Date :

 05-07, July 2008

Place :

 Chung-Yuan Christian University, Chungli

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

 Institute of Physics of Academia Sinica (Taipei)

 Chung-Yuan Christian University (Chungli)

  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

Hotel Info. :

 GIORGIO Hotel (喬爵大飯店)

 Address:桃園縣中壢市延平路216號（新街國小旁，約15分鐘車程）

 Tel: (886)-3-4622345

 Website: http://giorgio-hotel.myweb.hinet.net/

 (Charge: Single Room: NT$1400-Daily)

 皇家賓館

 Address:桃園縣中壢市中北路信陽街27巷15號（中原大學旁）

 Tel: (886)-3-4662969

 (Charge: Single Room: NT$960-Daily)

 If you need to reserve a room, please contact with Miss Chang (張慧美, Tel:(886)-3-2653201).

 Hotel expense will be paid by yourself (except for invited speakers).

Speakers :

Prof. Sow-Hsin Chen

Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, USA

E-mail: sowhsin@mit.edu

Neutron Scattering Studies of Liquid-Liquid Phase Transition and the Associated Second Critical Point in Supercooled Confined Water

    We have observed a fragile-to-strong dynamic crossover phenomenon of a relaxation time [1] and self-diffusion constant [2] in deeply supercooled 1-d confined water.  The a relaxation time is measured by Quasi-Elastic Neutron Scattering (QENS) experiments and the self-diffusion constant by Nuclear Magnetic Resonance (NMR) experiments.  Water is confined in 1-d geometry in cylindrical pores of porous silica material, MCM-41 and in Double-Wall Carbon Nanotubes (DWNT) [4].

    The crossover phenomena can also be observed by measuring the Mean Square Hydrogen Atom Displacement derived from an Incoherent Elastic Neutron Scattering and from appearance of a Boson peak in an Incoherent Inelastic Neutron Scattering.  We observe a pronounced violation of the Stokes-Einstein relation at and below the crossover temperature at ambient pressure [2].  Upon applying pressure to the confined water, the crossover temperature is shown to track closely the Widom line emanating from the existence of a liquid-liquid critical point buried in an unattainable deeply supercooled state of bulk water [1].  Relation of the dynamic crossover phenomena to the existence of a density minimum in supercooled confined water [3] will be discussed. The crossover temperature is shown to be sensitively dependent on the degree of hydrophilicity of the confining substrate [4].

References

1. Li Liu and Sow-Hsin Chen et al, Pressure dependence of fragile-to-strong transition and a possible second critical point in supercooled confined water, PRL 95, 117802 (2005).

2. Sow-Hsin Chen and Francesco Mallamace et al, The violation of the Stokes-Einstein relation in supercooled water, PNAS 103, 12974 (2006).

3. Dazhi Liu and Sow-Hsin Chen et al, Observation of the density minimum in deeply supercooled confined water, PNAS, 104, 9570 (2007).

4. Xiang-Qiang Chu, Alexander I. Kolesnikov, A. P. Moravsky, V. Garcia-Sakai, and Sow-Hsin Chen, Observation of a Dynamic Crossover in Water Confined in Double-wall Carbon Nanotubes, Physical Review E 76, 021505 (2007).

Prof. Michael W. Deem

Department of Bioengineering and Department of Physics and Astronomy, Rice University, Houston, USA
E-mail: mwdeem@rice.edu

Quasispecies Theory for Horizontal Gene Transfer and Recombination
    I discuss generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population.  The effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population will be discussed, through an analytic field theoretic mapping.  Both horizontal gene transfer from a population and recombination between pairs of individuals will be considered. Somewhat surprisingly, these nonlinear generalizations of quasispecies theory to modern biology are analytically solvable. For recombination there are two selected phases, one of which is spectrally rigid. I present numerical and analytical results as well as phase diagrams for different cases.

Amino Acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small Library Thoroughly or a Large Library Sparsely?
    I will discuss simulations of directed laboratory evolution of antibodies constructed from reduced amino-acid alphabets of sizes of 2, 5, and 20 [1]. The binding free energy of the antibody was evolved, starting from an initially modest level. The free energy of substrate binding decreased as the number of rounds of evolution increased. Ranked amino acid usage frequencies are in agreement with observations of the CDR-H3 variable region of human antibodies.  Antibodies constructed from the largest alphabet sizes were the most functional. That is, antibodies of higher affinity are found by searching a library with a larger alphabet sparsely than by searching a smaller library thoroughly, even with well-designed, reduced amino-acid alphabet libraries. This result is perhaps the reason for the diversity of amino acids found in nature and suggests a general motivation for the search to discover and incorporate unnatural amino acids in protein evolution experiments.

References
[1] E. Munoz and M. W. Deem, Protein Engineering, Design & Selection 21 (2008) 311-317.
　

