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At least 199 records · Page 11Linked to original sources
PubMed2000

The finite element model for the propagation of light in scattering media: a direct method for domains with nonscattering regions.

We present a method for handling nonscattering regions within diffusing domains. The method develops from an iterative radiosity-diffusion approach using Green's functions that was computationally slow. Here we present an improved implementation using a finite element method (FEM) that is direct. The fundamental idea is to introduce extra equations into the standard diffusion FEM to represent nondiffusive light propagation across a nonscattering region. By appropriate mesh node ordering the computational time is not much greater than for diffusion alone. We compare results from this method with those from a discrete ordinate transport code, and with Monte Carlo calculations. The agreement is very good, and, in addition, our scheme allows us to easily model time-dependent and frequency domain problems.

Biophysical Phenomena↗
PubMed2006

M5 mesoscopic and macroscopic models for mesenchymal motion.

In this paper mesoscopic (individual based) and macroscopic (population based) models for mesenchymal motion of cells in fibre networks are developed. Mesenchymal motion is a form of cellular movement that occurs in three-dimensions through tissues formed from fibre networks, for example the invasion of tumor metastases through collagen networks. The movement of cells is guided by the directionality of the network and in addition, the network is degraded by proteases. The main results of this paper are derivations of mesoscopic and macroscopic models for mesenchymal motion in a timely varying network tissue. The mesoscopic model is based on a transport equation for correlated random walk and the macroscopic model has the form of a drift-diffusion equation where the mean drift velocity is given by the mean orientation of the tissue and the diffusion tensor is given by the variance-covariance matrix of the tissue orientations. The transport equation as well as the drift-diffusion limit are coupled to a differential equation that describes the tissue changes explicitly, where we distinguish the cases of directed and undirected tissues. As a result the drift velocity and the diffusion tensor are timely varying. We discuss relations to existing models and possible applications.

Algorithms↗
PubMed2006

Diffusion of transcription factors can drastically enhance the noise in gene expression.

We study by Green's Function Reaction Dynamics the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels for a gene that is under the control of a repressor. We find that spatial fluctuations due to diffusion can drastically enhance the noise in gene expression. After dissociation from the operator, a repressor can rapidly rebind to the DNA. Our results show that the rebinding trajectories are so short that, on this timescale, the RNA polymerase (RNAP) cannot effectively compete with the repressor for binding to the promoter. As a result, a dissociated repressor molecule will on average rebind many times, before it eventually diffuses away. These rebindings thus lower the effective dissociation rate, and this increases the noise in gene expression. Another consequence of the timescale separation between repressor rebinding and RNAP association is that the effect of spatial fluctuations can be described by a well-stirred, zero-dimensional, model by renormalizing the reaction rates for repressor-DNA (un) binding. Our results thus support the use of well-stirred, zero-dimensional models for describing noise in gene expression. We also show that for a fixed repressor strength, the noise due to diffusion can be minimized by increasing the number of repressors or by decreasing the rate of the open complex formation. Lastly, our results emphasize that power spectra are a highly useful tool for studying the propagation of noise through the different stages of gene expression.

Algorithms↗
PubMed2006

Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies.

Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize (Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R (2) equaling 0.78 (n=120).

Light↗
PubMed1991

[The application of in vivo diffusion weighted magnetic resonance imaging to intracranial disorders].

We have developed a magnetic resonance (MR) spin echo method to obtain diffusion weighted imaging using motion-probing gradient (MPG) pulses in one or three orthogonal directions before and after a 180 degree pulse. Phantom models containing water and acetone, normal volunteers and patients with brain tumors, brain edema and infarction were examined. Experimental models of brain edema including triethyltin intoxication and cold injuries were also examined in Wistar rats. MRI was performed at a 1.0-T clinical machine or a 4.7-T experimental machine using spin echo pulse sequences with or without additional MPGs on one or three orthogonal axes. The one direction method was useful to define diffusion anisotropy of myelinated axonal fibers in white matter. Faster diffusion was detected in the white matter parallel to the direction of MPGs. On the other hand, slower diffusion was detected perpendicular to the direction of MPGs because the myelin sheath restricted water diffusion. The three orthogonal gradients method was useful to demonstrate the difference in the diffusion coefficients in various diseases due to its larger total gradient strength. The clear distinction between the cytotoxic edema, which revealed slower diffusion, and the vasogenic edema, which revealed faster diffusion, was demonstrated in the experimental models using diffusion weighted image. In the clinical cases, faster diffusion was demonstrated in the brain tumor and perifocal vasogenic edema, which was in agreement with the results in the experimental models of rats. Brain tumors such as low grade astrocytoma with microcysts and perifocal vasogenic edema have very wide extracellular space.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1996

