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Biomedical subjects

Qi Ouyang

Publications and source records attributed to Qi Ouyang.

At least 19 recordsLinked to original sources
PubMed2006

Robustness and modular design of the Drosophila segment polarity network.

Biomolecular networks have to perform their functions robustly. A robust function may have preferences in the topological structures of the underlying network. We carried out an exhaustive computational analysis on network topologies in relation to a patterning function in Drosophila embryogenesis. We found that whereas the vast majority of topologies can either not perform the required function or only do so very fragilely, a small fraction of topologies emerges as particularly robust for the function. The topology adopted by Drosophila, that of the segment polarity network, is a top ranking one among all topologies with no direct autoregulation. Furthermore, we found that all robust topologies are modular-each being a combination of three kinds of modules. These modules can be traced back to three subfunctions of the patterning function, and their combinations provide a combinatorial variability for the robust topologies. Our results suggest that the requirement of functional robustness drastically reduces the choices of viable topology to a limited set of modular combinations among which nature optimizes its choice under evolutionary and other biological constraints.

Animals↗
PubMed2006

Resonant-pattern formation induced by additive noise in periodically forced reaction-diffusion systems.

We report frequency-locked resonant patterns induced by additive noise in periodically forced reaction-diffusion Brusselator model. In the regime of 2:1 frequency-locking and homogeneous oscillation, the introduction of additive noise, which is colored in time and white in space, generates and sustains resonant patterns of hexagons, stripes, and labyrinths which oscillate at half of the forcing frequency. Both the noise strength and the correlation time control the pattern formation. The system transits from homogeneous to hexagons, stripes, and to labyrinths successively as the noise strength is adjusted. Good frequency-locked patterns are only sustained by the colored noise and a finite time correlation is necessary. At the limit of white noise with zero temporal correlation, irregular patterns which are only nearly resonant come out as the noise strength is adjusted. The phenomenon induced by colored noise in the forced reaction-diffusion system is demonstrated to correspond to noise-induced Turing instability in the corresponding forced complex Ginzburg-Landau equation.

Journal Article↗
PubMed2006

Propagation of wave modes and antispiral waves in a reaction-diffusion system.

Since the observation of antispirals by Vanag et al. in a reaction-diffusion system, the study of its origin becomes a focus of nonlinear science and pattern formation. It was shown that antispirals may exist in a reaction-diffusion system when the system is near the onset of Hopf bifurcation. Here, we demonstrate that antispiral waves can also exist in a relaxational oscillatory medium, which is far from Hopf onset. Furthermore, we clarify the previously unclear concept of group velocity in inharmonic nonlinear waves, and prove that the group velocity v(g)=domega/dk is physically significant and valid both for excitable media and for oscillatory media. From this formula, we identify two types of wave propagating fronts: gentle mode front and steep mode front. Finally, we discuss the origin of counterpropagating waves and propose necessary conditions for antispiral formation. A direct deduction from these criteria is that antispirals cannot exist in an excitable medium.

Journal Article↗
PubMed2006

Dynamic studies of scaffold-dependent mating pathway in yeast.

The mating pathway in Saccharomyces cerevisiae is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to current understanding of the mating pathway, we construct a system of ordinary differential equations to describe the process. Our model is consistent with a wide range of experiments, indicating that it captures some main characteristics of the signal transduction along the pathway. Investigation with the model reveals that the shuttling of the scaffold protein and the dephosphorylation of kinases involved in the MAPK cascade cooperate to regulate the response upon pheromone induction and to help preserve the fidelity of the mating signaling. We explored factors affecting the dose-response curves of this pathway and found that both negative feedback and concentrations of the proteins involved in the MAPK cascade play crucial roles. Contrary to some other MAPK systems where signaling sensitivity is being amplified successively along the cascade, here the mating signal is transmitted through the cascade in an almost linear fashion.

Biophysics↗
PubMed2006

Stochastic model of coliphage lambda regulatory network.

The dynamic properties of the regulatory network governing the choice between lytic and lysogenic growths of coliphage lambda is studied using a Markov chain stochastic model. Our computer simulation confirms the finding by Li et al. [Proc. Natl. Acad. Sci. USA 101, 4781 (2004)] on the dynamics of budding yeast: that the biological stationary states are global attractors; the biological pathways of lytic and lysogenic growths are attracting trajectories; and the network functions are robustly designed against structural perturbations. In addition, our model shows the stochastic switch from lysogen to lytic growth, which has been observed in experiments. A definition of pseudoenergy is introduced in the network dynamics to reveal a transitionlike behavior in the system.

