Date :

 November 27-29, 2003

Place :

 The First Meeting Room, 5F, Institute of Physics, Academia Sinica (Taipei)

Schedule :

 27 November (Thursday)

10:00-10:50

Softmatter Catalytic Wheels and the Brownian Motor Mechanism

Professor Tian Yow Tsong (Institute of Physics, Academia Sinica)

11:00-11:50

Multiscale Molecular Modeling of Membrane Proteins

Professor Jung-Hsin Lin (School of Pharmacy, National Taiwan University)

Scaling and Marginal Stability of Globular Proteins

Professor Mai Suan Li (Institute of Physics, Polish Academy of Sciences, Poland)

15:00-15:50

Stretching and Circular Permutation of Proteins

Professor Mai Suan Li (Institute of Physics, Polish Academy of Sciences, Poland)

The Immune System. Overview.

Dr. Tigran Davtian (Laboratory of Immunology and Virology, "Armenicum" Research Center, Armenia)

17:10-18:00

Regulation of the Immune Response.

Dr. Tigran Davtian (Laboratory of Immunology and Virology, "Armenicum" Research Center, Armenia)

 28 November (Friday)

Immunity to Viruses and Retroviruses.

Dr. Tigran Davtian (Laboratory of Immunology and Virology, "Armenicum" Research Center, Armenia)

11:00-11:50

Virus Evolution and Viral Quasispecies Emergence.

Dr. Tigran Davtian (Laboratory of Immunology and Virology, "Armenicum" Research Center, Armenia)

Lunch

Exact Solution of Kamp-Bornholdt Host-parasite Coevolution Model

Dr. David B. Saakian (Yerevan Physics Institute, Yerevan , Armenia)

DNA Adsorption Model

Dr. Zhyrair Gevorgian (Yerevan Physics Institute, Yerevan , Armenia)

The DNA Wrapping around a Protein

Professor Yan-Chr Tsai (Dept. of Physics, National Chung Cheng University)

Theory for the Force-stretched Double-stranded Chain Molecule

Professor Zhong-can Ou-Yang (Institute of Theoretical Physics, Chinese Academy of Sciences, China)

 29 November (Saturday)

Thinking with Simple Computer Models
Professor Kan Chen (Dept. of Computational Science, National University of Singapore, Singapore)

11:00-11:50

Which Matters for Survival,  Risk Preference or Forecasting Accuracy ? -- An Analysis based on Agent-Based Artificial Stock Markets

Professor Shu-Heng Chen (Department of Economics, National Chengchi University)

Conditional Probabilities of Price Change in Stock Market Data and a Simple Model for trend and trend reversal
Professor Kan Chen (Dept. of Computational Science, National University of Singapore, Singapore)

Modeling Cooperative Activities in Financial Fluctuations

Dr. Wen-Jong Ma (Institute of Physics, Academia Sinica)

16:10-17:00

Minority Games for Complex Adaptive Systems

Professor Chin-Kun Hu (Institute of Physics, Academia Sinica)

Flexoelectric Origin of Nanomechanic Deflection in DNA-Microcantilever System

Professor Zhong-can Ou-Yang (Institute of Theoretical Physics, Chinese Academy of Sciences, China)

 Speakers' contact information and lecture abstracts:  (ordered by speakers' last names)

 Professor Kan Chen ( Dept. of Computational Science, National University of Singapore, Singapore )

                                 E-mail: cscchenk@leonis.nus.edu.sg

Thinking with Simple Computer Models
     In this talk I illustrate the importance of simple computer models for understanding social and natural phenomena as well as for practical application. Computer simulations on Schelling's segregation model, spatial game of prisoners' dilemma, and the sand pile model (with potential use in secure communication) will be shown and discuss.

Conditional Probabilities of Price Change in Stock Market Data and a Simple Model for trend and trend reversal
     We analyze the minute-by-minute data of the Hang Seng Index as well as the daily closing prices of the indices of a number of stock markets. We found that the conditional probability of price change is strongly correlated with the price change in the previous interval due to non-Gaussian market trend and trend reversal. A simple model based on short-time trend and trend reversal is constructed. We show that the model exhibits statistical properties and market swings similar to those of the real market.

 Professor Shu-Heng Chen ( Department of Economics, National Chengchi University )

                                          E-mail: chchen@nccu.edu.tw

Nov. 29

Which Matters for Survival,  Risk Preference or Forecasting Accuracy ? -- An Analysis based on Agent-Based Artificial Stock Markets

     Blume and Easley (1992) show that if agents have the same savings rule, an expected discounted logarithmic utility maximizer with correct beliefs will dominate. If no agent adopts this rule, then agents with incorrect beliefs, but equally averse to risk as logarithmic utility maximizers, may eventually hold more wealth than the agent with correct beliefs. In other words, a trader with correct beliefs can   be driven out of the market by traders with incorrect beliefs.  However,  Sandroni (2000) shows that, among agents who have the same intertemporal discount factor and who choose savings endogenously, the most prosperous will be those making accurate predictions.  Agents with inaccurate predictions will be driven out of the market regardless of their preferences.  By using the extended agent-based artificial stock market, we simulate the evolution of portfolio behavior, and investigate the characteristics of the long-run surviving population of investors. Our agent-based simulation results are largely consistent with Blume and Easley (1992), and we conclude that preference is the key  factor determining agents' survivability.