Reduction of excitotoxicity-induced brain damage by the competitive NMDA antagonist CGP 40116: a longitudinal study using diffusion-weighted imaging.

The cerebroprotective properties of the competitive N-methyl-D-aspartate (NMDA) antagonist CGP 40116 were evaluated in a rat model of excitotoxicity-induced brain damage using direct intrastriatal injection of quinolinic acid and subsequent (5 or 45 min later) i.p. administration of the drug. Diffusion-weighted magnetic resonance imaging (DWI) was used to follow the temporal lesion growth during the acute phase (4 h) and T2-weighted MRI (T2WI) to quantify vasogenic edema extent 2 days later. For control animals, we found a rapid increase in lesion volume during the first hour followed by a moderate growth over the following hours. The DWI-visible hyperintensity was partially reversible after treatment with CGP 40116. The onset of action of CGP 40116 was immediate. The final outcome (63% reduction of lesion volume within 2-4 h post-surgery) was independent of the time of drug administration. DWI data after 4 h correlated well with those obtained by T2WI 2 days later. DWI is a valuable method for early prediction of the outcome of therapeutic interventions of excitotoxic insults.

2-Amino-5-phosphonovalerate↗
PubMed1993

An estimate of the rate of direct drug diffusion from the surface of heart and kidney--implications for their representation as compartments.

In many regional pharmacokinetic experiments and models, the anatomical boundaries of the heart and kidney are intrinsically assumed to be barriers for drug diffusion such that these organs can be represented as one or more compartments. To test this, an experimental preparation was developed in which the heart and kidney of anaesthetized sheep were surrounded with 0.9% saline. The rate of drug diffusion from the surface of the organs into the saline was examined during constant-rate i.v. drug infusions. It was found that the maximum clearances of lidocaine and procainamide into the pericardial saline were 10.3-11.6 and 0.6-2.1 ml min-1 respectively, and the values for the kidney were 0.3-0.6, 0.1-1.0 and 0.4-1.3 ml min-1, for lidocaine, procainamide, and meperidine respectively. These corresponded to calculated times of 4-481 min to reach the steady-state saline concentration depending on the drug and the organ. The steady-state ratio of the saline concentrations over the arterial blood drug concentrations usually ranged from 0.5-1.0. It is concluded that drugs can rapidly enter regions of low or no perfusion surrounding these organs, and that the concept of treating the heart and kidney as compartments may not be valid in certain 'worst-case' situations.

Animals↗
PubMed1993

The role of myoglobin in retarding oxygen depletion in skeletal muscle.

Myoglobin retards the development of anoxia in a poorly perfused region of skeletal muscle by facilitating diffusion into this region from adjacent normally perfused regions and by releasing bound oxygen directly into the tissue. We examine these phenomena by analyzing a mathematical model of time-dependent myoglobin-facilitated oxygen transport. The governing equations are solved using similarity transformations and multiple-scale techniques. We find that when perfusion of a region is suddenly decreased, oxygen depletion is significantly retarded by direct release of myoglobin-bound oxygen into the tissue and that myoglobin-facilitated diffusion of oxygen from adjacent regions becomes significant at very low oxygen concentration.

Animals↗
PubMed1995

Investigation of the mechanism of phosphoribosylamine transfer from glutamine phosphoribosylpyrophosphate amidotransferase to glycinamide ribonucleotide synthetase.

