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PubMed2004

Kinetic modeling of Q-switched high-power ytterbium-doped fiber lasers.

We present a kinetic model for Q-switched, cladding-pumped, high-power Yb-doped fiber lasers that are based on the rate equation, in a difference equation form, of ion population and propagation equations for both pumping and signal light. The effects of fiber-laser parameters, such as doping, length, pump power, and repetition rate on pulse characteristics are analyzed. This model is used to analyze the performance of Q-switched multicore fiber lasers and to show the output pulses with enhanced characteristics.

Journal Article↗
PubMed1993

A cell kinetics model of radiation-induced myelopoiesis: rate coefficient estimates for mouse, rat, sheep, swine, dog, and burro irradiated by photons.

Rate coefficients in the model of cell kinetics and mortality introduced by Jones et al. (Radiat. Res. 128, 258-266, 1991) are estimated using mortality data from 27 animal experiments. Adjustments are made for the six species and three nominal classes of gamma radiation represented in these studies. The model fits most of the mortality data quite well when the rate coefficient representing cellular proliferation is fitted to individual species and each of the other coefficients is given a single value across the entire data set. Results are qualitatively similar to those reported by Morris et al. (Radiat. Res. 128, 267-275, 1991) who estimated the rate coefficients from a limited number of mouse studies involving only 250 kVp X rays. As in the earlier study, estimates here lead to greater cell survival than is observed for marrow cells in the amplification division compartment.

Animals↗
PubMed1998

Equations for progress curves of some kinetic models of enzyme-single substrate-single slow binding modifier system.

A procedure is described by means of which the equations for progress curves for the kinetic models that include fast and slow reaction steps can be derived. It is based on combined assumptions of equilibrium and steady-state and uses Laplace transformation for solving the systems of differential equations. The progress curve equations and the significance of the corresponding parameters are given for some most frequently occurring models describing the influence of a slow binding modifier on a single substrate enzyme reaction.

Binding Sites↗
PubMed2003

Kinetic modeling of triamterene intestinal absorption and its inhibition by folic acid and methotrexate.

The aim of this work was to study the intestinal absorption process of triamterene in situ in rats in order to gain insight on its absorption mechanism. The study shows an example of application of a pharmacokinetic model for drug disappearance from a compartment by simultaneous first order and Michaelis-Menten processes to the intestinal drug disappearance by absorption in a non-steady state system. The parameter used to quantify absorption was the absorption rate constant, determined in situ by means of a loop perfusion technique, performed in colon and in whole small intestine of rat at three pHs (5.00, 7.00 and 8.00) and in the presence of folic acid and methotrexate. Different concentrations of the drug were perfused in each condition. The concentrations versus time data were modeled with different kinetic absorption and inhibition differential equations to obtain the passive and active transport components and to elucidate the inhibition mechanisms. The results obtained confirm that triamterene is absorbed by means of passive diffusion and by a transporter or transporters related to folates. Folic acid and methotrexate are able to inhibit triamterene absorption. The results do not allow the selection of a competitive or non-competitive model for inhibition and this fact could be due to the presence of different carriers. The possibility of the existence of a secretion process sensitive to verapamil is also discussed.

Animals↗
PubMedDate not supplied

Formal analytical solution to a regional blood flow and diffusion based urea kinetic model.

At the beginning of hemodialysis (HD), urea in arterial blood drops rapidly, whereas a pronounced postdialytic urea rebound (PDUR) can be observed when HD is discontinued. In a new approach to this observation, the authors suggest that solute flux from remote body compartments to the dialyzer is governed by 1) diffusion of solutes from the tissue to the blood perfusing the tissue, and 2) by regional blood flow distribution, cardiopulmonary recirculation, and access recirculation, respectively. These concepts were incorporated into a variable volume, two compartment model that could be treated as an eigenvalue problem and solved analytically. The resulting equations were used to model intradialytic and postdialytic urea profiles with the help of a commercial spreadsheet program. The significance of hemodynamic model parameters such as cardiac output (CO) and regional blood flow distribution on PDUR was modeled in simulation runs, where PDUR increased from 5% to 15% when CO fell from 7 to 3 l/min with standard treatment parameters (t = 3h, KD = 0.3 l/min, V = 35l, UFV = 2.8l, fQHFS = 0.8, QAc = 0.8l/min). Thus, this urea kinetic model establishes a previously missing link between hemodynamics and solute removal.

Biological Transport, Active↗
PubMed2002

Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleases.

