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At least 613 records · Page 34Linked to original sources
PubMed2005

Estimation of anisotropic optical parameters of tissue in a slab geometry.

The scattering and absorption coefficients of many homogeneous biological tissues such as muscle, skin, white matter in the brain, and dentin are often anisotropically oriented with respect to their bounding interface. In consequence the curves of equal intensity of re-emitted light on the surface of the slab will no longer be circular. We here consider the problem of determining the parameters allowing one to estimate the angles defining anisotropy, directional bias of diffusive spreading, and scattering and absorbing coefficients from data obtained from time-gated measurements of light intensity transmitted through a slab of the tissue. Our model can be solved exactly and leads to accurate approximations in which measured values of the surface intensity are shown to be elliptical. The parameters of the ellipses suffice to estimate the anisotropy of the tissue interior. A summary of the parameter estimates with the observables from which they are found is given in a table. Our analysis is based on a diffusion model.

Algorithms↗
PubMed2005

Multicellular tumor spheroid in an off-lattice Voronoi-Delaunay cell model.

We study multicellular tumor spheroids by introducing a new three-dimensional agent-based Voronoi-Delaunay hybrid model. In this model, the cell shape varies from spherical in thin solution to convex polyhedral in dense tissues. The next neighbors of the cells are provided by a weighted Delaunay triangulation with on average linear computational complexity. The cellular interactions include direct elastic forces and cell-cell as well as cell-matrix adhesion. The spatiotemporal distribution of two nutrients--oxygen and glucose--is described by reaction-diffusion equations. Viable cells consume the nutrients, which are converted into biomass by increasing the cell size during the G1 phase. We test hypotheses on the functional dependence of the uptake rates and use computer simulations to find suitable mechanisms for the induction of necrosis. This is done by comparing the outcome with experimental growth curves, where the best fit leads to an unexpected ratio of oxygen and glucose uptake rates. The model relies on physical quantities and can easily be generalized towards tissues involving different cell types. In addition, it provides many features that can be directly compared with the experiment.

Animals↗
PubMed1979

Experimental glomerulonephritis induced by in situ formation of immune complexes in glomerular capillary wall.

An experimental model of glomerulonephritis was produced by the in situ formation of immune complexes directly in the glomerular capillary wall. Perfusing the lectin concanavalin A (Con A) into the left renal arteries of rats led to its binding diffusely to the glycoproteins of the glomerular capillary wall of only that kidney in each animal. The subsequent reaction with anti-Con A antibody (either administered systemically or actively induced) resulted in an exudative and proliferative glomerulonephritis confined to the Con A perfused kidney. Immunofluorescence disclosed the diffuse deposition of immunoglobulin, Con A, and C3 in the perfused, but not the unperfused kidney. The quantitative relationship between antigen and antibody binding and histologic outcome was determined. Since lectins have been found in mammalian tissues, as well as in infectious agents that are pathogenic in man, a series of events conceptually similar to this in situ model may occur in some cases of glomerulonephritis in man.

Animals↗
PubMed2001

Quantitative measurement of water diffusion lifetimes at a protein/DNA interface by NMR.

Hydration site lifetimes of slowly diffusing water molecules at the protein/DNA interface of the vnd/NK-2 homeodomain DNA complex were determined using novel three-dimensional NMR techniques. The lifetimes were calculated using the ratios of ROE and NOE cross-relaxation rates between the water and the protein backbone and side chain amides. This calculation of the lifetimes is based on a model of the spectral density function of the water-protein interaction consisting of three timescales of motion: fast vibrational/rotational motion, diffusion into/out of the hydration site, and overall macromolecular tumbling. The lifetimes measured ranged from approximately 400 ps to more than 5 ns, and nearly all the slowly diffusing water molecules detected lie at the protein/DNA interface. A quantitative analysis of relayed water cross-relaxation indicated that even at very short mixing times. 5 ms for ROESY and 12 ms for NOESY, relay of magnetization can make a small but detectable contribution to the measured rates. The temperature dependences of the NOE rates were measured to help discriminate direct dipolar cross-relaxation from chemical exchange. Comparison with several X-ray structures of homeodomain/DNA complexes reveals a strong correspondence between water molecules in conserved locations and the slowly diffusing water molecules detected by NMR. A homology model based on the X-ray structures was created to visualize the conserved water molecules detected at the vnd/NK-2 homeodomain DNA interface. Two chains of water molecules are seen at the right and left sides of the major groove, adjacent to the third helix of the homeodomain. Two water-mediated hydrogen bond bridges spanning the protein/DNA interface are present in the model, one between the backbone of Phe8 and a DNA phosphate, and one between the side chain of Asn51 and a DNA phosphate. The hydrogen bond bridge between Asn51 and the DNA might be especially important since the DNA contact made by the invariant Asn51 residue, seen in all known homeodomain/DNA structures, is critical for binding affinity and specificity.

