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Results for “bistability”

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PubMed1999

Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA.

Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.

Animals↗
PubMed1988

Left-right visual field asymmetry in bistable motion perception.

Twelve observers viewed two alternating frames, each consisting of three rectangular bars which were displaced laterally by one cycle in one frame with respect to the other. At long interframe intervals (IFIs) observers perceived a group of three elements moving as a whole (group movement), whereas with IFIs shorter than 40-60 ms the overlapping elements in each frame appeared stationary while the third element appeared to move from one end of the display to the other (end-to-end movement). The percentage of group movement responses in central viewing was compared to those obtained for stimulus presentation in the left and right visual fields (4 deg eccentricity), for opposite horizontal directions of motion. All ten right-handed subjects showed a left-field advantage in sensitivity to group movement. The two left-handed subjects showed a similar advantage in sensitivity with right-field presentation. The effects of monocular vision, hand used in the task, spatial frequency, and contrast on visual field asymmetry were all investigated in two right-handed subjects. None of these factors affected the left-right asymmetry.

Cerebral Cortex↗
PubMed2005

Eutrophication of aquatic ecosystems: bistability and soil phosphorus.

Eutrophication (the overenrichment of aquatic ecosystems with nutrients leading to algal blooms and anoxic events) is a persistent condition of surface waters and a widespread environmental problem. Some lakes have recovered after sources of nutrients were reduced. In others, recycling of phosphorus from sediments enriched by years of high nutrient inputs causes lakes to remain eutrophic even after external inputs of phosphorus are decreased. Slow flux of phosphorus from overfertilized soils may be even more important for maintaining eutrophication of lakes in agricultural regions. This type of eutrophication is not reversible unless there are substantial changes in soil management. Technologies for rapidly reducing phosphorus content of overenriched soils, or reducing erosion rates, are needed to improve water quality.

Ecosystem↗
PubMed1999

Dynamics of 1:2 Coordination: Temporal Scaling, Latent 1:1, and Bistability.

The simplest interlimb multifrequency coordination of 1:2 can be performed at different speeds and in at least two different styles or modes. The effects of speed and mode (in-phase or antiphase) were evaluated in a bimanual 1:2 rhythmic task in which participants (N = 8) oscillated hand-held pendulums with identical or different uncoupled frequencies. A motion equation in relative phase that captures the asymmetries of components and task predicted the 1:2 coordination equilibria resulting from temporal scaling. According to the experimental results, both coordination modes proved to be equally stable. More detailed analyses of individual trials showed signs that the more fundamental 1:1 coordination intruded into the 1:2 coordination.

Journal Article↗
PubMed2006

Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network.

MOTIVATION: The stochastic kinetics of a well-mixed chemical system, governed by the chemical Master equation, can be simulated using the exact methods of Gillespie. However, these methods do not scale well as systems become more complex and larger models are built to include reactions with widely varying rates, since the computational burden of simulation increases with the number of reaction events. Continuous models may provide an approximate solution and are computationally less costly, but they fail to capture the stochastic behavior of small populations of macromolecules. RESULTS: In this article we present a hybrid simulation algorithm that dynamically partitions the system into subsets of continuous and discrete reactions, approximates the continuous reactions deterministically as a system of ordinary differential equations (ODE) and uses a Monte Carlo method for generating discrete reaction events according to a time-dependent propensity. Our approach to partitioning is improved such that we dynamically partition the system of reactions, based on a threshold relative to the distribution of propensities in the discrete subset. We have implemented the hybrid algorithm in an extensible framework, utilizing two rigorous ODE solvers to approximate the continuous reactions, and use an example model to illustrate the accuracy and potential speedup of the algorithm when compared with exact stochastic simulation. AVAILABILITY: Software and benchmark models used for this publication can be made available upon request from the authors.

Algorithms↗