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At least 1,225 records · Page 68Linked to original sources
PubMed1996

A general model for exposure and uptake from consumer products.

To assess exposure to and uptake of chemical compounds from consumer products, a general model framework is proposed. The model framework separates exposure into the components contact, potential exposure, and potential uptake rate, and establishes the relation between the three. It adds a contact function and a spatial component to other exposure modeling concepts. Before the model framework can be used, its components need to be specified. A simple diffusional model is built as an example of specifying functions for exposure and uptake. A case study of 1,1,1 trichloroethane in some shoe impregnating product, partly based on the diffusional uptake model, illustrates the inclusion of the contact component. In the latter example, the exposure is calculated for the user and then, by only modifying the contact component, for a nonuser randomly walking in the house.

Consumer Product Safety↗
PubMed2006

A Bayesian mixture model for partitioning gene expression data.

In recent years there has been great interest in making inference for gene expression data collected over time. In this article, we describe a Bayesian hierarchical mixture model for partitioning such data. While conventional approaches cluster the observed data, we assume a nonparametric, random walk model, and partition on the basis of the parameters of this model. The model is flexible and can be tuned to the specific context, respects the order of observations within each curve, acknowledges measurement error, and allows prior knowledge on parameters to be incorporated. The number of partitions may also be treated as unknown, and inferred from the data, in which case computation is carried out via a birth-death Markov chain Monte Carlo algorithm. We first examine the behavior of the model on simulated data, along with a comparison with more conventional approaches, and then analyze meiotic expression data collected over time on fission yeast genes.

Bayes Theorem↗
PubMed1990

How do leucocytes perceive chemical gradients?

Chemoattractants determine not only the direction of leucocyte locomotion (chemotaxis) but also its speed (chemokinesis). Various mechanisms by which leucocytes may detect chemotactic gradients, including spatial and temporal detection, are briefly reviewed. These mechanisms as originally proposed did not address the question how attractants cause leucocytes to migrate in persistent random paths in the absence of a gradient. Stochastic models have recently been presented in which leucocytes either respond by polarizing and migrating in the direction from which they receive their first signal, or respond to random fluctuations in the perceived attractant concentration. Stochastic models allow an explanation for the persistent random walk shown by cells in uniform concentrations of attractant as well as for directional locomotion in gradients. They suggest that, at the biochemical level, the mechanisms by which attractants stimulate chemotaxis and chemokinesis are probably the same.

Animals↗
PubMed2005

Translocation through the nuclear pore complex: selectivity and speed by reduction-of-dimensionality.

Translocation through the nuclear pore complex (NPC), a large transporter spanning the nuclear envelope, is a passive, diffusion-driven process, paradoxically enhanced by binding. To account for this mystery, several models have been suggested. However, recent experiments with modified NPCs make reconsideration necessary. Here, we suggest that nuclear transport receptors (NTRs) such as the karyopherins, in accordance with their peculiar boat-like structure, act as nanoscopic ferries transporting cargos through the NPC by sliding on a surface of phenylalanine glycine (FG) motifs. The dense array of FG motifs that covers the cytoplasmic filaments of the NPC is thought to continue on the wall of the large channel permeating the central framework of the NPC and on parts of the nuclear filaments to yield a coherent FG surface. Nuclear transport receptors are assumed to bind to the FG surface at filaments or at the channel entrance and then to rapidly search the FG surface by a two-dimensional random walk for the channel exit where they are released. The passage of neutral molecules is restricted to a narrow tube in the center of the central channel by a loose network of peptide chains. The model features virtual gating, is compatible with but not dependent on FG affinity gradients and tolerates deletions and transpositions of FG motifs. Implications of the model are discussed and tests are suggested.

Active Transport, Cell Nucleus↗
PubMedDate not supplied

Computing "anomalous" contaminant transport in porous media: the CTRW MATLAB toolbox.

