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Critical properties of the reaction-diffusion model 2A-->3A, 2A-->0.

The steady-state phase diagram of the one-dimensional reaction-diffusion model 2A-->3A, 2A-->0 is studied through the non-Hermitian density matrix renormalization group. In the absence of single-particle diffusion the model reduces to the pair-contact process, which has a phase transition in the universality class of directed percolation (DP) and an infinite number of absorbing steady states. When single-particle diffusion is added, the number of absorbing steady states is reduced to 2 and the model no longer shows DP critical behavior. The exponents theta=nu(parallel)/nu(perpendicular) and beta/nu(perpendicular) are calculated numerically. The value of beta/nu(perpendicular) is close to the value of the parity conserving universality class, in spite of the absence of local conservation laws.

Journal Article↗

Application of reaction-diffusion models to cell patterning in Xenopus retina. Initiation of patterns and their biological stability.

We have examined the behavior of two reaction-diffusion models, originally proposed by Gierer & Meinhardt (1972) and by Kauffman, Shymko & Trabert (1978), for biological pattern formation. Calculations are presented for pattern formation on a disc (approximating the geometry of a number of embryonic anlagen including the frog eye rudiment), emphasizing the sensitivity of patterns to changes in initial conditions and to perturbations in the geometry of the morphogen-producing space. Analysis of the linearized equations from the models enabled us to select appropriate parameters and disc size for pattern growth. A computer-implemented finite element method was used to solve the non-linear model equations reiteratively. For the Gierer-Meinhardt model, initial activation (varying in size over two orders of magnitude) of one point on the disc's edge was sufficient to generate the primary gradient. Various parts of the disc were removed (remaining only as diffusible space) from the morphogen-producing cycle to investigate the effects of cells dropping out of the cycle due to cell death or malfunction (single point removed) or differentiation (center removed), as occur in the Xenopus eye rudiment. The resulting patterns had the same general shape and amplitude as normal gradients. Nor did a two-fold increase in disc size affect the pattern-generating ability of the model. Disc fragments bearing their primary gradient patterns were fused (with gradients in opposite directions, but each parallel to the fusion line). The resulting patterns generated by the model showed many similarities to results of "compound eye" experiments in Xenopus. Similar patterns were obtained with the model of Kauffman's group (1978), but we found less stability of the pattern subject to simulations of central differentiation. However, removal of a single point from the morphogen cycle (cell death) did not result in any change. The sensitivity of the Kauffman et al. model to shape perturbations is not surprising since the model was originally designed to use shape and increasing size during growth to generate a sequence of transient patterns. However, the Gierer-Meinhardt model is remarkably stable even when subjected to a wide range of perturbations in the diffusible space, thus allowing it to cope with normal biological variability, and offering an exciting range of possibilities for reaction-diffusion models as mechanisms underlying the spatial patterns of tissue structures.

Animals↗

Min-protein oscillations in Escherichia coli with spontaneous formation of two-stranded filaments in a three-dimensional stochastic reaction-diffusion model.

We introduce a three-dimensional stochastic reaction-diffusion model to describe MinD/MinE dynamical structures in Escherichia coli. This model spontaneously generates pole-to-pole oscillations of the membrane-associated MinD proteins, MinE ring, as well as filaments of the membrane-associated MinD proteins. Experimental data suggest MinD filaments are two-stranded. In order to model them we assume that each membrane-associated MinD protein can form up to three bonds with adjacent membrane-associated MinD molecules and that MinE induced hydrolysis strongly depends on the number of bonds MinD has established.

Adenosine Triphosphatases↗

Diffusion model for drug release from suspensions II: release to a perfect sink.

Numerical mathematical methods are applied to a diffusion model based on physicochemical principles to predict drug release from suspensions of drug in semisolid vehicles. The predicted mass of drug released versus time curves using this model are in agreement with some reported experimental data but differ from predictions using the classical model for semisolid suspensions. The differences are discussed in relation to the drug dissolution rate and diffusion rate in the vehicle.

Biological Transport↗

Slow dynamics and aging in a constrained diffusion model.

