Akinori Awazu

Dynamics of Two Equivalent Lanes Traffic Flow Model: Self-Organization of the Slow Lane and Fast Lane

A simple two-lanes traffic flow model using cellular automaton is investigated. In this model, if the car density is set within a certain range, the following characteristic behavior of traffic flow is observed. i) The self-organization of the slow and fast lanes in spite of the symmetry between these two lanes. ii) The appearance of several branches and hysteresis in the relation between traffic flow and car density.

Risk stratification of ventricular fibrillation in Brugada syndrome using noninvasive scoring methods

BACKGROUND Risk stratification for ventricular fibrillation (VF) in patients with Brugada syndrome (BrS) remains controversial. OBJECTIVE The purpose of this study was to construct a novel prediction model for VF risk in BrS patients using noninvasive parameters. METHODS A total of 143 Japanese BrS patients with VF (n = 35) and without VF (n = 108) were retrospectively enrolled. We built a logistic regression model predicting VF occurrence and evaluated it by cross-validation. RESULTS Frequencies of history of syncope and spontaneous type 1 ECG, r-J interval in V1, QRS duration in V6, and LAS40, Tpeak-Tend dispersion, and max T-wave alternans were significantly associated with VF occurrence in univariate analyses. The history of syncope, r-J interval in V1, QRS duration in V6, and Tpeak-Tend dispersion were identified as independent predictors by multivariate logistic regression analysis. The predictive model was constructed using all these parameters with good discrimination of VF occurrence (area under the curve 0.869 with 97.1% sensitivity and 65.7% specificity). The area under the curve based on leave-one-out cross-validation was 0.845, with 97.1% sensitivity and 63.0% specificity suggesting good performance of the model. Retrospective survival analysis revealed that the cumulative VF event rate was significantly higher in patients at high risk than in those with low risk using the log rank test (P = 2.97 × 10(-8)). Notably, no BrS patient below the cutoff value developed a subsequent VF event. CONCLUSION This novel prediction method may effectively assesses VF risk in BrS patients, especially when determining implantable cardioverter-defibrillator placement for asymptomatic BrS patients.

Liquid-solid phase transition of a system with two particles in a rectangular box.

We study the statistical properties of two hard spheres in a two-dimensional rectangular box. In this system, a relation similar to the van der Waals equation is obtained between the width of the box and the pressure working on the sidewalls. The autocorrelation function of each particles position is calculated numerically. This calculation shows that, near the critical width, the time at which the correlation becomes zero gets longer as the height of the box increases. Moreover, fast and slow relaxation processes such as the alpha and beta relaxations in supercooled liquids are observed when the height of the box is sufficiently large. These relaxation processes are discussed with reference to the probability distribution of the relative positions of the two particles.

Swarming of Self-Propelled Camphor Boats

When an ensemble of self-propelled camphor boats move in a one-dimensional channel, they exhibit a variety of collective behaviors. Under certain conditions, the boats tend to cluster together and move in a relatively tight formation. This type of behavior, referred to as clustering or swarming here, is one of three types recently observed in experiment. Similar clustering behavior is also reproduced in simulations based on a simple theoretical model. Here we examine this model to determine the clustering mechanism and the conditions under which clustering occurs. We also propose a method of quantifying the behavior that may be used in future experimental work.

Localized Bioconvection of Euglena Caused by Phototaxis in the Lateral Direction

Localized pattern of bioconvection was newly observed in a suspension of Euglena gracilis , which was a photosensitive micro-organism. The suspension was exposed bright illumination from the bottom, in which the cells swam away from the light source. Then high-density spots, i.e., settling the cells, were formed at a part of a sealed chamber. This localized pattern was contrast with a general bioconvection where pattern was generated whole of a chamber. The experimental observations were reproduced by a mathematical model that was based on the phototaxis of individual cells in both vertical and lateral directions. Our results indicate that convection is maintained by upward swimming, as with general bioconvection, and the localization originates from lateral phototaxis.

Cellular automaton rule 184++C. A simple model for the complex dynamics of various particles flow

Abstract A cellular automaton named Rule 184++ C is proposed as a meta-model to investigate the flow of various complex particles. In this model, unlike the granular pipe flow and the traffic flow, not only the free-jam phase transition but also the free-intermediate, the intermediate-jam, and the dilute-dense phase transitions appear. Moreover, the freezing phenomena appear if the system contains two types of different particles.

Localized Bioconvection Patterns and Their Initial State Dependency in Euglena gracilis Suspensions in an Annular Container

Localized patterns of bioconvection in Euglena gracilis suspensions were experimentally analyzed in an annular container. Near the critical mean density of convection, we succeeded in isolating two basic types of localized convection patterns. One was an almost stationary pattern consisting of two convection cells centered by an isolated high-density region of the microorganism where a downflow was generated, which we call a “bioconvection unit”. The other was a traveling wave pattern consisting of an array of moving high-density waves bounded in a certain area. The effect of the mean density of E. gracilis on the emergence of the localized convection pattern was also examined. Near the critical mean density, we found that the emergence probability of the localized convection pattern depends on the initial state, i.e., whether E. gracilis has a uniform or localized distribution, which suggests that the system is bistable. Such bistability is often accompanied by localized structures in spatially extended ...

Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition

Motivation: Nucleosome positioning plays important roles in many eukaryotic intranuclear processes, such as transcriptional regulation and chromatin structure formation. The investigations of nucleosome positioning rules provide a deeper understanding of these intracellular processes. Results: Nucleosome positioning prediction was performed using a model consisting of three types of variables characterizing a DNA sequence—the number of five-nucleotide sequences, the number of three-nucleotide combinations in one period of a helix, and mono- and di-nucleotide distributions in DNA fragments. Using recently proposed stringent benchmark datasets with low biases for Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster, the present model was shown to have a better prediction performance than the recently proposed predictors. This model was able to display the common and organism-dependent factors that affect nucleosome forming and inhibiting sequences as well. Therefore, the predictors developed here can accurately predict nucleosome positioning and help determine the key factors influencing this process. Contact: awa@hiroshima-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Bifurcation Analysis of the Transition of Dune Shapes under a Unidirectional Wind

A bifurcation analysis of dune shape transition is made. By use of a reduced model of dune morphodynamics, the Dune Skeleton model, we elucidate the transition mechanism between different shapes of dunes under unidirectional wind. It was found that the decrease in the total amount of sand in the system and/or the lateral sand flow shifts the stable state from a straight transverse dune to a wavy transverse dune through a pitchfork bifurcation. A further decrease causes wavy transverse dunes to shift into barchans through a Hopf bifurcation. These bifurcation structures reveal the transition mechanism of dune shapes under unidirectional wind.

Ubiquitous "glassy" relaxation in catalytic reaction networks

Study of reversible catalytic reaction networks is important not only as an issue for chemical thermodynamics but also for protocells. From extensive numerical simulations and theoretical analysis, slow relaxation dynamics to sustain nonequlibrium states are commonly observed. These dynamics show two types of salient behaviors that are reminiscent of glassy behavior: slow relaxation along with the logarithmic time dependence of the correlation function and the emergence of plateaus in the relaxation-time course. The former behavior is explained by the eigenvalue distribution of a Jacobian matrix around the equilibrium state that depends on the distribution of kinetic coefficients of reactions. The latter behavior is associated with kinetic constraints rather than metastable states and is due to the absence of catalysts for chemicals in excess and the negative correlation between two chemical species. Examples are given and generality is discussed with relevance to bottleneck-type dynamics in biochemical reactions as well.