Date :

 10-12 November 2006

Place :

 Lecture hall, at 4F, Village of Holistic Education (全人教育村), Chung-Yuan Christian University, Chung Li, Taiwan

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems focus group)

 Institute of Physics of Academia Sinica (Taipei)

 Department of Physics, Chung-Yuan Christian University (CYCU)

 Miss Hui-Mei Chang (Secretary, Department of Physics, CYCU)

 Tel:(886)-3-2653201; Fax:(886)-3-2653299; E-mail: huimei@phys.cycu.edu.tw

 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

Registration :

 Please complete the Registration Form (PDF / DOC) and send it to Miss Hui-Mei Chang (huimei@phys.cycu.edu.tw)

 1. There will be one bus from Taipei to CYCU. The bus will leave from Institute of Physics, Academia Sinica at 10:00 am.

 2. Shuttle buses of CYCU from Taipei to CYCU are also available. Time-table for shuttle bus (PDF)

Accommodation :

 Hotel information (PDF / DOC)

Speakers :

Dr. Bidhan Chandra Bag

Institute of Physics, Academia of Sinica, TAIWAN

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

Colored non-Gaussian noise induced anomalous diffusion and current inversion

     We consider colored non Gaussian noise driven stochastic process. Our investigation shows that non Gaussian noise can induce ballistic diffusion in noise driven free particle process. Applying it to the flashing ratchet model we have observed that there is a current inversion in the variation of the current with half cycle period which accounts potential on-off operation. The current inversion disappears if one switches from non Gaussian to Gaussian character of the noise. The phenomena of current inversion is also found to occur as the asymmetric character of the ratchet potential grows. On increasing noise correlation time (τ) mean velocity of a particle first increases and then decreases after passing through a maximum if the noise is non Gaussian in character. For Gaussian noise current monotonically decreases. The current is enhanced if the noise is more departure from Gaussian behavior. Our present study is relevant to the transport through quasi-one-dimensional structures as pores, ion channels, zeolites and the operation mechanism of molecular motors etc.

Prof. Moo Young Choi

Department of Physics and Astronomy, Seoul National University, Seoul 151-747, KOREA
Korea Institute for Advanced Study, Seoul 130-722, KOREA

E-mail: mychoi@snu.ac.kr

1. Stability and collective oscillations in a globally coupled rotors

     We study a system of globally coupled rotors governed by a set of Langevin equations. The corresponding Fokker-Planck equation is solved to yield a number of solutions in both the microcanonical and canonical ensembles. The stability of these solutions, which allow various degrees of cluster motion, varies differently with the temperature, disclosing the inequivalence between the two ensembles. Also discussed is the relation of the cluster motion and the dynamical order.

2. Molecular dynamics of protein PDC-109: Potential of mean force between the two domains

     Protein PDC-109, which consists of two domains, guides the motion of bull sperm, forming dimers. To understand such dimerization and domain-domain association, we consider both explicit and implicit solvent models to compute the potential of mean force. Various methods including thermodynamic integration, umbrella sampling, generalized Born model, and Poisson-Boltzmann model are considered and the results are compared. The discrepancy between them are discussed.

3. Dynamic model for failures: criticality and resonance

     We present a dynamic model for failures in biological organisms, where each cell becomes dead under sufficiently strong stress and is then allowed to be healed with some probability. Revealed is the characteristic time evolution that the system tends to resist the stress longer than the system without healing, followed by sudden breakdown with some fraction of cells surviving. The distributions of the clusters of failed cells and associated power spectra are also examined with regard to the possibility of self-organized criticality. Under periodic stress, the average fraction of intact cells decays stepwise or exhibits oscillating behavior, depending on the stress and healing. The power spectrum at the stress frequency at first increases with the healing parameter, then decreases, which may be called healing resonance. In case thathealing varies periodically with time, the system undergoes a transition from the unhealthy state to the healthy one as the healing frequency increases. This suggests how to adjust the frequency of medical treatment to the optimum.

Dr. Chung-ke Chang

Institute of Biomedical Science, Academia Sinica, TAIWAN
E-mail: chungke@ibms.sinica.edu.tw

Modelling of SARS coronavirus nucleocapsid protein with small-angle X-ray scattering

Miss Chun-Ling Chang

Institute of Physics, Academia of Sinica, TAIWAN
E-mail: labthpp@phys.sinica.edu.tw

Complex network in Taiwan earthquakes

     The complex growing network of earthquakes based on Taiwan’s earthquake database is constructed and its topological properties such as the connectivity distribution, the clustering coefficient, and the degree of separation are studied. It is found that the network is characterized by the power-law nature of the distribution of connectivity, a large value of the clustering coefficient and a small value of the degree of separation between vertices. The clustering coefficient is 63 times larger than the completely random network in the case. These features mark the seismicity as a complex phenomenon.

