Biomedical subjects

Qi Ouyang

Publications and source records attributed to Qi Ouyang.

31 records · Page 2Linked to original sources

PubMed2004

Spatiotemporal chaos control with a target wave in the complex Ginzburg-Landau equation system.

An effective method for controlling spiral turbulence in spatially extended systems is realized by introducing a spatially localized inhomogeneity into a two-dimensional system described by the complex Ginzburg-Landau equation. Our numerical simulations show that with the introduction of the inhomogeneity, a target wave can be produced, which will sweep all spiral defects out of the boundary of the system. The effects exist in certain parameter regions where the spiral waves are absolutely unstable. A theoretical explanation is given to reveal the underlying mechanism.

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PubMed2004

Chemical waves with line defects in the Belousov-Zhabotinsky reaction.

We report our experimental observations of line-defected chemical waves in a quasi-two-dimensional reaction-diffusion system of Belousov-Zhabotinsky reaction. The observed line defects are explicit, which can be directly monitored in real time. In the parameter space, the state of the chemical waves with line defects is located between two regimes of the defect-mediated turbulence. The line defects appear in target waves as well as in spiral waves. We demonstrate that the line defects come out in traveling waves as the later reorganize their spatial topologies to adapt to the change in the local dynamics from simple to complex oscillations or vice versa.

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PubMed2004

The yeast cell-cycle network is robustly designed.

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.

Cell Cycle↗

PubMed2003

Studies of temperature-dependent electronic transduction on DNA hairpin loop sensor.

A self-assembly monolayer (SAM) of hairpin DNA can be formed on a gold substrate in order to make special biosensors. Labeling the hairpin loop probes with electroactive compositions rather than a fluorophore illustrates interesting profiles of redox current versus temperature. For a biosensor interacting with perfectly complementary targets, the profile shows a characteristic plateau, which disappears when the targets have a single base variation. The plateau is split into multiple steps by tuning the hybridization temperature. We propose that the phenomena are due to hairpin loop compartmentalization. The novel characteristics lead to a thermal gradient detection method that permits perfect discrimination of a target sequence from single nucleotide mismatches.

Base Sequence↗

PubMed2003

Dynamics of DNA in vitro evolution with Mnt-repressor: simulations and analysis.

The dynamics of DNA in vitro evolution with Mnt-repressor has been studied numerically and analytically. Based on experimental data and realistic energy landscape for DNA-Mnt-repressor interaction, we investigated the dynamics of DNA in vitro evolution using stochastic simulations. The binding energy of DNA to Mnt-repressor was considered to consist of two parts: the DNA sequence specific and nonspecific. The crossover observed in real experiments is numerically recovered. We demonstrate that the evolution trajectories are drastically dispersed and no typical evolution passage exists during the evolution. Particularly, Fisher's theorem of natural selection is verified. A theoretical analysis for the evolution is also included.

DNA↗

PubMed2003

Transition from spiral waves to defect-mediated turbulence induced by gradient effects in a reaction-diffusion system.

The transition from spiral waves to defect-mediated turbulence was studied in a spatial open reactor using Belousov-Zhabotinsky reaction. The experimental results show a new mechanism of the transition from spirals to spatiotemporal chaos, in which the gradient effects in the three-dimensional system are essential. The transition scenario consists of two stages: first, the effects of gradients in the third dimension cause a splitting of the spiral tip and a deletion of certain wave segments, generating new wave sources; second, the waves sent by the new wave sources undergo a backfire instability, and the back waves are laterally unstable. As a result, defects are automatically generated and fill all over the system. The result of numerical simulation using the FitzHugh-Nagumo model essentially agrees with the experimental observation.

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PubMed2003

[Predict SARS infection with the small world network model].

We report of our numerical simulation of SARS infection dynamics with the small world network model. The negative feedback mechanism and the effect of information flow are added in the model. The simulation fits well with the observed data. The main results of our simulation are that the feedback mechanism can effectively slow down the SARS infecting rate, but it may cause sustained oscillations in number of infection cases. Moreover, keeping the transparency of information is a key factor to resist SARS in the society.

