Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “directional 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 631 records · Page 35Linked to original sources
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↗
PubMed2006

Permeability of the reconstructed human epidermis model Episkin in comparison to various human skin preparations.

The objective of this work was to compare the barrier function of the small diameter reconstructed human epidermis model Episkin (d=12 mm) to human skin in vitro. For that purpose a modification for the Franz diffusion cell (d=15mm) had to be developed so as to allow direct comparison with the following human skin preparations: Full thickness skin (FTS), split thickness skin (STS), heat-separated epidermis (HSE), and trypsin isolated stratum corneum (TISC). Among the tested preparations, HSE appeared to be the most preferable due to its clear morphological structure and ease of preparation. The lipid profile of HSE and Episkin was analyzed and showed significant differences in terms of cholesterol, ceramides and triglycerides contents, whereas cholesterol esters and fatty acids were not different. Permeation data with HSE and Episkin were then gathered using caffeine and testosterone. Both test compounds permeated much faster through Episkin than through HSE. Moreover, opposed to Episkin, HSE differentiated between the two test compounds. In spite of the remarkable progress in developing RHEs in the past years at this time Episkin can obviously not yet fully replace human skin for in vitro permeability experiments.

Ceramides↗
PubMed2002

Anisotropic diffusion in mitral cell dendrites revealed by fluorescence correlation spectroscopy.

Fluorescence correlation spectroscopy (FCS) can be used to measure kinetic properties of single molecules in drops of solution or in cells. Here we report on FCS measurements of tetramethylrhodamine (TMR)-dextran (10 kDa) in dendrites of cultured mitral cells of Xenopus laevis tadpoles. To interpret such measurements correctly, the plasma membrane as a boundary of diffusion has to be taken into account. We show that the fluorescence data recorded from dendrites are best described by a model of anisotropic diffusion. As compared to diffusion in water, diffusion of the 10-kDa TMR-dextran along the dendrite is slowed down by a factor 1.1-2.1, whereas diffusion in lateral direction is 10-100 times slower. The dense intradendritic network of microtubules oriented parallel to the dendrite is discussed as a possible basis for the observed anisotropy. In somata, diffusion was found to be isotropic in three dimensions and 1.2-2.6 times slower than in water.

Animals↗
PubMedDate not supplied

CK flux or direct ATP transfer: versatility of energy transfer pathways evidenced by NMR in the perfused heart.

How the myocardium is able to permanently coordinate its intracellular fluxes of ATP synthesis, transfer and utilization is difficult to investigate in the whole organ due to the cellular complexity. The adult myocardium represents a paradigm of an energetically compartmented cell since 50% of total CK activity is bound in the vicinity of other enzymes (myofibrillar sarcolemmal and sarcoplasmic reticulum ATPases as well as mitochondrial adenine nucleotide translocator, ANT). Such vicinity of enzymes is well known in vitro as well as in preparations of skinned fibers to influence the kinetic properties of these enzymes and thus the functioning of the subcellular organelles. Intracellular compartmentation has often been neglected in the NMR analysis of CK kinetics in the whole organ. It is indeed a methodological challenge to reveal subcellular kinetics in a working organ by a global approach such as NMR. To get insight in the energy transfer pathway in the perfused rat heart, we developed a combined analysis of several protocols of magnetization transfer associated with biochemical data and quantitatively evaluated which scheme of energetic exchange best describes the NMR data. This allows to show the kinetic compartmentation of subcellular CKs and to quantify their fluxes. Interestingly, we could show that the energy transfer pathway shifts from the phosphocreatine shuttle in the oxygenated perfused heart to a direct ATP diffusion from mitochondria to cytosol under moderate inhibition of ATP synthesis. Furthermore using NMR measured fluxes and the known kinetic properties of the enzymes, it is possible to model the system, estimate local ADP concentrations and propose hypothesis for the versatility of energy transfer pathway. In the normoxic heart, a 3-fold ADP gradient was found between mitochondrial intermembrane space, cytosol and ADP in the vicinity of ATPases. The shift from PCr to ATP transport observed when ATP synthesis decreases might result from a balance in the activity of two populations of ANT, either coupled or uncoupled to CK. We believe this NMR approach could be a valuable tool to reinvestigate the control of respiration by ADP in the whole heart reconciling the biochemical knowledge of mitochondrial obtained in vitro or in skinned fibers with data on the whole heart as well as to identify the implication of bioenergetics in the pathological heart.

