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Results for “directional diffusion models”

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PubMed2005

The diffusive vesicle supply center model for tip growth in fungal hyphae.

We propose the diffusive vesicle supply center model for tip growth in fungal hyphae. The model is based on the three-dimensional vesicle supply center (VSC) model [Gierz, G., Bartnicki-García, S., 2001. A three-dimensional model of fungal morphogenesis based on the vesicle supply center concept: J. Theor. Biol. 208, 151-164], but incorporates two aspects of a more realistic vesicle delivery mechanism: vesicle diffusion from the VSC and a finite rate constant for vesicle fusion with the cell membrane. We develop a framework to describe tip growth for a general class of models based on the vesicle supply center concept. Combining this with a method for calculating the steady state distribution of diffusive vesicles we iteratively solve for stationary cell shapes. These show a blunter tip than predicted by the original VSC model, which we attribute to increased forward-directed vesicle delivery via diffusion. The predicted distance between the VSC and the utmost tip of the cell is set by the ratio between the diffusion constant and the rate constant for vesicle exocytosis. Combined with the cell radius, these define the only dimensionless parameter for our model.

Cytoplasmic Vesicles↗
PubMed1994

Water diffusion coefficient measurements in the finger by magnetic resonance imaging.

Diffusion coefficients of water have been measured in the fingers of humans by magnetic resonance imaging. It was found that the measured diffusion coefficients increased with subject age in certain regions of the finger but that these regions differed between males and females. The observation of an increased diffusion coefficient with age appears to be inconsistent with a direct-hydration model and possible explanations are given using other models. It is conjectured that the measured diffusion coefficient of water increases with age as a result of structural changes to proteins.

Adult↗
PubMedDate not supplied

[Treatment of surface burns with proteolytic enzymes: mathematic description of lysis kinetics].

The lysis of necrotic tissue by a proteolytic enzyme applied to the surface of a burn wound was studied. A mathematical model was proposed, which describes changes in the thickness of necrotic tissue as a function of the proteolytic activity of the enzyme. The model takes into account the inward-directed diffusion of the enzyme, the counterflow of interstitial fluid (exudates) containing specific inhibitors, and the extracellular matrix proteolysis. It was shown in terms of the quasi-stationary approach that the thickness of the necrotic tissue layer decreases exponentially with time; i.e., the lysis slows down as the thickness of the necrotic tissue layer decreases. The dependence of the characteristic time of this decrease on enzyme concentration was obtained. It was shown that, at high enzyme concentrations (more than 5 mg/ml), the entire time of lysis (after the establishment of quasi-stationary equilibrium) is inversely proportional to the concentration of the enzyme.

Burns↗
PubMed2003

Origin of directionality in the fish stripe pattern.

The formation of stripe patterns in animal skin has been explained by the reaction-diffusion (RD) system, a hypothetical chemical reaction proposed by A. Turing. Although animal stripes usually have directionality, the RD model alone cannot explain how the direction is specified. To investigate the mechanism regulating the direction of stripes, we studied stripe pattern formation in two species of Genicanthus during sexual conversion. These species share almost identical morphologic properties, except for their stripe direction. In both species, spots transiently arise at random positions and then combine and rearrange to form directional stripes. Computational analysis has shown that diffusion anisotropy is very effective at specifying the direction of stripes formed by the RD system. Model simulations reproduce the transient dynamics of directional pattern formation observed in fish as well as the resulting stripes. In cases where the magnitude and direction of diffusion anisotropy of the substances are identical, the resulting stripes are not directional. However, if they differ, stripes become directional. As only a small difference in anisotropy is required for this effect, any kind of structure with directional conformation might cause a marked change in stripe direction. Scales are the most likely candidate structure for generating anisotropic interactions in skin.

Animals↗
PubMed2006

Side diffusion modeling by the explicit consideration of a space-charge buildup under the mask during strip waveguide formation in the Ag+ -Na+ field-assisted ion-exchange process.

A space-charge buildup under the blocking mask in a field-assisted Ag+ -Na+ ion-exchange modeling is assumed. It results in the distortion of electric field lines in the direction under the mask edges. As a result, side diffusion occurs and the numerical model shows the same range of side diffusion as the experimental data. Explicit consideration of the space-charge buildup under the mask and solving the Poisson equation for the electric field determination make it possible to use more realistic boundary conditions in the numerical model, compared to the boundary conditions generally used.

