Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Random walk”

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 739 records · Page 41Linked to original sources
PubMed2001

Dynamics and critical behavior of the q model.

The q model, a random walk model rich in behavior and applications, is investigated. We introduce and motivate the q model via its application proposed by Coppersmith et al. to the flow of stress through granular matter at rest. For a special value of its parameters the q model has a critical point that we analyze. To characterize the critical point we imagine that a uniform load has been applied to the top of the granular medium and we study the evolution with depth of fluctuations in the distribution of load. Close to the critical point explicit calculation reveals that the evolution of load exhibits scaling behavior analogous to thermodynamic critical phenomena. The critical behavior is remarkably tractable: the harvest of analytic results includes scaling functions that describe the evolution of the variance of the load distribution close to the critical point and of the entire load distribution right at the critical point, values of the associated critical exponents, and determination of the upper critical dimension. These results are of intrinsic interest as a tractable example of a random critical point. Of the many applications of the q model, the critical behavior is particularly relevant to network models of river basins, as we briefly discuss. Finally we discuss circumstances under which quantum network models that describe the surface electronic states of a quantum Hall multilayer can be mapped onto the classical q model. For mesoscopic multilayers of finite circumference the mapping fails; instead a mapping to a ferromagnetic supersymmetric spin chain has proved fruitful. We discuss aspects of the superspin mapping and give an elementary derivation of it making use of operator rather than functional methods.

Journal Article↗
PubMed2001

The time course of perceptual choice: the leaky, competing accumulator model.

The time course of perceptual choice is discussed in a model of gradual, leaky, stochastic, and competitive information accumulation in nonlinear decision units. Special cases of the model match a classical diffusion process, but leakage and competition work together to address several challenges to existing diffusion, random walk, and accumulator models. The model accounts for data from choice tasks using both time-controlled (e.g., response signal) and standard reaction time paradigms and its adequacy compares favorably with other approaches. A new paradigm that controls the time of arrival of information supporting different choice alternatives provides further support. The model captures choice behavior regardless of the number of alternatives, accounting for the log-linear relation between reaction time and number of alternatives (Hick's law) and explains a complex pattern of visual and contextual priming in visual word identification.

Choice Behavior↗
PubMed1997

Indicator-dilution dispersion models and cardiac output computing methods.

The general theory of indicator-dilution methods provides a basis for computing improved cardiac output estimates. Interpretation is via indicator-dispersion modeling with Brownian motion of drifting particles. Detected curves indicate the distribution of passage times from the injection site: the local density random walk (LDRW) function of a Wiener process. Fitting the LDRW to 70 dye curves by nonlinear regression for examples, I show how all possible undistorted curves can, in principle, be simulated. I show via semilogarithmic plots that conventional exponential decay constructs systematically underestimate cardiac output by up to 8%. To help reconcile the predictions of LDRW-fitted dilution curves and contemporary practice, I show how curve-shape asymmetry (skewness) dramatically affects the enclosed areas. Mean transit times may overestimate blood volumes by 15-100% in very skewed thermodilution curves if the dispersion effects are overlooked. Triangle constructions, which accounted for hundreds of experimental findings, also have theoretical explanations. Curve-fitting methods reduce the extrapolation biases inherent in many computers and in any respiration-induced artifacts. Compatibility of cardiac output predictions from various dilution methods and modules becomes feasible.

Artifacts↗
PubMedDate not supplied

Is the heart preadapted to hypoxia? Evidence from fractal dynamics of heartbeat interval fluctuations at high altitude (5,050 m).

The dynamics of heartbeat interval time series over large time scales were studied by a modified random walk analysis introduced recently as Detrended Fluctuation Analysis. In this analysis, the intrinsic fractal long-range power-law correlation properties of beat-to-beat fluctuations generated by the dynamical system (i.e., cardiac rhythm generator), after decomposition from extrinsic uncorrelated sources, can be quantified by the scaling exponent (alpha) which, in healthy subjects, for time scales of approximately 10(4) beats is approximately 1.0. The effects of chronic hypoxia were determined from serial heartbeat interval time series of digitized twenty-four-hour ambulatory ECGs recorded in nine healthy subjects (mean age thirty-four years old) at sea level and during a sojourn at 5,050 m for thirty-four days (EvK2-CNR Pyramid Laboratory, Sagarmatha National Park, Nepal). The group averaged alpha exponent (+/- SD) was 0.99 +/- 0.04 (range 0.93-1.04). Longitudinal assessment of alpha in individual subjects did not reveal any effect of exposure to chronic high altitude hypoxia. The finding of alpha approximately 1 indicating scale-invariant long-range power-law correlations (1/f noise) of heartbeat fluctuations would reflect a genuinely self-similar fractal process that typically generates fluctuations on a wide range of time scales. Lack of a characteristic time scale along with the absence of any effect from exposure to chronic hypoxia on scaling properties suggests that the neuroautonomic cardiac control system is preadapted to hypoxia which helps prevent excessive mode-locking (error tolerance) that would restrict its functional responsiveness (plasticity) to hypoxic or other physiological stimuli.

