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At least 1,207 records · Page 67Linked to original sources
PubMed2005

Strong-coupling dynamics of a multicellular chemotactic system.

Chemical signaling is one of the ubiquitous mechanisms by which intercellular communication takes place at the microscopic level, particularly via chemotaxis. Such multicellular systems are popularly studied using continuum, mean-field equations. In this Letter we study a stochastic model of chemotactic signaling. The Langevin formalism of the model makes it amenable to calculation via nonperturbative analysis, which enables a quantification of the effect of fluctuations on both the weak and the strongly coupled biological dynamics. In particular, we show that the (i) self-localization due to autochemotaxis is impossible. (ii) When aggregation occurs, the aggregate performs a random walk with a renormalized diffusion coefficient D(R) proportiuonal to epsilon-2N-3. (iii) The stochastic model exhibits sharp transitions in cell motile behavior for negative chemotaxis, behavior that has no parallel in the mean-field Keller-Segel equations.

Cell Communication↗
PubMed2005

Entangled networks, synchronization, and optimal network topology.

A new family of graphs, entangled networks, with optimal properties in many respects, is introduced. By definition, their topology is such that it optimizes synchronizability for many dynamical processes. These networks are shown to have an extremely homogeneous structure: degree, node distance, betweenness, and loop distributions are all very narrow. Also, they are characterized by a very interwoven (entangled) structure with short average distances, large loops, and no well-defined community structure. This family of nets exhibits an excellent performance with respect to other flow properties such as robustness against errors and attacks, minimal first-passage time of random walks, efficient communication, etc. These remarkable features convert entangled networks in a useful concept, optimal or almost optimal in many senses, and with plenty of potential applications in computer science or neuroscience.

Animals↗
PubMed2006

Anomalous diffusion of inertial, weakly damped particles.

The anomalous (i.e., non-Gaussian) dynamics of particles subject to a deterministic acceleration and a series of "random kicks" is studied. Based on an extension of the concept of continuous time random walks to position-velocity space, a new fractional equation of the Kramers-Fokker-Planck type is derived. The associated collision operator necessarily involves a fractional substantial derivative, representing important nonlocal couplings in time and space. For the force-free case, a closed solution is found and discussed.

Journal Article↗
PubMed2006

Reproducibility of dynamical heterogeneities and metabasin dynamics in glass forming liquids: the influence of structure on dynamics.

The discovery that the propensity for particle motion in a supercooled liquid is completely determined by the initial structure pointed to the existence of a causal link between structure and dynamics in glassy systems. Here we demonstrate that this underlying influence of structure is only local in time, fading out beyond the metabasin lifetime much before the relaxation time. Thus, our results reveal the irreproducibility of metabasin dynamics and support the scenario of a random walk on metabasins for the long time diffusion.

Computer Simulation↗
PubMed2006

Subdiffusion and long-time anticorrelations in a stochastic single file.

The subdiffusion of a stochastic single file is interpreted as a jumping process. Contrary to the current continuous time random walk models, its statistics is characterized by finite averages of the jumping times and square displacements. Subdiffusion is then related to a persistent anticorrelation of the jump sequences. In continuous time representation, this corresponds to negative power-law velocity autocorrelations, attributable to the restricted geometry of the file diffusion.

Journal Article↗
PubMed2006

Field-induced dispersion in subdiffusion.

We discuss the response of continuous-time random walks to an oscillating external field within the generalized master equation approach. We concentrate on the time dependence of the two first moments of the walker's displacement. We show that for power-law waiting-time distributions with 0<alpha<1 corresponding to a semi-Markovian situation showing nonstationarity, the mean particle position tends to a constant; namely, the response to the external perturbation dies out. On the other hand, the oscillating field leads to a new additional contribution to the dispersion of the particle position, proportional to the square of its amplitude and growing with time. These new effects, amenable to experimental observation, result directly from the nonstationary property of the system.

Journal Article↗
PubMed1996

Dynamics of temperature dependent optical properties of tissue: dependence on thermally induced alteration.

