Biomedical subjects
Publications and source records attributed to Tianshou Zhou.
Lyapunov exponents of a synchronized coupled system consist of those of the underlying individual systems and the transverse systems, based on a mode decomposition along the synchronization manifold. Estimates of bounds on the Lyapunov exponents (including transverse Lyapunov exponents) are derived. Several examples are used to validate the theoretical estimates.
We model a synthetic gene regulatory network in a microbial cell, and investigate the effect of noises on cell-cell communication in a well-mixed multicellular system. A biologically plausible model is developed for cellular communication in an indirectly coupled multicellular system. Without extracellular noises, all cells, in spite of interaction among them, behave irregularly due to independent intracellular noises. On the other hand, extracellular noises that are common to all cells can induce collective dynamics and stochastically synchronize the multicellular system by actively enhancing the integrated interchange of signaling molecules.
The responses of nonlinear dynamics of two classes to coupling are investigated. It is shown both analytically and numerically that coupling has an excitation ability in a network of the linearly coupled systems. That is, when an uncoupled system is degenerated to a stable steady state from a limit cycle but in the "marginal" state due to the system parameter, an appropriate coupling strength can excite the limit cycle such that the coupled systems exhibit synchronous oscillation; when the uncoupled system is in a stable limit cycle but close to a chaotic attractor, a certain coupling strength can induce the chaotic attractor such that the coupled systems reach chaotic synchronization. Such excitation functions of coupling are different from its traditional role where coupling mainly synchronizes the coupled systems with the original dynamics of the uncoupled system.
MOTIVATION: All cell components exhibit intracellular noise on account of random births and deaths of individual molecules, and extracellular noise because of environment perturbations. Gene regulation in particular, is an inherently noisy process with transcriptional control, alternative splicing, translation, diffusion and chemical modification reactions, all of which involve stochastic fluctuations. Such stochastic noises may not only affect the dynamics of the entire system but may also be exploited by living organisms to actively facilitate certain functions, such as cooperative behavior and communication. RESULTS: We have provided a general model and an analytic tool to examine the cooperative behavior of a multicell system with both intracellular and extracellular stochastic fluctuations. A multicell system with a synthetic gene network is adopted to demonstrate the effects of noises and coupling on collective dynamics. These results establish not only a theoretical foundation but also a quantitative basis for understanding essential roles of noises on cooperative dynamics, such as synchronization and communication among cells.
Protein structure alignment plays a key role in protein structure prediction and fold family classification. An efficient method for multiple protein structure alignment in a mathematical manner is presented, based on deterministic annealing technique. The alignment problem is mapped onto a nonlinear continuous optimization problem (NCOP) with common consensus chain, matching assignment matrices and atomic coordinates as variables. At each step in the annealing procedure, the NCOP is decomposed into as many sub-problems as the number of protein chains, each of which is actually an independent pairwise structure alignment between a protein chain and the consensus chain and hence can be efficiently solved by the parallel computation technique. The proposed method is robust with respect to choice of iteration parameters for a wide range of proteins, and performs well in both multiple and pairwise structure alignment cases, compared with existing alignment methods.
MOTIVATION: Protein structure alignment is one of the most important computational problems in molecular biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and so on. From the viewpoint of computational complexity, a pairwise structure alignment is also a NP-hard problem, in contrast to the polynomial time algorithm for a pairwise sequence alignment. RESULTS: We propose a method for solving the structure alignment problem in an accurate manner at the amino acid level, based on a mean field annealing technique. We define the structure alignment as a mixed integer-programming (MIP) problem. By avoiding complicated combinatorial computation and exploiting the special structure of the continuous partial problem, we transform the MIP into a reduced non-linear continuous optimization problem (NCOP) with a much simpler form. To optimize the reduced NCOP, a mean field annealing procedure is adopted with a modified Potts model, whose solution is generally identical to that of the MIP. There is no 'soft constraint' in our mean field model and all constraints are automatically satisfied throughout the annealing process, thereby not only making the optimization more efficient but also eliminating many unnecessary parameters that depend on problems and usually require careful tuning. A number of benchmark examples are tested by the proposed method with comparisons to several existing approaches.
An effective method of chaotification via time-delay feedback for a simple finite-dimensional continuous-time autonomous system is made rigorous in this paper. Some mathematical conditions are derived under which a nonchaotic system can be controlled to become chaotic, where the chaos so generated is in a rigorous mathematical sense of Li-Yorke in terms of the Marotto theorem. Numerical simulations are given to verify the theoretical analysis.
This paper investigates a general coupled noisy system for a cell-cell communication in a multi-cell system. The main conclusion is that appropriate noise intensity and coupling strength are capable of driving the coupled system to synchrony, which may be exploited by biological organisms to actively facilitate mutual communication. A multi-cell system with a synthetic gene network with both noises and delays is adopted to demonstrate the effect of noises on cellular communication.
A simple, fast and reliable method, based on capillary zone electrophoresis with amperometric detection, for the separation and determination of sucrose, glucose, and fructose in Chinese traditional drugs, namely Astragalus Membranceus (Fish.) Bge, Angelica and Codonopsis pilosula (Franch.) Nannf. was described in this paper. A copper disk electrode was used as working electrode. The optimal conditions of separation and detection were 0.05 mol/l sodium hydroxide buffer (pH 12.7), 5 kV for the separation voltage and +0.65 V (vs. Ag/AgCl) for the detection potential. The linear ranges were from 5.0x10(-6) to 5.0x10(-4) mol/l for all three sugars. The all regression coefficients were more than 0.999. The detection limits were 1.0x10(-6) mol/l for glucose and fructose, and 4.0x10(-6) mol/l for sucrose. The method built in this paper was directly applied to the separation and determination of the three sugars in three Chinese traditional drugs without prior derivatization, and the content for every sugar in the drugs was first assayed. The assay results were satisfactory.
This paper introduces a new chaos generator, a switching piecewise-linear controller, which can create chaos from a three-dimensional linear system within a wide range of parameter values. Basic dynamical behaviors of the chaotic controlled system are investigated in some detail. (c) 2002 American Institute of Physics.