Date :

  15-16 April, 2013

Place :

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

 16  April :P101 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)

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

Speakers :

Dr. Sasun G. Gevorgyan

Yerevan Physics Institute, Yerevan, Armenia

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

Hierarchical structure of biological materials: from the creation of a new method to new results

  Many biological materials are hierarchically structured. They are designed from the nano- to the macro-scale in a sometimes self-similar way. Interestingly, there are hardly any investigations that systematically interconnect mechanical properties of different length scales. Investigations of mechanical properties are most often focused on either nano-indentation or bulk mechanical testing characterizing properties at the smallest or largest size scale. The principle of mechanical (and micro-mechanical) methods of experimentation is quite simple: the sample undergoes deformation by an external force and recovers it initial form due to elastic forces. The rate of recovery and the degree of deformation define the viscous-elastic properties of sample’s material. By tweaking the degree and frequency of external force we can perform acoustic spectroscopy. The main principle of acoustic spectroscopy is measuring the stress-deformation function for different frequencies and different values of deforming force. The constant and smooth monitoring of the external force becomes more difficult from macro to micro scale of the experiment. The problems, depending on the scale of the experiment, are the precise measuring of the external force and its alteration and possibility of controlling it. This becomes obvious during the examination of biopolymers in solid state. In this case the instability of a sample itself verges on the value of the external force. And frailness of the samples makes the requirements for the external force and for methods of sample preparation even more fundamental. The main goal of our work is to develop a method that allows researching mechanical properties of solid state biopolymers while the samples are less than 1 µm in diameter and about 100 µm in length. In our method light pressure is used to deviate a sample from the equilibrium position, and the force of gravity is overcome by the elasticity of the sample. With this method we investigated visco-elastic properties of DNA fibers less than 1µm in diametr. This scale corresponds to "DNA - organelle - chromosome" hierarchy, where molecules are assembled into chromatin. The results demonstrate the presence of a stable structural form between B- and A- forms of DNA.

Prof. Chin-Kun Hu

Institute of Physics, Academia Sinica, Taipei, Taiwan

 E-amil: huck@phys.sinica.edu.tw

Slow dynamics in lattice models, polymer chains, and proteins

  How a biological system can maintain in a non-equilibrium state for a very long time and why proteins aggregate are still not well understood. In this talk, we first review critical slow down of the Ising model [1] and slow relaxation of a spin-glass model at low temperatures [2]. The data indicate that relaxation of the spin glass model at low temperatures can be slower than the critical slowing down of the Ising model [3]. We then review recent molecular dynamics results for the slow relaxation of polymer chains [4] and experimental data for the glassy behavior of proteins, including collagen fibrils [5] and hemoglobin [6]. The slow dynamics in polymer chains and proteins can provide clues for understanding why a biological system can maintain in a non-equilibrium state for a very long time, and how to slow down protein aggregation related to neurodegenerative diseases [3].

References: 

[1] F. G. Wang and C.-K. Hu, Phys. Rev. E 56, 2310 (1997). 

[2] C. Dasgupta, S. K. Ma, and C.-K. Hu, Phys. Rev. B 20, 3837 (1979).

[3] C.-K. Hu, AIP Conf. Proc. 1518, 541 (2013). (2010).

[4] W.-J. Ma and C.-K. Hu, J. Phys. Soc. Japan 79, 024005, 024006, 054001, 104002 (2010).

[5] S. G. Gevorkian, A. E. Allahverdyan, D. S. Gevorgyan and C.-K. Hu, EPL 95, 23001 (2011).

[6] S. G. Gevorkian, A. E. Allahverdyan, D. S. Gevorgyan and C.-K. Hu, preprint.

Dr. Ban-Chiech Huang

Institute of Physics, National Chiao-Tung University, Taiwan

E-mail: bjhuang0802@gmail.com

The multifractalfinite-size scaling of thelocalization-delocalization transition of the instantaneous normalmodes in fluids

  While localization-delocalization transition (LDT) widely exists in general wave systems, our knowledge on its precise location and critical behavior is restricted to rather limited number of systems. Here we present these properties on the vibrations of liquid in terms of the instantaneous normal mode (INM) analysis. It has helped clarifying liquid dynamics extracted from Infrared or vibrational Raman spectra. The INMs are shown to exhibit multifractal fluctuations while approaching the LDT. Combining the multifractality and finite size scaling, we can precisely determine the critical frequency and correlation length exponent ν.

  Simulations of up to 18000 water molecules on the fSPC/E water model provide nearly 106 instantaneous normal modes. In the imaginary frequency branch, the critical frequency is quantified by the multifractal finite-size scaling method to be I_m-ω = −130.9±0.6 cm^-1. This ν = 1.62±0.14 is close to those of the Anderson model, the truncated Lennard-Jones system, and the disordered lattice, indicating that they belong to the same universality class. The fractal spectrum f(α) and the maximum position, <α_m> = 4.00 ± 0.02, of the local vibrational distribution of the critical modes of fSPC/E coincide with those of other three systems, showing another universal feature among systems.

Mr. Yu-Feng Huang

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

E-mail: 100755001@nccu.edu.tw

Time scale dependence of stock-stock correlations : an analysis of cross correlation matrices

Prof. Nobuyasu Ito

Department of Applied Physics, School of Engineering, the University of Tokyo, Japan

E-mail: ito@ap.t.u-tokyo.ac.jp

 Society-in-silico with exascale computer

  Speed of computer reached 10PFLOPS, and this performance is connecting microscopic dynamics with macroscopic phenomena. And the next challenge will be an exascale computer around the year 2020.