Adaptation, Physiological↗
PubMed1997

Evolution of model proteins on a foldability landscape.

We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non self-averaging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process.

Biopolymers↗
PubMed2001

Generalized-ensemble algorithms for molecular simulations of biopolymers.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Algorithms↗
PubMed2001

An exactly solvable Ogston model of gel electrophoresis. VI. Towards a theory for macromolecules.

In this article, we present a generalized version of our lattice model of low-field gel electrophoresis that allows us to treat the case of macromolecules such as short linear or circular oligomers and semi-flexible rods. We show that free-solution electrophoresis problems can be seen as random walks in the conformational space of the analyte. For sufficiently small molecules, our mathematical approach provides exact mobilities. In a quenched gel-like environment, however, both conformational and positional degrees of freedom must be used, but exact solutions can also be obtained. As an example, we then investigate several two-dimensional model gels, as well as a simple channel system where we see evidence of entropic effects that cannot be captured by the traditional Ogston concept of free volume.

Electrophoresis, Agar Gel↗
PubMedDate not supplied

Modeling stability and change in strength development: a study in adolescent boys.

The purpose of this study was to investigate stability and change in different expressions of strength development in adolescent boys using structural equation modeling. Three models were used: Markov simplex to study stability or tracking, Wiener or random walk to investigate fanning-out or spread effects in change, and latent growth to study differences in individual pathways of change as well as group changes. In the Leuven Growth Study, 588 male subjects were followed for 6 years with a mean age of 12.7 years at the onset of the study. Vertical jump, arm pull, and bent arm hang were used to mark the following strength factors: explosive strength, static strength, and functional strength. All models were tested with robust estimation procedures based on the software EQS 6.0. Main results and conclusions are as follows: 1) all strength factors showed moderate to high tracking, with low values of instability in relative position of the subjects in their developmental channels; 2) the fanning-out effect is not obvious, although some evidence showed a spread effect in functional and explosive strength; 3) there are marked interindividual differences in developmental pathways of strength manifestations; 4) strength development is linear and also has some curvilinearity, something akin to a breaking effect; 5) linear trend is negatively correlated with initial status and the leveling-off effect is also negatively correlated with the linear change.

Adolescent↗
PubMed1985

Increased adhesiveness of trisomy 21 cells and atrioventricular canal malformations in Down syndrome: a stochastic model.

Based on the finding that fetal trisomy 21 fibroblasts explanted from lungs and endocardial-cushion-derived structures appear more adhesive in vitro than those from normal control individuals, we present a stochastic model for atrioventricular (AV) canal malformations in Down syndrome (DS). Computer simulations were performed to model the normal anatomic sequences of cushion-to-cushion and cushion-to-septum fusion in AV canal development. In these simulations, random-walking endocardial cells were allowed to migrate, divide, and adhere with programmable probabilities. Low values of intercellular adhesiveness engendered simulations resembling normal AV canal development; higher values of adhesiveness yielded deficiencies of AV canal development as seen in DS. Moderately high levels of adhesiveness resulted in abnormalities in only a proportion of multiple, independently performed simulations. The model successfully predicts the temporospatial sequence of anatomic events in cushion-to-septum fusion, clinical variability among individuals with the same genotype based on chance alone, and amplified developmental instability as observed in individuals with DS.

Cell Adhesion↗
PubMed2006

Noise-enhanced balance control in patients with diabetes and patients with stroke.

OBJECTIVE: Somatosensory function declines with diabetic neuropathy and often with stroke, resulting in diminished motor performance. Recently, it has been shown that input noise can enhance human sensorimotor function. The goal of this study was to investigate whether subsensory mechanical noise applied to the soles of the feet via vibrating insoles can be used to improve quiet-standing balance control in 15 patients with diabetic neuropathy and 15 patients with stroke. Sway data of 12 healthy elderly subjects from a previous study on vibrating insoles were added for comparison. METHODS: Five traditional sway parameters and three sway parameters from random-walk analysis were computed for each trial (no noise or noise). RESULTS: Application of noise resulted in a statistically significant reduction in each of the eight sway parameters in the subjects with diabetic neuropathy, the subjects with stroke, and the elderly subjects. We also found that higher levels of baseline postural sway in sensory-impaired individuals was correlated with greater improvements in balance control with input noise. INTERPRETATION: This work indicates that noise-based devices could ameliorate diabetic and stroke impairments in balance control.