Prof. Victor J. Hruby

E-mail: hruby@email.arizona.edu

Direct Examination of Binding and Signaling Via Integral Membrane Proteins Using a New Biophysical Method, Plasmon Waveguide Resonance (PWR) Spectroscopy and Related Methods

    Efforts to directly examine structural changes that accompany ligand interactions with transmembrane proteins such as seven transmembrane G-protein coupled receptors has been difficult due to their anisotropic structures in membrane environments, which also are highly anisotropic both structurally and dynamically. We have been developing a new technology to help overcome these problems. PWR spectroscopy is a variant of conventional surface phasmon resonance (SPR) spectroscopy. In PWR optical excitations of plasmons occur in a thin metal (e.g. Ag) film overcoated by a thicker dielectric film (e.g. silica) deposited on the surface of a right angle prism. A sample to be analyzed (e.g. a GPCR in a membrane bilayer) is immobilized at the surface of the prism. It interacts with the evanescent field and changes the characteristics of the resonance. In PWR (as opposed to SPR where only the p-polarized resonance is excited) both p-polarized and s-polarized light excitation occurs producing two separate resonances that occur at different incident angles. This leads to not only a large enhancement in sensitivity of this method over SPR(fentomolar molar quantities of GPCRs can be examined), but most importantly for examining GPCRs, it provides information that can distinguish structural changes from simple mass changes utilizing Maxwell’s equations. We will illustrate the power of these methods with several examples of new insights that can be obtained in examining signaling of GPCRs: 1) binding of agonist, antagonist, partial agonists and inverse agonist ligands to a GPCR lead to different structures; 2) there is no necessary direct correlation between the affinity of agonist binding to a GPCR and G-protein binding interactions with the GPCR with signaling via GDP/GTP exchange; 3) membrane rafts can be directly detected via PWR spectroscopy; and 4) GPCR-ligand interactions lead to specific segregation into membrane domains depending on the nature of the ligand. These and related findings will be discussed in terms of a new model for GPCR-ligand signaling.

    Supported in part by the National Science Foundation and U.S. Public Health Service, National Institutes of Health.

Prof. Gang Hu

Department of Physics, Beijing Normal University, CHINA

E-mail: ganghu@bnu.edu.cn

可激发系统中螺旋波与缺陷湍流的控制及在心脏除颤中的可能应用 

    该报告讨论了用局域周期驱动消除可激发介质中螺旋波与缺陷湍流的控制方法。研究了用控制波除去螺旋波和湍流波的条件，以及这些条件对可激发系统参数空间的要求，同时研究提高控制效率和拓宽参数空间中可控区窗口的有效方法。由于心肌组织是一种典型的可激发介质，并且螺旋波和破碎螺旋波是心动过速和心颤的重要原因，我们期望以上控制方法对心颤控制提供有意义的启示。
　

Prof. Mai-Suan Li

Institute of Physics, Polish Academy of Science, POLAND

E-mail: masli@ifpan.edu.pl

New Force Replica Exchange Method and Mechanical Unfolding of Proteins

    We present our new force replica exchange method for efficient configurational sampling of long biomolecules subjected to external force [1]. This method was applied to obtain the temperature-force phase diagram of the three-domain Ubiquitin.  Concerning mechanical unfolding, it is shown that the resistance of proteins to mechanical perturbation is defined by their secondary structures [2].  Helix-rich proteins are mechanically less stable compared to beta-rich proteins.  The distance between the native state and the transition state depends on the helix content linearly.  The contact order, which is a measure of fraction of local contacts, was found to strongly correlate with the stability and the shape of free energy landscapes.  Thus our study reveals that the nature of mechanical resistance of proteins is surprisingly simple: mechanical stability and the distance from the transition to the native state are determined either by the content of secondary structure or by the contact order. We have found simple equations to describe this relationship [2].

References
1. M. Kouza, C.K. Hu, and Mai Suan Li, J. Chem. Phys 128, 045103 (2008)
2. Mai Suan Li, Biophys J. 93, 2644 (2007)

Prof. David Mukamel

Department of Physics of Complex Systems, ISRAEL

E-mail: fnmukaml@wisemail.weizmann.ac.il

Phase Transitions in Biopolymers I: Statistical Mechanics of Interacting Loops
Phase Transitions in Biopolymers II: Dynamics of Loops

    Phase transitions which take place in double stranded DNA and in single stranded RNA molecules will be reviewed. Examples include thermal denaturation, or melting,  of DNA in which the two strands unbind upon heating, unzipping of DNA in which the unbinding of the two strands is induced by an external pulling force and conformational changes which take place in RNA.  Theoretical modeling of these transitions will be presented and the effect of excluded volume interactions, which play an important role in these transitions, will be discussed. In the second talk the dynamics of loops, which mediate the denaturation process will be  considered.
　

