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PubMed2002

General models for water transport across leaky epithelia.

The group of leaky epithelia, such as proximal tubule and small intestine, have several common properties in regard to salt and water transport. The fluid transport is isotonic, the transport rate increases in dilute solutions, and water can be transported uphill. Yet, it is difficult to find common features that could form the basis for a general transport model. The direction of transepithelial water transport does not correlate with the direction of the primary active Na+ transport, or with the ultrastucture as defined by the location of apical and basolateral membranes, of the junctional complex and the lateral intercellular spaces. The presence of specific water channels, aquaporins, increases the water permeability of the epithelial cell membranes, i.e., the kidney proximal tubule. Yet other leaky epithelia, for example, the retinal pigment epithelium, have no known aquaporins. There is, however, a general correlation between the direction of transepithelial transport and the direction of transport via cotransporters of the symport type. A simple epithelial model based on water permeabilities, a hyperosmolar compartment and restricted salt diffusion, is unable to explain epithelial transport phenomena, in particular the ability for uphill water transport. The inclusion of cotransporters as molecular water pumps in these models alleviates this problem.

Animals↗

PubMed1999

Backbone dynamics of the N-terminal domain of the HIV-1 capsid protein and comparison with the G94D mutant conferring cyclosporin resistance/dependence.

Nuclear magnetic resonance (NMR) (15)N relaxation methods have been used to characterize the backbone dynamics of the N-terminal core domain of the HIV-1 capsid protein (CA(151)). The domain, which has an unusually flat, triangular shape, tumbles in solution at 28 degrees C with an effective rotational correlation time of 11.5 ns. Relaxation data for backbone amides in the domain's seven alpha-helices are indicative of fully anisotropic rotational diffusion. The principal axes of the rotational diffusion tensor calculated from the NMR data are aligned to within 12-23 degrees of the principal axes of the inertial tensor, with the axis of fastest rotational diffusion coincident with that of minimal inertia, and vice versa. Large variations in the (15)N-(1)H nuclear Overhauser effects for individual amino acids correlate with the degree of convergence in the previously calculated NMR structure. In particular, the partially disordered residues Val86-Arg97 that contain the human cyclophilin A (CypA) packaging signal have (15)N heteronuclear NOEs and transversal relaxation rates consistent with a high degree of dynamic conformational averaging. The N-terminal domain of a CA mutant (G94D) that confers both resistance to and dependence on cyclosporin A analogues was also analyzed. Our results indicate that this mutation does not influence the conformation or dynamics of CA(151), and therefore probably affects the function of the protein by modifying essential intermolecular CA-CA interactions.

Amino Acid Substitution↗

PubMed2004

The mitochondrial respiratory chain is partially organized in a supercomplex assembly: kinetic evidence using flux control analysis.

The model of the respiratory chain in which the enzyme complexes are independently embedded in the lipid bilayer of the inner mitochondrial membrane and connected by randomly diffusing coenzyme Q and cytochrome c is mostly favored. However, multicomplex units can be isolated from mammalian mitochondria, suggesting a model based on direct electron channeling between complexes. Kinetic testing using metabolic flux control analysis can discriminate between the two models: the former model implies that each enzyme may be rate-controlling to a different extent, whereas in the latter, the whole metabolic pathway would behave as a single supercomplex and inhibition of any one of its components would elicit the same flux control. In particular, in the absence of other components of the oxidative phosphorylation apparatus (i.e. ATP synthase, membrane potential, carriers), the existence of a supercomplex would elicit a flux control coefficient near unity for each respiratory complex, and the sum of all coefficients would be well above unity. Using bovine heart mitochondria and submitochondrial particles devoid of substrate permeability barriers, we investigated the flux control coefficients of the complexes involved in aerobic NADH oxidation (I, III, IV) and in succinate oxidation (II, III, IV). Both Complexes I and III were found to be highly rate-controlling over NADH oxidation, a strong kinetic evidence suggesting the existence of functionally relevant association between the two complexes, whereas Complex IV appears randomly distributed. Moreover, we show that Complex II is fully rate-limiting for succinate oxidation, clearly indicating the absence of substrate channeling toward Complexes III and IV.

Adenosine Triphosphate↗

PubMed1994

Compartmentalized structure of the plasma membrane for receptor movements as revealed by a nanometer-level motion analysis.