Adenosine Triphosphate↗
PubMed2006

Exploration of molecular dynamics during transient sorption of fluids in mesoporous materials.

In recent years, considerable progress has been made in the development of novel porous materials with controlled architectures and pore sizes in the mesoporous range. An important feature of these materials is the phenomenon of adsorption hysteresis: for certain ranges of applied pressure, the amount of a molecular species adsorbed by the mesoporous host is higher on desorption than on adsorption, indicating a failure of the system to equilibrate. Although this phenomenon has been known for over a century, the underlying internal dynamics responsible for the hysteresis remain poorly understood. Here we present a combined experimental and theoretical study in which microscopic and macroscopic aspects of the relaxation dynamics associated with hysteresis are quantified by direct measurement and computer simulations of molecular models. Using nuclear magnetic resonance techniques and Vycor porous glass as a model mesoporous system, we have explored the relationship between molecular self-diffusion and global uptake dynamics. For states outside the hysteresis region, the relaxation process is found to be essentially diffusive in character; within the hysteresis region, the dynamics slow down dramatically and, at long times, are dominated by activated rearrangement of the adsorbate density within the host material.

Journal Article↗
PubMed2005

Diffusion-limited phase separation in eukaryotic chemotaxis.

The ability of cells to sense spatial gradients of chemoattractant factors governs the development of complex eukaryotic organisms. Cells exposed to shallow chemoattractant gradients respond with strong accumulation of the enzyme phosphatidylinositol 3-kinase (PI3K) and its D3-phosphoinositide product (PIP(3)) on the plasma membrane side exposed to the highest chemoattractant concentration, whereas PIP(3)-degrading enzyme PTEN and its product PIP(2) localize in a complementary pattern. Such an early symmetry-breaking event is a mandatory step for directed cell movement elicited by chemoattractants, but its physical origin is still mysterious. Here, we propose that directional sensing is the consequence of a phase-ordering process mediated by phosphoinositide diffusion and driven by the distribution of chemotactic signal. By studying a realistic reaction-diffusion lattice model that describes PI3K and PTEN enzymatic activity, recruitment to the plasma membrane, and diffusion of their phosphoinositide products, we show that the effective enzyme-enzyme interaction induced by catalysis and diffusion introduces an instability of the system toward phase separation for realistic values of physical parameters. In this framework, large reversible amplification of shallow chemotactic gradients, selective localization of chemical factors, macroscopic response timescales, and spontaneous polarization arise naturally. The model is robust with respect to order-of-magnitude variations of the parameters.

Chemotaxis↗
PubMed2002

Fluctuation-dissipation ratio for compacting granular media.

In this paper we investigate the possibility of a dynamical definition of an effective temperature for compacting granular media in the framework of the fluctuation-dissipation (FD) relations. We have studied two paradigmatic models for the compaction of granular media, which consider particles diffusing on a lattice, with either geometrical (tetris model) or dynamical (Kob-Andersen model) constraints. Idealized compaction without gravity has been implemented for the tetris model, and compaction with a preferential direction imposed by gravity has been studied for both models. In the ideal case of an homogeneous compaction, the obtained FD ratio is clearly shown to be in agreement with the prediction of Edwards' measure at various densities. Similar results are obtained with gravity only when the homogeneity of the bulk is imposed. In this case the FD ratio obtained dynamically for horizontal displacements and mobility and from Edwards' measure coincide. Finally, we propose experimental tests for the validity of the Edwards' construction through the comparison of various types of dynamical measurements.

