Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Diffusion models”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources
PubMed1992

Pharmacokinetic analysis of drug absorption from muscle based on a physiological diffusion model: effect of molecular size on absorption.

In a rabbit hind leg perfusion experiment, the absorption of radiolabeled water and carbohydrates of various molecular sizes from muscle was analyzed using a physiological diffusion model and, also, by statistical moment analysis. The model takes into account diffusion in the interstitial space, transcapillary movement, and removal by the blood circulation and pharmacokinetic parameters representing these processes were computed by curve-fitting. The apparent diffusion coefficients of water and small sugars in the interstitial space (Dm) were proportional to their free diffusion coefficients in water (Df), whereas the diffusion of 14C-inulin was hampered by interstitial structures. The first moments of each absorption process were also determined to assess the quantitative contribution of each absorption process to overall absorption. For carbohydrate molecules, residence time in the depot (td) accounted for most of the absorption time after injection, whereas for 3H-water, residence times in muscle (tm) and in the depot (td) were similar.

Absorption↗
PubMed2006

Tropical--parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images.

UNLABELLED: Tropical is a software for simulation and parameter estimation of reaction-diffusion models. Based on spatio-temporal microscopy images, Tropical estimates reaction and diffusion coefficients for user-defined models. Tropical allows the investigation of systems with an inhomogeneous distribution of molecules, making it well suited for quantitative analyses of microscopy experiments such as fluorescence recovery after photobleaching (FRAP). AVAILABILITY: Tropical is available free of charge for academic use at http://www.dkfz.de/tbi/projects/modellingAndSimulationOfCelluarSystems/tropical.jsp after signing a material transfer agreement.

Algorithms↗
PubMed2006

A comparison of monodomain and bidomain reaction-diffusion models for action potential propagation in the human heart.

A bidomain reaction-diffusion model of the human heart was developed, and potentials resulting from normal depolarization and repolarization were compared with results from a compatible monodomain model. Comparisons were made for an empty isolated heart and for a heart with fluid-filled ventricles. Both sinus rhythm and ectopic activation were simulated. The bidomain model took 2 days on 32 processors to simulate a complete cardiac cycle. Differences between monodomain and bidomain results were extremely small, even for the extracellular potentials, which in case of the monodomain model were computed with a high-resolution forward model. Propagation of activation was 2% faster in the bidomain model than in the monodomain model. Electrograms computed with monodomain and bidomain models were visually indistinguishable. We conclude that, in the absence of applied currents, propagating action potentials on the scale of a human heart can be studied with a monodomain model.

Action Potentials↗
PubMed1992

Random genetic drift and selection in a triallelic locus: a continuous diffusion model.

The Kolmogorov forward diffusion equation is used to examine the evolution of three alleles at one locus under viability selection and random genetic drift. Separation of variables and Chebyschev approximations are employed to solve this equation for long times. As an example, one artificial viability set is examined in detail; its general implications for the evolution at a triallelic locus are discussed.

Alleles↗
PubMed2002

Spatial resonances and superposition patterns in a reaction-diffusion model with interacting Turing modes.

Spatial resonances leading to superlattice hexagonal patterns, known as "black-eyes," and superposition patterns combining stripes and/or spots are studied in a reaction-diffusion model of two interacting Turing modes with different wavelengths. A three-phase oscillatory interlacing hexagonal lattice pattern is also found, and its appearance is attributed to resonance between a Turing mode and its subharmonic.

Diffusion↗
PubMed1997

Using a simple diffusion model to predict residual monomer migration--considerations and limitations.

A simple mathematical equation based on a diffusion model has been utilized recently to estimate migration of both acrylonitrile and styrene from polymers produced from these monomers which are used under a wide variety of food-contact applications. These calculated migration values have subsequently been used to estimate the US consumer's exposure to acrylonitrile and styrene from food stored in these materials. The basic assumptions integral to the model are discussed in relation to potential errors in migration estimates that could be experienced if the assumptions are not true. In addition to the discussion of the basic assumptions, factors affecting the migration predictions such as polymer 'ageing', temperature changes during the lifetime of the polymeric article, the effects of polymer-modifying materials (plasticizers, impact modifiers), and the physical form of the article or test sample are discussed.

Acrylonitrile↗
PubMed1992

Replication of viruses in a growing plaque: a reaction-diffusion model.

An understanding of the viral replication process commonly referred to as "plaque growth" is developed in the context of a reaction-diffusion model. The interactions among three components: the virus, the healthy host, and the infected host are represented using rates of viral adsorption and desorption to the cell surface, replication and release by host lysis, and diffusion. The solution to the full model reveals a maximum in the dependence of the velocity of viral propagation on its equilibrium adsorption constant, suggesting that conditions can be chosen where viruses which adsorb poorly to their hosts will replicate faster in plaques than those which adsorb well. Analytic expressions for the propagation velocity as a function of the kinetic and diffusion parameters are presented for the limiting cases of equilibrated adsorption, slow adsorption, fast adsorption, and large virus yields. Hindered diffusion at high host concentrations must be included for quantitative agreement with experimental data.