Movements of transferrin and alpha 2-macroglobulin receptor molecules in the plasma membrane of cultured normal rat kidney (NRK) fibroblastic cells were investigated by video-enhanced contrast optical microscopy with 1.8 nm spatial precision and 33 ms temporal resolution by labeling the receptors with the ligand-coated nanometer-sized colloidal gold particles. For both receptor species, most of the movement trajectories are of the confined diffusion type, within domains of approximately 0.25 microns2 (500-700 nm in diagonal length). Movement within the domains is random with a diffusion coefficient approximately 10(-9) cm2/s, which is consistent with that expected for free Brownian diffusion of proteins in the plasma membrane. The receptor molecules move from one domain to one of the adjacent domains at an average frequency of 0.034 s-1 (the residence time within a domain approximately 29 s), indicating that the plasma membrane is compartmentalized for diffusion of membrane receptors and that long-range diffusion is the result of successive intercompartmental jumps. The macroscopic diffusion coefficients for these two receptor molecules calculated on the basis of the compartment size and the intercompartmental jump rate are approximately 2.4 x 10(-11) cm2/s, which is consistent with those determined by averaging the long-term movements of many particles. Partial destruction of the cytoskeleton decreased the confined diffusion mode, increased the simple diffusion mode, and induced the directed diffusion (transport) mode. These results suggest that the boundaries between compartments are made of dynamically fluctuating membrane skeletons (membrane-skeleton fence model).

Animals↗

PubMed2001

Non-contact measurement of thermal diffusivity in tissue.

We demonstrate the application of an infrared (IR) imaging technique for non-contact determination of thermal diffusivity in biological materials. The proposed method utilizes pulsed laser excitation to produce an initial three-dimensional temperature distribution in tissue, and records IR images of subsequent heat diffusion. The theoretical model assumes that the time-dependent temperature increase following pulsed laser exposure is due to independent heat diffusion in longitudinal and lateral directions. A nonlinear least-squares algorithm is used to compute the lateral thermal point spread function from a pair of recorded IR images and to determine the thermal diffusivity of a test specimen. The recorded time-sequence of IR images is used to compute thermal diffusivity as a function of increasing time interval between two IR emission images. Experimental application of the method was demonstrated using tissue phantoms, ex vivo samples of hydrated cartilage and in vivo epidermis.

Adult↗

PubMed2006

Edge-forming methods for color image zooming.

This paper introduces edge-forming schemes for image zooming of color images by general magnification factors. In order to remove/reduce artifacts arising in image interpolation, such as image blur and the checkerboard effect, an edge-forming method is suggested to be applied as a postprocess of standard interpolation methods. The method is based on nonconvex nonlinear partial differential equations. The equations are carefully discretized, incorporating numerical schemes of anisotropic diffusion, to be able to form reliable edges satisfactorily. The alternating direction implicit (ADI) method is employed for an efficient simulation of the model. It has been numerically verified that the resulting algorithm can form clear edges in 2 to 3 ADI iterations. Various results are given to show th eeffectiveness and reliability of the algorithm.

Algorithms↗

PubMed2003

A framework for evaluating comprehensive community initiatives.

This article describes a model and design for evaluating a comprehensive community health promotion initiative. The theoretically based model was designed by the authors to evaluate a countywide initiative based on developmental assets, a framework for healthy youth development promoted by the Search Institute in Minneapolis, Minnesota. The model includes the components of a typical logic model and incorporates concepts proposed by diffusion of innovations, social cognitive theory, and Search Institute's conceptual model for community change. The model highlights the priorities of local stakeholders and directs evaluation activities in multiple community sectors over time. The evaluation design is presented according to the Centers for Disease Control and Prevention framework for program evaluation in public health.

Academies and Institutes↗

PubMed2005

MR quantitation of volume and diffusion changes in the developing brain.