 Dr. Tigran Davtian ( Laboratory of Immunology and Virology, "Armenicum" Research Center, Armenia )

                              E-mail: tigdav@excite.com

The Immune System. Overview.

    The immune system of vertebrates is characterized by a remarkable set of adaptive processes that enable the individual organism to produce, on demand as it were, an immense variety of specifically reactive proteins and cells that can recognize and cause the destruction of an almost limitless variety of foreign substances. These processes, called immune responses, are essential for survival, for they constitute the principal means of natural defense against infection by pathogenic microorganisms; they probably also contribute to defenses against some host cells that undergo transformation into cancer cells.
    The present talk is concerned with general features that underline the immune system and its responses as a whole: the origin of immunology; the immune system's cells; antigenic determinants; an overview of cellular and humoral immunity; lymphocytes and network hypothesis; immunoglobulin genes; the major histocompatibility complex; immune cells signaling and tolerance to self. The combinatorial immune system defined by the presence of antigen-specific recognition units from immunoglobulin family of vertebrates apparently arose as an evolutionary "big bang" involving the generation and duplication of genetic segments from an unknown precursor within the brief evolutionary span of 10-20 million years.

Regulation of the Immune Response.

    The central nervous system receives a wide spectrum of energies (electromagnetic, sound, pressure, gravitational, etc) and transforms these inputs into information useful to the survival of the organism. The connection between immunology and the information science are less natural. To effect molecular integrity of the individual, the immune system has a gather antigenic information and respond in meaningful way. How does the immune system create information and meaning forms this input? This talk aims to place the immune system into an informational framework.
    The immune system exists to protect us from antigens, including infection agents. As a corollary, it evolved through constant encounter with infectious microbes. During this co-evolution, many immunologic systems become dichotomous by nature: the mediators of specific or adaptive immunity and innate immunity. Innate immune responses are elicited almost immediately following antigen entry, and consist of stereotyped responses, whereas adaptive immune responses appear later and consist of specific arms of molecules and receptors. Here we will discuss balancing immunity and tolerance and deleting and tuning immune repertoires.

Immunity to Viruses and Retroviruses.

    Through cellular and humoral mechanisms, the immune system constrains virus infection and replication. Low amounts of viruses cause disease, since they rely on intracellular multiplication. That, in spite of the immune system, viruses can cause life-threatening disease indicate that viruses and the immune system must establish a delicate equilibrium, where neither virus infection nor immune responses are completely effective. Viruses may have defective infectious pathways or the immune system may be unable to eliminate rapidly and completely virus infections, or viruses may have evolved strategies to overcome immune detection, and immune system's sophisticated mechanisms to detect virus infection.
    In this talk we will describe the above strategies of immunity and virus adaptation in HIV infection model as well as the structure, expression and regulation of HIV genome and HIV replication in CD4 T lymphocytes. Special attention will be devoted to host mechanisms of anti-HIV resistance.

Virus Evolution and Viral Quasispecies Emergence.

    Like many other RNA viruses, HIV and HCV circulates within the host as a mixture of genetically distinct but closely related viruses, referred to as quasispecies. The quasispecies nature of HIV and HCV is principally due to the rapid kinetics of viral replication and the lack of RNA polymerase or revertase proof-reading which allows the virus to rapidly accumulate mutations with an estimated rate of 0,4 x 10-3 to 1,2 x 10-3 base substitutions per site per year]. Differential host selection pressures directed against the various viral proteins are through to affect the rate of fixation of mutations, which varies along the viral genome. In particular, a higher rate of sequence heterogeneity is observed in the hypervariable regions which contains epitopes recognised by neutralising antibodies, and thus, it is likely to be subject to continuous selection by the immune response. We will discuss the recent challenges in mathematical models of viral evolution under the pressure of adaptive immune response and as a optimal mutation rates for viral escape as well as co-evolution and quasispecies as a viral error catastrophe.

 Dr. Zhyrair Gevorgian ( Yerevan Physics Institute, Yerevan , Armenia)

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

Nov. 28

DNA Adsorption Model

     DNA adsorption problem is studied within a simple theoretical mode. It is shown that an adsorbed state of DNA at the surface is much more stable than that one of a single polymer chain. This effect due to the weak bound states of a system of interacting particles at the surface in an analogy with those in the quantum mechanical three-body problem. Experimental manifestations of the obtained results are discussed.