Journal Article↗
PubMed2006

A new antibacterial carrier of hyaluronic acid gel.

BACKGROUND: Postoperative infection following total joint arthroplasty is thought to be one of the most serious and devastating complications. To develop an effective treatment for this complication, we tested a bioabsorbable antibacterial carrier that is made from novel cross-linked hyaluronic acid (HA) gel and gentamicin (GM). METHODS: Antibacterial activity of the carrier was evaluated by the agar diffusion test, direct contact test, in vivo mouse model, and in vivo rabbit osteomyelitis model. RESULTS: GM-containing HA gel suppressed bacterial growth both in vitro and in vivo. In the rabbit osteomyelitis model, beads coated with HA gel containing GM did not disturb bone ongrowth in the femoral stem. CONCLUSIONS: Our bioabsorbable carrier of antibiotic-containing HA gel is effective for prophylactic treatment or treatment of an actual deep infection following total joint arthroplasty.

Animals↗
PubMed2006

Continuous and tractable models for the variation of evolutionary rates.

We propose a continuous model for variation in the evolutionary rate across sites and over the phylogenetic tree. We derive exact transition probabilities of substitutions under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in financial applications. The model directly extends the standard gamma distributed rates across site model, with one additional parameter governing changes in rate down the tree. The parameters of the model can be estimated directly from two well-known statistics: the index of dispersion and the gamma shape parameter of the rates across sites model. The CIR model can be readily incorporated into probabilistic models for sequence evolution. We provide here an exact formula for the likelihood of a three-taxon tree. The likelihoods of larger trees can be evaluated using Monte-Carlo methods.

Base Sequence↗
PubMed2006

Probing lipid vesicles by bimolecular association and dissociation trajectories of single molecules.

Vesicles prepared by DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) and SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid molecules having sizes smaller than the diffraction-limited focused laser beam have been used to confine single molecules in the laser focus. The confinement of single molecules in a volume smaller than the focused laser beam leads to a Gaussian distribution of single molecule fluorescence intensity. The interactions of single Nile Red molecules with DMPC and SOPC lipid bilayers were studied by single molecule fluorescence confocal microscopy. Nile Red molecules were observed to associate with and dissociate from individual DMPC and SOPC vesicles adsorbed on a glass surface, generating on-and-off fluctuations in a fluorescence signal representing a very low noise two-state trajectory. Off-time statistics were used to investigate the mean radius of the vesicles and the size distribution functions. The means of the on-time distributions of Nile Red in DMPC and SOPC vesicles were significantly different. The association and dissociation reactions of single Nile Red molecules with a vesicle have been studied. Features of the bimolecular interaction between the probe Nile Red and the vesicle were evaluated from the uncorrelated mean on-time and vesicle radius distributions, and the linear Nile Red concentration dependence of the mean off-time. Nile Red is shown to be a useful probe of the structural fluctuations and heterogeneity of these membrane structures, and it is a useful model with which to directly study a diffusion-influenced reversible bimolecular reaction.

Dimyristoylphosphatidylcholine↗
PubMed2004

Adsorption and diffusion on a stepped surface: atomic hydrogen on Pt(211).

We present density functional theory calculations for atomic hydrogen interacting with a stepped surface, the Pt(211) surface. The calculations have been performed at the generalized gradient approximation level, using a slab representation of the surface. This is the state-of-the-art method for calculating the interaction of atoms or molecules with metal surfaces, nevertheless only few studies have used it to study atoms or molecules interacting with stepped surfaces, and none, to the best of our knowledge, have considered hydrogen interacting with stepped platinum surfaces. Our goal has been to initiate a systematic study of this topic. We have calculated the full three-dimensional potential energy surface (PES) for the H/Pt(211) system together with the vibrational band structure and vibrational eigenfunctions of H. A deep global minimum of the PES is found for bridge-bonded hydrogen on the step edge, in agreement with experimental results for the similar H/Pt(533) system. All the local vibrational excitations at the global minimum have been identified, and this will serve as a helpful guide to the interpretation of future experiments on this (or similar) system(s). Furthermore, from the calculated PES and vibrational band structure, we identify a number of consequences for the interpretation or modelling of diffusion experiments studying the coverage and directional dependence of atomic hydrogen diffusion on stepped platinum surfaces.