BACKGROUND AND PURPOSE: Brain volume and diffusion change during maturation. Quantitation of these changes may be helpful in understanding normal brain development. We used diffusion-weighted imaging to characterize the volumetric and diffusion changes in vivo. METHODS: We recruited 30 pediatric volunteers (aged 1 month-17 years; 14 male, 16 female). Diffusion was measured in three orthogonal directions with a b value of 1000 s/mm2. The diffusion parameters from the entire brain were calculated and fitted to a triple gaussian model. In addition, region-of-interest measurements were made in caudate, thalamus, genu and splenium of the corpus callosum, and periventricular white matter (PVWM). The brain volume was measured by counting pixels and by using the model. RESULTS: Water diffusion of the whole brain, caudate, thalamus, genu and splenium of the corpus callosum, and PVWM decreased during maturation, with the most significant change within the first 2 years. Robust negative correlations were found between age and the measured average diffusion constant (Dav) values in each of the measured locations (P <.005). Volumes of different cerebral compartments and the total intracranial volume (ICV) increased rapidly during the first 2 years of life and then had a slower growth process through adolescence. Age was correlated with the ICV and the volume of each brain compartment (P <.005). CONCLUSION: Brain diffusion decreases and brain volume increases during maturation, with the most significant changes occurring within the first 2 years of life. The brain model used in this study provides a good estimate of the increasing brain volume.

Adolescent↗

PubMed2006

Effects of mesh style and grid convergence on particle deposition in bifurcating airway models with comparisons to experimental data.

A number of research studies have employed a wide variety of mesh styles and levels of grid convergence to assess velocity fields and particle deposition patterns in models of branching biological systems. Generating structured meshes based on hexahedral elements requires significant time and effort; however, these meshes are often associated with high quality solutions. Unstructured meshes that employ tetrahedral elements can be constructed much faster but may increase levels of numerical diffusion, especially in tubular flow systems with a primary flow direction. The objective of this study is to better establish the effects of mesh generation techniques and grid convergence on velocity fields and particle deposition patterns in bifurcating respiratory models. In order to achieve this objective, four widely used mesh styles including structured hexahedral, unstructured tetrahedral, flow adaptive tetrahedral, and hybrid grids have been considered for two respiratory airway configurations. Initial particle conditions tested are based on the inlet velocity profile or the local inlet mass flow rate. Accuracy of the simulations has been assessed by comparisons to experimental in vitro data available in the literature for the steady-state velocity field in a single bifurcation model as well as the local particle deposition fraction in a double bifurcation model. Quantitative grid convergence was assessed based on a grid convergence index (GCI), which accounts for the degree of grid refinement. The hexahedral mesh was observed to have GCI values that were an order of magnitude below the unstructured tetrahedral mesh values for all resolutions considered. Moreover, the hexahedral mesh style provided GCI values of approximately 1% and reduced run times by a factor of 3. Based on comparisons to empirical data, it was shown that inlet particle seedings should be consistent with the local inlet mass flow rate. Furthermore, the mesh style was found to have an observable effect on cumulative particle depositions with the hexahedral solution most closely matching empirical results. Future studies are needed to assess other mesh generation options including various forms of the hybrid configuration and unstructured hexahedral meshes.

Computer Simulation↗

PubMed2001

Particle-scale investigation of PAH desorption kinetics and thermodynamics from sediment.

Dredged sediment from Milwaukee Harbor showed two primary classes of particles in the <2 mm size range: a lighter-density coal- and wood-derived fraction with 62% of total PAHs and a heavier-density sand, silt, and clay fraction containing the remaining 38% of the PAHs. Room-temperature PAH desorption kinetic studies on separated sediment fractions revealed slow desorption rates for the coal-derived particles and fast desorption rates for the clay/silt particles. The effect of temperature on PAH release was measured by thermal program desorption mass spectrometry to investigate the desorption activation energies for PAHs on the different sediment particles. Three activated diffusion-based models and an activated first-order rate model were used to describe the thermal desorption of PAHs for four molecular weight classes. PAH binding with the coal-derived particles was associated with high activation energies, typically in the range of 115-139 kJ/mol. PAHs bound to the clay/silt material had much lower activation energy, i.e., in the range of 37-41 kJ/ mol for molecular weight 202. Among the desorption models tested, a spherical diffusion model with PAHs located like a rind on the outer 1-3 microm region best described the PAH thermal desorption response for coal-derived particles. This internal PAH distribution pattern on coalderived particles is based on prior direct measurement of PAH locations at the subparticle scale. These studies reveal that heterogeneous particle types in sediment exhibit much different amounts and binding of PAHs. PAHs associated with coal-derived particles aged over several decades in the field appear to be far from reaching an equilibrium sorption state due to the extremely slow diffusivities through the polymer-like coal matrix. These results provide an improved mechanistic perspective for the understanding of PAH mobility and bioavailability in sediments.

Adsorption↗

PubMed2004

Interpretation of injection-withdrawal tracer experiments conducted between two wells in a large single fracture.