Digestion of linear DNA by type I restriction endonucleases is generally activated following the head-on collision of two translocating enzymes. However, the resulting distributions of cleavage loci along the DNA vary with different enzymes; in some cases, cleavage is located in a discrete region midway between a pair of recognition sites while in other cases cleavage is broadly distributed and occurs at nearly every intervening locus. Statistical models for DNA translocation, collision, and cleavage are described that can account for these observations and that are generally applicable to other DNA-based motor proteins. If translocation is processive (stepping forward is significantly more likely than DNA dissociation), then the linear distribution of an ensemble of proteins can be described simply using a Poisson relationship. The pattern of cleavage sites resulting from collision between two processive type I enzymes over a distance d can then be described by a binomial distribution with a standard deviation 0.5 x d1/2. Alternatively, if translocation is nonprocessive (stepping forward or dissociating become equally likely events), the linear distribution is described by a continuum of populated states and is thus extended. Comparisons of model data to the kinetics of DNA translocation and cleavage discount the nonprocessive model. Instead, the observed differences between enzymes are due to asynchronous events that occur upon collision. Therefore, type I restriction enzymes can be described as having processive DNA translocation but, in some cases, nonprocessive DNA cleavage.

Base Sequence↗
PubMed1985

Glucose response to bursting-spiking pancreatic beta-cells by a barrier kinetic model.

A mathematical model of the pancreatic beta-cell electrical activity was developed using a barrier kinetic model. Our model incorporates the glucose sensitive channel which is known to conduct K+ in the absence of glucose. The model also incorporates Cai sensitive K+ channels which are inhibited by intracellular H+ ions. It is described by three non-linear simultaneous differential equations. Numerical integration of these equations allowed us to examine the effect of glucose and of external Ca2+ ions on the electrical and cellular activity of the beta-cell. Our results show that the contribution of glucose-sensitive channel activity, if not completely inhibited, plays a very important role in determining the bursting periodicity. Our results also shows that even a small decrease in pHi is sufficient to change a bursting beta-cell to a spiking one. The voltage dependence of calcium sensitive K+ channels, however, affects little to the bursting mode of the electrical activity. Our simulation supports an incomplete selectivity of the voltage dependent calcium channel for calcium ions with low external [Ca2+]. It also supports the role of [Ca]i as an inhibitor of this channel when [Ca]i becomes unusually high.

Animals↗
PubMed2006

A two-dimensional adsorption kinetic model for thermal hysteresis activity in antifreeze proteins.

Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs), collectively abbreviated as AF(G)Ps, are synthesized by various organisms to enable their cells to survive in subzero environments. Although the AF(G)Ps are markedly diverse in structure, they all function by adsorbing to the surface of embryonic ice crystals to inhibit their growth. This adsorption results in a freezing temperature depression without an appreciable change in the melting temperature. The difference between the melting and freezing temperatures, termed thermal hysteresis (TH), is used to detect and quantify the antifreeze activity. Insights from crystallographic structures of a number of AFPs have led to a good understanding of the ice-protein interaction features. Computational studies have focused either on verifying a specific model of AFP-ice interaction or on understanding the protein-induced changes in the ice crystal morphology. In order to explain the origin of TH, we propose a novel two-dimensional adsorption kinetic model between AFPs and ice crystal surfaces. The validity of the model has been demonstrated by reproducing the TH curve on two different beta-helical AFPs upon increasing the protein concentration. In particular, this model is able to accommodate the change in the TH behavior observed experimentally when the size of the AFPs is increased systematically. Our results suggest that in addition to the specificity of the AFPs for the ice, the coverage of the AFPs on the ice surface is an equally necessary condition for their TH activity.

Adsorption↗
PubMed2000

A kinetic model for the metabolic interaction of two substrates at the active site of cytochrome P450 3A4.

In many cases, CYP3A4 exhibits unusual kinetic characteristics that result from the metabolism of multiple substrates that coexist at the active site. In the present study, we observed that alpha-naphthoflavone (alpha-NF) exhibited a differential effect on CYP3A4-mediated product formation as shown by an increase and decrease, respectively, of the carboxylic acid (P(2)) and omega-3-hydroxylated (P(1)) metabolites of losartan, while losartan was found to be an inhibitor of the formation of the 5,6-epoxide of alpha-NF. Thus, to address this problem, a kinetic model was developed on the assumption that CYP3A4 can accommodate two distinct and independent binding domains for the substrates within the active site, and the resulting velocity equations were employed to predict the kinetic parameters for all possible enzyme-substrate species. Our results indicate that the predicted values had a good fit with the experimental observations. Therefore, the kinetic constants can be used to adequately describe the nature of the metabolic interaction between the two substrates. Applications of the model provide some new insights into the mechanism of drug-drug interactions at the level of CYP3A4.

Benzoflavones↗
PubMed2005

Integrating cell-level kinetic modeling into the design of engineered protein therapeutics.

Functional genomics and proteomics are identifying many potential drug targets for novel therapeutic proteins, and both rational and combinatorial protein engineering methods are available for creating drug candidates. A central challenge is the definition of the most appropriate design criteria, which will benefit critically from computational kinetic models that incorporate integration from the molecular level to the whole systems level. Interpretation of these processes will require mathematical models that are refined in combination with relevant data derived from quantitative assays, to correctly set biophysical objectives for protein design.