Computer Simulation↗

PubMed2002

Turbulence control by developing a spiral wave with a periodic signal injection in the complex Ginzburg-Landau equation.

Turbulence control in the two-dimensional complex Ginzburg-Landau equation is investigated. An approach is proposed for the purpose of control. In the presence of a small spiral wave seed initiation, a fully developed turbulence can be completely annihilated by injecting a single periodic signal into a small fixed space area around the spiral wave tip. The control is achieved in a parameter region where the spiral wave of the uncontrolled system is absolutely unstable. The robustness, convenience, and high control efficiency of this method are emphasized, and the mechanism underlying these practical advantages is intuitively understood.

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PubMed2002

Relation between the wave front and the tip movement of spirals.

The relation between the movement of spiral waves and their tip for a simple spiral is experimentally investigated in a spatial open reactor using the Belousov-Zhabotinsky reaction. In the quasi-two dimensional regime, our results agree with the combustion model proposed by Lázár et al. [Chaos 5, 443 (1995)] which states that the speed of spiral tip movement is proportional to the speed of spiral waves, c(tip) infinity c(front), when expressed in the radius of the spiral tip trajectory R and the spiral wavelength lambda, R infinity lambda. The measurement shows that the slope of the linear R-lambda curve is about 0.13, independent of the control parameter. This observation is also consistent with the combustion model.

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PubMed2002

Scale-free network model of node and connection diversity.

A network model with node and connection diversity is proposed in this paper. Distinctly from to other models whose nodes and connections are represented by identical simple points and lines, we investigate inhomogeneous networks with two kinds of sites and link by growth of preferential attachment. Scale-free networks with varied centralizations and exponents (ranging from 2.0 to theoretically infinity) are obtained, and the influences of the relative ratio of the two kinds of sites p, the number of links connected from each site m, and initial attractiveness delta are studied. A mean-field theory that agrees well with our numerical results was proposed and analyzed. The theory gives the analytical scaling exponent of the form gamma=2+p+delta/m-delta(1-p)/(mp+m+delta).

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PubMed2002

Effect of colored noises on spatiotemporal chaos in the complex Ginzburg-Landau equation.

The effect of colored noises, which are correlated both in space and time, on spatiotemporal chaos in the complex Ginzburg-Landau equation has been studied numerically. The correlations of spatiotemporal patterns as a function of characteristics of noise were calculated. We found that there exists an optimal correlation length of noise where the system establishes its maximal spatial correlation; a small temporal correlation of noise corresponds to a larger correlation length in the system; and that an increase of noise intensity enhances the spatial correlation of the spatiotemporal patterns. Besides, the frequency of temporal correlation function, which is a complicated oscillation, also depends on properties of the noise.

Journal Article↗

PubMed2002

Experimental study of the dimensionality of black-eye patterns.

The spatial structure of one type of Turing pattern named "black eyes" is studied in experiments using the chlorite-iodide-malonic acid reaction in spatial open reactor. The purpose of the work is to verify (or falsify) two possible theoretical interpretations of black-eye pattern formation: the projection of a body-centered-cubic (bcc) structure onto the plane vertical to the body diagonal and the spatial resonance of larger wave vectors with the fundamental ones. The latter happens when the mode of the larger wave vectors becomes linearly unstable, as the system goes far beyond the onset of Turing bifurcation. Our experimental results give evidence that black-eye patterns are not a projection of the bcc structure, so that the interpretation of a three-dimensional structure can be ruled out. The observations in the experiment also suggest another possible mechanism for the formation of black eyes.

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PubMed1993

Rhombic patterns: Broken hexagonal symmetry.

Landau-Ginzburg equations derived to conserve two-dimensional spatial symmetries lead to the prediction that rhombic arrays with characteristic angles slightly differ from 60 degrees should form in many systems. Beyond the bifurcation from the uniform state to patterns, rhombic patterns are linearly stable for a band of angles near the 60 degrees angle of regular hexagons. Experiments conducted on a reaction-diffusion system involving a chlorite-iodide-malonic acid reaction yield rhombic patterns in good accord with the theory.

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