Prof. Zh. S. Gevorkian

Yerevan Physics Institute, ARMENIA
Institute of Radiophysics and Electronics, ARMENIA
Institute of Physics, Academia of Sinica, TAIWAN
E-mail: gevorkia@phys.sinica.edu.tw

Adhesion-induced DNA naturation

     DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface, the entropy gain is smaller than in the bulk, leading to a stronger binding and, upon neglecting self-avoidance, absence of a denatured phase. Now consider conditions where the binding potentials are too weak for naturation, and the surface potential too weak to adsorb single strands. In a variational approach it is shown that their combined action may lead to a naturated adsorbed phase. Conditions for the absence of naturation and adsorption are derived too. The phase diagram is constructed qualitatively.

Prof. Ding-Wei Huang

Department of Physics, Chung-Yuan Christian University, TAIWAN

E-mail: dwhuang@phys.cycu.edu.tw

A simple model for city traffic

     We study the influence of traffic lights on city traffic, which is simulated in the cellular automata framework. Vehicles on road are treated as particles hopping on lattice. The microsimulations of traffic flow are obtained with different settings of signal period and time delay. Both numerical results and analytical approximations are presented. In a closed system, the green-light wave solutions can be realized for undersaturated traffic. For saturated traffic, the correlations among the traffic signals have no effect on the throughput. The benefits of synchronization are manifest only when stochastic noise is suppressed for oversaturated traffic. The results in an open system are also discussed.

Prof. Norden E. Huang

Research Center for Data Analysis, National Central University, TAIWAN
E-mail: norden@ncu.edu.tw

What should we look for in data from a nonlinear and nonstationary world ?
     Traditionally, we made the critical linear and stationary assumption even before we look at any data. But the world we live in is neither stationary nor linear. Facing with such reality, what should we look for in the data? The existing methods of probability theory and spectral analysis are certainly inadequate, for they are all based on stationary and linear assumptions. For example, spectral analysis is synonymous with the Fourier based analysis. As Fourier spectrum can only give meaningful interpretation to linear and stationary process, its application to data from nonlinear and nonstationary processes is problematical. And probability distributions can only represent global properties, which imply homogeneity in the population. To break away from this limitation, we should let data speak for themselves so that the results could reveal the full range of consequence of nonlinearity and nonstationarity. To do so, we need new paradigm of data analysis methodology without a priori basis to fully accommodating the variations of the underlying driving mechanisms. We should develop adaptive data analysis techniques.

     A new method, Hilbert-Huang Transform (HHT), for analyzing nonlinear and nonstationary data is developed precisely for this purpose. The key part of HHT is the Empirical Mode Decomposition method with which any complicated data set can be decomposed into a finite and often small number of Intrinsic Mode Functions (IMF). This decomposition method is adaptive, and, therefore, highly efficient. Since the decomposition is based on the local characteristic time scale of the data, it is applicable to nonlinear and nonstationary processes. With the Hilbert transform, the Intrinsic Mode Functions yield instantaneous frequencies as functions of time that give sharp identifications of imbedded structures. The final presentation of the results is an energy-frequency-time distribution, designated as the Hilbert Spectrum. Classical nonlinear system models are used to illustrate the roles played by the nonlinear and nonstationary effects in the energy-frequency-time distribution. Other applications of HHT will also be presented.

Prof. Tai-Huang Huang

Institute of Biomedical Science, Academia Sinica, TAIWAN
E-mail: bmthh@ibms.sinica.edu.tw

Structural biology of SARS coronavirus
　

Mr. Maksim Kouza

Institute of Physics, Polish Academy of Science, POLAND

E-mail: kouza@ifpan.edu.pl

Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin

     The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C_a Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force quench refolding times scale as D_F ~ exp(f_qDx_F/k_BT), where Dx_F ≈ 0.96 nm is the location the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to Dx_F ≈ 0.8 nm obtained from the force-clamp experiments [J. M. Fernandez and H. Li, Science 303, 1674-1678 (2004)]. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing N-terminus of ubiquitin changes its mechanical unfolding pathways much more dramatically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state Dx_UF ≈ 0.24 nm which is in reasonable agreement with the experimental data.