Bacteriophage lambda↗
PubMed2006

Chemical turbulence and line defects induced by gradient effects in a three-dimensional reaction-diffusion system.

We report experimental observations of chemical turbulence and line defects in a three-dimensional (3-D) Belousov-Zhabotinsky (BZ) reaction-diffusion system. Transitions from spiral waves to 3-D chemical turbulence to line defects are observed. These transitions are caused by concentration gradients across the third dimension in the 3-D reaction medium, indicating the observed line defects have a 3-D structure. The line defects come out of the 3-D turbulent state, and become smooth with the increase of the control parameter. Simulation with the two-variable Oregonator model in the 3-D system reproduces similar line defects.

Catalysis↗
PubMed2006

Picoliter-volume aqueous droplets in oil: electrochemical detection and yeast cell electroporation.

An electrochemical detection method was introduced for aqueous droplet analysis in oil phase of microfluidic devices. This method is based on the electrochemical signal difference between aqueous and oil. Applying a low alternating current (AC) voltage to a couple of Au microelectrodes, this method can offer size information and ion concentration range from 0.02 mmol/L to 1 mol/L of tens of picoliter to nanoliter aqueous droplets. Alternatively, applying a relative high AC voltage (18 Vpp) at a frequency of 1 kHz leads to electroporation of yeast cells encapsulated into picoliter droplets. We believe that this simple technique is useful for a number of aqueous droplet-based chemical and biological analyses as well as cell electroporation.

Electrochemistry↗
PubMed2005

Design of a network with state stability.

Designing a network with given functions or reconstruct a network based on its dynamical behavior is an important problem in the study of complex systems. In this paper, we put forward certain principles in constructing a network with state stability. We show that a necessary and sufficient condition to design networks with a global fixed point is that active nodes inhibit inactive nodes, while the latter activate the former directly or indirectly. We also designed networks based on basic modules, where each basic module consists a sub-network, they communicate through the inhibition link from each activator in lower module to the inhibitor of upper module. We found that long activation links, i.e. indirect activation links are important to the formation of convergence trajectory. We believe that these principles may help us to understand the topology of biological networks.

Animals↗
PubMed2005

Spontaneous scroll ring creation and scroll instability in oscillatory medium with gradients.

Scroll waves in a quasi-three-dimensional reaction-diffusion medium with a gradient in the third dimension are studied by numerical simulations using the Fitzhugh-Nagumo model. Under a simple initial condition with only one straight filament, we show a spontaneous creation of twisted scroll rings surrounding the initial filament when the control parameter is increased across a threshold. We find that due to the presence of the gradient, the difference of oscillation frequencies in the third dimension is the underlying cause of the phenomenon. Further increase of the control parameter will lead to the spiral breakups, as a result of the interaction of filaments. Observations in the experiments conducted in the same type of medium with the Belousov-Zhabotinsiky reaction qualitatively agree with our simulation results.

Journal Article↗
PubMed2005

Wave grouping of a meandering spiral induced by Doppler effects and oscillatory dispersion.

A new type of meandering spiral pattern, in which the dense waves form groups while the sparse waves keep evenly spaced, is observed in a spatial open reactor using a ferroin-catalyzed Belousov-Zhabotinsky reaction. Such a phenomenon is related to both the Doppler effect of a meandering spiral and the oscillatory dispersion relation of the system. Simulation in the two-dimensional Oregonator reaction-diffusion model with an oscillatory dispersion relation gives very similar results.

Colloids↗
PubMed2005

PDMS microfludic device for optical detection of protein immunoassay using gold nanoparticles.

A simple but highly specific immunoassay system for goat anti-human IgG has been developed using gold nanoparticles and microfluidic techniques. The assay is based on the deposition of gold nanoparticles that are coated with protein antigens in the presence of their corresponding antibodies to microfluidic channel surface. The effects of time accumulation, the flow velocity, and the concentration of antibodies to the red light absorption percentage (RAP) of deposition were investigated with an ordinary optical microscope. By controlling the reaction time and flow velocity, a dynamic range of 3 orders of magnitude and a detection sensitivity of 10 ng ml(-1) of goat anti-human IgG were achieved. Because of its simplicity and flexibility, this new technique should be useful for fast, highthroughput screening of antibodies in clinical diagnostic applications.