Journal Article↗
PubMed2006

Smectic order parameters from diffusion data.

Microcanonical molecular dynamics simulations have been performed in the smectic A phase of an elementary liquid-crystal model. Smectic order parameters and diffusion coefficients along directions parallel and perpendicular to the director have been calculated during the same trajectory for a number of state points. This has permitted the satisfactory testing of a procedure, adopted in the analysis of experimental self-diffusion coefficients, leading to an estimate of the temperature dependence of the smectic order parameters. This methodology has been then confidently applied to two smectogenic thermotropic liquid crystals belonging to the 4,4(')-di-n-alkyl-azoxybenzene series. The derived smectic order parameters are larger for the homologue compound with the longest alkyl chains. This is consistent with the well-established increased tendency, for members of a homologue series, to form a smectic phase as their alkyl chains become longer.

Journal Article↗
PubMed2006

Segregation instabilities of moving interfaces.

The segregation of solute particles on a moving interface leads to the appearance of two types of instabilities near competing velocity thresholds. This behavior is shown to occur in a variety of exactly solvable models where the interface motion is coupled to a diffusion process of the solute particles. These models directly apply to the propagation of internal domain walls, but can also be generalized to surfaces of growing crystals in the kinetics-limited regime.

Journal Article↗
PubMed2000

Hypothesis: do voltage-gated H(+) channels in alveolar epithelial cells contribute to CO(2) elimination by the lung?

Although alveolar epithelial cells were the first mammalian cells in which voltage-gated H(+) currents were recorded, no specific function has yet been proposed. Here we consider whether H(+) channels contribute to one of the main functions of the lung: CO(2) elimination. This idea builds on several observations: 1) some cell membranes have low CO(2) permeability, 2) carbonic anhydrase is present in alveolar epithelium and contributes to CO(2) extrusion by facilitating diffusion, 3) the transepithelial potential difference favors selective activation of H(+) channels in apical membranes, and 4) the properties of H(+) channels are ideally suited to the proposed role. H(+) channels open only when the electrochemical gradient for H(+) is outward, imparting directionality to the diffusion process. Unlike previous facilitated diffusion models, HCO(-)(3) and H(+) recombine to form CO(2) in the alveolar subphase. Rough quantitative considerations indicate that the proposed mechanism is plausible and indicate a significant capacity for CO(2) elimination by the lung by this route. Fully activated alveolar H(+) channels extrude acid equivalents at three times the resting rate of CO(2) production.

Acid-Base Equilibrium↗
PubMed1984

Allometry of water vapor absorption in two species of tenebrionid beetle larvae.

Water vapor absorption is compared in the two tenebrionid larvae Tenebrio molitor and Onymacris marginipennis. Thresholds for absorption and "absorption capacity," which depend on ion transport by Malpighian tubules, are consistently different over the entire size range of the two species. Because of lower thresholds, uptake rates of Onymacris are over double those of Tenebrio in larvae of the same size at identical ambient water activities. By contrast, passive determinants of uptake, rectal conductance, and morphometry are similarly scaled with size in the two species. A ventilatory mechanism of vapor entry into the rectum is proposed for both species, since the anal canal is too long and narrow for exclusively diffusional entry. Vapor uptake in relation to larval mass was described by a simple diffusion model through rectal tissue, where flux varied directly with surface area and inversely with the distance between the lumen and Malpighian tubules. Failure of rectal conductance to increase proportionally with body mass means that size-specific vapor uptake declines with larval size in both species.

Absorption↗
PubMed1999

A Lagrangian Stochastic Model for Heavy Particle Deposition.

A Lagrangian stochastic model for the deposition of heavy particles from turbulent flows is presented. Heavy particles are treated as tracer particles moving in a virtual fluid having heavy particle velocity statistics. These velocity statistics are deduced from the particle momentum equation. The model satisfies the well-mixed condition for this virtual fluid and is consistent with similarity theory. Model agreement with experimental data for the "inertia-moderated" regime and the upper half of the "diffusion-impaction" regime (nondimensional particle relaxation time, tau+p > 5) is excellent. In accord with the results of direct numerical simulations for the diffusion-impaction regime, the model predicts a build-up of particle concentration in the viscous sublayer. Such a build-up concentration is not predicted by current Lagrangian stochastic models nor by models utilizing the "diffusion/free-flight" concept. Copyright 1999 Academic Press.