Prof. Macoto Kikuchi

Cybermedia center, Osaka University, JAPAN

E-mail: kikuchi@cmc.osaka-u.ac.jp

1. Simulations and experiments of highway traffic flow
     I will give a brief review of computer simulation models, mainly ones based on the optimal velocity model, of the highway traffic flow and their phase transitions (i.e., emergence of a traffic jam). Then, some results from our circuit experiment will be presented, in which we demonstrated that a traffic jam can occur ithout a bottleneck. Also discussed will be a power-law fluctuations recently observed on an expressway in Japan by means of the detrended fluctuation analysis.

2. Free-energy landscape of lattice protein model
     Recent development of the funnel picture of protein folding have revealed that the folding process of a protein is deduced from its free-energy landscape. Most importantly, it has become a consensus that the folding route of a protein is largely determined by its native state topology. In this talk, I will describe our recent study of free-energy landscapes of proteins using lattice protein model and an extended ensemble Monte Carlo method. The following two subjects will mainly be focused on: (1)Possible diversity in folding routes of proteins having the same native topology (2)Thermodynamical mechanism of aggregation of two proteins.

3. Fluctuation and relaxation of motor proteins
     Motion mechanism of biological molecular motors are still open. Although relevance of ratchet mechanism to the motion has long been discussed, ratchet-type models are too much simplified so that connection to the real molecular motor is rather vague. We are currently studying motor proteins such as Kinesin and Myosin using coarse-grained protein model (Go-like model) for understanding how the chains behaves during the motion. I will present in this talk our recent results on the structural fluctuation of Kinesin and the structural relaxation of Myosin.

Dr. Po-Han Lee

Affiliated Senior High School, National Taiwan Normal University, TAIWAN

E-mail: leepohan@yahoo.com.tw

The studies of clique polynomial embedded in the protein-protein interaction networks

     We study the clique polynomials of topological structures embedded in the protein-protein interaction networks for seven species, including E. coli, H. pylori, C. elegans, D. melanogaster, H. sapiens, M. musculus and S. cerevisiae and the data analyzed here are gathered from the DIP database. The protein-protein interaction plays an important role in the processes of the biochemical synthesis, metabolism of living cell and so on. Through the analysis of the clique polynomials of the protein-protein interaction networks (PINs), we can find the possible grouping interaction of the proteins existed in the complex networks, which means that we can build the unknown biochemical pathway of interactions among the proteins. Measuring these networks, we also obtain the small world and hierarchical properties embedded in the seven networks. These findings suggest the possibility of constructing the topological relationships of the protein-protein interaction networks and of methods for uncovering the unknown pathways of protein-protein interactions.

Prof. Chai-Yu Lin

Department of Physics, National Chung Cheng University, TAIWAN

E-mail: lincy@phys.ccu.edu.tw

Bulk dissipation as a tuning parameter in Manna model

     Bulk dissipation is one of the factors for building and maintaining a self-organized criticality system. Here, we use bulk dissipation as a tuning parameter to study the behavior a two-state sandpile model (Manna model). We find the scaling as a function of bulk dissipation is well described by the exponents obtained from the moment analysis method. The related scaling behaviors reveal that the criticality of Manna model could be described by the picture of the traditional critical phenomena.
　

Dr. Cui-Lian Li

Institute of Physics, Academia of Sinica, TAIWAN
E-mail: clli@phys.sinica.edu.tw

The behavior of confined counter-ions in two-dimensional suspension

     We present our Monte Carlo simulation results for the behavior of counter-ions confined between a charged colloidal particle and a charged ring in two-dimensional suspension at the reduced temperature from 0.002 to 0.050. Our results reveal a completely different distribution of confined counter-ions from the predictions of both Poisson-Boltzmann (PB) theory and strong coupling (SC) theory. We further perform the Gibbs ensemble simulation to examine systematically the phase behavior of the counter-ions, obtain phase diagram and determine the critical temperature which can be considered as a criterion whether PB theory is valid.

Prof. Mai Suan Li

Institute of Physics, Polish Academy of Science, POLAND

E-mail: masli@ifpan.edu.pl

Mechanism of oligomerization of short peptides

    Nonfibrillar soluble oligomers, which are likely to be transient intermediates in the transitions from monomers to amyloid fibrils, may be the toxic species in Alzheimer's disease. Thus it is very important to understand early events that direct assembly of amyloidogenic peptides. Using all-atom simulations with the GROMOS96 force field 43a1 in explicit water we have shown that the oligomerization of Ab_16-22 peptides obeys the dock-lock mechanism. We have also proposed a toy lattice model which allows us to ascertain this conclusion but for a much larger number of monomers. In this talk we review our all-atom as well as lattice simulation results on the dock-lock mechanism which is probably a generic mechanism for fibril elongation of full length Ab-peptides.