We carry out a complete analysis of the schematic diffusive model recently introduced for the description of supercooled liquids and glassy systems above the glass temperature. The model is described by a trivial equilibrium measure and the presence of kinetics constraints is mimicked through a rapidly decreasing mobility at high particle density. The governing equation describing a sudden quench process is investigated analytically in a mean field approach and by means of numerical simulations. For deep quenches a long lasting off-equilibrium dynamics is observed in dense systems before equilibration is achieved, where time translational invariance lacks and the system ages. The kinetics is slow in this time domain since the average particle diffusivity D decreases in time, as opposed to the standard diffusion case of a constant D, that is recovered only in equilibrium. The autocorrelation function decays slower than an exponential, falling in mean field as an enhanced power law. The linear response function is computed and the modalities of the break-down of the fluctuation dissipation theorem are analytically investigated, showing that an effective temperature can be defined which slowly approaches the bath temperature from above.

Journal Article↗

Comparative analysis of percutaneous absorption enhancement by d-limonene and oleic acid based on a skin diffusion model.

Percutaneous absorption-enhancing effects of d-limonene and oleic acid were investigated using three model drugs with different lipophilicities in in vitro diffusion experiments with guinea pig skin. Pretreatment of the skin with d-limonene resulted in a large penetration enhancement for the lipophilic butylparaben (BP) and amphiphilic 6-mercaptopurine (6-MP) but had little effect on the hydrophilic mannitol (MT). Oleic acid caused a large effect only on 6-MP penetration. The penetration profiles were analyzed with a two-layer skin diffusion model consisting of stratum corneum with polar and nonpolar routes and viable epidermis plus dermis. Through curve-fitting, six parameters corresponding to drug diffusivity and partitioning in these three regions of the skin were obtained, and the mechanisms of enhancers were assessed in comparison with those of 1-geranylazacycloheptan-2-one (GACH) reported previously. Increased penetration was caused mainly by modification of the barrier property of the nonpolar route in the stratum corneum in all cases. In the nonpolar route, d-limonene increased mainly drug diffusivity, while GACH enhanced predominantly drug partitioning. On the other hand, oleic acid moderately increased both parameters.

Animals↗

Determination of ionic conductivity and its impact on proton diffusion model for nickel hydroxide.

The ionic conductivity is an important but previously ignored aspect for the nickel hydroxide used in alkaline batteries. With a specially designed device, the ionic conductivity is determined for single beads of spherical nickel hydroxide in KOH solutions. The apparent ionic conductivity is found on the order of 10(-3)-10(-2) S cm-1 in 6 M KOH and to change with the conductivity of the solution in which the bead is immersed. The ionic conductivity of the bead can be mainly attributed to the electrolyte absorbed in the bead. On the basis of these findings, the dual structure model for proton diffusion in spherical nickel hydroxide is refined by specifying nanoparticles to be the component showing a large apparent proton diffusion coefficient (on the order of 10(-7) cm2 s-1). This refined model is able to interpret the main features of the diffusion coefficients reported in the literature, including the unusually large scattering (up to 6 orders of magnitude) and inconsistency in the dependence of proton diffusion coefficient on the state of the charge. Besides, this refined model is supported by the influence of bulk KOH concentration on chronoamperometry and transmission electron microscopy observations.

Journal Article↗

Persistence in reaction diffusion models with weak allee effect.

We study the positive steady state distributions and dynamical behavior of reaction-diffusion equation with weak allele effect type growth, in which the growth rate per capita is not monotonic as in logistic type, and the habitat is assumed to be a heterogeneous bounded region. The existence of multiple steady states is shown, and the global bifurcation diagrams are obtained. Results are applied to a reaction-diffusion model with type II functional response, and also a model with density-dependent diffusion of animal aggregation.

Animals↗

Re-evaluation of the oxygen diffusion model for predicting minimum contact lens Dk/t values needed to avoid corneal anoxia.