DNA↗
PubMed2006

Movement toward better environments and the evolution of rapid diffusion.

We study a reaction-diffusion-advection model for two ecologically equivalent competitors with different dispersal strategies inhabiting a spatially heterogeneous environment. The competitors represent different phenotypes of the same species. One is assumed to disperse by simple diffusion, the other by diffusion together with directed movement toward more favorable environments. We show that under suitable conditions on the underlying spatial domain, the competitor that moves toward more favorable environments may have a competitive advantage even if it diffuses more rapidly than the other competitor. This is in contrast with the case in which both competitors disperse by pure diffusion, where the competitor that diffuses more slowly always has the advantage. We determine competitive advantage by examining the invasibility, i.e. stability or instability, of steady states with only one competitor present. The mathematical approach is a perturbation analysis of principal eigenvalues.

Algorithms↗
PubMed2001

Cell dynamics simulations of shear-induced alignment and defect annihilation in stripe patterns formed by block copolymers.

The effect of large amplitude oscillatory shear on two-dimensional stripe patterns formed by block copolymers was investigated using cell dynamics simulations. A global orientational order parameter S and a correlation function for stripe normals G(r-r(')) were used to characterize the degree of stripe orientation under shear. The kinetics of stripe alignment, quantified by S, at various shear and quench conditions were studied as a function of strain amplitude, shear frequency, and temperature. The mechanisms of shear alignment and defect annihilation were investigated. A critical shear condition for complete alignment of stripes along the shear direction was also identified.

Diffusion↗
PubMed1997

Health impacts of large releases of radionuclides. Transport and processes in freshwater ecosystems.

The partition coefficient (Kd) and the water retention rate (RR) are fundamental components of dynamic, mass-balance models, not just for radionuclides in fresh water but also for contaminants in all aquatic ecosystems. Kd may be regarded as an 'entry gate' and RR an 'exit gate'. Uncertainties in Kd and RR cause uncertainties in model predictions. Uncertainties in important rates for processes within ecosystems (such as sedimentation, diffusion, advection, bio-uptake and excretion) cannot be adequately evaluated when uncertainties exist for Kd and RR. Empirical data show that there may be a variation in Kd of two orders of magnitude with environmental factors such as pH. This is important because Kd regulates the amount of radionuclides in dissolved and particulate phases, and hence also pelagic and benthic transport. Pelagic transport is directly linked to the outflow and retention of substances in the water mass, and thus also to concentrations and ecological effects. There are many approaches for sub-models of Kd and RR. Which provide the best predictive power? This chapter gives a brief overview and discussion of the benefits and drawbacks of different alternatives for Kd and RR within the framework of a lake model for radiocaesium.

Animals↗
PubMed2004

Efficient solution technique for solving the Poisson-Boltzmann equation.

The Poisson-Boltzmann (PB) equation has been extensively used to analyze the energetics and structure of proteins and other significant biomolecules immersed in electrolyte media. A new highly efficient approach for solving PB-type equations that allows for the modeling of many-atoms structures such as encountered in cell biology, virology, and nanotechnology is presented. We accomplish these efficiencies by reformulating the elliptic PB equation as the long-time solution of an advection-diffusion equation. An efficient modified, memory optimized, alternating direction implicit scheme is used to integrate the reformulated PB equation. Our approach is demonstrated on protein composites (a polio virus capsid protomer and a pentamer). The approach has great potential for the analysis of supramillion atoms immersed in a host electrolyte.

Algorithms↗
PubMed1982

Distribution of receptors and functions on cell surfaces: quantitation of ligand-receptor mobility and a new model for the control of plasma membrane topography.