Phosphoribosylamine (PRA) is a product of glutamine phosphoribosylpyrophosphate amidotransferase (PRPP-AT) and a substrate for glycinamide ribonucleotide synthetase (GAR-syn), the first two enzymes in the de novo purine biosynthetic pathway. PRA has a half-life of 5 s under physiological conditions, hydrolyzing to ribose 5-phosphate. The instability of this purine precursor brings to question how the efficiency of transfer from one active site to the next is ensured: Is PRA transferred by free diffusion, or is it transferred directly from one enzyme to the next through a process defined as substrate channeling? Kinetic investigations of reactions containing both enzymes monitoring the appearance of the intermediate PRA and/or the product GAR were performed and compared with the predicted kinetics assuming a free diffusion mechanism of transfer. A significant discrepancy exists between the free diffusion model and the experimental data when the ratios of the two enzymes are varied. To accommodate this discrepancy, a direct transfer mechanism is proposed that is facilitated by protein-protein interactions. Experiments to provide evidence for these stable protein-protein interactions including gel chromatography, fluorescence spectroscopy, chemical cross-linking, and affinity gel chromatography; however, have all been unsuccessful. These results suggest that the requisite channeling interaction between PRPP-AT and GAR-syn, which is indicated by the kinetic results, must be a transient one.

Amidophosphoribosyltransferase↗
PubMed2004

Analysis of functional coupling: mitochondrial creatine kinase and adenine nucleotide translocase.

The mechanism of functional coupling between mitochondrial creatine kinase (MiCK) and adenine nucleotide translocase (ANT) in isolated heart mitochondria is analyzed. Two alternative mechanisms are studied: 1), dynamic compartmentation of ATP and ADP, which assumes the differences in concentrations of the substrates between intermembrane space and surrounding solution due to some diffusion restriction and 2), direct transfer of the substrates between MiCK and ANT. The mathematical models based on these possible mechanisms were composed and simulation results were compared with the available experimental data. The first model, based on a dynamic compartmentation mechanism, was not sufficient to reproduce the measured values of apparent dissociation constants of MiCK reaction coupled to oxidative phosphorylation. The second model, which assumes the direct transfer of substrates between MiCK and ANT, is shown to be in good agreement with experiments--i.e., the second model reproduced the measured constants and the estimated ADP flux, entering mitochondria after the MiCK reaction. This model is thermodynamically consistent, utilizing the free energy profiles of reactions. The analysis revealed the minimal changes in the free energy profile of the MiCK-ANT interaction required to reproduce the experimental data. A possible free energy profile of the coupled MiCK-ANT system is presented.

Adenosine Diphosphate↗
PubMed2006

Computational approaches to visual decision making.

Computational models based on diffusion processes have been proposed to account for human decision making behaviour in a variety of tasks. This study explores whether such models account for the speed and accuracy of perceptual decisions in a reaction-time random dot motion direction-discrimination task and whether they explain the decision-related activity of neurons recorded from the parietal cortex (area LIP) of monkeys performing the task. While a relatively simple diffusion model can explain the psychometric function and the mean response times, it fails to account for the response time distributions. By adding an 'urgency mechanism' to the diffusion model the psychometric function, the mean response times, and the shape of the response time distributions can be explained. Such an urgency mechanism could be implemented in different ways, but the best match between the physiological data and model predictions is provided by a diffusion process with a time-variant gain of the sensory signals. It can be shown that such a time-variant decision process allows the monkey to perform optimally (in the sense of maximizing reward rate) given the risk of aborting a trial by breaking fixation before a choice can be reported.

Animals↗
PubMed1992

The effect of convection on bidirectional peritoneal solute transport: predictions from a distributed model.

A distributed model of the peritoneum has been proposed as an alternative to the standard membrane model for describing peritoneal solute transport. The effect of convection on bidirectional peritoneal solute transport is studied theoretically using the distributed model. Approximate analytical and exact numerical solutions to the distributed model yield predictions similar to those when using a membrane model of peritoneal solute transport. Difficulties in interpretation of the membrane transport parameters may arise, however, when interstitial tissue, not the capillary wall, is the dominant diffusive solute transport resistance. Under such conditions the effect of convection on peritoneal solute transport is dependent on the transport direction. Moreover, predictions from the distributed model are similar to those for a membrane model containing two transport barriers in series. Thus, both the distributed model and a membrane model containing two serial transport barriers equivalently describe the effect of convection on bidirectional peritoneal solute transport.