Thermal damage in heated bovine myocardial tissue is assessed from measured changes in total reflection and transmission of light. Mathematical expressions, based on random walk analysis of light propagation within tissue slabs, are used to relate the diffuse reflection and transmittance to the absorption coefficient, mu a, and effective scattering coefficient, mu's, for samples of myocardial tissue which were subjected to rapid step changes in temperature. Time-dependent changes in mu's, indicate two processes, one with a fast and temperature-dependent rate the other with a slow and apparently temperature-independent rate. For final temperatures above 56.8 degrees C and for the first 500 s after the temperature change, the optical parameters are well fit by exponential forms that exhibit temperature-dependent time constants as predicted by Arrhenius reaction rate theory of thermal damage. The scattering changes are associated with an apparent activation energy, delta E, of 162 kJ/mole and a frequency constant, A, of 3 x 10(23) s-1. This method provides a means for estimating optical coefficients which are needed to assess laser tissue dosimetry.

Absorption↗
PubMed2005

Multi-scale hierarchical structure prediction of helical transmembrane proteins.

As the first step toward a multi-scale, hierarchical computational approach for membrane protein structure prediction, the packing of transmembrane helices was modeled at the residual and atomistic levels, respectively. For predictions at the residual level, the helix-helix and helix-lipid interactions were described by a set of knowledge-based energy functions. For predictions at the atomistic level, CHARMM19 force field was employed. To facilitate the system to overcome energy barriers, Wang-Landau sampling was carried out by performing a random walk in the energy and conformational spaces. Native-like structures were predicted at both levels for 2- and 7-helix systems. Interestingly, consistent results were obtained from simulations at residual and atomistic levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane structure prediction.

Algorithms↗
PubMed2004

Visual tracking and recognition using appearance-adaptive models in particle filters.

We present an approach that incorporates appearance-adaptive models in a particle filter to realize robust visual tracking and recognition algorithms. Tracking needs modeling interframe motion and appearance changes, whereas recognition needs modeling appearance changes between frames and gallery images. In conventional tracking algorithms, the appearance model is either fixed or rapidly changing, and the motion model is simply a random walk with fixed noise variance. Also, the number of particles is typically fixed. All these factors make the visual tracker unstable. To stabilize the tracker, we propose the following modifications: an observation model arising from an adaptive appearance model, an adaptive velocity motion model with adaptive noise variance, and an adaptive number of particles. The adaptive-velocity model is derived using a first-order linear predictor based on the appearance difference between the incoming observation and the previous particle configuration. Occlusion analysis is implemented using robust statistics. Experimental results on tracking visual objects in long outdoor and indoor video sequences demonstrate the effectiveness and robustness of our tracking algorithm. We then perform simultaneous tracking and recognition by embedding them in a particle filter. For recognition purposes, we model the appearance changes between frames and gallery images by constructing the intra- and extrapersonal spaces. Accurate recognition is achieved when confronted by pose and view variations.

Algorithms↗
PubMed2006

Shape representation and classification using the poisson equation.

We present a novel approach that allows us to reliably compute many useful properties of a silhouette. Our approach assigns, for every internal point of the silhouette, a value reflecting the mean time required for a random walk beginning at the point to hit the boundaries. This function can be computed by solving Poisson's equation, with the silhouette contours providing boundary conditions. We show how this function can be used to reliably extract various shape properties including part structure and rough skeleton, local orientation and aspect ratio of different parts, and convex and concave sections of the boundaries. In addition to this, we discuss properties of the solution and show how to efficiently compute this solution using multigrid algorithms. We demonstrate the utility of the extracted properties by using them for shape classification and retrieval.

Algorithms↗
PubMed2002

Surface-related phase noise in SAW resonators.

With the advent of nanotechnologies, electronic devices are shrinking in thickness and width to reduce mass and, thereby, increase frequency and spe Lithographic approaches are capable of creating metal connections with thickness and lateral dimensions down to about 20 nm, approaching the molecular scale. As a result, the dimensions of outer particles are comparable with, or even larger than, those of active or passive regions in electronics devices. Therefore, directing our attention toward the effect of surface fluctuations is of practical significance. In fact, electronic device surface-related phenomena have already received more and more attention as device size decreases. In connection with surface phase noise, selection of a suitable device with high surface sensitivity is important. In this paper, high Q-value surface acoustic wave resonators were employed because of their strong sensitivity to surface perturbation. Phase noise in SAW resonators related to surface particle motion has been examined both theoretically and experimentally. This kind of noise has been studied from the point of view of a stochastic process resulting from particle molecular adsorption and desorption. Experimental results suggest that some volatile vapors can change flicker noise 1/f and random walk noise 1/f2. An analysis has been made indicating that these effects are not associated with Q value variation, but are generated by the change in the dynamic rate of adsorption and desorption of surface particles. Research on particle motion above the device substrate might explain the differences observed from the model based only on the substrate itself. Results might lead to a better understanding of the phase noise mechanism in micro-electronic devices and help us to build oscillators with improved performance.