We describe the continuous time random walk (CTRW) MATLAB toolbox, a collection of MATLAB scripts and functions that compute breakthrough curves (BTCs) and one-dimensional/two-dimensional (1D/2D) resident concentration profiles for passive tracer dispersion. The transport model is based on the CTRW theory. CTRW includes as special cases the classical Fickian dispersion based advection-dispersion equation, multirate and mobile-immobile models, and the fractional-in-time derivative transport equation. Several models for treating the memory effects responsible for the anomalous character of dispersion have been implemented in the CTRW toolbox. In the current version of the toolbox, it is possible to solve explicitly for the forward problem (concentration prediction) in 1D and 2D and for the inverse problem (parameter identification from experimental BTC data) in 1D. Future extensions will include explicit treatment of sorbing tracers, simple subroutines for treating radial flow from wells, introduction of arbitrary initial conditions, treatment of heterogeneous domains by use of the Fokker-Planck with Memory equation, and treatment of transport in multidimensional systems.

Environmental Monitoring↗
PubMedDate not supplied

Influence of small-scale heterogeneities on contaminant transport in fractured crystalline rock.

We present a sequence of purely advective transport models that demonstrate the influence of small-scale geometric inhomogeneities on contaminant transport in fractured crystalline rock. Special weight is placed on the role of statistically generated variable fracture apertures. The fracture network geometry and the aperture distribution are based on information from an in situ radionuclide retardation experiment performed at Grimsel test site (Swiss Alps). The obtained breakthrough curves are fitted with the advection dispersion equation and continuous-time random walks (CTRW). CTRW is found to provide superior fits to the late-arrival tailing and is also found to show a good correlation with the velocity distributions obtained from the hydraulic models. The impact of small-scale heterogeneities, both in fracture geometry and aperture, on transport is shown to be considerable.

Computer Simulation↗
PubMed1994

Resolution limits for optical transillumination of abnormalities deeply embedded in tissues.

Random walk theory is used to calculate the line spread function (LSF) of photons as they cross the midplane of a slab of finite thickness. The relationship between the LSF and the photon transit time in transillumination time-resolved experiments is investigated. It is found that the LSF is approximately Gaussian distributed, with a standard deviation, sigma, which can be used as a criterion of the spatial resolution of the imaging system. Results are substantiated by comparison with actual data in the literature. Any given resolution can be improved by reducing the excess transit time delta t, but heterogeneity of the scattering medium and low levels of detected light enormously complicate the achievement of subcentimeter spatial resolution. The latter point is discussed by using optical parameters of breast tissues for visible and near-infrared radiation (NIR) light.

Breast Diseases↗
PubMed1996

Experimental test of theoretical models for time-resolved reflectance.

Four different expressions, derived from the diffusion theory or the random walk model, were used to fit time-resolved reflectance data for the evaluation of tissue optical properties. The experimental reflectance curves were obtained from phantoms of known optical parameters (absorption and transport scattering coefficients) covering the range of typical values for biological tissues between 600 and 900 nm. The measurements were performed using an instrumentation for time-correlated single-photon counting. The potential of the four methods in the assessment of the absorption and transport scattering coefficients was evaluated in terms of absolute error, linearity error, and dispersion of data. Each method showed different performances depending on the optical properties of the sample and the experimental conditions. We propose some criteria for the optimal choice of the fitting method to be used in different applications.

Biophysical Phenomena↗
PubMed2002

Two-photon imaging of lymphocyte motility and antigen response in intact lymph node.

Lymphocyte motility is vital for trafficking within lymphoid organs and for initiating contact with antigen-presenting cells. Visualization of these processes has previously been limited to in vitro systems. We describe the use of two-photon laser microscopy to image the dynamic behavior of individual living lymphocytes deep within intact lymph nodes. In their native environment, T cells achieved peak velocities of more than 25 micrometers per minute, displaying a motility coefficient that is five to six times that of B cells. Antigenic challenge changed T cell trajectories from random walks to "swarms" and stable clusters. Real-time two-photon imaging reveals lymphocyte behaviors that are fundamental to the initiation of the immune response.

Adoptive Transfer↗
PubMed1973

Dynamics of number fluctuations: motile microorganisms.

The time dependence of the intensity of light scattered from motile Escherichia coli bacteria is studied in population densities so low that the intensity autocorrelation function reflects fluctuations in the total number of particles in the scattering region. Measured correlation functions are analyzed by using a random walk model of bacterial motion.

Escherichia coli↗
PubMed1993

Patchiness and correlations in DNA sequences.

The highly nonrandom character of genomic DNA can confound attempts at modeling DNA sequence variation by standard stochastic processes (including random walk or fractal models). In particular, the mosaic character of DNA consisting of patches of different composition can fully account for apparent long-range correlations in DNA.