Dr. Wen-Jong Ma

Institute of Physics, Academia of Sinica, TAIWAN

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

Short time dynamic properties in polymer-fluid mixture

     We study the dynamic properties of a model composed of polymer molecules mixed in simple atomic fluids. By numerically combining several molecular dynamics simulation techniques, we are able to probe the extremes of nonequilibrium situations, with only the excluded volume effect and the chain connectivity considered as of relevance. While the motions of the fluid particles in such system are strongly affected by the local agitations caused by the untamed structural forces of the random polymer chains, the polymer molecules are found tending to have stable velocity distributions described by the so-called q-statistics. The result reveals novel issues concerning the description of nonequilibrium dense polymer systems.
　

Dr. Karen Petrosyan

Yerevan Physics Institute, ARMENIA

E-mail: pkaren@yerphi.am

Anomalous latent heat in nonequilibrium phase transitions

     We study first-order phase transitions in a two-temperature system, where due to the time-scale separation all the basic thermodynamical quantities (free energy, entropy, etc.) are well defined. The sign of the latent heat is found to be counterintuitive: it is positive when going from the phase where the temperatures and the entropy are higher to the one where these quantities are lower. The effect exists only out of equilibrium and requires conflicting interactions. It is displayed on a lattice gas model of ferromagnetically interacting spin-1/2 particles.

Prof. Jiunn-Ren Roan

Department of Physics, National Chung-Hsing University, TAIWAN

E-mail: roan@phys.nchu.edu.tw

Soft nanopolyhedra
    Computer simulations show that end-grafted immiscible homopolymers can confer multivalence to nanoparticles, resulting in soft nanopolyhedra with structures identical to those found in small clusters of colloidal microspheres. Unprecedented structure tunability is demonstrated by several structure transition sequences, including a reentrant transition, induced by varying composition, polymer lengths, or grafting patterns. These results suggest a new method for fabricating nanoparticles with precisely controlled numbers and locations of functional sites.

Dr. Shura Hayryan

Institute of Physics, Academia Sinica, TAIWAN

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

Application of Wang-Landau algorithm to Monte Carlo simulation of peptide fragment PrP(214-226) of cellular human prion protein (PrP)

     Thermodynamical and structural properties of 13-residue synthetic peptide, P1, from the C-terminal a-helix part of the human Prion Protein (PrP) are studied. All-atom energy potential function is used for simulation of P1 peptide in a vacuum and in aqueous solution with normal PH factor, using Solvent Accessible Surface Area method for calculation of peptide-solvent interaction energy. The Wang-Landau algorithm is used for calculating the density of states of the system. Temperature dependences of thermodynamical quantities such as average energy, specific heat, relative free energy and entropy are calculated from the density of states. A cooperative helix-coil transition with double-well structure of the relative free energy is found. Using the estimates of density of states several multicanonical production runs were performed to sample configurations of the system. Temperature dependences of average structural parameters such as helicity, gyration radius, end-to-end distance and number of beta-sheet-like residues are calculated from the multicanonical production runs of 10⁶ sweeps. With SMMP program's force field we found that P1 peptide is a two-state self folding peptide with helical structure. This result is in a agreement with the PDB structure of the P1 peptide as part of the human Prion Protein, PrP(214-226): (CITQYERESQAYY), but in contradiction with some experimental data.

Dr. Ming-Chya Wu

Institute of Physics, Academia Sinica, TAIWAN

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

Phase statistics of electrocardiograms during ventricular fibrillation in humans

Mr. Shu-Hao Yeh

School of Pharmacy, National Taiwan University, TAIWAN

E-mail: r94423004@ntu.edu.tw

Recognition and dynamic gating in DNA intercalation

     Anthracyclines such as doxorubicin and daunomycin are important anti-cancer agents and are well-known DNA intercalators. However, the dynamic intercalating processes of these intercalators are seldom discussed. Here we conducted molecular dynamics simulation with the umbrella sampling technique to investigate the dynamic association and dissociation processes of these intercalators. For comparison of solvent models, the DNA-intercalator complexes were first equilibrated with the generalized Born model and explicit waters, respectively, and then the dissociation process was performed by dragging the intercalators out of DNA with many successive windows. It was observed that after the intercalators have left the intercalation site, the distance between base pairs soon recovered to a normal range. Subsequently, the simulation for the association process was performed to investigate the recognition and dynamic opening of the intercalation site. Finally, the potentials of mean force (PMF) were calculated by the weighted histogram analysis method (WHAM) and the dissociation rate constants were estimated and compared with the experimental values.