  What is a main target of exascale machines? I am expecting that it will be a simulation of our global society. Socity is a complex system which comprises various subsystems like economic, traffic, environmental, and political systems. Such "society-in-silico" simulation will contribute security and safety of our future.

Prof. Henri Orland

Institut de Physique Th´eorique, CEA, France

E-mail: henri.orland@cea.fr

1. Prediction of RNA structures with pseudoknots

  After reviewing some elementary properties of RNA, we discuss how statistical mechanics can be used to determine the secondary structure of RNA. First, one has to parametrize as precisely as possible the free energy of secondary structures. Given such a parametrization, we review some methods used to predict secondary structures without pseudoknots. To include pseudoknots, we propose a classification of RNA structures in terms of their topological genii. This topological classification stems from a matrix field- theory representation of the RNA folding problem. The free energy is parametrized so as to include a penalty proportional to the genus of the RNA structure. We show how this can be used to efficiently predict RNA structures with pseudoknots.

2. Transition Paths in Protein Folding

  Protein folding can be described in terms of Langevin dynamics. This dynamics can in turn be represented by a path integral (analogous to a Feynmann path integral in quantum mechanics), which is a weighted sum over all paths joining the denatured state to the native state of the protein.We first show how one can compute the dominant paths (paths with largest weight) and how one can calculate dynamical quantities (such as rates or transition path times) from these paths. The method and its limitations are illustrated on some simple examples. Then, we show how the Langevin dynamics can be modified to obtain a stochastic equation which samples directly and efficiently the transition paths. This new method is illustrated on a simple example.

Dr. David B. Saakian

Yerevan Physics Institute, Yerevan, Armenia

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

Some exact results for the multifractals

  We investigate the probability distribution function for the hierarchic tree model with quenched disorder and continuous branching, one of simplest cases of the multifractals. The PDF is the solution of special PDE. For two specific case of the noise on hierarchic tree, this equation is becoming Peinleve equation. These two special cases corresponds to the Kolmogorov-62 and Yakhot-98 models of turbulence.

Prof. Shinji Saito

Institute for Molecular Science, Japan

E-mail: shinji@ims.ac.jp

Molecular origin of anomalous temperature dependence of isobaric heat capacity of supercooled water

  Molecular origin of the well-known specific heat anomaly in supercooled liquid water is investigated by using molecular dynamics simulations and theoretical analyses. A sharp increase in the isobaric specific heat with lowering temperature and the weak temperature dependence of isochoric specific heat in the same range are reproduced in simulations.  We calculate the spatio-temporal correlation among temperature fluctuations and examine the frequency dependent specific heat. We find the emergence of the temporally slow and spatially long ranged large temperature fluctuations at low temperatures. The emergence of the correlated region is more significant under constant pressure condition than constant volume condition. Temperature dependence of the relaxation time of the correlation function can be fitted to Vogel-Fulcher-Tamermann expression which provides a quantitative measure of the fragility of the liquid. We find that the rapid growth in the relaxation time of TFCF with lowering temperature undergoes a sharp crossover from a markedly fragile state to a weakly fragile state around 220 K.

Prof. Kei Tokita

Department of Complex Systems Science, Graduate School of Information Science, Nagoya University, Japan

E-mail: kei.tokita@gmail.com

A neutral fitness model in ecology

  Hubbell's neutral model of biodiversity has been criticized for its neutrality assumption that all individuals of different species have a same birth, death and dispersal rate. It is, however, one of the few models of population dynamics which predicts realistic species abundance distributions (SADs) observed in nature. From a theoretical point of view one of the fundamental questions is why such unrealistic neutral assumption provides a good approximation although species in any community are apparently not neutral. In my talk, after a brief review of recent theoretical studies on neutral models, it is demonstrated that the "neutral fitness model" with different values of species' parameters but same fitness still predicts the same SADs as the fully neutral model. It is moreover shown that the neutral fitness model predicts a special correlation between dispersion length and species rank, which is also observed in nature but is never reproduced by the fully neutral model in principle. High efficiency of GPGPU simulations of 2D lattice neutral model is also reported.

Prof. Fa-Yueh Wu

Department of Physics, Northeastern University, USA

E-mail: fywu@neu.edu

Potts models on kagome-type lattices

  The kagome lattice structure first studied by Syozi has been prominent in recent advances in statistical mechanics and high-temperature superconductivity. We present evidence that the kagome design has been known in China for thousands of years tracing back to Zhu Ge Wu Hou (諸葛武侯) 2,250 years ago. We discuss the homogeneity hypothesis associated with the kagome-type lattice Potts model introduced by Wu in 1979, and apply the hypothesis to various kagome-type Potts lattices.  The results are compared with numerical findings from highly accurate finite-size determinations and are shown to be extremely accurate. It was in 2012 that Jacobsen and Scullard finally settled the question whether the hypothesis is actually exact. Using a 1980 graphical analysis of the Potts model due to Wu and Lin, they showed that the homogeneity hypothesis is, after all, the first-order approximate in a sequence of well-defined approximations. Their results are presented.