Bacterial Physiological Phenomena↗
PubMed1992

A general diffusion model for analyzing the efficacy of synaptic input to threshold neurons.

We describe a general diffusion model for analyzing the efficacy of individual synaptic inputs to threshold neurons. A formal expression is obtained for the system propagator which, when given an arbitrary initial state for the cell, yields the conditional probability distribution for the state at all later times. The propagator for a cell with a finite threshold is written as a series expansion, such that each term in the series depends only on the infinite threshold propagator, which in the diffusion limit reduces to a Gaussian form. This procedure admits a graphical representation in terms of an infinite sequence of diagrams. To connect the theory to experiment, we construct an analytical expression for the primary correlation kernel (PCK) which profiles the change in the instantaneous firing rate produced by a single postsynaptic potential (PSP). Explicit solutions are obtained in the diffusion limit to first order in perturbation theory. Our approximate expression resembles the PCK obtained by computer simulation, with the accuracy depending strongly on the mode of firing. The theory is most accurate when the synaptic input drives the membrane potential to a mean level more than one standard deviation below the firing threshold, making such cells highly sensitive to synchronous synaptic input.

Computer Simulation↗
PubMed2000

Broad spectrum diffusion model for room acoustics ray-tracing algorithms

Geometrical acoustics methods have already been transformed to account for diffusely reflecting boundaries. In randomized ray-tracing algorithms, the sound rays are either specularly reflected or scattered, according to the value of a random number which is compared with the diffusion factor. However, this method becomes inefficient if this factor depends on frequency, since the process must then be repeated for each frequency band. A method is proposed in this paper to compute all frequency components simultaneously in a single pass. The diffuse reflection model is based on the definition of a new concept: the "splitting coefficient," which can differ from the diffusion factor. First, the randomized ray-tracing method is described and the diffusion model is applied to a single diffusing surface in free field. It is shown that the results computed by the program are in accordance with theoretical results. Then, the method is shown to work properly when it is applied to more realistic enclosures: This is proved in theory and illustrated by some examples. A particular problem is the increase of the statistical error which has been solved by an appropriate control of the splitting coefficient.

Journal Article↗
PubMed2006

A hand-over-hand diffusing model for myosin-VI molecular motors.

Single molecules of dimeric myosin-VI have been demonstrated to be able to move processively towards the pointed end of actin filament with a mean step size of approximately 36 nm. Here we present a hand-over-hand diffusing mechanism for this unidirectional movement. Based on this mechanism, its dynamical behaviors such as the step-size distribution, dwell-time distributions and mean dwell time at various ATP and ADP concentrations and under various loads are studied in detail. The calculated results show good agreement with previous experimental results. The processive movement of mutant myosin-V with its neck domains truncated to only one IQ motif can also be explained by using this hand-over-hand diffusing model.

Actins↗
PubMed2001

Combined diffusion model for the sorption of cadmium, copper, and zinc ions onto bone char.

The ability of bone char to remove three single-component metals (namely, cadmium, copper and zinc) from aqueous solutions has been studied. Equilibrium isotherms have been measured and analyzed using a Langmuir isotherm model. A series of batch contact time experiments were performed to study the effect of sorbent mass and initial metal ion concentration for the three systems. A new film-pore diffusion model has been applied to the batch contact time results, and good correlation is obtained between theoretical predictions and experimental data. A further extension to the new model was made to include a surface diffusion term. The agreement between theoretical results and experimental data improved as the sum of the squares of the errors (SSE) improved by around 20% for cadmium and zinc but by 50% for copper. Therefore, the sorptions of cadmium and zinc ions onto bone char are primarily film-pore diffusion controlled, but for the copper system film-pore-surface diffusion must be considered.

Adsorption↗
PubMed1990

Transport of inert gases in mammalian myocardium: comparison with a convection-diffusion model.

Because tracer techniques are gaining an increasing importance for imaging flow (and metabolism) in the heart, experimental evidence is needed on the role of convection and diffusion in the transcoronary transport of solutes. In the present work, the transport of four different inert gases through the coronary system is studied in five closed-chest dog experiments and is compared with a digital multicapillary convection-diffusion model. Transport may be defined as flow dependent, as judged by the gross similarity of shape of the time-normalized dilution curves. However, the results show that the transcoronary transport of helium and xenon is more dispersed than that of argon and krypton, probably because of differences in diffusibility and solubility. A comparison of the animal and model experiments emphasizes the importance of diffusive transport of the gases. It is suggested that there is a diffusion shunt that is mainly located within the capillary network itself rather than between conduit vessels. Only for helium (which has the highest diffusivity) was a small arteriovenous shunt fraction seen that is thought to bypass the capillary exchange region. The conclusion is that although there is evidence of diffusional shunting at a capillary level, the inert gas kinetics in the heart are compatible with a basically flow-limited transport.