Adult↗
PubMed2025

Genetic Architecture of Idiopathic Inflammatory Myopathies From Meta-Analyses.

OBJECTIVE: Idiopathic inflammatory myopathies (IIMs, myositis) are rare systemic autoimmune disorders that lead to muscle inflammation, weakness, and extramuscular manifestations, with a strong genetic component influencing disease development and progression. Previous genome-wide association studies identified loci associated with IIMs. In this study, we imputed data from two prior genome-wide myositis studies and analyzed the largest myositis data set to date to identify novel risk loci and susceptibility genes associated with IIMs and its clinical subtypes. METHODS: We performed association analyses on 14,903 individuals (3,206 patients and 11,697 controls) with genotypes and imputed data from the Trans-Omics for Precision Medicine reference panel. Fine-mapping and expression quantitative trait locus colocalization analyses in myositis-relevant tissues indicated potential causal variants. Functional annotation and network analyses using the random walk with restart (RWR) algorithm explored underlying genetic networks and drug repurposing opportunities. RESULTS: Our analyses identified novel risk loci and susceptibility genes, such as FCRLA, NFKB1, IRF4, DCAKD, and ATXN2 in overall IIMs; NEMP2 in polymyositis; ACBC11 in dermatomyositis; and PSD3 in myositis with anti-histidyl-transfer RNA synthetase autoantibodies (anti-Jo-1). We also characterized effects of HLA region variants and the role of C4. Colocalization analyses suggested putative causal variants in DCAKD in skin and muscle, HCP5 in lung, and IRF4 in Epstein-Barr virus (EBV)-transformed lymphocytes, lung, and whole blood. RWR further prioritized additional candidate genes, including APP, CD74, CIITA, NR1H4, and TXNIP, for future investigation. CONCLUSION: Our study uncovers novel genetic regions contributing to IIMs, advancing our understanding of myositis pathogenesis and offering new insights for future research.

Humans↗
PubMed2005

Locally adaptive function estimation for binary regression models.

In this paper we present a nonparametric Bayesian approach for fitting unsmooth or highly oscillating functions in regression models with binary responses. The approach extends previous work by Lang et al. for Gaussian responses. Nonlinear functions are modelled by first or second order random walk priors with locally varying variances or smoothing parameters. Estimation is fully Bayesian and uses latent utility representations of binary regression models for efficient block sampling from the full conditionals of nonlinear functions.

Bayes Theorem↗
PubMed1990

Applications of simulated annealing to peptides.

We report the application of a new conformation searching algorithm called simulated annealing to the location of the global minimum energy conformation of peptides. Simulated annealing is a Metropolis Monte Carlo approach to conformation generation in which both the energy and temperature dependence of the Boltzmann distribution guides the search for the global minimum. Both uphill and downhill moves are possible, which allows the molecule to escape from local minima. Applications to the 20 natural amino acid "dipeptide models" as well as to polyalanines up to Ala80 are very successful in finding the lowest energy conformation. A history file of the simulated annealing process allows reconstruction and examination of the random walk around conformation space. A separate program, Conf-Gen, reads the history file and extracts all low-energy conformations visited during the run.

Algorithms↗
PubMed1991

Fluctuating bond model of DNA gel electrophoresis.

We present a Monte Carlo algorithm that allows a small length scale numerical study of DNA gel electrophoresis in high electric fields, similar to the fluctuating bond model for dynamical properties of polymeric systems. This approach combines advantages of lattice Monte Carlo methods with those from continuous Brownian dynamics algorithms, and also takes into account the persistence length of DNA, as well as the random nature of the gel. The initial orientation and acceleration of a random-walk DNA conformation shows a number of features that can be related to experimental results. The detailed description of DNA motion provided by this approach may lead to a first realistic computer study of the process of DNA sequencing.

DNA↗
PubMed2006

Multibaric-multithermal ensemble molecular dynamics simulations.