Analysis of Variance↗
PubMed2002

Mechanisms and rates of bacterial colonization of sinking aggregates.

Quantifying the rate at which bacteria colonize aggregates is a key to understanding microbial turnover of aggregates. We used encounter models based on random walk and advection-diffusion considerations to predict colonization rates from the bacteria's motility patterns (swimming speed, tumbling frequency, and turn angles) and the hydrodynamic environment (stationary versus sinking aggregates). We then experimentally tested the models with 10 strains of bacteria isolated from marine particles: two strains were nonmotile; the rest were swimming at 20 to 60 microm s(-1) with different tumbling frequency (0 to 2 s(-1)). The rates at which these bacteria colonized artificial aggregates (stationary and sinking) largely agreed with model predictions. We report several findings. (i) Motile bacteria rapidly colonize aggregates, whereas nonmotile bacteria do not. (ii) Flow enhances colonization rates. (iii) Tumbling strains colonize aggregates enriched with organic substrates faster than unenriched aggregates, while a nontumbling strain did not. (iv) Once on the aggregates, the bacteria may detach and typical residence time is about 3 h. Thus, there is a rapid exchange between attached and free bacteria. (v) With the motility patterns observed, freely swimming bacteria will encounter an aggregate in <1 day at typical upper-ocean aggregate concentrations. This is faster than even starving bacteria burn up their reserves, and bacteria may therefore rely solely on aggregates for food. (vi) The net result of colonization and detachment leads to a predicted equilibrium abundance of attached bacteria as a function of aggregate size, which is markedly different from field observations. This discrepancy suggests that inter- and intraspecific interactions among bacteria and between bacteria and their predators may be more important than colonization in governing the population dynamics of bacteria on natural aggregates.

Bacteria↗
PubMed1998

Unique regulation of carbohydrate chemotaxis in Bacillus subtilis by the phosphoenolpyruvate-dependent phosphotransferase system and the methyl-accepting chemotaxis protein McpC.

The phosphoenolpyruvate-dependent phosphotransferase system (PTS) plays a major role in the ability of Escherichia coli to migrate toward PTS carbohydrates. The present study establishes that chemotaxis toward PTS substrates in Bacillus subtilis is mediated by the PTS as well as by a methyl-accepting chemotaxis protein (MCP). As for E. coli, a B. subtilis ptsH null mutant is severely deficient in chemotaxis toward most PTS carbohydrates. Tethering analysis revealed that this mutant does respond normally to the stepwise addition of a PTS substrate (positive stimulus) but fails to respond normally to the stepwise removal of such a substrate (negative stimulus). An mcpC null mutant showed no response to the stepwise addition or removal of D-glucose or D-mannitol, both of which are PTS substrates. Therefore, in contrast to E. coli PTS carbohydrate chemotaxis, B. subtilis PTS carbohydrate chemotaxis is mediated by both MCPs and the PTS; the response to positive stimulus is primarily McpC mediated, while the duration or magnitude of the response to negative PTS carbohydrate stimulus is greatly influenced by components of the PTS and McpC. In the case of the PTS substrate D-glucose, the response to negative stimulus is also partially mediated by McpA. Finally, we show that B. subtilis EnzymeI-P has the ability to inhibit B. subtilis CheA autophosphorylation in vitro. We hypothesize that chemotaxis in the spatial gradient of the capillary assay may result from a combination of a transient increase in the intracellular concentration of EnzymeI-P and a decrease in the concentration of carbohydrate-associated McpC as the cell moves down the carbohydrate concentration gradient. Both events appear to contribute to inhibition of CheA activity that increases the tendency of the bacteria to tumble. In the case of D-glucose, a decrease in D-glucose-associated McpA may also contribute to the inhibition of CheA. This bias on the otherwise random walk allows net migration, or chemotaxis, to occur.

Bacillus subtilis↗
PubMed2006

Sgs1 regulates gene conversion tract lengths and crossovers independently of its helicase activity.