Prof. Zhong-Can Ou-Yang

Institute of Theoretical Physics, Chinese Academy of Science, CHINA

E-mail: oy@itp.ac.cn

Exact Shape Equation of Lipid Monolayer Domain and Its Kindney-Boojum-Like Solutions: Cusp removes Neumann’s Type Divergence

    Solid lipid monolayer domain surround by a fluid phase is studied by the equilibrium between line tension and long range dipole-dipole interaction. An exact domain shape equation is derived in form without introducing an artificial cutoff distance between dipoles. We found that a kinked shape solution (i.e., a cusp appears in the boundary) can prevent divergence induced by the electrostatic dipole-dipole energy, a double line integral same as the Neumann’s formula for self-inductance of a single coil. Our results reveal that nature has more intelligent technique to remove the Neumann’s type divergence than previous treatment of human being by introducing an artificial cutoff in calculation.

References

[1] M. Iwamoto and Ou-Yang Zhong-can, Phys. Rev. Lett. 93, 206101 (2004)

[2] M. Iwamoto, Liu Fei, and Ou-Yang Zhong-can, J. Chem. Phys. 125, 224701 (2006)

Prof. Rahul Pandit

Department of Physics, Indian Institute of Science, INDIA

E-mail: rahul@physics.iisc.ernet.in

Spiral- and Scroll-Wave Turbulence in Mathematical Models for Cardiac Tissue

Prof. Tien-Tzou Tsong

Institute of Physics, Academia Sinica, TAIWAN

E-mail: phtsong@ccvax.sinica.edu.tw

A Study of the Dynamics of Surface Atoms and Clusters at Atomic Resolution

Prof. Bing-Hong Wang

Department of Modern Physics, University of Science and Technology of China, CHINA

E-mail: bhwang@ustc.edu.cn

Some Recent Research Progress on Complex Systems

Prof. Fa-Yueh Wu

Department of Physics, Northeastern University, USA

E-mail: fywu@lepton.neu.edu

Professor C. N. Yang and Statistical Mechanics

    Professor Chen Ning Yang has made seminal and influential contributions in many different areas in theoretical physics. This talk focuses on his contributions in statistical mechanics, a field in which Professor Yang has held a continual interest for over sixty years. His Master's thesis was on a theory of binary alloys with multi-site interactions, some 30 years before others studied the problem. Likewise, his other works opened the door and led to subsequent developments in many areas of modern day statistical mechanics and mathematical physics. He made seminal contributions in a wide array of topics, ranging from the fundamental theory of phase transitions, the Ising model, Heisenberg spin chains, lattice models, and the Yang-Baxter equation, to the emergence of Yangian in quantum groups. These topics and their ramifications will be discussed in this talk.
　

Prof. Boming Yu

Department of Physics, Huazhong University of Science, CHINA

E-mail: yuboming2003@yahoo.com.cn

Introduction to Complex Networks

    近年來，越來越多的數學家和物理學家開始關注現實世界中各種複雜網絡的拓樸結構，並發現了諸如小世界效應、無標度網絡、等級結構等特性。網絡的複雜性研究成為物理學界的一大熱點。對普通人而言，首先想到的是互聯網。除了互聯網以外，複雜網絡的例子在我們生活中到處存在，比如說把一個萬維網作為一個節點，可以說至少和我們人類的數目相當，所以萬維網也是極其複雜的網絡。又例如，每個人都有自己的關係網。學校校長與教職員工及學生也形成網絡關係等等。演員之間形成合作網絡，論文的引用形成引用網絡等。網絡無處不在！

    本演講主要內容將介紹複雜網絡的基本概念、基本理論、基本研究方法和若干應用。

Prof. Jian-Min Yuan

Department of Physics, Drexel University, USA
E-mail: yuanjm@drexel.edu

Sensitivity and Dynamic Studies on Cancer- and Diabetes-Related Signaling Pathways

    Human diseases, such as cancers, diabetes, and heart diseases, are often related to networks of cellular signaling pathways.  In view of their importance, we have applied thermodynamic, physical, and engineering methodologies in the investigation of mathematical models of signaling pathways.  The goals are to understand the dynamics, the effects of cross-talks and feedback loops, and design principles of these pathways.  Related to cancers, we have analyzed a mathematical model of the coupled MAPK and PI3K pathways, two better-known pathways of the Ras network.  For diabetes, on the other hand, we have studied phenomenological models of Quon, et al.  Time-dependent sensitivity analysis has been used to reveal information about the time scales and the interaction strengths of protein-protein interactions, intricate interplays of cross-talks and feedback loops, as well as the rankings of vulnerable nodes of these pathways.   On the other hand, non-equilibrium thermodynamic concepts, such as affinities, fluxes, energy dissipated rates, and efficiency, allow us to probe deeper into the design principles of these pathways.  Furthermore, dynamics of these variables plus the time-dependent sensitivity information allow us to achieve certain degree of control over important output signals, which are related to cell growth and differentiation in the case of the Ras network and related to glucose transportation into tissue cells in the case of the insulin pathways.