We present new generalized-ensemble molecular dynamics simulation algorithms, which we refer to as the multibaric-multithermal molecular dynamics. We describe three algorithms based on (1) the Nosé thermostat and the Andersen barostat, (2) the Nosé-Poincaré thermostat and the Andersen barostat, and (3) the Gaussian thermostat and the Andersen barostat. The multibaric-multithermal simulations perform random walks widely both in the potential-energy space and in the volume space. Therefore, one can calculate isobaric-isothermal ensemble averages in wide ranges of temperature and pressure from only one simulation run. We test the effectiveness of the multibaric-multithermal algorithm by applying it to a Lennard-Jones 12-6 potential system.

Journal Article↗
PubMed2004

Characterization of monolithic columns for HPLC.

Monolithic stationary phases and columns have rapidly become highly popular separation media for liquid chromatography, in spite of their recent discovery. However, their most important features have not yet been completely clarified. A complete understanding of their performance and of their intrinsic characteristics will require the systematic acquisition of many series of reliable experimental data and their consistent analysis from different points of view. Progress in their design and production requires now that the chromatographic behavior of monolithic columns be studied in close connection with their physico-chemical and structural properties. The main goal of this review is to summarize fundamental information on some physico-chemical and chromatographic characteristics of monolithic stationary phases and columns for RPLC. The material reviewed deals only with silica-based monolithic columns. First, structural information on the porosities and the size of the pores in monolithic columns is reported. Second, results of chromatographic studies that deal with the characterization of monolithic columns are summarized. Third, results of detailed studies made on the adsorption equilibrium and the surface heterogeneity of monolithic stationary phases are presented. Finally, results on the mass transfer kinetics in monolithic columns derived from the applications of the classical random-walk model and of the moment theory to a new model of the monolith are discussed.

Adsorption↗
PubMed1991

Laser beam diameter for port wine stain treatment.

Optimal port wine stain treatment requires the selective absorption of light by the ectatic blood vessels. We investigated whether deeper blood vessels can be coagulated, without damaging other cutaneous structures, by varying the laser beam diameter. The penetration of the light was simulated with a random walk (Monte Carlo) program. Scattering of the light plays a major role: practically all light that is absorbed in a blood vessel in the dermis is scattered light. In the epidermis, where the distribution is more centered, a larger beam diameter does not increase the energy density as much as deeper within the dermis where the blood vessels lie and where the light is totally diffuse. Increasing the laser beam diameter from 200 microns to 1 mm or more, makes a typical blood vessel absorb 2.5 times more energy, while the energy absorbed by the epidermis remains the same. The larger the laser beam diameter the better the treatment.

Absorption↗
PubMed2004

Functional optical detection based on pH dependent fluorescence lifetime.

BACKGROUND AND OBJECTIVES: Detection of possible alterations of physiological parameters (e.g., pH and temperature), resulting from malignant transformation of initially healthy tissue, can be a powerful diagnostic tool for earlier cancer detection. Such variations can be observed by comparing these parameters with those of healthy tissue surrounding the abnormality. Time-resolved spectroscopy of specifically targeted fluorescent labeled antibodies can be sensitive to such variations and provide a high resolution functional image of the region of interest. The goal of this study was to establish a forward experimental setup for calibration of the lifetime dependencies of near-IR fluorescent dyes on physiological parameters, and to develop analytical solutions, taking into account the effects of light propagation in turbid media (e.g., tissue), that was able to extract an original lifetime fluorescence signal from time-of-flight intensity distributions, measured in vivo from a deeply embedded live organ for further analysis. STUDY DESIGN/MATERIALS AND METHODS: Tissue-like phantoms with embedded fluorescent dyes and background optical properties simulating those of live tissues were designed and created. Fluorescence decay curves were measured for different fluorophore positions, and pH values. Those measurements were made with a system based on a time-correlated single photon counting (TCSPC) instrument and a tunable femtosecond Ti-Sapphire system built by our group. RESULTS: Decay curves were recorded for fluorophore depths of up to 5 mm and source-detector separation of 7 mm. It was shown that a forward model, based on the random walk theory, adequately described the experimental data. Measured pH dependencies of the fluorescence lifetime were characterized for two different dyes. CONCLUSIONS: Good correlation between experimental data and predictions of the theoretical model allows the use of close-form analytical solutions to separate the effects of photon time delays due to multiple scattering in tissues from the original intensity fluorescence time decay curve, determined by the fluorophore itself and its immediate surroundings. It is the latter dependence that can be diagnostically important. Experimentally obtained scaling between lifetime and a parameter of interest can be used in vivo to obtain a map of physiological parameter changes which can serve as a base for an in vivo specific diagnostic system.

Animals↗