The long-range movements of membrane ligand-receptor complexes into surface caps and into the pseudopods of cells performing phagocytosis, the uropods of motile cells and the cleavage furrows of dividing cells appear to be analogous processes. A common mechanism to explain these movements must take into account several recent observations. First, laser photobleaching studies have indicated that Concanavalin A-receptor movement occurs unidirectionally; and analyses of Con A redistribution by quantitative video intensification microscopy (QUAVIM) have shown that movement may exceed the maximum rates measured for protein diffusion in membranes. These are the results predicted for a process of directed migration but not for a process of diffusion with entrapment. In addition it has been found that membrane receptors may segregate out of as well as into cap, pseudopod, uropod and cleavage furrow regions and that topographical heterogeneity on asymmetric cells is not restricted to membrane molecular determinants but extends to a range of endocytic functions and to a macromolecular complex, the coated pit. All dynamic surface events are arrested during mitosis. A new model for the regulation of plasma membrane topography has been developed from these diverse quantitative, functional and morphological data. Its essence is the entrainment of selected membrane determinants on membrane waves directed towards regions such as caps, pseudopods, uropods and cleavage furrows. The waves are initiated by tension due to asymmetric microfilament-membrane interaction.

Animals↗
PubMed1998

Extinction rate of a population under both demographic and environmental stochasticity.

We examined the asymptotic rate of population extinction beta when the population experiences density-dependent population regulation, demographic stochasticity, and environmental stochasticity. We assume discrete-generation population dynamics, in which some parameters fluctuate between years. The fluctuation of parameters can be of any magnitude, including both fluctuation traditionally treated as diffusion processes and fluctuation from catastrophes within a single scheme. We develop a new approximate method of calculating the asymptotic rate of population extinction per year, beta=integralinfinity0 exp(-x) u(x) dx, where u(x) is the stationary distribution of adult population size from the continuous-population model including environmental stochasticity and population-regulation but neglecting demographic stochasticity. The method can be regarded as a perturbation expansion of the transition operator for population size. For several sets of population growth functions and probability distributions of environmental fluctuation, the stationary distributions can be calculated explicitly. Using these, we compare the predictions of this approximate method with that using a full transition operator and with the results of a direct Monte Carlo simulation. The approximate formula is accurate when the intrinsic rate of population increase is relatively large, though the magnitude of environmental fluctuation is also large. This approximation is complementary to the diffusion approximation.

Adult↗
PubMed1983

Concentration profile in the intestinal tract and drug absorption model: two-dimensional laminar flow in a circular porous tube.

The calculation method of the concentration profile in the intestinal tract was developed by adapting the two-dimensional laminar flow in a circular porous tube to the fluid flow and considering a small water absorption or secretion in the intestinal perfusion experiment. The concentration profile was changed by the axial component of velocity, the radial component of velocity, the membrane permeability coefficient, the reflection coefficient and so on. According to the calculated values, the concentration decreased from the center of the intestinal tract to the intestinal membrane as well as from the inlet to the outlet of the intestinal tract. The concentration at the aqueous-intestinal membrane interface increased when water was absorbed and decreased when water was secreted. Consequently, the drug absorption (or secretion), not only because of the effect of the solvent drag but also because of the increase (or decrease) of the concentration gradient at the aqueous-intestinal membrane interface. Using the proposed model in the present study, the concentration at the aqueous-intestinal membrane interface can be calculated directly under the various conditions. Therefore, the true membrane permeability coefficient can be obtained by a graphic method, without correcting the apparent membrane permeability coefficient by the effective thickness of the aqueous diffusion layer (the unstirred water layer).

Animals↗
PubMed1999

Modeling the influence of ectodomain affinities on the spatial distribution of membrane receptors.

We have previously shown that the glycosylphosphatidyl-inositol (GPI)-linked urokinase-type plasminogen activator receptor (uPAR) reversibly associates with the integrins complement receptor type 3 (CR3; alphaMbeta2) and CR4 (alphaxbeta2) during leukocyte motility. These receptor-to-receptor interactions could potentially be accounted for by diffusion-controlled reactions or by directed transport phenomena. To address these alternatives, we have used computer simulation techniques. Our results show that a diffusion-controlled interaction between uPAR and CR4 during accumulation at lamellipodia is not physically reasonable. This suggests that a directed transport mechanism participates in establishing uPAR-integrin association.

