Date :

 12-13, 15 December 2008

Place :

 12-13 December: Hsiao Fong Memorial Hall (曉峰紀念館) 1st Conference Room, Chinese Culture University, Taipei

 15 December: The auditorium on 1st floor, Institute of Physics, Academia Sinica, Taipei

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

 Institute of Physics, Academia Sinica (Taipei)

 Department of Physics, Chinese Culture University (Taipei)

 Chinese Culture University

 Hsiao Fong Memorial Hall (曉峰紀念館)  (The Building 1)

 Bus Info. (12 December)

  10:00 Get on a bus at Institute of Physics of Academia Sinica

  10:20 Bus from Academia Sinica to Chinese Culture University

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

  Mr. Lee-Min Chang (鄭立明)  (Department of Physics, Chinese Culture University)

 Tel:(886)-2-28610511 ext. 25205; Fax(886)-2-28610577; E-mail: crsspy@staff.pccu.edu.tw

Hotel Info. :

 International Hotel (陽明山國際大旅館)

 Address: 台北市陽明山湖山路一段7號

 Tel: (886)-2-28617100

 Website: http://www.ihhotel.com.tw, http://www.hotspringtour.com/beautifulsecene/nation/slideshow.html

 If you need to reserve a room, please contact with Mr. Lee-Min Chang (鄭立明, Tel:(886)-2-28610511 ext. 25205).

 Hotel expense will be paid by yourself .

Speakers :

Prof. Hsuan-Yi Chen
Department of Physics, National Central University, TAIWAN
E-mail: hschen@mail.phy.ncu.edu.tw

Statistical Mechanics of Reversible Non-Covalent Bonds:  From Single Molecule Experiment to Cell Adhesion

    Adhesion on subcellular scale is mediated by specific non-covalent molecular bond working cooperatively.  Experimental studies on the adhesion molecules have been focusing on characterizing the strength of a single complex under external force, but little attention has paid to the cooperative effect in multiple parallel bonds.  I shall begin with a discussion on the characteristics of single adhesion complex, including the rupture rate under weak and strong force, the effect of rebinding, and the interpretation of existing experimental data.  After discussing single adhesion complex, I will show that by constructing the effective free energy of a cluster of parallel adhesion complexes, a system of multiple parallel bonds under external force can be studied by theoretical methods similar to those used for single adhesion complexes. 

Dr. Yi-Chiuan Chen

Institute of Mathematics, Academia Sinica, TAIWAN

E-mail: ycchen@math.sinica.edu.tw

Anti-Integrable Limit and Chaotic Scattering Billiards

    In this talk, some scattering billiards will be introduced and discussed. Instead of horseshoes, I shall explain  how  we may understand their chaotic orbits via the theory of anti-integrable limit.

Prof. Chung-I Chou
Department of Physics, Chinese Culture University, TAIWAN
E-mail: cichou@faculty.pccu.edu.tw

Statistical Physics Approach to Elections

    This presentation is a summary of our works in two issues of Socio-Physics: the political districting problem and the problem of distribution of votes among candidates.

    The aim of the Political Districting Problem is to partition a territory into electoral districts subject to some constraints such as contiguity, population equality, etc. In this report, we will show how to transform the political districting problem to a q-state Potts model in which the constraints can be written as interactions between sites or external fields acting on the system. Districting into q voter districts is equivalent to finding the ground state of this q-state Potts model. Searching for an optimal solution for the ground state becomes an optimization problem and some optimization algorithms such as the Monte Carlo method, simulated annealing method, genetic algorithm and Knowledge-based Evolution Algorithm can be employed here.

    For the distribution of votes among candidates, there are at least two types of the voting distribution of elections. One is the power-law behavior which has been reported on Brazilian parliamentary elections. Another is the lognormal distribution on German, French, Italian and Polish elections. In this report, we will show our studies on the voting distributions of Legislature elections in Taiwan and Japan. These distributions show a mixed behavior of power-law-like and lognormal-like distribution. We will also show how to use a simple model to simulate the results in these countries.