PURPOSE: (1) To update Fatt's mathematical model of the distribution of oxygen tension (pO2) across the cornea and contact lens (CL) to include the recent finding that corneal oxygen consumption increases with the acidification that occurs with CL wear. (2) To estimate the minimum transmissibility (CL Dk/t) to avoid epithelial anoxia or to avoid stromal anoxia. METHODS: A five-layer static and one-dimensional mathematical model of oxygen diffusion through the cornea based on Fatt's models was used. The relationships between acidosis and increased QO2, and acidosis and CL Dk/t were used to estimate corneal QO2 for a given CL Dk/t. RESULTS: (1) Revised model predictions are in agreement with direct tear pO2 measurements beneath CLs in the rabbit. (2) For the human eye, the minimum CL Dk/t for oxygen delivery to the basal epithelial cells was determined to be 23 for the open eye and 89 for the closed eye. To prevent anoxia throughout the entire corneal thickness the Dk/t requirements are 35 for the open eye and 125 for the closed eye. CONCLUSIONS: (1) Model predictions of the oxygen distribution beneath contact lenses are significantly lower than previous models that did not include the effect of acidosis on corneal QO2. (2) Minimum Dk/t values that allow oxygen delivery to the basal epithelium are in agreement with the Dk/t needed to avoid corneal edema.

Acidosis↗

Reaction-diffusion models of within-feather pigmentation patterning.

Feathers are complex, branched keratin structures that exhibit a diversity of pigmentation patterns. Feather pigments are transferred into developing feather keratinocytes from pigment cells that migrate into the tubular feather germ from the dermis. Within-feather pigment patterns are determined by differential pigmentation of keratinocytes within independent barb ridges during feather development. Little is known about the molecular mechanisms that determine which keratinocytes receive pigment. We apply reaction-diffusion models to the growth of within-feather pigment patterns based on a realistic model of feather growth. These models accurately simulate the growth of a diversity of the within-feather pigmentation patterns found in real feathers, including a central patch, a 'hollow' central patch, concentric central patches, bars, chevrons, a central circular spot, rows of paired spots, and arrays of offset dots. The models can also simulate the complex transitions between distinct pigmentation patterns among feathers observed in real avian plumages, including transitions from bars to chevrons, bars to paired dots, and bars to arrays of dots. The congruence between the developmental dynamics of the simulated and observed feather patterns indicates that the reaction-diffusion models provide a realistic and accurate description of the determination of pigment pattern within avian feather follicles. The models support the hypothesis that within-feather pigmentation patterning is determined by antagonistic interactions among molecular expression gradients within the tubular follicle and feather germ.

Animals↗

Generalized diffusion model in optical tomography with clear layers.

We introduce a generalized diffusion equation that models the propagation of photons in highly scattering domains with thin nonscattering clear layers. Classical diffusion models break down in the presence of clear layers. The model that we propose accurately accounts for the clear-layer effects and has a computational cost comparable to that of classical diffusion. It is based on modeling the propagation in the clear layer as a local tangential diffusion process. It can be justified mathematically in the limit of small mean free paths and is shown numerically to be very accurate in two- and three-dimensional idealized cases. We believe that this model can be used as an accurate forward model in optical tomography.

Diffusion↗

Radon diffusion modelling.

A mathematical model has been developed that examines the ingress of radon into houses, through a vertical crack in an otherwise impervious concrete floor. Initially, the model considered the diffusive flow of radon from its soil source and this simulation has highlighted the dependency of the flux of radon into the house on the magnitude of various parameters, such as the diffusion coefficient of radon in soil. A preliminary investigation of the modelling of pressure-driven flow into a building is presented, and the potential of this type of analysis is discussed.

Diffusion↗

Reaction diffusion model of the enzymatic erosion of insoluble fibrillar matrices.

Predicting the time course of in vivo biodegradation is a key issue in the design of an increasing number of biomedical applications such as sutures, tissue analogs and drug-delivery devices. The design of such biodegradable devices is hampered by the absence of quantitative models for the enzymatic erosion of solid protein matrices. In this work, we derive and simulate a reaction diffusion model for the enzymatic erosion of fibrillar gels that successfully reproduces the main qualitative features of this process. A key aspect of the proposed model is the incorporation of steric hindrance into the standard Michaelis-Menten scheme for enzyme kinetics. In the limit of instantaneous diffusion, the model equations are analogous to the standard equations for enzymatic degradation in solution. Invoking this analogy, the total quasi-steady-state approximation is used to derive approximate analytical solutions that are valid for a wide range of in vitro conditions. Using these analytical approximations, an experimental-theoretical method is derived to unambiguously estimate all the kinetic model parameters. Moreover, the analytical approximations correctly describe the characteristic hyperbolic dependence of the erosion rate on enzyme concentration and the zero-order erosion of thin fibers. For definiteness, the analysis of published experimental results of enzymatic degradation of fibrillar collagen is demonstrated, and the role of diffusion in these experiments is elucidated.

