Date :

 12-14, 16 January 2006

Place :

 The first meeting room of the 5th floor, Institute of Physics, Academia Sinica, Taipei

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

 Institute of Physics of Academia Sinica (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

          Speaker :　

Dr. Chi-Fon Chang

Genomics Research Center, Academia Sinica, TAIWAN

chifon@gate.sinica.edu.tw

The transacylase (E2) subunit of the branched-chain -ketoacid dehydrogenase (BCKD) complex carries three independently folded domains which are linked together by flexible loops: The amino-terminal lipoyl-bearing domain (hbLBD, 1-84), the interim E1/E3-binding domain (hbSBD, 104-152), and the carboxy-terminal inner-core domain. The hbLBD and hbSBD play central role in substrate channeling and substrate recognition. We have employed multidimensional heteronuclear NMR techniques to determine the structure and dynamics of three truncated fragments of the human BCKD complex: the hbLDB (a.a. 1-84), hbSBD (a.a. 104-152) and a di-domain (hbDD) comprising residues 1–168 of the E2 component. Solution structures of hbLBD and hbSBD have been determined. NMR results showed that solution structures of hbLBD and hbSBD determined in separate fragments are indistinguishable from that in hbDD. Analysis of backbone ¹⁵N-T¹, ¹⁵N-T₂ and ¹H-¹⁵N-NOE relaxation data of hbDD showed the linker region is highly flexible. Together with the isothermal calorimetric titrations data, NMR studies of interactions between hbDD and branched-chain-ketoacid decarboxylase (E1) or dihydrolipoamide dehydrogenase (E3) will be discussed.

Prof. Iksoo Chang

National Research Laboratory for Computational Proteomics and Biophysics, Department of Physics, Pusan National Univ., KOERA

chang@random.phys.pusan.ac.kr

Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment

Although a coarse-grained description of proteins is a simple and convenient way to attack the protein folding problem, the construction of a global pairwise energy function which can simultaneously recognize the native folds of many proteins has resulted in partial success. We have sought the possibility of a systematic improvement of this pairwise-contact energy function as we extended the parameter space of amino acids, incorporating local environments of amino acids, beyond a 20x20 matrix. We have studied the pairwise contact energy functions of 20x20, 60x60, and 180x180 matrices depending on the extent of parameter space, and compared their effect on the learnability of energy parameters in the context of a gapless threading, bearing in mind that a 20x20 pairwise contact matrix has been shown to be too simple to recognize the native folds of many proteins. In this paper, we show that the construction of a global pairwise energy function was achieved using 1006 training proteins of a homology of less than 30%, which include all representatives of different protein classes. After parametrizing the local environments of the amino acids into nine categories depending on three secondary structures and three kinds of hydrophobicity (desolvation), the 16290 pairwise contact energies (scores) of the amino acids could be determined by perceptron learning and protein threading. These could simultaneously recognize all the native folds of the 1006 training proteins. When these energy parameters were tested on the 382 test proteins of a homology of less than 90%, 370 (96.9%) proteins could recognize their native folds. We set up a simple thermodynamic framework in the conformational space of decoys to calculate the unfolded fraction and the specific heat of real proteins. The different thermodynamic stabilities of E.coli ribonuclease H (RNase H) and its mutants were well described in our calculation, agreeing with the experiment.

Prof. Chi-Ning Chen

Department of Physics, National Dong-Hwa University, TAIWAN

cnchen@mail.ndhu.edu.tw

The exact partition functions of the ±J Ising spin glasses on finite lattices are computed by recursive counting, which sums up not only spin configurations, but also bond configurations. The partition function zeros show different patterns with different percentages of antiferromagnetic bonds. The results lead to a conjecture that for ±J Ising spin glass on the square lattice, when the density of fully frustrated plaquettes increases to reach the critical point of site percolation, the order-disorder critical temperature T_c decreases to zero.

          Speaker :　

Dr. Syamal Kumar Dana

Instrument Division Indian Institute of Chemical Biology, Calcutta 32, INDIA

sdana_ecsu@yahoo.com

Bursting is an important phenomenon mainly observed in neural systems by which neurons process information and communicate with each other. Bursting is found in many biological systems where a slow variable controls the fast variable. We report our observations of various bursting events, point-cycle and cycle-cycle bursting in physical systems like Josephson junction and in Chua circuit. We find in numerical simulation of a Josepshon junction model that it shows parabolic bursting when a periodic signal with much lower frequency than the natural frequency of the junction is applied to the junction. Such parabolic bursting is possible in the superconducting junction near saddle-node on limit cycle bifurcation. In an electronic experiment, such parabolic bursting is observed near homoclinic bifurcation in Chua oscillator when it is forced by an external sinusoidal signal with much lower frequency than the natural frequency of the circuit. In another electronic experiment, we also observed autonomous cycle-cycle bursting in asymmetric Chua circuit near homoclinic bifurcation.