Journal Article↗
PubMed1993

Visual-response properties of units in the turtle cerebellar granular layer in vitro.

1. Single units were recorded extracellularly in the turtle's cerebellar cortex from an isolated brain preparation during visual stimulation. Only a small fraction of the isolated units responded to visual stimuli. For these visually responsive units, the most effective visual stimulus was a moving check pattern that covered the entire surface of the retinal eyecup. The visually responsive units had little or no spontaneous spike activity, nor were they driven by flashes of diffuse light or stationary patterns. 2. All the visually responsive units were direction sensitive and were driven exclusively by the contralateral eye. This direction tuning was well fit by a limaçon model (mean correlation coefficient, 0.89). The distribution of the entire sample indicates a slight preponderance of upward preferred directions. 3. The direction tuning of these cerebellar units was independent of stimulus contrast or the pattern's configuration (such as checkerboards or random check or dot patterns). In the preferred direction, a unit's spike frequency increased monotonically as a function of stimulus velocity until approximately 10 degrees/s, but remained direction sensitive (relative to the opposite direction) at speeds as fast as 100 degrees/s. 4. In some experiments the ventrocaudal brain stem was transected in the frontal plane just caudal to the cerebellar peduncles. Although this lesion presumably removes climbing fiber input from the inferior olivary nuclei, the visual-response properties in the cerebellar cortex were unaffected. 5. The response properties of these units indicate that they encode retinal slip information in the cerebellum.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1989

The localization of an inductive response.

Combinations of tissues from Xenopus blastulae have been used to identify several mechanisms that limit the number of animal cells forming muscle after induction by vegetal cells. The results disagree with a model in which direct physical contact or very close proximity between animal and vegetal cells restricts the number of cells that receive the inductive signal. Rather it seems that a diffusible inducer is released by vegetal cells, and spreads through 4-8 animal cell diameters, equivalent to a distance of 80 microns, from the nearest vegetal cells. Several factors seem to cooperate to prevent the further spread of the mesoderm-forming induction. These include the slow diffusion and/or instability of the inducer, the time of loss of competence of animal cells to respond to induction, and the amount of vegetal tissue that releases inducer for a limited time. The combination of these, and perhaps other, processes seems to ensure that a consistent minority of animal cells are induced to form muscle, thereby leaving other animal cells available to form the nervous system and epidermis.

Animals↗
PubMed1982

Adverse effects of drugs on muscle.

A variety of drugs used in clinical practice may cause myopathy or interfere with neuromuscular transmission. The precise incidence of such disorders is not known, but it is almost certainly higher than is generally suspected. An important aspect of drug-induced muscular disorders is their reversibility if the offending agent is withdrawn, whereas failure to do so may lead to unnecessary morbidity. The study of drug effects on muscle provides a means of investigating the pathological reactions of muscle, and of producing experimental models of naturally occurring myopathies. Drug-induced myopathies may result from a direct toxic effect, which may be local when the drug is injected into a muscle or more diffuse when the drug is taken systemically, or may be secondary to electrolyte disturbances, muscle compression, ischaemia, neural activation or to the development of an immunological reaction directed against muscle. Repeated injections of antibiotics or drugs of addiction may lead to severe muscle fibrosis and contractures. A variety of drugs may cause an acute or subacute painful necrotising myopathy which may be associated with myoglobinuria, at times leading to acute renal failure. Clofibrate and epsilon aminocaproic acid are the drugs most frequently implicated, but a similar syndrome may occur in alcoholics and heroin addicts. Certain hypocholesterolaemic agents may induce myotonia by altering the sterol composition of the muscle cell membrane, while certain drugs including beta-adrenergic blockers and agonists, succinylcholine and diuretics may exacerbate or unmask pre-existing myotonia. In the syndrome of malignant hyperpyrexia, halothane, succinylcholine and various other agents may induce a potentially fatal state of muscular rigidity and hypermetabolism in susceptible individuals as a result of a defect in the calcium transport function of the sarcoplasmic reticulum and possibly of other cellular membranes. In corticosteroid myopathy, which is the most common form of drug-induced myopathy, there is selective atrophy of type 2 muscle fibres and the primary metabolic effect is an inhibition of RNA and protein synthesis, although protein degradation is also increased. Chloroquine and a number of related drugs with amphiphilic cationic properties may induce lysosomal storage myopathy, which may be associated with cardiomyopathy and with a more widespread form of lipidosis.