Tracer experiments conducted using a flow field established by injecting water into one borehole and withdrawing water from another are often used to establish connections and investigate dispersion in fractured rock. As a result of uncertainty in the uniqueness of existing models used for interpretation, this method has not been widely used to investigate more general transport processes including matrix diffusion or advective solute exchange between mobile and immobile zones of fluid. To explore the utility of the injection-withdrawal method as a general investigative tool and with the intent to resolve the transport processes in a discrete fracture, two tracer experiments were conducted using the injection-withdrawal configuration. The experiments were conducted in a fracture which has a large aperture (>500 microm) and horizontally pervades a dolostone formation. One experiment was conducted in the direction of the hydraulic gradient and the other in the direction opposite to the natural gradient. Two tracers having significantly different values of the free-water diffusion coefficient were used. To interpret the experiments, a hybrid numerical-analytical model was developed which accounts for the arcuate shape of the flow field, advection-dispersion in the fracture, diffusion into the matrix adjacent to the fracture, and the presence of natural flow in the fracture. The model was verified by comparison to a fully analytical solution and to a well-known finite-element model. Interpretation of the tracer experiments showed that when only one tracer, advection-dispersion, and matrix diffusion are considered, non-unique results were obtained. However, by using multiple tracers and by accounting for the presence of natural flow in the fracture, unique interpretations were obtained in which a single value of matrix porosity was estimated from the results of both experiments. The estimate of porosity agrees well with independent measurements of porosity obtained from core samples. This suggests that: (i) the injection-withdrawal method is a viable tool for the investigation of general transport processes provided all relevant experimental conditions are considered and multiple conservative tracers are used; and (ii) for the conditions of the experiments conducted in this study, the dominant mechanism for exchange of solute between the fracture and surrounding medium is matrix diffusion.

Diffusion↗

PubMed1985

Biased intrachromosomal gene conversion in a chromosome lineage.

A model for the evolution of a family of tandemly repeated genes in a single chromosome lineage under intrachromosomal gene conversion [43] is analyzed further and extended. Direct and diffusion approximations are derived for the exact fixation probabilities, mean time to fixation or loss, and mean conditional fixation time of Nagylaki and Petes [43]. The distribution of the number of variant repeats under the joint action of gene conversion and reversible mutation is investigated; exact and approximate expressions are derived for the stationary distribution. It is shown that conversional bias greatly increases the amount of sequence homogeneity at equilibrium. The diffusion processes studied here also apply to selection and mutation in a finite population, and some new results are established for that classical problem.

Alleles↗

PubMed2005

Evaluation of migration models that might be used in support of regulations for food-contact plastics.

Materials and articles intended to come into contact with food must be shown to be safe because they might interact with food during processing, storage and the transportation of foodstuffs. Framework Directive 89/109/EEC and its related specific Directives provide this safety basis for the protection of the consumer against inadmissible chemical contamination from food-contact materials. Recently, the European Commission charged an international group of experts to demonstrate that migration modelling can be regarded as a valid and reliable tool to calculate 'reasonable worst-case' migration rates from the most important food-contact plastics into the European Union official food simulants. The paper summarizes the main steps followed to build up and validate a migration estimation model that can be used, for a series of plastic food-contact materials and migrants, for regulatory purposes. Analytical solutions of the diffusion equation in conjunction with an 'upper limit' equation for the migrant diffusion coefficient, D(P), and the use of 'worst case' partitioning coefficients K(P,F) were used in the migration model. The results obtained were then validated, at a confidence level of 95%, by comparison with the available experimental evidence. The successful accomplishment of the goals of this project is reflected by the fact that in Directive 2002/72/EC, the European Commission included the mathematical modelling as an alternative tool to determine migration rates for compliance purposes.

Diffusion↗

PubMed1993

Lateral diffusion in an archipelago. Single-particle diffusion.

Several laboratories have measured lateral diffusion of single particles on the cell surface, and these measurements may reveal an otherwise inaccessible level of submicroscopic organization of cell membranes. Pitfalls in the interpretation of these experiments are analyzed. Random walks in unobstructed systems show structure that could be interpreted as free diffusion, obstructed diffusion, directed motion, or trapping in finite domains. To interpret observed trajectories correctly, one must consider not only the trajectories themselves but also the probabilities of occurrence of various trajectories. Measures of the asymmetry of obstructed and unobstructed random walks are calculated, and probabilities are evaluated for random trajectories that resemble either directed motion or diffusion in a bounded region.