Cell Physiological Phenomena↗
PubMed1999

Modeling of irreversible thermal protein denaturation at varying temperature. II. The complete kinetic model of Lumry and Eyring.

The model for thermal denaturation of proteins involving consecutive reversible and irreversible steps (Lumry and Eyring model) has been analyzed. The most general case, when equilibrium in the first step is established slowly in comparison with the rate of the second step and the heat effect value for the second step is either greater than or less than zero, has been considered. The theoretical dependences of excess heat capacity on temperature have been constructed. The variation of the shape of the theoretical curves with varied values of the enthalpy change for the second step, Arrhenius equation parameters for both steps, and the scanning rate has been studied.

Escherichia coli↗
PubMed1991

Is urea kinetic modelling an appropriate tool for guiding ultrashort high-flux dialysis therapy?

High-flux dialysers are frequently used for highly efficient ultrashort treatment schedules. To avoid the risk of inadequately low dialysis dose in this treatment strategy where 'every minute counts', it is often advocated to monitor the treatment quality by means of urea kinetic modelling (UKM). However, careful computational analysis of concentration curves generated by UKM versus more realistic two-pool model curves indicates the risk of substantial overestimation of the protein catabolic rate (PCR). Therefore conventional UKM should not be used to monitor and/or guide treatment schedules with dialyser urea clearance greater than 250 ml/min and dialysis time less than 3 h. Under these conditions, PCR can be overestimated by as much as 20%.

Humans↗
PubMed1990

Competitive inhibition of lipolytic enzymes. I. A kinetic model applicable to water-insoluble competitive inhibitors.

It is now becoming clear from the abundant lipolytic enzyme literature that any meaningful interpretation of inhibition data has to take into account the kinetics of enzyme action at the lipid/water interface. We attempt in the present paper to provide a kinetic model applicable to water-insoluble competitive inhibitors, in order to quantitatively compare the results obtained at several laboratories. We derived kinetic equations applicable to the pre-steady state as well as steady state. By measuring the inhibitory power, as described in the present paper, it is possible to obtain a normalized estimation of the relative efficiency of various potential inhibitors. Furthermore, with the kinetic treatment developed here, it is possible to make quantitative comparisons with the same inhibitor placed under various physico-chemical situations, i.e., micellar or monolayer states.

Binding, Competitive↗
PubMed2004

The evaluation of electrical energy per order (E(Eo)) for photooxidative decolorization of four textile dye solutions by the kinetic model.

Photooxidative decolorization of four textile dyestuffs, C.I. Acid Orange 7 (AO7), C.I. Acid Orange 8 (AO8), C.I. Acid Orange 52 (AO52) and C.I. Acid Blue 74 (AB74), by UV/H2O2 was investigated in a laboratory scale photoreactor equipped with a 15 W low pressure mercury vapour lamp. The decolorization of the dyes was found to follow pseudo-first-order kinetics, and hence the figure-of-merit electrical energy per order (E(Eo)) is appropriate for estimating the electrical energy efficiency. The E(Eo) values were found to depend on the concentration of H2O2, concentration and basic structure of the dye. This study shows that these textile dyes can be treated easily and effectively with the UV/H2O2 process with E(Eo) values between 0.4 and 5 kW h m-3 order-1, depending on the initial concentrations of dyes and H2O2. The kinetic model, based on the initial rates of degradation, provided good prediction of the E(Eo) values for a variety of conditions.

Azo Compounds↗
PubMed2005

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection.

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an important reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macroscopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities. Proc. Natl. Acad. Sci. U.S.A. 84, 663-667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, including the actual time to insert a nucleotide plus delays due to polymerase detachment from either the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are expressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the influence of G + C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a competition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

DNA-Directed DNA Polymerase↗
PubMed1999

Kinetic model of phase separation in binary mixtures with hard mobile impurities.

We develop a mean-field rate-equation model for the kinetics of phase separation in binary mixtures with hard mobile impurities. For impurities preferentially wet by one of the components, the phase separation is arrested in the late stage. The "steady-state" domain size depends strongly on both the particle diffusion constant and the particle concentration. We compare theoretical results with the simulation data and find good qualitative agreement.

Journal Article↗
PubMed1993

[Tracer kinetic modeling in nuclear medicine].

For the quantitative measurement of the function of the organs, the data analysis with the modeling has been performed. The basic concepts and assumptions of the modeling in nuclear medicine are described. In the data analysis with tracer kinetic modeling, there are three important factors to be considered. They are the pharmacokinetics of the tracer in the tissue, the conditions of the study such as data acquisition method and study protocol, and the mathematical methods. We mention many effects of these factors on the values and the interpretation of the results of the examination. For the clinical practice, more simplex methods of measurements and mathematical analysis are desired.

Autoradiography↗