Date :

 09 July 2012

Place :

 The first meeting room on 5th 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)

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

Speakers :

Mr. Hsin-Lin Chiang

Department of Physics, National Tsing Hua University, Hsinchu, Taiwan

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

All-atom molecular dynamics simulations indicate that polyglutamine dimer prefer anti-parallel conformations

  Polyglutamine peptides form protofibrils composed by β-sheets. The aggregation of these protofibrils causes amyloidosis. It was not yet clear how polyglutamine chains aggregate and form β-sheets. For probing polyglutamine conformation in the β-sheets, we performed all-atom molecular dynamics simulations on pairs of the polyglutamine fragments in explicit water which consist of 10 repeated glutamine residues from parallel, perpendicular, and anti-parallel initial conditions. Our results shows that the simulation formed anti-parallel β-sheets and the number of β-bridges increased gradually. It indicates that polyglutamine dimer prefer anti-parallel β-sheet conformation than parallel conformation. This agrees well with previous researches by experiments and a coarse-grained molecular dynamics simulation. A free-energy barrier was also found at the structures with no β-bridge, which makes the transformation between parallel and anti-parallel β-sheets difficult.

Dr. Shura Hayryan

Institute of Physics, Academia Sinica, Taipei, Taiwan

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

Folding microRNAs from Stretched Conformation

  We obtained the 3D structures of 2 microRNA sequences (pdb codes 2jxv and 2kpv) by performing replica-exchange molecular dynamics simulations using iFoldRNA software. We define the native structure as a structure of the minimum free energy obtained throughout the simulation. The root mean square distance (RMSD) between the simulated and the experimentally found structures is about 2.8A. Our calculations show that such similarity is of high statistical significance. We conclude that the iFoldRNA package is a reliable tool for calculation of microRNA structures from scratch.

Prof. Yao-Chen Hung

Department of Electronic Engineering, National Formosa University, Yunlin, Taiwan

E-mail: ychung@nfu.edu.tw

Modeling Intrinsic Noise in Disorder Cellular Automata

  Noise has crucial effects on biological dynamics, chemical reactions, and various chaotic systems. Here we explore the statistical properties of the noise in a special-temporal system, the disorder cellular automata, where the stochasticity may cause significant deviations from deterministic descriptions. Such noise is intrinsic and due to the discreteness of the dynamics in finite populations. Applying the methods from statistical physics and nonlinear dynamics, we illustrate the dynamical characteristics of the inherent noise. Finally, a modified mean-field model is proposed to mimic the stochastic dynamics revealed by the discrete system.

Prof. Wen-Jong Ma

Graduate Institute of Applied Physics, National Chengchi University, Taipei, Taiwan

E-mail: mwj@nccu.edu.tw

Role of Backbone Connectivity on the Collective Aggregation Processes in Model Polymer Systems

Dr. Karen Petrosyan

Institute of Physics, Academia Sinica, Taipei, Taiwan

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

Entropy, information and fluctuation relations for complex biophysical systems

  We extend a non-equilibrium statistical physics framework for description of nonlinear stochastic processes that describe complex biophysical systems. Specifically, we consider biological processes that can be modelled via master equation approach. Using the Poisson representation technique we map the master equation to the equivalent set of stochastic differential equations with exactly derived diffusion matrices. Then using the large-deviation principle we obtain corresponding stochastic actions for probability distribution functions. This provides with the statistical physics description of the underlying processes and allows us to apply methods developed in the field. In particular, Jarzynski and Sagawa-Ueda equalities are derived for arbitrary nonlinear non-equilibrium stochastic processes taking place in a variety of biological systems ranging from systems biology and molecular evolution to ecology.

Mr. Kuo-Ting Tsai

Department of Physics, National Kaohsiung Normal University, Kaohsiung, Taiwan

E-mail: kuoting.tsai@gmail.com

The overnight effect on Taiwan stock market

  This study examines statistical regularities among three components of stocks and indices: daytime (trading hour) return, overnight (off-hour session) re-turn, and total (close-to-close) return. Owing to that the Taiwan Stock Ex-change (TWSE) has the longest non-trading periods among major markets. TWSE is selected to explore the correlation among the three components and compare it with major markets such as the New York Stock Exchange (NYSE) and the National Association of Securities Dealer Automated Quotation (NASDAQ). Analysis results indicate a negative cross correlation between the sign of daytime return and the sign of overnight return possibly explain why most stocks feature a negative cross correlation between daytime return and overnight return [F. Wang et al., Phys. Rev. E 79, 056109 (2009)]. Additionally, the cross correlation between the magnitude of returns is analyzed. According to those results, a larger magnitude of overnight return implies a higher probability that the sign of the following daytime return is opposite of the sign of overnight return. Namely, the predictability of daytime return might be improved when a stock undergoes a large magnitude of overnight return. Furthermore, the cross correlations of 29 indices of worldwide markets are discussed.

Mr. Xinye Wu

Department of Physics of Beijing Normal University, Beijing, China

E-mail: wuxinye@mail.bnu.edu.cn

A preliminary work on the Foreign Exchange: networks and minimum spanning tree

  Foreign Exchange (FX) Market is the largest financial market in the world for a $4 trillion daily average turnover (Bank for International Settlements, BIS,2010),almost 10 times that of the global stock market. Like the stock market, there should be some structures or patterns in the FX market. Based on a group of exchange rates, our work is to study the FX market by the following methods: correlation coefficient, minimum spanning tree, and complex networks.
　

Prof. Jian-Min Yuan

Department of Physics, Drexel University, Philadelphia, USA

E-mail: yuanjm@drexel.edu

1. Statistical Mechanical and Kinetic Studies of Protein Aggregation

  Motivated by neurodegenerative diseases and bio-macromolecules as new materials, we studied various systems of protein aggregations using effective Hamiltonian, partition functions, transfer matrices as well as kinetic methods. Numerical results obtained are compared to experimental results.

2. Depletion Forces on Proteins and Signaling Pathways

  Proteins function inside cells which are usually crowded with other proteins, DNA, lipids, etc. This crowdedness change the properties of proteins in fundamental ways. We will discuss basic ideas behind these macromolecular crowding effects. We will also discuss systems biology approaches to signaling pathways related to cancer and diabetes. We try to unearth drug-targets and underlying design principles of pathways using sensitivity analysis and non-equilibrium thermodynamics.