Cell Membrane↗

PubMed1989

An analysis of factors influencing diffusion from dental plaque into a moving film of saliva and the implications for caries.

Recent studies have indicated that saliva in the mouth is present as a film only about 0.1 mm thick, and that this film moves at different rates (about 0.8 to 7.6 mm/min) in different regions of the oral cavity. The clearance rates of KCl, as a model diffusant, from agarose gels at different sites in the mouth have also been found to vary markedly, and it has been proposed that these variations are related to differences in the velocity of the salivary film. A computer model has been developed for prediction of clearance half-times for substances diffusing from plaque of variable dimensions into a film of fluid 0.1 mm thick, moving at different velocities. The results show that over the range of velocities calculated to occur in the mouth, the clearance half-times are directly related to the length of plaque over which the fluid passes, and inversely related to the salivary film velocity. The predictions of the model are in good agreement with experimental results from a physical model. Tests were made of the predicted effect of salivary film velocity on the shape of the pH curve initiated by exposure of plaque to a saturated sucrose solution, followed by normal salivary clearance. With a low salivary film velocity, the fall in pH was greater and more prolonged.(ABSTRACT TRUNCATED AT 250 WORDS)

Dental Caries↗

PubMed2005

Kinetics of androstendione-radioactive immunocomplex substitution reaction.

A kinetic model is put forward for the study of the antigen-antibody reactions involved in the coated tube radioimmunoassay (RIA) of androstendione. Twenty experiments were conducted to determine the influence of initial concentrations, ionic strength, viscosity, and temperature on the substitution reaction of 125I-androstendione (M) by unlabelled androstendione (Q) in the immunocomplex PM (P = anti-androstendione antibody). The results obtained are in line with the proposed model. The concentration of radioactive immunocomplex is directly proportional to the initial concentration of labelled androstendione and independent of the concentration of unlabelled androstendione, ionic strength, and viscosity. The reaction is not diffusion-controlled.

Androstenedione↗

PubMed2004

Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness.

We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem of diffusion in a potential into free diffusion in the presence of an absorbing zone spanning the entrance to the binding funnel. The free diffusion problem is solved using a recently derived analytic expression for the rate of association of asymmetrically oriented molecules. Despite the required high steric specificity and the absence of long-range attractive interactions, the computed rates are typically on the order of 10(4)-10(6) M(-1) sec(-1), several orders of magnitude higher than rates obtained using a purely probabilistic model in which the association rate for free diffusion of uniformly reactive molecules is multiplied by the probability of a correct alignment of the two partners in a random collision. As the association rates of many protein-protein complexes are also in the 10(5)-10(6) M(-1) sec(-1) range, our results suggest that free energy barriers arising from desolvation and/or side-chain freezing during complex formation or increased ruggedness within the binding funnel, which are completely neglected in our simple diffusional model, do not contribute significantly to the dynamics of protein-protein association. The transparent physical interpretation of our approach that computes association rates directly from the size and geometry of protein-protein binding funnels makes it a useful complement to Brownian dynamics simulations.

Computer Simulation↗

PubMed1988

Light dosimetry in optical phantoms and in tissues: I. Multiple flux and transport theory.

This is the first of two papers on the quantitative measurement of light energy fluence rates in optical phantoms and in tissues, in vitro and in vivo. The theory discussed in the present paper will be used in a forthcoming experimental paper to quantitatively check measurements of light energy fluence rates. A simple multiple flux model, which is equivalent to the diffusion approximation, is derived from the equation of transfer in a plane as well as in a spherical geometry. The equations obtained are similar to those of the Kubelka-Munk and related heuristic models. This permits conclusions regarding the limitations of these models and the values of their constants. The heuristic models are equivalent to diffusion theory for diffuse incident light, but not for collimated incident light. We also present a simple calculation of the radiance as a function of direction in the diffusion domain. This, together with the effective attenuation coefficient, permits indirect experimental determination of both the albedo and the anisotropy factor (g) of the scattering function. Similarity relations are discussed, as they result from the so called delta-Eddington approximation, leading to the conclusion that far from boundaries and sources light propagation characteristics do not change very much when g and omega s are varied, provided omega s (1-g) is kept constant (omega s = scattering coefficient). Therefore, only two optical constants are required to approximately describe light propagation in homogeneous and isotropic media in the diffusion approximation.

Mathematics↗