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The efficient computation of the cumulative distribution and probability density functions in the diffusion model.

An algorithm is described to efficiently compute the cumulative distribution and probability density functions of the diffusion process (Ratcliff, 1978) with trial-to-trial variability in mean drift rate, starting point, and residual reaction time. Some, but not all, of the integrals appearing in the model's equations have closed-form solutions, and thus we can avoid computationally expensive numerical approximations. Depending on the number of quadrature nodes used for the remaining numerical integrations, the final algorithm is at least 10 times faster than a classical algorithm using only numerical integration, and the accuracy is slightly higher. Next, we discuss some special cases with an alternative distribution for the residual reaction time or with fewer than three parameters exhibiting trial-to-trial variability.

Algorithms↗

Why are cancers acidic? A carrier-mediated diffusion model for H+ transport in the interstitial fluid.

31P MRS studies have shown that the intracellular compartment ot tumours is kept near neutrality, whereas the interstitial fluid is acidic (pH 6.5-6.8). Why is this compartment acidic? Balance studies confirm that tumours produce excessive lactic acid, although less than usually supposed, but this cannot be the whole story, since Tannock and co-workers have shown interstitial acidity in glycolysis-deficient tumours. Another major acid load is caused by hydration of CO2 molecules to carbonic acid, catalysed by carbonic anhydrase. The distance that H+ must diffuse from cancer cells to capillaries is further than in normal tissue and this will increase acidification near the cells. We show that previous quantitative models based on simple H+ diffusion are unsatisfactory. This is because most H+ ions cross the interstitial space bound to buffers such as inorganic phosphate. Although these protonated buffers (i.e. conjugate acids) diffuse much more slowly than H+ ions they carry most of the protons, so the pH predicted by this model is closer to neutrality for a given proton production rate than that predicted by the dissolved H+ model. We have developed a mathematical model of this carrier-mediated system that predicts pHe values as low as those observed in some tumours.

Diffusion↗

Parametric dependence of conduction speed for a diffusive model of a myelinated axon.

A simple model of a myelinated axon, using ideas from cable theory and accounting for the diffusion of potential across the internode, is formulated and solved to obtain transcendental expressions relating conduction velocity and various model parameters. Numerical simulations are performed to obtain graphs of several parameter relationships.

Action Potentials↗

Diffusion models of ion-channel gating and the origin of power-law distributions from single-channel recording.

The lifetimes of the unitary currents from ion channels, as revealed from single-channel recording, are traditionally thought to follow exponential or multiexponential distributions. The interpretation of these event-time distributions is that the gating process follows Markov kinetics among a small number of states. There is recent evidence, however, that certain systems exhibit distributions that follow power laws or functions related to power laws. Likewise, it has been suggested that data sets that appear to be multiexponential may be fit to simple power laws as well. In this paper we propose a different view of ion-channel-gating kinetics that is consistent with these recent experimental observations. We retain the Markovian nature of the kinetics, but, in contrast to the traditional models, we suggest that ion-channel proteins have a very large number of states all of similar energy. Gating, therefore, resembles a diffusion process. We show that our simplest one-dimensional model exhibits single-channel distributions that follow power laws of the form t-a, where 1/2 less than or equal to a less than or equal to 3/2. Exponents determined from recent experiments approximately fall within this range. We believe that this model is consistent with modern views of protein dynamics and, thus, may provide a key to the molecular details of the gating process.

Computer Simulation↗

Effect of noise on defect chaos in a reaction-diffusion model.

The influence of noise on defect chaos due to breakup of spiral waves through Doppler and Eckhaus instabilities is investigated numerically with a modified Fitzhugh-Nagumo model. By numerical simulations we show that the noise can drastically enhance the creation and annihilation rates of topological defects. The noise-free probability distribution function for defects in this model is found not to fit with the previously reported squared-Poisson distribution. Under the influence of noise, the distributions are flattened, and can fit with the squared-Poisson or the modified-Poisson distribution. The defect lifetime and diffusive property of defects under the influence of noise are also checked in this model.

Artifacts↗

A stochastic diffusion model of the time path of nuptiality.

"The time path of nuptiality is approximated by means of the log normal diffusion process. The drift coefficient is estimated by the method of maximum likelihood. Swedish and Canadian data on nuptiality have been utilised to illustrate the model. A piece-wise fitting of the log-normal model to the Swedish data reveals that the drift coefficient is changing over time. The use of mixing distribution is suggested to remedy this problem. On the whole the Hajnal theory of nuptiality transition is supported. It is also seen that the Hajnal transition is one in a series of transitions."

Americas↗

Periodic spatiotemporal patterns in a two-dimensional two-variable reaction-diffusion model.

Periodic spatiotemporal two-dimensional (2D) asymptotic patterns in an excitable two-variable thermochemical (reaction-diffusion) system are shown. In a one-dimensional system the traveling impulse which reflects from impermeable boundaries is a stable asymptotic solution if the diffusion coefficient of the reactant is greater than the thermal diffusivity of the system. Periodic patterns of two symmetries are presented in the 2D system: the impulse of excitation propagating along the diagonal of a square spatial domain and a structure consisting of curved impulses which propagate in the direction perpendicular to one side of a rectangular domain.

Journal Article↗

Calcium diffusion models and transmitter release in neurons.