Prof. Nikolay V. Dokholyan

Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA

E-mail: dokh@med.unc.edu

1. Simplified Approaches to Complex Biological Systems

    Some of the emerging goals in modern medicine are to uncover the molecular origins of human diseases, and ultimately contribute to the development of new therapeutic strategies to rationally abate disease. Of immediate interests are the roles of molecular structure and dynamics in certain cellular processes leading to human diseases and the ability to rationally manipulate these processes. Despite recent revolutionary advances in experimental methodologies, we are still limited in our ability to sample and decipher the structural and dynamic aspects of single molecules that are critical for their biological function. Thus, there is a crucial need for new and unorthodox techniques to uncover the fundamentals of molecular structure and interactions. We follow a hypothesis-driven approach which is based on tailoring simplified protein models to the systems of interest.  Such an approach allows significantly extending the length and time scales for studies of complex biological systems. I will describe several recent studies that signify the predictive power of simplified protein models within the hypothesis-driven modeling approach utilizing developed in our laboratory rapid Discrete Molecular Dynamics (DMD) simulations.

2. Molecular Mechanisms of Polypeptide Aggregation in Human Diseases

    Protein aggregation-related toxicity is implicated in a plethora of neurodegenerative diseases including Alzheimer's, Parkinson's, prion, and motor neuron diseases. The proteins found to aggregate in diseases are unrelated in their native structures and primary sequences, but form similar fibrils with characteristic cross-ß sheet morphologies (amyloid) in the aggregated state. We will discuss commonalities in and differences in protein aggregation processes and in morphologies of protein aggregates. We will use three systems as examples: (1) Cu, Zn superoxide dismutase, aggregation of which is associated with the Amyotrophic Lateral Sclerosis, (2) polyglutamine-containing proteins associated with nine neurodegenerative diseases, and (3) an artificially designed peptide ccß. The latter peptide exhibits a temperature-dependent conformational conversion from a three-helix bundle to ß-rich amyloid fibrils.  We will demonstrate that while the processes that lead to aggregates are drastically different, there are underlying principles that govern these processes.

3. Scale-Free Evolution: From Proteins to Organisms

    The bottom-up approach to understanding the evolution of organisms is by studying molecular evolution. We have discovered peculiar patterns that nature imprints on protein structural space in the course of evolution. In particular, we have found that the universe of protein structures is organized hierarchically into a scale-free network. We propose a model that explains the hierarchical organization of proteins in fold families. The model, which is based on the evolutionary selection of proteins by their native state stability, reproduces patterns of amino acids conserved across protein families. Due to its dynamic nature, the model sheds light on the evolutionary time-scales. By studying the relaxation of the correlation function between consecutive mutations at given position in proteins, we observe separation of the evolutionary time-scales: at short time intervals families of proteins with similar sequences and structures are formed, while at long time intervals the families of structurally similar proteins that have low sequence similarity are formed.

Prof. Dominik Gront

University of Washington, USA; Faculty of Chemistry, Warsaw University, POLAND

E-mail: dgront@gmail.com

1. Lattice Models in Protein Structure Prediction

    Despite remarkable progress in the field of protein structure prediction that has been made in recent years the problem still remains unsolved. Conformational space of a protein grows exponentially with the length of its sequence which renders the problem extremely difficult as we try to investigate large proteins and macromolecular complexes. Lattice models are one of possible remedies offering enormous increase of sampling speed. In this presentation I will introduce the world of on-lattice simulations: assumptions they are based on, and typical algorithms. I will also summarize the most successful methods.

2. Multiscale Modeling of Proteins

    All atom simulations of proteins offer detailed insight into their structure and dynamics. Contemporary all-atom force fields are able to detect hi resolution model within a group of decoys. These models alone however are not able to sample conformations space of a protein.  This leads to a multiscale algorithm which is a combination of two modeling approaches, 1) a simplified approach to sample conformational space effectively, and 2) a high-resolution model is employed to refine and score crude results created by the reduced one.

CAVE: A Fortran Program for Detection and Analysis of Internal Cavities in Proteins

    An efficient FORTRAN code is presented for detection of the internal cavities of proteins and for calculation their surface area, volume and other quantitative characteristics. The algorithm is based on a newly invented enveloping triangulation method for detection of the cavities. The program is tested by calculating the internal cavities for a number of protein structures from PDB database, and the results are compared with the other published data.  The results of testings are presented.  Testings have shown that the algorithm is correct and the code is efficient.
　

