Date :

 29-30 June 2007

Place :

 29 June: Room 312, Department of Physics, National Taiwan University, Taipei

 30 June: The meeting room on the 7th floor, Institute of Physics of Academia Sinica, Taipei

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems Focus Group)

 Institute of Physics of Academia Sinica (Taipei)

 Department of Physics, National Taiwan university (Taipei)

  Miss Chia-Chi Liu (Secretary, Physics Division, NCTS)
 Tel:(886)-2-33665566; Fax:(886)-2-33665565; E-mail: ccliu@phys.ntu.edu.tw

 Miss Shu-Min Yang (Assistant of LSCP, Institute of Physics, Academia Sinica)

 Tel: (886)-2-2782-2467, or (886)-2-27880058 ext. 6012; FAX: (886)-2-2782-2467; E-mail: shumin@phys.sinica.edu.tw

Speakers :

Dr. Chung-Ke Chang

Institute of Biomedical Science, Academia Sinica, TAIWAN

E-mail: chungke@ibms.sinica.edu.tw

An Introduction to SARS Virus

Prof. Chi-Ming Chen

Department of Physics, National Taiwan Normal University, TAIWAN

E-mail: cchen@phy03.phy.ntnu.edu.tw 

Driven Polymer Transport Through a Nanopore Controlled by a Rotating Electric Field

    The driven translocation kinetics of a single strand polynucleotide chain through a nanopore is studied using off-lattice Monte Carlo simulations, by which the authors demonstrate a novel method in controlling the driven polymer transport through a nanopore by a rotating electric field. The recorded time series of blockade current from the driven polynucleotide transport are used to determine the sequence of polynucleotides by implementing a modified Monte Carlo algorithm, in which the energy landscape paving technique is incorporated to avoid trapping at deep local minima. It is found that only six-time series of block current are required to completely determine the polynucleotide sequence if the average missing rate (AMR) of current signals in these time series is smaller than 20%. For those time series with AMR greater than 20%, the error rate in sequencing an unknown polynucleotide decreases rapidly by increasing the number of time series. To find the most appropriate experimental conditions, the authors have investigated the dependence of AMR of current signals and qualified rate of measured time series of blockade current on various controllable experimental variables.

Prof. Yeng-Long Chen

Institute of Physics, Academia Sinica, TAIWAN

E-mail: yenglong@phys.sinica.edu.tw

Thermodiffusion and Shear-induced Manipulation of DNA in Confined Channels

    Microfluidic transport of DNA molecules plays a significant role in the device design for high accuracy/throughput bio-chemical analysis. We performed lattice Boltzmann simulations coupled with Brownian dynamics to investigate the dynamics of DNA molecules undergoing pressure-driven shear flow and temperature-driven diffusion in microfluidic channels. The dimensions of the channels are comparable the full chain contour length. In pressure-driven flow, the DNA molecule stretches and also migrates towards the center of the channel due to hydrodynamic interactions, leading to higher average velocity for the chains. Under a temperature gradient, the DNA molecules are found to migrate towards the colder surface. We find that by combining the flow and the thermal gradient, we can manipulate the distribution of the DNA molecules in the microchannel, with possible applications to DNA separation or templating.

Dr. Hsiao-Ping Hsu

Condensed Matter Theory Group, Institut fuer Physik, Johannes Gutenberg-Universitaet, GERMANY

E-mail: hsu@uni-mainz.de

1. What is the Order of 2d Escape Transition of Single Compressed Polymer Chains?

    An end-grafted flexible polymer chain compressed by two pistons in 3D undergoes an abrupt transition when the number of monomers in the chain, N, reaches a critical value. In 2D, the situation is much more complicated. The excluded volume interactions between monomers of a chain confined in a strip of finite length 2L transform the coil conformation into a linear string of blobs in a blob picture. This raises questions on the nature of this escape transition.  To check the theoretical predictions based on the blob picture we study 2d single polymer chains with one end grafted in the middle of a strip of length 2L and width H by simulating self-avoiding walks on a square lattice with the pruned-enriched-Rosenbluth method (PERM). A small but finite jump is observed on the results of the end-to-end distance, the number of imprisoned monomers, and the order parameter in the thermodynamic limit of large N and L but finite L/N. We also present a theoretical description based on the Landau free energy approach, which is in good agreement with the simulation results. A two-minima scenario of the distribution of the order parameter is also given by PERM. Both simulation results and the analytical theory indicate that the 2d escape transition is a weak first-order phase transition.

2. Simulations of Bottle-Brush Polymers: Scaling Considerations and Phase Separation

    The structure of bottle-brush polymers with a rigid backbone and flexible side chains is studied in three dimensions, varying the grafting density, the side chain length, and the solvent quality. For one-component bottle-brush polymers in a good solvent, scaling considerations yield predictions for the monomer density profile and the linear dimensions of the side chains. These predictions are compared to Monte Carlo results obtained from a variant of the pruned-enriched Rosenbluth method (PERM), allowing for simultaneous growth of all side chains in the Monte Carlo sampling. For a symmetrical binary (A,B) bottle-brush polymer, where two types (A,B) of flexible side chains are grafted with one chain end to the backbone. Choosing repulsive binary interactions between unlike monomers and varying the solvent quality, it is found that phase separation into an A-rich part of the cylindrical molecule and a B-rich part can occur only locally. Long range order (in the direction of the backbone) does not occur, and hence the transition from the randomly mixed state of the bottle brush to the phase-separated structure is strongly rounded, in contrast to corresponding mean field predictions, a sharp transition to "Janus cylinder" phase-separated structure. This lack of a phase transition can be understood from an analogy with spin models in one dimension. By estimating the correlation length for this phase separation along the backbone as a function of side chain length and solvent quality, we give the quantitative proof that no sharp phase transition occurs.