Abnormalities, Drug-Induced↗
PubMed1999

Extracellular links in Kir subunits control the unitary conductance of SUR/Kir6.0 ion channels.

Potassium (K+) channels are highly selective for K+ ions but their unitary conductances are quite divergent. Although Kir6.1 and Kir6.2 are highly homologous and both form functional K+ channels with sulfonylurea receptors, their unitary conductances measured with 150 mM extracellular K+ are approximately 35 and 80 pS, respectively. We found that a chain of three amino acid residues N123-V124-R125 of Kir6.1 and S113-I114-H115 of Kir6.2 in the M1-H5 extracellular link and single residues M148 of Kir6.1 and V138 of Kir6.2 in the H5-M2 link accounted for the difference. By using a 3D structure model of Kir6.2, we were able to recognize two independent plausible mechanisms involved in the determination of single channel conductance of the Kir6.0 subunits: (i) steric effects at Kir6.2V138 or Kir6.1M148 in the H5-M2 link influence directly the diffusion of K+ ions; and (ii) structural constraints between Kir6.2S113 or Kir6. 1N123 in the M1-H5 link and Kir6.2R136 or Kir6.1R146 near the H5 region control the conformation of the permeation pathway. These mechanisms represent a novel and possibly general aspect of the control of ion channel permeability.

Amino Acid Sequence↗
PubMed1999

[Factors influencing transperitoneal transport of glucose in vitro].

UNLABELLED: The effect of mixing fluid intensification, damage of mesothelial cells and gentamicin on the diffusive glucose transport across the peritoneal membrane were evaluated in the presented in vitro studies. A mathematical model of the mass transport was used to calculate the diffusive permeability, expressed as a diffusive permeability coefficient P [cm x s-1], for the investigated specimens. In the control conditions glucose transfer from the interstitial to the mesothelial side of membrane (I-->M) and in the opposite direction (M-->I) remained constant and P value at mean was 2.731 +/- 1.493 [cm x s-1 x 10(-4)]. The change of the stirring rate from 5.5 to 11 mL/min increased P values by about 74% for transport direction I-->M and 58% for M-->I, but change from 11 to 22 mL/min enhanced P at mean by about 42% for the both direction. The damage of the mesothelial layer, using of sodium deoxycholate (2.5 mmol/L; 103.6 mg%), increased the glucose transfer from the interstitial to the mesothelial side of the peritoneum by 41% and to the opposite direction by 57%. Furthermore, gentamicin did not change the I-->M transfer, but diminished M-->I transport by about 12%. IN CONCLUSION: 1. The reducing of unstirred fluid layer at the mesothelium and interstitium--fluid interface and the mesothelium damage increase the diffusive glucose transport in vitro; 2. The unstirred fluid layer restricts glucose transfer more than tissue barrier (mesothelium); 3. The peritoneal glucose transport, directed from the mesothelial to the interstitial side of the peritoneum (but not transfer to the opposite direction), decreases slightly after gentamicin introduction.

Animals↗
PubMed1989

The motile response of alveolar macrophages. An experimental study using single-cell and cell population approaches.