We report our observation of transition from in-phase and antiphase synchronization in coupled Chua oscillators with intermediate mixed states with coupling strength. The mixed state evolves in time from in-phase to antiphase. This is true for both limit cycle and chaotic oscillators. Most interestingly, for delay coupled systems, we report a transition from in-phase to antiphase with intermediate amplitude death regime in both simulations of many systems like Rossler, Lorenz systems and in electronic experiment with Chua oscillators.

Dr. Hsien-Kuei Hwang

Institute of Statistical Science, Academia Sinica, Nankang, Taipei 11529, TAIWAN

hkhwang@stat.sinica.edu.tw

Phase changes in random search trees and related models

I will present the phase change phenomena in several classes of random search trees issuing from computer data structures. These random trees, having a more discrete nature, are closely related to some continuous models in random fragmentation processes (and others). A brief survey of several other related models in diverse disciplines will also be given.

Prof. Naoki Kawashima

ISSP, University of Tokyo, JAPAN

kawashima@issp.u-tokyo.ac.jp

Recent Developments in Quantum Monte Carlo Methods

The world-line Monte Carlo method proposed in 1976 by M. Suzuki made it possible to deal with quantum many-body problems with no approximation. The method is based on the Feynman path-integral and the artificial discretization of the imaginary time was introduced. Before 1993, however, there were few numerical works that is reliable enough to discuss critical behaviors of quantum many-body problems. Aside from the notorious negative-sign problem, this is due to very limited system size and/or the slow computational relaxations. The global update algorithm, known as the loop algorithm, was proposed in 1993 and it removed the difficulties from the world-line method. Since then, several variants and improvements of the method has been invented and they are producing interesting results, such as very accurate estimation of critical behaviors, novel phases in spin systems with high-order interactions, ground state properties of the SU(N) generalization of the Heisenberg model, etc.

Spin Glasses --- A Review

Like other physical problems, study of spin glasses started from observation and understanding of real materials. However, the spin glass problem has exceptionally broad and profound connections to other branches of science, such as brain science (through neural network models), theory of communications, and computational complexities. It seems that the spin glass problem has something universal, universal even beyond the boundary of conventional physics, that lies at the core of various complex systems. In this series of review talks, I summarize basic established facts in the field and recent attempts at understanding spin glasses, mostly by numerical means, as well as connections to some particularly interesting fields. Subjects of three talks, respectively, are

  1. Mean-Field vs. Droplet Picture
  2. Some Numerical Approaches
  3. Computational Complexity

Prof. Jürgen Kurths

Interdisciplinary Centre for Dynamics of Complex Systems and Institute of Physics, Potsdam University Am Neuen Palais 10, D-14415 Potsdam, GERMANY

jkurths@gmx.de

http://www.agnld.uni-potsdam.de/~juergen/juergen.html

Synchronization phenomena are abundant in nature, science, engineering and social life. Synchronization was first recognized by Christiaan Huygens in 1665 for coupled pendulum clocks; this was the beginning of nonlinear sciences. First, several examples of synchronization in periodic systems are presented, such as in clocks, organ pipes, fireflies and even in the mechanics of bridges.
Second synchronization phenomena in coupled complex systems with rather simple geometry are discussed. Then it is explained how to identify such phenomena in experimental data, such as in plasma tubes and in physiological measurements, such as EEG or heart rate data.
Third I present two approaches to detect and quantify phase synchronization in attractors with a more complicated geometry, called non-phase coherent oscillators which have a strong phase diffusion. The first is based on the general idea of curvature and the second one on the concept of recurrence. It is shown that the second method is applicable even to noisy data. Applications to electrochemical experiments, to measurements of visual perception and to climatological data, as Indian Monsoon, are given.
References (selection)
1. M. Rosenblum, A. Pikovsky, and J. Kurths, Phys. Rev. Lett. 1996, 76, 1804.
2. A. Pikovsky, M. Rosenblum, and J. Kurths, Synchronization – A Universal Concept in Nonlinear Sciences, Cambridge

    University Press 2001.
3. S. Boccaletti, J. Kurths, G. Osipov, D. Valladares, and C. Zhou, Phys. Rep. 2002, 366, 1.
4. G. Osipov, B. Hu, C. Zhou, and J. Kurths, Phys. Rev. Lett. 2003, 91, 024101.
5. M. Romano, M. Thiel, J. Kurths, and W. von Bloh, Phys. Lett. A 2004, 330, 214.
6. M. Romano, M. Thiel, J. Kurths, I. Kiss, and J. Hudson, Europhys. Lett. 2005, 71, 466-472.
7. F. Meinecke, A. Ziehe, J. Kurths, and K. Muller, Phys. Rev. Lett. 2005, 94, 084102.