Dr. Yao-Chen Hung

Institute of Physics, Academia Sinica, TAIWAN

E-mail: ychung@phys.sinica.edu.tw

Detecting Essential Nodes in Complex Networks From Measured Noisy Time Series

    A nonlinear measure, namely multi-interdependency, is proposed to detect the essential nodes in heterogeneously dynamical networks.  The method is based upon the conceptions of the nearest conditional neighbors and singular value decomposition (SVD).  Numerical results show that the value of multi-interdependency is positively correlated with the degree of nodes, which is beneficial to identify the nodes of topological and functional importance. Moreover, such a method has been demonstrated being robust against the effect of intrinsic noise.

Prof. Yn-Hwang Lin

The Department of Applied Chemistry, National Chiao-Tung University, TAIWAN

E-mail: yhlin@mail.nctu.edu.tw

Monte Carlo Simulations of Stress Relaxation of Entanglement-Free Fraenkel Chains. I. Linear Polymer Viscoelasticity

    Shear stress relaxation modulus G(S)(t) curves of entanglement-free Fraenkel chains have been calculated using Monte Carlo simulations based on the Langevin equation, carrying out both in the equilibrium state and following the application of a step shear deformation. While the fluctuation-dissipation theorem is perfectly demonstrated in the Rouse-chain model, a quasiversion of the  fluctuation-dissipation theorem is observed in the Fraenkel-chain model. In both types of simulations on the Fraenkel-chain model, two distinct modes of dynamics emerge in G(S)(t), giving a line shape  similar to that typically observed experimentally. Analyses show that the fast mode arises from the segment-tension fluctuations or reflects the relaxation of the segment tension created by segments being stretched by the applied step strain-an energetic-interactions-driven process-while the slow mode arises from the fluctuations in segmental orientation or represents the randomization of the segmental-orientation anisotropy induced by the step deformation-an entropy-driven process. Furthermore, it is demonstrated that the slow mode is well described by the Rouse theory in all aspects: the magnitude of modulus, the line shape of the relaxation curve, and the number- of-beads (N) dependence of the relaxation times. In other words, one Fraenkel segment substituting for one Rouse segment, it has been shown that the entropic-force constant on each segment is not a required element to give rise to the Rouse modes of motion, which describe the relaxation modulus of an entanglement-free polymer over the long-time region very well. This conclusion provides an explanation resolving a long-standing fundamental paradox in the success of Rouse-segment-based molecular theories for polymer viscoelasticity- namely, the paradox between the Rouse segment size being of the same order of magnitude as that of the Kuhn segment (each Fraenkel segment with a large force constant H-F can be regarded as basically equivalent to a Kuhn segment) and the meaning of the Rouse segment as defined in the Rouse-chain model. The general agreement observed in the comparison of the simulation and experimental results indicates that the Fraenkel-chain model, while being still relatively simple, has captured the key element in energetic interactions-the rigidity on the segment-in a polymer system.

Dr. Wen-Jong Ma

Institute of Physics, Academia Sinica, TAIWAN

E-mail: mwj@gate.sinica.edu.tw

Velocity Distributions and Extended Statistical Mechanics for Non-Equilibrium Systems of Polymers and Lennard-Jones Particles

Prof. Chi-Tin Shih

Department of Physics, Tung-Hai University, TAIWAN

E-mail: ctshih@thu.edu.tw

Characteristic Length Scale of Electric Transport Properties of Genomes

    A tight-binding model together with a statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete  genomes. A correlation parameter Omega is defined to analyze the relation. For some particular propagation length w(max), the transport behaviors of the coding and noncoding sequences are very different and the correlation reaches its maximal value Omega(max). w(max) and Omega(max) are characteristic values for each species. A possible reason for the difference between the features of transport properties in the coding and noncoding regions is the mechanism of DNA damage repair processes together with natural selection.

Prof. Chyi-Yeou Soong

Department of Aerospace and Systems Engineering, Feng-Chia University, TAIWAN
E-mail: cysoong@fcu.edu.tw

Control and Anti-Control of Chaos with Perturbations of Minimum Power

    Recent study on a non-feedback chaos control/anti-control with perturbations of minimum power is presented. Different from previous methods, the present one is of two characteristic features: (1) the parameters of the controlling signal are optimized by a genetic algorithm (GA) with the largest Lyapunov exponent (LLE) used as an index of the stability, and (2) the optimization is justified by a fitness function defined with closeness of the target LLE and minimization of the controlling power taken into account. On the noted autonomous (Rossler and Lorenz) and non-autonomous (Murali-Lakshmanan-Chua) systems, this novel approach has been tested with and without the presence of noise and the control effectiveness and robustness demonstrated. In the last part, anti-control of chaos with a prescribed target LLE is dealt with.Performance of the GA-optimized signals in triggering chaos at an ordered state as well as further enhancing chaoticity at a chaotic state is explored. Results of numerical experiments and the related physical mechanisms are discussed.

Miss Da-Lun Tseng

Institute of Physics, Academia Sinica, TAIWAN

E-mail: dltseng@phys.sinica.edu.tw

1. An Introduction to Influenza Virus

2. Expression Evolution in Yeast Genes of Single-Input Modules

Mr. Shih-Chieh Wang

Institute of Physics, Academia Sinica, TAIWAN

E-mail: d9454104@mail.nchu.edu.tw

Correlation Matrix Approach to Taiwan Stocks