Animals↗
PubMed2005

Model analysis of flux enhancement across hairless mouse skin induced by chemical permeation enhancers.

Previous permeant partitioning studies with hairless mouse skin (HMS) in the presence of several chemical skin permeation enhancers have revealed that, when such enhancers induce significant skin permeability coefficient enhancement, it is accompanied by significant enhancement in the equilibrium uptake (partitioning) of the permeant into the intercellular lipid component of the stratum corneum (SC). Particularly, it was found that the 1-alkyl-2-pyrrolidones and the 1-alkyl-2-azacycloheptanones, at aqueous solution concentrations that gave skin permeation enhancement (E) of 10 for corticosterone (CS, the permeant), enhanced the equilibrium uptake of beta-estradiol (E2beta, a surrogate permeant) from the aqueous phase into the intercellular lipids of HMS SC by a factor of 5-7. This finding raised the question of whether this uptake enhancement induced by the permeation enhancer under equilibrium conditions would be essentially the same as that determined kinetically from time-dependent permeation experiments utilizing appropriate SC membrane models and Fick's laws of diffusion to treat the data. HMS transport experiments were conducted with CS as the permeant and 1-octyl-2-pyrrolidone (OP) and 1-hexyl-2-azacyloheptanone (HAZ) as the enhancers. In treating the experimental data, a one-layer skin transport model (SC only) and a two-layer model (SC layer and the epidermis/dermis layer) were both investigated. Both the partition coefficient enhancement (E(K)) and the diffusion coefficient enhancement (E(D)) were deduced from the data treatment. The results showed that when the total transport enhancement of CS was around 11, E(K) was in the range of 6-8 and E(D) was in the range of 1.5-1.9 using both the one-layer and the two-layer models. This E(K) value was found to be in good agreement with the E2beta partition enhancement obtained directly under equilibrium conditions in previous studies. This indicates that (a) the rate-limiting domain for the transport of the lipophilic permeants across HMS and the HMS SC intercellular lipid domain probed in the equilibrium partitioning experiments are essentially the same, and (b) the total flux enhancement (E) of lipophilic permeants across HMS was driven mainly by enhancing the partitioning of the permeant into the rate-limiting domain (E(K)) and secondarily by enhancing the diffusion coefficients (E(D)) of the permeant in the domain. Comparison of the one-layer and two-layer skin model results revealed that non-steady-state transport of lipophilic compounds across HMS was better described by the two-layer model because the dermis/viable epidermis played a significant role in lipophilic permeant binding.

Algorithms↗
PubMed2006

The integrity of welded interfaces in ultra high molecular weight polyethylene: Part 1-Model.

The difficulty of eradicating memory of powder-particle interfaces in UHMWPE for bearing surfaces for hip and knee replacements is well-known, and 'fusion defects' have been implicated frequently in joint failures. During processing the polymer is formed into solid directly from the reactor powder, under pressure and at temperatures above the melting point, and two types of inter-particle defect occur: Type 1 (consolidation-deficient) and Type 2 (diffusion-deficient). To gain quantitative information on the extent of the problem, the formation of macroscopic butt welds in this material was studied, by (1) modelling the process and (2) measuring experimentally the resultant evolution of interface toughness. This paper reports on the model. A quantitative measure of interface structural integrity is defined, and related to the "maximum reptated molecular weight" introduced previously. The model assumes an idealised surface topography. It is used to calculate the evolution of interface integrity during welding, for given values of temperature, pressure, and parameters describing the surfaces, and a given molar mass distribution. Only four material properties are needed for the calculation; all of them available for polyethylene. The model shows that, for UHMWPE typically employed in knee transplants, the rate of eradication of Type 1 defects is highly sensitive to surface topography, process temperature and pressure. Also, even if Type 1 defects are prevented, Type 2 defects heal extremely slowly. They must be an intrinsic feature of UHMWPE for all reasonable forming conditions, and products and forming processes should be designed accordingly.

Adhesiveness↗
PubMed1993

Preoperative assessment and prediction of postoperative results in an artificial arterial network using computer simulation.