Acoustics↗
PubMed2004

Contrast echocardiography for pulmonary blood volume quantification.

Pulmonary blood volume quantification is important both for diagnosis and for monitoring of the circulatory system. It requires employment of transpulmonary indicator dilution techniques, which are very invasive due to the need for double catheterization. This paper presents a new minimally invasive technique for blood volume quantification. An ultrasound contrast agent bolus is injected peripherally and detected by an ultrasound transducer in the central circulation. Several echocardiographic views permit simultaneous detection of contrast in different cardiac cavities and central vessels, and acoustic backscatter measurements produce multiple indicator dilution curves (IDCs). Contrast mean-transit-time differences are derived from the IDC analysis and multiplied times cardiac output for the assessment of blood volumes between different detection sites. For pulmonary blood volume estimates, the right ventricle and the left atrium IDCs are measured. The mean transit time of the IDC is estimated by specific modelling. The Local Density Random Walk and the First Passage Time models were tested for IDC interpolation and interpretation. The system was validated in vitro for a wide range of flows. The results show very accurate volume measurements. The volume estimate determination coefficient is greater than 0.999 for both model fits. A preliminary study in patients shows promising results.

Algorithms↗
PubMed2004

A cryogenic open-cavity sapphire reference oscillator with low spurious mode density.

In this paper, we describe the implementation of a microwave cryogenic sapphire oscillator (CSO) at the Laboratoire de Physique et Métrologie des Oscillateurs. In our realization we solved the problem of the spurious modes by operating the sapphire resonator in an open cavity. The CSO compared to a hydrogen maser demonstrates a frequency stability better than 3 x 10(-14) at short term. Its long-term frequency instability of the order of 3 x 10(-12)/day is limited by a random walk process. A first attempt to use this reference oscillator to characterize other signal sources is presented.

Journal Article↗
PubMed2000

Generating probabilistic spatially-explicit individual and population exposure estimates for ecological risk assessments.

Exposure to chemical contaminants in various media must be estimated when performing ecological risk assessments. Exposure estimates are often based on the 95th-percentile upper confidence limit on the mean concentration of all samples, calculated without regard to critical ecological and spatial information about the relative relationship of receptors, their habitats, and contaminants. This practice produces exposure estimates that are potentially unrepresentative of the ecology of the receptor. This article proposes a habitat area and quality-conditioned exposure estimator, E[HQ], that requires consideration of these relationships. It describes a spatially explicit ecological exposure model to facilitate calculation of E[HQ]. The model provides (1) a flexible platform for investigating the effect of changes in habitat area, habitat quality, foraging area, and population size on exposure estimates, and (2) a tool for calculating E[HQ] for use in actual risk assessments. The inner loop of a Visual Basic program randomly walks a receptor over a multicelled landscape--each cell of which contains values for cell area, habitat area, habitat quality, and concentration--accumulating an exposure estimate until the total area foraged is less than or equal to a given foraging area. An outer loop then steps through foraging areas of increasing size. This program is iterated by Monte Carlo software, with the number of iterations representing the population size. Results indicate that (1) any single estimator may over- or underestimate exposure, depending on foraging strategy and spatial relationships of habitat and contamination, and (2) changes in exposure estimates in response to changes in foraging and habitat area are not linear.

Animals↗
PubMed2001

A case study comparing static and spatially explicit ecological exposure analysis methods.

