↗
PubMed2005

Development of a biosensor for measuring plasma fibrinogen based on an enzyme kinetic model.

A biosensor has been designed for measuring plasma fibrinogen concentrations based on an enzyme kinetic model. The values obtained correspond linearly to those of a clinical method but have a higher sensitivity within the normal range of fibrinogen. By using the disposable biosensor technology, this method is easy to follow, quick (within 2 min) and precise (with coefficients of variation to be as low as below 5%) and requires only a small amount of plasma sample (<50 microl). This biosensor technology also holds potential for use in point-of-care diagnostics.

Animals↗
PubMed2005

Fractional kinetic model for chaotic transport in nonintegrable Hamiltonian systems.

We propose a kinetic model of transport in nonintegrable Hamiltonian systems, based on a fractional kinetic equation with spatially dependent diffusion coefficient. The diffusion coefficient is estimated from the remainder of the optimal normal form for the given region of the phase space. After partitioning the phase space into building blocks, a separate equation can be constructed for each block. Solving the kinetic equations approximately and estimating the diffusion time scales, we convolve the solutions to get the description of the macroscopic behavior. We show that, in the limit of infinitely many blocks, one can expect an approximate scaling relation between the Lyapunov time and the diffusion (or escape) time, which is either an exponential or a power law. We check our results numerically on over a dozen Hamiltonians and find a good agreement.

Journal Article↗
PubMed2006

[Trans-membrane transport kinetic models in peritoneal dialysis].

The peritoneum is a biologic semi-permeable membrane. This article presents some kinetic models of fluid and solute trans-peritoneal transport in peritoneal dialysis including the membrane model, the three-pore model, the extended three-pore model and the distributed model. In these models different trans-peritoneal transport mechanisms were revealed. The three-pore model is emphasized.

Animals↗
PubMed1993

Urea kinetic modeling: comparing the options.

In this study 6 commercially produced kinetic modeling packages utilizing a variable volume, single pool urea model, as well as formulae to determine the delivery of therapy, have been compared by applying to each the same set of rigorously collected data for a group of 12 patients. Comparison of the kinetically derived parameters (urea generation rate [G], urea distribution volume [V], delivery of therapy [Kt/V], and normalized protein catabolic rate [nPCR]) showed that the values obtained for both G and V differed between packages owing to the numerical methods and the clearance used in the solution of the differential equations. Although a broad agreement between the values established for Kt/V and nPCR was noted, the 95% limits of agreement indicated that it would be prudent to exercise caution when comparing results established by different modeling packages.

Adult↗
PubMed1991

Patch-clamp studies on the anomalous mole fraction effect of the K+ channel in cytoplasmic droplets of Nitella: an attempt to distinguish between a multi-ion single-file pore and an enzyme kinetic model with lazy state.

Patch-clamp studies have been employed in order to check whether the assumption of a multi-ion single-file pore is necessary for the explanation of the anomalous mole fraction effect or whether this effect can also be explained by a single-barrier enzyme kinetic model. Experiments in the cell-attached configuration were done on the tonoplast membrane of cytoplasmic droplets of Nitella in solutions containing 150 mol m-3 of K+ plus Tl+ with seven different K+/Tl+ ratios. At first sight, the results seem to support the multi-ion single-file pore, because apparent open channel conductivity displays the anomalous mole fraction effect, whereas open-probability has not been found to be dependent on the K+/Tl+ ratio. Changes in open probability would be expected for a single-barrier enzyme kinetic model with a lazy state. On the other hand, the lazy-state model is more successful in explaining the measured I-V curves. The entire slope of the apparent open channel current-voltage curves rotates with changing K+/Tl+ ratios in the whole voltage range between -100 and +80 mV. Numerical calculations on the basis of multi-ion single-file pores could create the anomalous mole fraction effect only in a limited voltage range with intersecting I-V curves. The apparent absence of an effect on open probability which is postulated by the lazy-state model can be explained if switching into and out of the lazy state is faster than can be resolved by the temporal resolution of 1 msec.

Biological Transport↗
PubMed2001

Pre-steady-state kinetics of initiation of transcription by T7 RNA polymerase: a new kinetic model.

In order to begin to understand the mechanism of the initiation of transcription in the model bacteriophage T7 RNA polymerase system, the simplest possible reaction, the synthesis of a dinucleotide, has been followed by quench-flow kinetics and numerical integration of mechanism-specific rate equations has been used to test specific kinetic models. In order to fit the observed time dependence in the pre-steady-state kinetics, a model for dinucleotide synthesis is proposed in which rebinding of the dinucleotide to the enzyme-DNA complex must be included. Separate reactions using dinucleotide as a substrate confirm this mechanism and the determined rate constants. The dinucleotide rebinding observed as inhibition under these conditions forms a productive intermediate in the synthesis of longer transcripts, and must be included in future kinetic mechanisms. The rate-limiting step leading to product formation shows a substrate dependence consistent with the binding of two substrate GTP molecules, and at saturating levels of GTP, is comparable in magnitude to the product release rate. The rate of product release shows a positive correlation with the concentration of GTP, suggesting that the reaction shows base-specific substrate activation. The binding of another substrate molecule, presumably via interaction with the triphosphate binding site, likely facilitates displacement of the dinucleotide product from the complex.

Bacteriophage T7↗
PubMed1999

A new kinetic model of protein adsorption on suspended anion-exchange resin particles.

The kinetics of adsorption of bovine serum albumin on an anion-exchange resin were measured in a batch system using a flow cell and ultraviolet absorbance, as a function of initial liquid-phase protein concentration and solid-to-liquid phase ratio. A new mathematical model for adsorption kinetics is presented that fits the experimental data to give a highly linear relationship with time, following a short transient period. Numerical integration of the differential form of the new composite nonlinear (CNL) kinetic model, containing three independent parameters, is shown to describe the dynamics of batch adsorption much better than alternative lumped parameter models. Although the new model is phenomenological rather than mechanistic, its principal parameter is shown to be a direct linear function of a physically measurable quantity. This study demonstrates that the model can accurately simulate protein concentration-time profiles using parameter estimates derived from correlations over a wide range of initial protein concentrations and phase ratios. The new CNL model is shown to be considerably superior to the Langmuir and solid-film linear kinetic models in this regard, having the additional advantage that an equilibrium isotherm for the system is not required.

Adsorption↗