RecQ helicases maintain genome stability and suppress tumors in higher eukaryotes through roles in replication and DNA repair. The yeast RecQ homolog Sgs1 interacts with Top3 topoisomerase and Rmi1. In vitro, Sgs1 binds to and branch migrates Holliday junctions (HJs) and the human RecQ homolog BLM, with Top3alpha, resolves synthetic double HJs in a noncrossover sense. Sgs1 suppresses crossovers during the homologous recombination (HR) repair of DNA double-strand breaks (DSBs). Crossovers are associated with long gene conversion tracts, suggesting a model in which Sgs1 helicase catalyzes reverse branch migration and convergence of double HJs for noncrossover resolution by Top3. Consistent with this model, we show that allelic crossovers and gene conversion tract lengths are increased in sgs1Delta. However, crossover and tract length suppression was independent of Sgs1 helicase activity, which argues against helicase-dependent HJ convergence. HJs may converge passively by a "random walk," and Sgs1 may play a structural role in stimulating Top3-dependent resolution. In addition to the new helicase-independent functions for Sgs1 in crossover and tract length control, we define three new helicase-dependent functions, including the suppression of chromosome loss, chromosome missegregation, and synthetic lethality in srs2Delta. We propose that Sgs1 has helicase-dependent functions in replication and helicase-independent functions in DSB repair by HR.

Chromosome Segregation↗
PubMed1977

Simulation of oviductal ovum transport.

The present note describes a Monte Carlo simulation of ovum transport in the rabbit oviduct. Ova execute a random walk through a one-dimensional oviduct and the jump probabilities at each point are obtained from in vitro electrical recordings of smooth muscle activity. Simulated transport are compared with experimental findings at 18 and 66-68 h after human chorionic gonadotropin injection.

Animals↗
PubMed2004

Exact lattice calculations of dispersion coefficients in the presence of external fields and obstacles.

We present a study of the field-dependent dispersion coefficient of point-like particles in various 2D overdamped systems with obstructions (periodic, percolating, and trapping distributions of obstacles). These calculations profit from the synthesis of a newly proposed Monte Carlo algorithm--the first such algorithm that correctly reproduces the free dispersion coefficient in the presence of finite external fields--and an asymptotically exact calculation technique. The resulting method efficiently produces algebraic and numerical results without the need to actually perform Monte Carlo simulations. When compared to such simulations, our exact method features a negligible computational cost and exponentially small errors. Utilizing the power of this numerical method, we engage in comprehensive parametric analysis of several model systems, revealing very subtle effects that would otherwise be swamped by statistical errors or incur prohibitive computational costs. The unified framework presented here serves as a template for further applications of lattice random-walk models of biased diffusion.

Algorithms↗
PubMed2005

Photon channelling in foams.

Experiments by Gittings, Bandyopadhyay and Durian (Europhys. Lett. 65, 414 (2004)) demonstrate that light possesses a higher probability to propagate in the liquid phase of a foam due to total reflection. The authors term this observation photon channelling which we investigate in this article theoretically. We first derive a central relation in the work of Gitting et al. without any free parameters. It links the photon's path-length fraction f in the liquid phase to the liquid fraction epsilon. We then construct two-dimensional Voronoi foams, replace the cell edges by channels to represent the liquid films and simulate photon paths according to the laws of ray optics using transmission and reflection coefficients from Fresnel's formulas. In an exact honeycomb foam, the photons show superdiffusive behavior. It becomes diffusive as soon as disorder is introduced into the foams. The dependence of the diffusion constant on channel width and refractive index is explained by a one-dimensional random-walk model. It contains a photon channelling state that is crucial for the understanding of the numerical results. At the end, we shortly comment on the observation that photon channelling only occurs in a finite range of epsilon.

Journal Article↗
PubMed2006

Smoothening transition of a two-dimensional pressurized polymer ring.

We revisit the problem of a two-dimensional polymer ring subject to an inflating pressure differential. The ring is modeled as a freely jointed closed chain of N monomers. Using a Flory argument, mean-field calculation and Monte Carlo simulations, we show that at a critical pressure, p(c) approximately N(-1), the ring undergoes a second-order phase transition from a crumpled, random-walk state, where its mean area scales as approximately N, to a smooth state with approximately N(2). The transition belongs to the mean-field universality class. At the critical point a new state of polymer statistics is found, in which approximately N(3/2). For p >> p(c) we use a transfer-matrix calculation to derive exact expressions for the properties of the smooth state.

Computer Simulation↗