Animals↗
PubMed2004

Collective diffusion model for water permeation through microscopic channels.

Water permeation through nanometric channels, generally a coupled many-body process, is described in this study by a single collective coordinate. A collective diffusion model is proposed in which water movement at equilibrium is characterized as an unbiased diffusion along this coordinate and water transport in the presence of a chemical potential difference is described as one-dimensional diffusion in a linear potential. The model allows one to determine the osmotic permeability of a water channel from equilibrium simulations.

Aquaporins↗
PubMed2002

Characterization of dupont photopolymer: determination of kinetic parameters in a diffusion model.

We investigate the recording dynamics of Omnidex photopolymer film from DuPont. We use a reviewed version of the diffusion model proposed by Zhao and Mouroulis [J. Mod. Opt. 41, 1929 (1994)] in order to describe the recording response that combined photopolymerization and free-monomer diffusion process. Two different experiments are detailed that lead to the determination of material kinetic parameters. These values are introduced in the numerical model to provide quantitative simulations of a grating formation under various holographic exposures. Theoretical results are experimentally checked as a validation of the model. We extend its applications to several secondary investigations, such as volume-shrinkage influence on refractive-index distribution and spectral selectivity of reflection gratings. This study improves the understanding of the recording process and consequently allows to build more accurate holographic components in this material to be built.

Journal Article↗
PubMed2004

Complex dynamics of the formation of spatially localized standing structures in the vicinity of saddle-node bifurcations of waves in the reaction-diffusion model of blood clotting.

Local activation in a one-dimensional three-component reaction-diffusion model of blood clotting may lead to a formation of spatially localized standing structures (peaks) via several complex scenarios. In the first scenario, two concentration pulses first propagate from the site of activation, then stop and transform into peaks [Zarnitsina et al., Chaos 11, 57 (2001)]. Here, we examine this scenario, and also describe a different scenario of peak formation. In this scenario, two trigger waves propagate initially in opposite directions away from the site of activation. Then they stop and change direction of propagation toward each other to the activation site, where they interact and form a peak. Both of these scenarios of stable peak formation are observed in the vicinity of saddle-node bifurcation and may be viewed as a memory of the extinct wave modes.

Animals↗
PubMed1999

The stochastic diffusion models of nerve membrane depolarization and interspike interval generation.

The first step to make the theory of stochastic diffusion processes that arise in connection with single neuron description more understandable is reviewing the deterministic leaky-integrator model. After this step the general principles of simple stochastic models are summarized which clearly reveal that two different sources of noise, intrinsic and external, can be identified. Many possible strategies of neuronal coding exist and one of these, the rate coding, for which the stochastic modeling is relevant, is pursued further. The rate coding is reflected, in experimental as well as theoretical studies, by an input-output curve and its properties are reviewed for the most common stochastic diffusion models. The results for the simplest stochastic diffusion model, the Wiener process, are presented and from them strong limitations of this model can be understood. The most common diffusion model is the Ornstein-Uhlenbeck process, which is one substantial step closer to reality since the spontaneous changes of the membrane potential are included in the model. Both these models are characterized by an additive noise. Taking into account the state dependency of the changes caused by neuronal inputs, we derive models where the noise has a multiplicative effect on the membrane depolarization. Two of these models are compared with the Wiener and Ornstein-Uhlenbeck models. How to identify the parameters of the models, which is an unavoidable task for the models verification, is investigated. The time-variable input is taken into account in the last part of the paper. An intuitive approach is stressed throughout the review.

Action Potentials↗
PubMed2005

Sorption kinetics of strontium in porous hydrous ferric oxide aggregates I. The Donnan diffusion model.

Sorption of ions by hydrous ferric oxide (HFO) often shows a fast initial sorption reaction followed by a much slower sorption process. The second step is diffusion-controlled and can continue for days or months before equilibrium is reached. In this paper, we demonstrate that the diffusion rate may be explained by electrostatic interactions. The internal and external surfaces of HFO are generally positively charged and therefore repel cations. This can result in extremely low cation concentrations in pores, and therefore a significant reduction in pore diffusion rate. The theory is demonstrated here for sorption of Sr(2+) in HFO aggregates. The ion concentrations in the pore space are calculated using a Donnan model and diffusion is calculated from the Donnan concentration and potential gradients. This diffusion model is compared with nonelectrostatic pore diffusion, which does not take electrostatic interactions into account. The Donnan model predicts very low concentrations of Sr(2+) in the pores and diffusion rates that are up to 8000 times lower than predicted with a nonelectrostatic model.

Journal Article↗