Prof. Ming-Chang Huang
Center for Nonlinear and Complex Systems and Department of Physics, Chung-Yuan Christian University, TAIWAN
E-mail: ming@phys.cycu.edu.tw

Stochastic Fluctuations and Gene Regulatory Networks

    The stochastic fluctuations, under the frame of Tsallis-type macroscopic distribution, can be either Gaussian or non-Gaussian colored noise determined by the Tsallis index q. The analytic study for the effect of stochastic fluctuations in

gene regulatory networks is extended to the cases of Gaussian and non-Gaussian colored noises in this work. Firstly, the solution of the corresponding Langevin equation with colored noise is expressed in terms of Ito integral. Then, two important lemmas concerning with the variance of a Ito integral and the covariance of two Ito integrals are shown. Based on the lemmas, we give explicitly the general formulae for the variance and covariance for a two-dimensional network near a stable equilibrium. Finally, we apply the formulae to two regulatory networks, auto-regulatory network and toggle switch. For Gaussian colored noises, we find that the finite correlation-time of noises reduces the fluctuations and enhances the correlation between the fluctuations of two molecular components.  For non-Gaussian cases, the fluctuations may enhances or reduces the fluctuations, relative to the Gaussian case, depending on the Tsallis index q < 1 or q > 1, and the correlation between the fluctuations shows the opposite way.

Dr. Yao-Chen Hung

Institute of Physics, Academia Sinica, TAIWAN

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

Resonant Apoptosis-Survival Switches on p53 Regulatory Network

    We study the effect of intrinsic noise on p53 regulatory network, the core of a cell's modulator for switching between survival and apoptosis.  The noise, originating from stochastic expression of p53-responsive genes, introduces marked advantages for the system to sense external stimuli. The performance of the sensitivity undergoes a maximum with the raise of noise level, indicating the occurrence of stochastic resonance.  Biological significance of such a phenomenon is under our discussion.

Dr. N.Sh. Izmailian
Yerevan Physics Institute, ARMENIA
E-mail: izmailan@phys.sinica.edu.tw

Finite-Size Correction Amplitudes and Universality of Their Ratios: Effect of Boundary Conditions

    In the vicinity of boundaries the bulk universality class of critical phenomena splits into several boundary universality classes, depending upon whether the tendency to order in the boundary is smaller or larger than in the bulk. For Ising universality class there are five different boundary universality classes: periodic, antiperiodic, free, fixed and mixed (mixture of the last two). In this letter we present the new set of the universal amplitude ratios for four boundary universality classes: periodic, antiperiodic, free and mixed.  The results are in perfect agreement with a perturbated conformal field theory scenario
proposed by Cardy.

Dr. Sing-Guan Kong

Graduate Institute of Systems Biology and Bioinformatics, National Central University, TAIWAN

E-mail: kensinro@gmail.com

Scale-Invariance and SOC in Genomes

    Scale-invariant is an important aspect of self-organized criticality (SOC), a phenomenon ubiquitous in nature [1,2]. Long-range correlation [3] and fractal structure [4] is known to exist in genomes. Here, we use a new method to observe long-range variation in genomes and analyzed over 1,000 complete chromosomes, including archaea, eubacteria, fungi, protozoa, plants, insects and vertebrates. Our study indicates that a high level of scale-invariance is universal in genomes. This suggests that genomes are in a state of SOC, which we infer to be a signature of a universal feature in the dynamics of genome growth and evolution [5,6].

1. Deepak Dhar. Self-Organized critical state of sandpile automaton models. Phys. Rev. Lett. 64, 1613-1616 (1990).

2. Per Bak et al. Self-organized criticality. Phys. Rev. A 38, 364-374 (1988).

3. C. K. Peng, et al. Long-range correlations in nucleotide sequences. Nature 356, 168-170 (1992).

4. B. L. Hao, H. C. Lee and S. Y. Zhang. Fractal related to long DNA sequences and complete genomes. Chaos, Solitons & Fractals 11, 825-836 (2000).

5. L. C. Hsieh, LF Luo, F. M. Ji and H. C. Lee. Minimal model for genome evolution and growth. Phys. Rev. Lett. 90, 018101 (2003).

6. H. D. Chen, C. H. Chang, L. C. Hsieh and H. C. Lee. Divergence and Shannon information in genomes Phys. Rev. Lett. 94, 178103 (2005).