In this report, we studied the applicability of a random walk model of individual cell motility in predicting the motile behavior of alveolar macrophage populations under agarose. The migration of a population of cells in the absence of a chemotactic or chemokinetic gradient can be characterized by the random motility coefficient, mu, which is analogous to a particle diffusion coefficient. Random walk theory relates this latter coefficient to particle speed and collision time (equivalent to the time between changes in particle direction). By analogy, according to a similar random walk theory for cell migration, mu for a cell population is a function of the speed and persistence time (with direction changes governed by cell behavioral processes rather than by collisions) of individual cells. To test the model, normal guinea pig alveolar macrophages were incubated in the presence or absence of uniform concentrations of the chemotactic tripeptide formyl-norleucyl leucyl phenylalanine (FNLLP) to elicit different levels of motile activity. Mu was calculated from cell population density profiles obtained by fixing and staining cultures after 2, 3, or 4 days. In parallel experiments, individual cell speeds and persistence times were measured from 1-h, time-lapse video microscopy recordings. The value of mu calculated from single-cell measurements was in good agreement with that from population studies for stimulated random migration (at 10(-7) to 10(-11) M FNLLP), but not in the absence of stimulant. Overall, these results support the applicability of the random walk model of individual cell migration to randomly migrating alveolar macrophage populations.

Animals↗
PubMed1991

Kinetic evaluation of pharmacological effects based on allosteric coupling of the benzodiazepine/gamma-aminobutyric acidA receptor in the brain.

A mathematical allosteric coupling model has been proposed to describe the process by which binding to the benzodiazepine/gamma-aminobutyric acid (GABA) receptor complex initiates a biological response. The model states that the first receptors (benzodiazepine receptors) can diffuse independently in the plane of the membrane and reversibly associate with the second receptors (GABA receptors) to regulate their activity (induction of increased chloride ion flux due to the opening of the chloride ion channel). The ratio of agonist-bound to total GABA receptor density was defined to be directly proportional to the biological response in the model. The analysis makes the following assumptions: i) the binding affinity of agonists (muscimol or benzodiazepine) to the benzodiazepine receptor/GABA receptor complex is much greater than that to each receptor alone; ii) the double receptor-single agonist (benzodiazepine, muscimol or GABA) ternary complex binds to the other agonist with a high binding affinity as compared with that of each agonist to an agonist-free receptor complex; iii) benzodiazepine receptor-GABA receptor interaction is enhanced in the presence of each agonist; iv) the GABA receptor is desensitized after the binding of GABA agonist (GABA or muscimol) to the receptor. The modeling exercise shows that the benzodiazepine concentration required for half-maximal biological response is lower than that required for half-maximal receptor binding. In the case of the GABA agonist, a linear relationship between receptor occupancy and biological response was observed. The degree of discrepancy between the two profiles (receptor occupancy and biological response) concerning benzodiazepine concentration dependency and time dependency increased with a decrease in the dissociation constants based on the benzodiazepine receptor-GABA receptor interaction.(ABSTRACT TRUNCATED AT 250 WORDS)

Brain↗
PubMed2004

Dynamical effects of diffusive cell coupling on cardiac excitation and propagation: a simulation study.

Cell coupling is considered to be important for cardiac action potential propagation and arrhythmogenesis. We carried out computer simulations to investigate the effects of stimulation strength and cell-to-cell coupling on action potential duration (APD) restitution, APD alternans, and stability of reentry in models of isolated cell, one-dimensional cable, and two-dimensional tissue. Phase I formulation of the Luo and Rudy action potential model was used. We found that stronger stimulation resulted in a shallower APD restitution curve and onset of APD alternans at a faster pacing rate. Reducing diffusive coupling between cells prolonged APD. Weaker diffusive currents along the direction of propagation steepened APD restitution and caused APD alternans to occur at a slower pacing rate in tissue. Diffusive current due to curvature changed APD but had little effect on APD restitution slope and onset of instability. Heterogeneous cell coupling caused APD inhomogeneities in space. Reduction in coupling strength either uniformly or randomly had little effect on the rotation period and stability of a reentry, but random cell decoupling slowed the rotation period and, thus, stabilized the reentry, preventing it from breaking up into multiple waves. Therefore, in addition to its effects on action potential conduction velocity, diffusive cell coupling also affects APD in a rate-dependent manner, causes electrophysiological heterogeneities, and thus modulates the dynamics of cardiac excitation. These effects are brought about by the modulation of ionic current activation and inactivation.

Action Potentials↗