Animals↗
PubMed1982

Pathology of an experimental extradural spinal T cell tumor.

Syngeneic mice injected intravenously with a T cell tumor line (line 13) induced by Gross' murine leukemia virus developed paraparesis and sensory loss below the midthoracic level 2 to 3 weeks after inoculation. Although signs of systemic disease coexisted, the animals survived through the development of the neurologic symptoms, and treatment with cytotoxic agents was not required. Pathologic study of the spinal cord and brain revealed tumoral infiltration of the meninges, confined to the extradural spaces, more markedly at spinal than cerebral levels. Equally severe infiltrates occurred in the paravertebral musculature. No leptomeningeal or parenchymal involvement was present, irrespective of the severity of the extradural infiltration. Marked bone marrow and visceral infiltration coexisted with central nervous system involvement. The topography of the extradural and muscular tumor cells collections related to the proximity of the involved bone marrow and areas of direct communication between these spaces were repeatedly identified. On the other hand, line 13 cells injected directly into the brain substance produced diffuse leptomeningeal tumoral infiltration without extradural involvement. These findings suggest that the pathogenesis of this model of spinal T cell tumor proliferation involves a first stage of bone marrow infiltration, followed by extradural involvement. This occurs by direct migration of bone marrow tumor cells through gaps in the vertebral bone. This model offers the opportunity for the study of malignancies that produce bone destruction as a mechanism for tumoral spread.

AKR murine leukemia virus↗
PubMed1982

Numerical solution of partial differential equation describing oxygenation rate of the red blood cell.

The non-linear partial differential equation for O2 diffusion was solved numerically in the three-dimensional red cell model by using the alternating-direction implicit method. The oxygenation rate factor of hemoglobin (FS) was assumed to decrease as the O2 saturation (SO2) increases, as given by FS = 2.1 x (1--S)2 (sec-1 . (mmHg)-1). The result obtained was compared with the solutions of the equations derived by Threws and Moll and also with those obtained from the sheet model. The oxygenation rate of the red cell largely depended on the diffusivity across the diffusion barrier around the red cell (eta). When eta = 2.5 x 10(-6) cm . sec-1 . (mmHg)-1 was inserted into the present equation, the numerical solution showed a good correlation with the experimental data. When the sheet model was applied, the eta value obtained from the same experimental data was about twice as great as that obtained in the disc model. One of the characteristic features of the SO2-time curves of the red cell was the decrease in steepness at a high SO2 range, which has been thought to occur due to the decrease in the oxygenation rate of hemoglobin. Therefore, the difference of the actual PO2 in the red cell from the fictitious, so-called "back-pressure" which is evaluated from the O2 dissociation curve through the actual SO2 has been expected to become greater as the SO2 increases. The result obtained from the present equation revealed that the above PO2 difference became as great as 20 mmHg at the maximum point. In the solutions obtained from Thew's and Moll's equations, however, the slope of the SO2-time curve was not significantly reduced at a high SO2 range.

Diffusion↗
PubMed1993

A physiologically based pharmacokinetic model for 2,3,7,8-tetrabromodibenzo-p-dioxin (TBDD) in the rat: tissue distribution and CYP1A induction.