Animals↗
PubMed2005

Frequency-locking phenomena of propagating wave fronts in reaction-diffusion systems.

We observe N:(N-1)(N>/=2) frequency-locking phenomena of propagating wave fronts when increasing the light intensity in a spatially extended system. The experiments were carried out using the light-sensitive form of the Belousov-Zhabotinsky reaction with Ru(bpy)(2+)3 as a catalyst. By constructing a mapping function, the characteristic devil's staircase can be reproduced when plotting wave period versus light intensity, in agreement with the experimental data.

2,2'-Dipyridyl↗
PubMed2005

Effect of noise on defect chaos in a reaction-diffusion model.

The influence of noise on defect chaos due to breakup of spiral waves through Doppler and Eckhaus instabilities is investigated numerically with a modified Fitzhugh-Nagumo model. By numerical simulations we show that the noise can drastically enhance the creation and annihilation rates of topological defects. The noise-free probability distribution function for defects in this model is found not to fit with the previously reported squared-Poisson distribution. Under the influence of noise, the distributions are flattened, and can fit with the squared-Poisson or the modified-Poisson distribution. The defect lifetime and diffusive property of defects under the influence of noise are also checked in this model.

Artifacts↗
PubMed2004

Reversibly switchable DNA nanocompartment on surfaces.

Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartments on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartments are used to encage molecules, switched by the collective effect of Watson-Crick base-pairing interactions. This effect is used to perform molecular recognition. Furthermore, we found that 'fuel' strands with single-base variation cannot afford an efficient closing of nanocompartments, which allows highly sensitive label-free DNA array detection. Our results suggest that DNA nanocompartments can be used as building blocks for complex biomaterials because its core functions are independent of substrates and mediators.

Base Pair Mismatch↗
PubMed2004

Hierarchical structure description of spatiotemporal chaos.

We develop a hierarchical structure (HS) analysis for quantitative description of statistical states of spatially extended systems. Examples discussed here include an experimental reaction-diffusion system with Belousov-Zhabotinsky kinetics, the two-dimensional complex Ginzburg-Landau equation, and the modified FitzHugh-Nagumon equation, which all show complex dynamics of spirals and defects. We demonstrate that the spatial-temporal fluctuation fields in the above-mentioned systems all display the HS similarity property originally proposed for the study of fully developed turbulence [Phys. Rev. Lett. 72, 336 (1994)]]. The derived values of a HS parameter beta from experimental and numerical data in various physical regimes exhibit consistent trends and characterize the degree of turbulence in the systems near the transition, and the degree of heterogeneity of multiple disorders far from the transition. It is suggested that the HS analysis offers a useful quantitative description for the complex dynamics of two-dimensional spatiotemporal patterns.

Journal Article↗
PubMed2004

Spiral breakup due to mechanical deformation in excitable media.

To address the problem of how cardiac muscle contraction affects the dynamics of rotating spiral waves, spiral breakup induced by mechanical deformation in excitable media is studied in two partial-differential-equation models. It is shown that spirals begin to break up at omega=0.5 omega(0) when we increase the amplitude of the mechanical deformation gradually. Our numerical results point to a new mechanism of transition from spirals to spatiotemporal chaos, in which the anisotropic time-dependent diffusion coefficient is essential.

Journal Article↗
PubMed2004

Attraction of spiral waves by localized inhomogeneities with small-world connections in excitable media.

Trapping and untrapping of spiral tips in a two-dimensional homogeneous excitable medium with local small-world connections are studied by numerical simulation. In a homogeneous medium which can be simulated with a lattice of regular neighborhood connections, the spiral wave is in the meandering regime. When changing the topology of a small region from regular connections to small-world connections, the tip of the spiral waves is attracted by the small-world region, where the average path length declines with the introduction of long distant connections. The "trapped" phenomenon also occurs in regular lattices where the diffusion coefficient of the small region is increased. The above results can be explained by the eikonal equation, the Luther equation, and the relation between the core radius and the diffusion coefficient.

Journal Article↗