 Professor Chin-Kun Hu ( Institute of Physics, Academia Sinica )

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

Nov. 29

Minority Games for Complex Adaptive Systems

 Professor Mai Suan Li ( Institute of Physics, Polish Academy of Sciences, Poland )

                                    E-mail: masli@ifpan.edu.pl

Scaling and Marginal Stability of Globular Proteins

    We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using simulations and the prefactor argument based on experimental data we argue that the dependence of the folding rate on N for real proteins can be described by a stretched exponential. Finite size effects on the cooperative thermal denaturation of proteins are discussed in detail. We show that a dimensionless measure of cooperativity scales as W_c~ N^z, where N is the number of amino acids. Surprisingly, we find that the exponent z is universal with z=1 + g, where the exponent g characterizes the divergence of the susceptibility for a self-avoiding walk. Lattice model simulations and experimental data are consistent with the theory. Our finding shows that the folding transition should be weakly first order rationalizing the marginal stability of proteins.

1. Cieplak M , Hoang T X, and Li M S, Phys Rev Lett 83,1684 (1999)
2. Li M S, Klimov D K and Thirumalai D, J Phys Chem B 106, 8302 (2002)
3. Li M S, Klimov D K and Thirumalai D, to appear in Polymer
4. Li M S, Klimov D K and Thirumalai D, submitted to Phys. Rev. Lett.

Stretching and Circular Permutation of Proteins

    We discuss key experiments on stretching and circular permutation of globular proteins. A possibility of finding the energy landscape from stretching experiments is considered. The effect of circular permutation on folding properties is studied using the three-dimensional lattice models with side chains. For the wild-type protein which is a two-state folder, the corresponding permutant may fold with or without intermediates depending on a cleavage at peptide bonds. This conclusion is based on the study of thermodynamic and kinetic properties and on the force stretching simulations. Our result is in qualitative agreement with experiments on a-spectrin SH₃ and chymotrypsin inhibitor 2.

 Dr. Wen-Jong Ma ( Institute of Physics, Academia Sinica )

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

Nov. 29

Modeling Cooperative Activities in Financial Fluctuations

     Using a model called 'coupled random walks', we are able to incorporate cooperative activities into a system of random walks, in conjunction with the analysis of cross-correlation matrix, that stock-stock correlation revealed from the market data can be correctly described. The formulation is based on the idea that the price of a stock changes when there is 'price gradient' between the stock and a group of related stocks. I will illustrate how the presence of such gradients among the stocks of whole market and among those in each separate group, generate the eigenmodes deviated from the bulk of continuously distributed eigenvalues obtained for the correlation matrix in real market. The formulation is potentially applicable to incorporate more elaborated correlations
or to systems in different contexts.

 Dr. David B. Saakian ( Yerevan Physics Institute, Yerevan , Armenia )

                                   E-mail: saakian@jerewan1.yerphi.am

Exact Solution of Kamp-Bornholdt Host-parasite Coevolution Model

     We consider Kamp-Bornholdt viral-immune system cooevolution model, where two quasispecies (viral and immune system) interact with each other. For the case, when after attack of immune system viral fitness peak jumps to the new configuration with several spin flipped, we can exactly solve the dynamics of the model. The resonance conditions are considered.

 Professor Yan-Chr Tsai ( Dept. of Physics, National Chung Cheng University )

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

The DNA Wrapping around a Protein

 Professor Zhong-can Ou-Yang ( Institute of Theoretical Physics, Chinese Academy of Sciences, China )

                                                E-mail: oy@itp.ac.cn

Theory for the Force-stretched Double-stranded Chain Molecule

    The statistical mechanical theory of conformation of chain biomolecules, such as RNA, single-strand DNA, and Beta-sheet proteins (S.-J. Chen and K.A. Dill, J. Chem. Phys. 109 (1998) 4602) is modified to describe the force-stretched extension of the mentioned chain molecules. The simulation study with the theory reveals that the mechanical behaviors of homogeneous RNA chains of hairpins conformation and second structures are quite different: the unfolding of the hairpin is two state while the unfolding of latter is one state.

Flexoelectric Origin of Nanomechanic Deflection in DNA-Microcantilever System

    The cantilever motion induced by adsorption of single-strand DNA and DNA hybrization reaction is studied by the biomembrane theory. The result shows good agreement with recent experiments. This is significant in the field of biosensors.

 Professor Tian Yow Tsong ( Institute of Physics, Academia Sinica )

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

Softmatter Catalytic Wheels and the Brownian Motor Mechanism

    An enzyme recycles in each catalytic process.  It is a catalytic wheel.  An enzyme is also a softmatter nanometer device.  In order for a molecular machine made of softmatter protein to work in a highly discipative environment it must follow certain rules. This lecture will consider one of these rules and discuss mechanisms of the Brownian Motor. I will use an ion pump as an example of a softmatter device which behavior is aptly explained by the Brownian Motor mechanism.