Calcium enters neurons or nerve terminals through the surface membrane, and then diffuses inwardly and is diluted. Calcium acts at membrane sites to release transmitter or modulate channels, or at organelles or the nucleus to regulate metabolism. Thus the average cytoplasmic calcium concentration is a poor predictor of calcium-dependent processes. Solutions of the diffusion equation with appropriate geometries and boundary conditions help considerably in our quantitative understanding of calcium-dependent processes in neurons.

Action Potentials↗

Myoglobin content and oxygen diffusion: model analysis of horse and steer muscle.

We test the hypothesis that myoglobin is important for O2 supply near the oxidative capacity of muscle. This hypothesis is evaluated with a simple model that incorporates the properties of heart and skeletal muscle tissue taken from steers and horses exercising at their maximum O2 consumption rate. These tissue samples allowed us to set the bounds on oxidative demand and O2 flux from red blood cells to the core of the muscle fiber, to estimate the blood and tissue capacities for O2 diffusion, and to define the capillary blood PO2 driving this O2 flux. A model combining blood convection with tissue diffusion indicates that O2 diffusion alone is insufficient to achieve the measured O2 fluxes in many samples. The myoglobin content of these fibers is significantly correlated with this O2 diffusion limitation and provides sufficient additional O2 flux to meet muscle O2 demand. The presence of myoglobin maintains the PO2 in the fiber core above anoxic levels for the majority of muscles. Thus myoglobin is critical to O2 supply at fluxes near the maximum and prevents anoxia by maintaining PO2 above levels needed to support mitochondrial function.

Animals↗

Closed-time distribution of ionic channels. Analytical solution to a one-dimensional defect-diffusion model.

A one-dimensional version of the model recently proposed by Läuger (1988) to explain the closed-time distribution of ionic channels in cell membranes is solved analytically. While the probability density f(t) for closed-time lengths may show a well-defined exponential behavior at short times, a power-law decay is predicted at long times. The influence of an additional random distribution of defects in the current-conducting protein is investigated and found to be dominating at long times. Explicit expressions that may be used for fitting experimental data are given for the closed-time distribution. Some of the available data are discussed and shown to be in good agreement with the predictions of the model.

Animals↗

Breaking of translational symmetry of a traveling planar impulse in a two-dimensional two-variable reaction-diffusion model.

The stability of a planar impulse in rectangular spatial domains for a two-variable excitable reaction-diffusion system is numerically studied. The dependence of the stability on the size of the domain perpendicular to the direction of the propagation of the impulse is shown. The instability results in asymptotic stable curved impulses or an asymptotic spatiotemporal structure, which is generated similarly to the one-dimensional backfiring phenomenon.

Journal Article↗

A diffusion-diffusion model for percutaneous drug absorption.

Several theories describing percutaneous drug absorption have been proposed, incorporating the mathematical solutions of differential equations describing percutaneous drug absorption processes where the vehicle and skin are regarded as simple diffusion membranes. By a solution derived from Laplace transforms, the mean residence time MRT and the variance of the residence time VRT in the vehicle are expressed as simple elementary functions of the following five pharmacokinetic parameters characterizing the percutaneous drug absorption: kd, which is defined as the normalized diffusion coefficient of the skin, kc, which is defined as the normalized skin-capillary boundary clearance, the apparent length of diffusion of the skin 1d, the effective length of the vehicle lv, and the diffusion coefficient of the vehicle Dv. All five parameters can be obtained by the methods proposed here. Results of numerical computation indicate that: concentration-distance curves in the vehicle and skin approximate two curves which are simply expressed using trigonometric functions when sufficient time elapses after an ointment application; the most suitable condition for the assumption that the concentration of a drug in the uppermost epidermis can be considered unchanged is the case where the partition coefficient between vehicle and skin is small, and the constancy of drug concentration is even more valid when the effective length of the vehicle is large; and the amount of a drug in the vehicle or skin and the flow rate of the drug from vehicle into skin or from skin into blood becomes linear on a semilogarithmic scale, and the slopes of those lines are small when Dv is small, when the partition coefficient between vehicle and skin is small, when lv is large, or when kc is small. A simple simulation method is also proposed using a biexponential for the concentration-time curve for the skin near the skin-capillary boundary, that is, the flow rate-time curve for drug passing from skin into blood.

Animals↗

Regulation of mitochondrial respiration in heart cells analyzed by reaction-diffusion model of energy transfer.

The purpose of this study is to investigate theoretically which intracellular factors may be important for regulation of mitochondrial respiration in working heart cells in vivo. We have developed a model that describes quantitatively the published experimental data on dependence of the rate of oxygen consumption and metabolic state of working isolated perfused rat heart on workload over its physiological range (Williamson JR, Ford G, Illingworth J, Safer B. Circ Res 38, Suppl I, I39-I51, 1976). Analysis of this model shows that for phosphocreatine, creatine, and ATP the equilibrium assumption is an acceptable approximation with respect to their diffusion in the intracellular bulk water phase. However, the ADP concentration changes in the contraction cycle in a nonequilibrium workload-dependent manner, showing the existence of the intracellular concentration gradients. The model shows that workload-dependent alteration of ADP concentration in the compartmentalized creatine kinase system may be taken, together with the changes in P(i) concentration, to be among the major components of the metabolic feedback signal for regulation of respiration in muscle cells.

Adenosine Diphosphate↗