Binding Sites↗

Traveling wave solutions of a reaction diffusion model for competing pioneer and climax species.

Presented is a reaction-diffusion model for the interaction of pioneer and climax species. For certain parameters the system exhibits bistability and traveling wave solutions. Specifically, we show that when the climax species diffuses at a slow rate there are traveling wave solutions which correspond to extinction waves of either the pioneer or climax species. A leading order analysis is used in the one-dimensional spatial case to estimate the wave speed sign that determines which species becomes extinct. Results of these analyses are then compared to numerical simulations of wave front propagation for the model on one and two-dimensional spatial domains. A simple mechanism for harvesting is also introduced.

Animals↗

Diffusion model of radon exhalation rates.

Radon migration through walls is considered using an effective diffusion model. One and two dimensional models as well as a spherical geometry are compared. It is concluded that either the 1-dimensional or spherical model, both having analytical solution, may be used for practical purposes. Application is made for typical cases in Athens, Greece.

Diffusion↗

Modeling diffusion in white matter in the brain: a composite porous medium.

We model diffusion in white matter fascicles as a problem of diffusion in an array of identical thick-walled cylindrical tubes immersed in an outer medium and arranged periodically in a regular lattice. The diffusing molecules have different diffusion coefficients and concentrations (or densities) within the tubes' inner core, membrane, myelin sheath, and within the outer medium. For an impermeable myelin sheath, diffusing molecules within the inner core are completely restricted, while molecules in the outer medium are hindered due to the tortuosity of the array of impenetrable tubes.

Animals↗

Reaction diffusion models in one dimension with disorder.

We study a large class of one-dimensional reaction diffusion models with quenched disorder using a real space renormalization group method (RSRG) which yields exact results at large time. Particles (e.g., of several species) undergo diffusion with random local bias (Sinai model) and may react upon meeting. We obtain a detailed description of the asymptotic states (i.e., attractive fixed points of the RSRG), such as the large time decay of the density of each specie, their associated universal amplitudes, and the spatial distribution of particles. We also derive the spectrum of nontrivial exponents which characterize the convergence towards the asymptotic states. For reactions which lead to several possible asymptotic states separated by unstable fixed points, we analyze the dynamical phase diagram and obtain the critical exponents characterizing the transitions. We also obtain a detailed characterization of the persistence properties for single particles as well as more complex patterns. We compute the decay exponents for the probability of no crossing of a given point by, respectively, the single particle trajectories (theta) or the thermally averaged packets (theta). The generalized persistence exponents associated to n crossings are also obtained. Specifying to the process A+A--> or A with probabilities (r,1-r), we compute exactly the exponents delta(r) and psi(r) characterizing the survival up to time t of a domain without any merging or with mergings, respectively, and the exponents deltaA(r) and psiA(r) characterizing the survival up to time t of a particle A without any coalescence or with coalescences, respectively. theta, psi, and delta obey hypergeometric equations and are numerically surprisingly close to pure system exponents (though associated to a completely different diffusion length). The effect of additional disorder in the reaction rates, as well as some open questions, are also discussed.

Journal Article↗

Calcium diffusion modeling in a spherical neuron. Relevance of buffering properties.

We have developed a calcium diffusion model for a spherical neuron which incorporates calcium influx and extrusion through the plasma membrane as well as three calcium buffer systems with different capacities, mobilities, and kinetics. The model allows us to calculate the concentration of any of the species involved at all locations in the cell and can be used to account for experimental data obtained with high-speed Ca imaging techniques. The influence of several factors on the Ca2+ transients is studied. The relationship between peak [Ca2+]i and calcium load is shown to be nonlinear and to depend on buffer characteristics. The time course of the Ca2+ signals is also shown to be dependent on buffer properties. In particular, buffer mobility strongly determines the size and time course of Ca2+ signals in the cell interior. The model predicts that the presence of exogenous buffer, such as fura-2, modifies the Ca2+ transients to a variable extent depending on its proportion relative to the natural, intrinsic buffers. The conclusions about natural calcium buffer properties that can be derived from Ca imaging experiments are discussed.

Animals↗