First, I present synchronization phenomena in chains of spiking and bursting systems. Second, synchronizability in heterogeneous networks with complex topological structure is discussed. It is shown that the synchronizability mainly depends on the mean degree and the heterogeneity of the network. Third the transition to synchronization in such networks is studied. The organization of synchronized behaviour is hierarchical and is mainly driven by the hubs.
References:
1. A. Motter, C. Zhou, J. Kurths: Phys. Rev. Lett., in press
2. C. Zhou, J. Kurths: CHAOS, in press
　

I will apply recently developed techniques from nonlinear data analysis, especially basing on recurrence plots, to detect and quantify laminar phases before a life-threatening cardiac arrhythmia. The corresponding results could be of importance for the therapy of malignant cardiac arrhythmias.

Dr. Sai-Ping Li

Institute of Physics, Academia Sinica, TAIWAN

spli@phys.sinica.edu.tw

The Political Districting Problem is mapped 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 in equivalent to finding the ground state of this q-state Potts model. We illustrate this by districting Taipei city in its 2008 Legislature Election. Statistical properties of the model are also studied.

Prof. Hongru Ma

Institute of Theoretical Physics, Shanghai Jiao Tong University, CHINA

hrma@sjtu.edu.cn

Colloidal dispersions: effective interaction, structure and dynamics

Colloidal dispersions are solid particles dispersed in continuous liquids. The particles may carry electric charge or neutral. The interaction, structure and dynamics of this system are very complicate and contains many interesting physics. In this series of talks (approximately 3 hours), I will give first a short account of the general properties of Soft Condensed Matter and colloidal dispersions. Then I will present the current understandings of effective interactions between colloid particles, the liquid structure and phase transitions of colloids and, finally the short time and long time dynamics of colloids. Emphases will be given to the Monte Carlo evaluation of effective interactions, the pair distribution function and its calculation and experiment measurement, and the important effects of hydrodynamic interactions on the diffusion of colloid particles.

Prof. Hui-Hsu Gavin Tsai

Department of Chemistry, National Central University, TAIWAN

hhtsai@cc.ncu.edu.tw

Recent research suggests that amyloidogenic oligomers may be the toxic species in cell cultures rather than the amyloid fibrils (1). Therefore, it is crucial to understand their interactions, structure and oligomerization mechanism in atomistic detail. By employing tens of fast CPUs and an advanced phase sampling algorithm, parallel-tempering molecular dynamics (PTMD), we have investigated the energy landscape of amyloidogenic peptide oligomerization in explicit water (2) A pentapeptide, DFNKF, derived from human clacitonin (hCT) (3)  and its mutant, DAFAF, was simulated with a total simulation time of ~500 ns. It has been characterized to be stable with a in-register parallel single-sheet by conventional molecular dynamics (4). The process of a parallel-sheet formation at 300K have been characterized. The assembly of a parallel-sheet from the amorphous state mainly occurs via a "bottleneck" channel where the inter-strand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking including both backbond and side chain hydrogen bonds. The Asn-Asn interactions work like "glue" by sticking the DFNKF strands together and assist the "on-pathway" oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder (or so-called amide stacking) commonly found in globular-helix proteins (5). A contral run shows that when Asn -s mutated to Ala, the stability and population of the DFAKF parallel-sheet  is significantly decreased. Furthermore, our in vitro mutagenesis experiments show that the  ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with their new atomic structure of amyloid-like fibrils composed of short peptides with sequence GNNQQNY (6). The atomic-resolved structure of GNNQQNY fibrils shows the in-register parallel "cross-" sheet with amide stacking along the bibrial axis similar to our observation from simulations. Bioinformatics analysis of parallel-helix, a putative structural motif of amyloids, also shows the significant amino acide stacking (7). Knowledge of the energy landscape of oligomerizaton and the structure of amyloids my provide hints for rational drug design preventing amyloid associated diseases.

References:

1. Hardy, J. & Selkoe, D. J. (2002) Science 297, 353-356.

2. Tsai, H.-H., Reches, M., Tsai, C.-J., Gunasekaran, K., Gazit, E. & Nussinov, R. (2005) PNAS 102, 8174-8179.

3. Reches, M., Porat, Y. & Gazit, E. (2002) Journal of Biological Chemistry 277, 35475-35480.

4. Tsai, H.-H., Zanury, D., Haspel, H. , Gunasekaran, K., Ma, B., Tsai, C. J. & Nussinov, R. (2004) Biophysical Journal 87,

     146-158.

5. Jenkins, J. & Pickersgill, R. (2001) Progress in Biophysics & Molecular Biology 77, 111-175.

6. Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005) Nature 435, 773-

    778.

7. Tsai, H.-H., Gunasekaran, K. & Nussinov, R. (2005) unpublished results.

Dr. Zhanchun Tu

Department of Physics, Tamkang University, TAIWAN

tzc@staff.tku.edu.tw

The crucial condition in the derivation of the Jarzynski equality (JE) from the fluctuation theorem is that the integral of the phase space contraction factor respect to time is exactly expressed as the entropy production resulting from the heat absorbed by the thermal system from the heat bath. This condition may not always hold because the phase space contraction factor depends on the microscopic dynamics the system. Hence a more general form of JE may exist.