Journal Article↗
PubMed2003

Radiation enhanced silicon self-diffusion and the silicon vacancy at high temperatures.

We report proton radiation enhanced self-diffusion (RESD) studies on Si-isotope heterostructures. Self-diffusion experiments under irradiation were performed at temperatures between 780 degrees C and 872 degrees C for various times and proton fluxes. Detailed modeling of RESD provides direct evidence that vacancies at high temperatures diffuse with a migration enthalpy of H(m)(V)=(1.8+/-0.5) eV significantly more slowly than expected from their diffusion at low temperatures, which is described by H(m)(V)<0.5 eV. We conclude that this diffusion behavior is a consequence of the microscopic configuration of the vacancy whose entropy and enthalpy of migration increase with increasing temperature.

Journal Article↗
PubMed2001

Performance of batch membrane reactor: Glycerol-3-phosphate synthesis coupled with adenosine triphosphate regeneration.

Glycerol-3-phosphate (G3P) was synthesized from glycerol using glycerol kinase (GK). This reaction requires adenosine triphosphate (ATP) and was coupled with the ATP regeneration reaction using acetate kinase (AK) in a batch-operated ultrafiltration hollow-fiber reactor. By taking into consideration the dynamic nature of the bioreactor performance under non-steady-state conditions, a model for the performance of a batch membrane reactor for G3P synthesis coupled with ATP regeneration was developed and studied. The simulation results showed good agreement with the experimental results. The simulation studies have provided some insight into the process dynamics of the coupled reactions in the reactor system studied. For the reactor operational model used, in which the enzymes are retained in the shell side and the substrates are also initially placed in the shell side, it was found that the substrate concentration in the lumen side increased to a level higher than that in the shell side, and a backdiffusion occurred from the lumen side to the shell side during reactor operation. The ratio of the reaction rate to diffusion rate goes through a sharp peak during the time that the direction of diffusion is reversed. For another reactor operational model, in which the substrates were initially placed in the lumen side and enzymes were retained in the shell side, it was found that the rate-controlling step between the reaction and diffusion was switched during the reactor operation. Initially, the reaction rate increased while the diffusion rate was high and the substrate concentrations increased in the shell side. The ratio of reaction rate to diffusion rate increased to a maximum and remained at a constant level as the diffusion rate decreased to a low level due to the nonlinear characteristics of mass transfer process. This study provides information that is useful for optimization of batch membrane enzyme reactor operation and for a fed-batch-type process with an intermittent feeding strategy for efficient use of substrates.

Acetate Kinase↗
PubMed2006

Testing predictions of macroscopic binary diffusion coefficients using lattice models with site heterogeneity.

Quantitatively predicting mass transport rates for chemical mixtures in porous materials is important in applications of materials such as adsorbents, membranes, and catalysts. Because directly assessing mixture transport experimentally is challenging, theoretical models that can predict mixture diffusion coefficients using only single-component information would have many uses. One such model was proposed by Skoulidas, Sholl, and Krishna (Langmuir, 2003, 19, 7977), and applications of this model to a variety of chemical mixtures in nanoporous materials have yielded promising results. In this paper, the accuracy of this model for predicting mixture diffusion coefficients in materials that exhibit a heterogeneous distribution of local binding energies is examined. To examine this issue, single-component and binary mixture diffusion coefficients are computed using kinetic Monte Carlo for a two-dimensional lattice model over a wide range of lattice occupancies and compositions. The approach suggested by Skoulidas, Sholl, and Krishna is found to be accurate in situations where the spatial distribution of binding site energies is relatively homogeneous, but is considerably less accurate for strongly heterogeneous energy distributions.

Journal Article↗
PubMed2000

Biased diffusion in anisotropic disordered systems

We investigate a diffusion process into an anisotropic disordered medium in the presence of a bias. The medium is modeled by a two-dimensional square lattice in which the anisotropic disorder is represented by a bond percolation model with different occupation probabilities on each direction. The biased diffusion process is mapped by a random walk with unequal transition probabilities along and against the field (in the [1,1] direction) by performing Monte Carlo simulations. We observe a transition from pure to drift diffusion when the bias reaches a threshold B(c). In order to estimate this B(c), an effective exponentis used to characterize the diffusion process. This B(c) is also compared with another estimation for the critical field.

Journal Article↗