Biologically based models serve as valuable tools for integration of mechanistic pharmacokinetic data by their explicit definition of important determinants of chemical disposition. The objective of the present work was to develop a physiologically based pharmacokinetic model to describe the disposition and enzyme induction properties of 2,3,7,8-tetrabromodibenzo-p-dioxin (TBDD). The TBDD model, which was based on models previously developed for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), incorporated: ternary interactions between TBDD, the Ah receptor, and specific DNA-binding sites; induction of a TBDD-binding protein specific to the liver; and diffusion-limited tissue uptake. In the model for TBDD, CYP1A2, which had been measured directly by radioimmunoassay, was assumed to be the hepatic binding protein. The model employed physiologic parameters based on recent data in unanesthetized rats, growing tissue compartments, transluminal excretion of parent TBDD via the gut into the feces, and a separate skin compartment. The model was developed using tissue distribution and excretion data following a single intravenous dose of 1 nmol [3H]TBDD per kilogram. The TBDD model was then used unchanged to analyze several experimental data sets illustrating the time, dose, and route of exposure dependency of TBDD disposition. The model successfully described the dose-dependent tissue distribution of [3H]TBDD following intravenous and oral administration and following a single dermal dose. These studies show that diffusional clearance from blood to tissue was slower for skin than for fat (PAsk approximately 0.1 PAf). When compared with TCDD: (i) TBDD had a higher fat partition coefficient (Pf = 1000 vs 400) and a lower diffusional clearance into fat (PAf = 0.1 vs 0.2) than TCDD; (ii) the binding affinity of CYP1A2 for TBDD was slightly lower than that for TCDD (9.0 vs 6.5 nM); and (iii) TBDD exhibited a slightly greater rate of metabolic elimination (2.0 vs 1.65). Small differences were noted in DNA binding parameters derived for the induction of CYP1A1 and CYP1A2 for TBDD versus TCDD. With minor modifications, the biologically based model for TCDD accurately described the behavior of the brominated congener. The present model, which relied on measured values of CYP1A2 and specified CYP1A2 as the hepatic dioxin binding species, successfully describes the hepatic disposition of TBDD, providing further evidence that CYP1A2 is the primary hepatic binding species in the rat.

Administration, Oral↗
PubMed2005

Thermo-kinetics study of laser-induced desorption of self-assembled monolayers from gold: case of laser micropatterning.

Laser-induced desorption of self-assembled monolayers (SAMs) from gold surfaces within context of the direct laser patterning methodology was investigated through combining results of a heat diffusion thermal model with desorption kinetics of alkanethiol SAMs. It was found that contrast plots of experimental scanning electron microscopy (SEM) images, which are correlated to surface coverage of SAMs desorbed after laser irradiation, agreed with the theoretically predicted surface composition of SAMs. The surface composition of SAM was then interpreted in terms of the wetting property of the resulting surface. The effect of incident laser beam power and size on the final spatial coverage of SAMs on the surface and feature sizes was investigated both experimentally and by modeling. Theoretical modeling and experimental evidence showed that the resulting feature sizes are wider when the surface is heated by a laser of higher power. Increasing the laser beam size results in broadening of feature sizes. Considering the correlation of the theoretical and experimental results, we concluded that the feature sizes are controllable in a predictable way (using the presented thermal-kinetics model) through varying laser beam power and beam size.

Journal Article↗
PubMed1998

Absorption of solar radiation by an ellipsoid sensor simulated the human body.

Assessment of heat gain in man caused by solar radiation is one of the most important problems in research of the human heat balance outdoors. The purpose of the present study was to investigate a new method for estimation of solar heat income. Absorption of short wave radiation (direct, diffuse and reflected) was measured with an ellipsoid sensor representing a simple, physical model of man. Measurements were performed in climatic chamber with the use of an iodide CSI solar lamp. The absorbed quantity of solar radiation varied as a result of sun altitude as well as of a colour and insulation of fabric covering the ellipsoid sensor. The new coefficients derived from our investigations for estimating doses of absorbed solar radiation should be applicable for a standing man. They correlate better with mean skin temperature observed on subjects outdoor than previous results obtained based on a cylinder as an analogue model of man. The ellipsoid sensor covered by a black fabric absorbed about 6 times more of solar radiation than when covered by a white textile.

Absorption↗
PubMed2003

Characterization and propagation of uncertainty in diffusion-weighted MR imaging.

A fully probabilistic framework is presented for estimating local probability density functions on parameters of interest in a model of diffusion. This technique is applied to the estimation of parameters in the diffusion tensor model, and also to a simple partial volume model of diffusion. In both cases the parameters of interest include parameters defining local fiber direction. A technique is then presented for using these density functions to estimate global connectivity (i.e., the probability of the existence of a connection through the data field, between any two distant points), allowing for the quantification of belief in tractography results. This technique is then applied to the estimation of the cortical connectivity of the human thalamus. The resulting connectivity distributions correspond well with predictions from invasive tracer methods in nonhuman primate.

Algorithms↗