A computer model has been developed that can be used to describe the human arterial system mathematically. It simulates the complex relationship of morphology and hydraulics in the vessel network. After entering patient data into a standard vessel model, the mean flow velocity, the flow direction, and the blood pressure at each specified point of the flow network can be calculated. The vessel picture can be altered and modified with the help of a graphic editor. Localized or diffuse stenoses, bypasses with simple or multiple anastomoses, end-to-end anastomoses, end-to-side anastomoses, etc., can be studied in terms of the hydraulic effects on the local situation or on the entire vessel system. Experimental results of ultrasonic mean flow data in vessel systems of leg and cerebral arteries of patients are compared with calculated values. The predicted and measured flow velocities show a mean difference of about 10% indicating that such a computer model may be successfully used in the optimal planning of bypass operations.

Arteries↗
PubMed1992

A novel directly coupled gradostat.

The original bidirectional compound chemostat (gradostat) described by Lovitt and Wimpenny has been simplified by making a more compact apparatus in which chemical gradients are established by diffusion between adjacent culture chambers. The experimental model (diffusion coupled (DC) gradostat) consisted of five chambers whose contents could be agitated by turbines rotating in the horizontal plane on a common shaft. Two biological experiments were designed to reveal the value of the DC gradostat. A methylotroph (Methylophilus methylotrophus) grown in a methanol gradient showed expected changes in cell viability as a function of position in the five vessel array. Cells of two species of photosynthetic bacteria (Rhodobacter capsulata and Rhodopseudomonas marina/agilis) with different salt sensitivities could be mixed and subsequently separated by the DC gradostat operating with a NaCl gradient of 0-3% w/v.

Bacteria↗
PubMed2000

Direct in situ measurements of labile inorganic and organically bound metal species in synthetic solutions and natural waters using diffusive gradients in thin films.

The emerging technique of DGT (diffusive gradients in thin films) is shown to be capable of performing new speciation measurements in situ in natural waters. In DGT, metals are bound to a resin layer after passing through a well-defined diffusion layer. Cd was measured in solutions containing glycine, EDTA, and fulvic (FA) and humic acids (HA) by atomic absorption spectroscopy (AAS), anodic stripping voltammetry (ASV), and DGT. DGT measured similar labile fractions to ASV, with detailed differences being consistent with a thicker diffusion layer allowing more dissociation of labile complexes and a slower diffusion of FA and HA complexes through the gel. When single measurements are made in complex solutions with DGT, precise quantification is impossible due to uncertainties concerning the distribution of species with different diffusion coefficients. A new procedure was proposed based on the advantage of DGT of being able to control the pore size of the diffusive gel layer. Small (inorganic) species diffuse freely through all gels but larger FA and HA (organic) complexes diffuse less freely in more constrained gels. When measurements were made on known solutions of Cu and FA or HA, it was possible to quantify the inorganic and organic species separately. They agreed well with predictions made using the WHAM speciation code. Multiple DGT units were also deployed in situ in a stream with high dissolved organic carbon (14.6 mg/L). The systematic differences between the devices with different gel compositions enabled determination, for the first time, of the in situ concentrations of both labile inorganic and organic species in natural water. A single DGT device with a constrained gel can be used to quantify inorganic species directly, providing absolute accuracy is not required. This ability of DGT to measure well-defined fractions of metals in situ using a simple device gives it considerable potential as a regulatory tool. A direct speciation measurement may be preferable to modeling approaches which require diverse input data that are difficult to determine.

Benzopyrans↗
PubMed1994

A general model of microcirculatory blood flow effects in gradient sensitized MRI.

A general expression is derived for the NMR signal from a fluid undergoing random directional flow such as encountered within the microcirculation. The dependence of the echo amplitude on flow velocity, sample morphology, and experimental parameters are described in terms of a temporal velocity autocorrelation function. The width of the correlation function determines whether the flow can properly be described as diffusive. Comparison is made between the velocity autocorrelation method outlined here and the IVIM model for tissue perfusion. Conditions for the validity of the latter approach for extracting physiologic information from apparent diffusion measurements are discussed. The approach outlined leads to a more robust measure of microcirculatory blood velocity from NMR measurements.

Biophysical Phenomena↗