Exposure to chemical contaminants must be estimated when performing ecological risk assessments. A previous article proposed a habitat area and quality conditioned population exposure estimator, E[HQ]P, and described an individual-based, random walk, Monte Carlo model (SE3M) to facilitate calculation of E[HQ]P. In this article, E[HQ]P was compared with exposure estimates from a baseline risk assessment that evaluated mink and great blue heron exposure to fluoride at a federal Superfund site. Calculation of E[HQ]P took into consideration a receptor's forage area, movement behavior, population size, and the areal extent and quality of suitable habitat. The baseline assessment used four methods that did (total and unit Tier 2) and did not (total and unit Tier 1) consider habitat area or quality; where "total" included all exposure units on site and "unit" only a given exposure unit. Total Tier 1 estimates were consistently higher than E[HQ]P (e.g., 169.1 mg/kg x d versus 21.6 mg/kg x d). Risk managers using total Tier 1 results for decision making would be unlikely to underestimate exposure; however, implementability of correspondingly lower remedial objectives could be challenging. Unit Tier 1 estimates were higher (e.g., 96.5 mg/kg x d versus 61.6 mg/kg x d) or lower (e.g., 3.5 mg/kg x d versus 51.1 mg/kg x d) than E[HQ]P depending on variations in landscape features. Total Tier 2 and E[HQ]P estimates were similar (e.g., 20.7 mg/kg x d versus 21.6 mg/kg x d) when an ecologically questionable average exposure was assumed. Unit Tier 2 estimates were consistently well below E[HQ]P (e.g., 17.8 mg/kg x d versus 61.6 mg/kg x d) when an average exposure was not assumed. Risk managers using unit Tier 1 or 2 results could be basing their decisions on potentially large underestimates of exposure. By forgoing average exposure assumptions, and explicitly addressing landscape heterogeneity, SE3M appears capable of yielding exposure estimates that are not as potentially misleading to risk managers as those produced with traditional averaging methods.

Aluminum↗
PubMed2006

Animal movement rates as behavioural bouts.

Johnson et al. (Journal of Animal Ecology, 2002, 71, 225-235) have proposed a new technique for identifying scales of movement in animals. Animals are located at certain time intervals, and movement rates between successive animal relocations are calculated. The null model of a nonscalar response predicts a decreasing linear relationship between log (frequency) vs. movement rate, while a scalar response predicts a monotonically decreasing curve with an inflection point at the separation between the processes. I tested this technique using three types of simulated movement paths: correlated random walks, directed walks, and movements in patchy habitat. None of the simulations showed the results expected by the technique. This occurs because the technique assumes that movement rates are exponentially distributed, which is highly unlikely. Thus before this technique can be applied to animal movement data we need to understand how spatial and temporal scale, as well as sampling interval, affect the frequency histogram of animal movement rates.

Animals↗
PubMed1990

Multilocus ordering strategies based on sperm typing.

Sperm typing is a promising new approach for fine-structure human gene mapping. We examine three-locus sperm typing and its implications for the estimation of recombination fractions and for locus ordering. In particular, we compare some sequential stopping rules for three-locus assignment and develop methods for approximating their mean stopping times and error probabilities. A stopping rule recently described by Thompson and Boehnke et al. appears to be nearly optimal. Under this rule, one stops sampling as soon as the number of sperm of the least frequent recombinant type is s fewer than the number of sperm of the next least frequent type. We develop a random-walk algorithm and some heuristic formulas for assessing the performance of this rule. Since the broader goal of linkage analysis is to order many more than three loci, we propose a trisection strategy for ordering a new locus relative to an existing ordered set of loci. The crux of the trisection strategy is to restrict attention to the smallest block of ordered loci among which the new locus can fall and to divide this block into thirds for the next comparison. This trisection strategy is optimal in the sense that it has the best worse-case performance of any strategy. When it is applied sequentially to order a collection of loci, it is only nearly optimal, as we demonstrate by specific counter-example. However, it does become asymptotically optimal as the size of the collection increases.

Chromosome Mapping↗
PubMed2006

Error estimation of the fractal dimension measurements of cranial sutures.

The fractal exponents used to quantify the complexity of cranial sutures were computed for 17 coronal and 17 sagittal sutures of adults from different populations, using the box-counting algorithm. This paper discusses the main sources of error for the fractal exponents, and gives the error estimates. We then compare our results with those obtained by other authors. We suggest that the usual error estimates implied by the standard deviation for the regression line are too low. We emphasize the crucial role played by the choice of regression line in the log-log plot. For the coronal and sagittal sutures we found mean fractal dimensions of 1.48 and 1.56, respectively. Our values are close to the value for Brownian random walk.

Adult↗