Dr. Po-Han Lee

Institute of Physics, Academia Sinica, TAIWAN

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

The Characterization and Application of a Synthetic Autoregulatory Circuit

    The genetic switch, a combination between the inducers and the regulators, is central for quantitatively analyzing genetic expression. With the regulated genetic networks by suitable titration of inducers, we are able to envision in detail the expression of reporter gene in the transcription or the protein level. In this paper, we focus on the synthetic autoregulation networks repressed by TetR protein and reported by the LacZ or GDH protein (glutamate dehydrogenase) in Escherichia coli. With the regulation of auto-repression network, we found that the autorepression circuit exhibits gradual tunable gene expression and also provides the more perspective for studying the regulation of Nitrogen pathway in Escherichia coli.

Dr. Wen-Jong Ma

Institute of Physics, Academia Sinica, TAIWAN

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

Molecular Dynamics Approach to Aggregation in a Mixed System of Polymer and Lennard-Jones Fluid

    We study the aggregation in a system of polymer chains mixed in Lennard-Jones fluid, using molecular dynamics simulation. The polymer chains are modelled by rigidly bonded monomer sites, with bending and torsion angle potentials. A small number of 'linker' sites are randomly assigned as the fluid-affiliated, in distinguishing from the rest fluid-repelling monomer sites.  We compare the process of clustering with that of a pure system in absence of fluid, with zero angle potentials. We found the differences in the structure and the dynamics of aggregation of polymer chains, which suggest the relevance of considering the effects of heterogeneity alone backbone in the study of aggregation of polypeptide or other soft matter materials.

Prof. A. N. Morozov

Inst Surface Chem, Natl Acad Sci Ukraine, UKRAINE

E-mail: a_n_morozov@yahoo.com

Dr. Karen Petrosyan
Institute of Physics, Academia Sinica, TAIWAN
E-mail: pkaren@phys.sinica.edu.tw

1. Effect of Time Delay on the Onset of Synchronization of the Stochastic Kuramoto Model

    We consider the Kuramoto model of globally coupled phase oscillators with time-delayed interactions, that is subject to the
Ornstein-Uhlenbeck and non-Gaussian noises. We investigate numerically the interplay between the influences of the finite
time correlation of noise and the time delay on the synchronization process. It is shown that the effect of time delay for the deterministic Kuramoto model is qualitatively equivalent to the effect of frequency fluctuations of the phase oscillators while for the stochastic Kuramoto model the critical coupling grows nonlinearly with the increase of the time delay. The linear dependence of the critical coupling on the noise intensity also changes to become nonlinear due to the additional de-phasing caused by the time delay. Generally, it is found that the de-phasing plays important role in the dynamics of the system when
the intrinsic correlations induced by the finite correlation time of the noise are small. It is also shown that the critical coupling is higher for the non-Gaussian noise compared to Gaussian one due to higher effective noise strength.

2.Physical Approaches to DNA Sequencing and Detection

    A review talk will be presented on recent developments in physical approaches to DNA sequencing and detection, including a very recently proposed technique for reading the base sequence of a single DNA molecule using a graphene nanogap.
　

Dr. D. B. Saakian
Yerevan Physics Institute, ARMENIA
E-mail: saakian@mail.yerphi.am

Solution of Evolution Models: Truncated Selection and Finite Population

    We found new evolution phase in case of truncated slection. In case of evolution with finite population we suggested a parameter to characterize the validuty of infinite population results.

Miss Chian-Yi Sue

Department of Life Science, National Taiwan Normal University, TAIWAN
E-mail: fillesue@yahoo.com.tw

Spatial Expression of ASR protein in Tomato

    A protein with molecular mass of ca. 15 kDa was revealed to be abundant in tomato fruits of various developmental stages and of different cultivars. Its encoding gene, designated as TF15, was screened from a fruit cDNA library and identified as a novel member of the ABA-, stress-, and ripening-induced (Asr) gene family in plants. While the previous in vitro study suggested the ASR protein’s nuclear localization and its DNA binding activity, the datum regarding to its in vivo localization has not been available. Using specific antibody probes, the cellular and subcellular localization of TF15 protein in tomato fruit was investigated. We examined different tissues of tomato fruit and found that the TF15 proteins were located within the cytoplasm and nucleus. In addition, some of the TF15 protein might exist in the apoplastic areas, although this requires further investigation. Overall, the current study identified a novel ASR protein in tomato and provided localization results for its cellular and subcellular distribution in the fruits.