Date :

 29-30 April 2011

Place :

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

 30 April: P101 meeting room 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 :

Porf. Sasun G. Gevorkian
Yerevan Physics Institute, Armenia

E-mail: sgevork@yerphi.am

Glassy state of native collagen fibril ?

  Our micromechanical experiments show that viscoelastic features of type I collagen fibril at physiological temperatures display essential dependence on the frequency and speed of heating. For temperatures 20-30^oC the internal friction has a sharp maximum for a frequency less than 2 kHz. Upon heating the internal friction displays a peak at a temperature T_soft(v) that essentially depends on the speed of heating v: T_soft near  70^o C for v = 1 ^oC/min, and T_soft near 25oC for v = 0,1 ^oC/min. At the same temperature T_soft(v) the Young's modulus passes through minimum. All these effects are specific for the native state of the fibril and disappear after heat-denaturation. Taken together with the known facts that the fibril is axially ordered as quasicrystal, but disordered laterally, we interpret our findings as indications of a glassy state,  where T_soft is the softening transition.

Dr. Shura Hayryan
Institute of Physics of Academia Sinica, Taipei, Taiwan

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

Wang-Landau simulation of RNA-like model on 3D lattices

  A three dimensional lattice model is suggested for Monte Carlo simulation of RNA folding. The proposed model takes into account slow change of the pattern of hydrogen bonds in comparison with nucleotides movement. Dependences of structural and thermodynamic quantities like end-to-end distance of the chain and the specific heat on temperature are calculated.

Prof. Sudhir Jain
School of Engineering and Applied Science ,Aston University, England

E-mail: s.jain@aston.ac.uk

Persistence and Financial Markets

  The persistence phenomenon in a financial context is explored by using a novel mapping of the time evolution of the values of shares in a portfolio onto Ising spins. The method is applied to historical data from the London Financial Times Stock Exchange 100 and the Japanese Nikkei 225 indices over arbitrarily chosen periods. We study the persistence behaviour in these markets by monitoring the “first passage crossing time”. We find clear evidence of a double-power law decay of the persistence. The long-time persistence exponent is estimated to be ~ 0.5. The persistence of sequences of consecutive positive/negative daily log returns is also discussed.

  In the second part of the seminar, we discuss the persistence phenomenon in a “toy” socio-econo dynamics model which appears to capture some of the essential features of real systems. Computer simulations on hypercubic lattices in dimensions up to 5 are performed at a finite temperature. The model includes a local “social” field which contains the magnetization at time t. We find no evidence of “blocking” in this model.

Dr. Peter Kopcansky

Slovak Academy of Sciences, Slovak Republic

E-mail: kopcan@saske.sk

The  Induced Structural Changes in Liquid Crystals Doped by Magnetic Nanoparticles

Liquid crystals (LCs) are very sensitive to an application of external electric field due to their large dielectric anisotropy of order e_a ~1.  On the other hand the change of properties of LCs with application of an external magnetic field is very limited due to their very small magnetic anisotropy c_a ~10^-7. One of the possibilities how to increase their sensitivity to magnetic field is to add the magnetic nanoparticles (MNPs) into the liquid crystal [1]. In this work was predicted new class of composite materials so called ferronematics (FN). The main assumption of this theoretical work was the rigid anchoring between liquid crystal molecules (LCM) and magnetic particles and the initial orientation between director of LCM and magnetic moment of MNP is parallel. However in real FNs the situation is more complicated since the initial orientation between director of LCM and magnetic moment of MNPs can be parallel (I- type of anchoring) or perpendicular (II- type of anchoring) [2]. The behavior of FNs in magnetic field depends significantly on type of anchoring i.e. in the I-type  the sensitivity of LCs is increasing while in II-type  is decreasing, respectively. Burylov and Raikher [2] introduced the parameter of theory w = Wd/K too (ratio the anchoring and elastic properties) where W is the anchoring energy, d is typical size of MNP and K is corresponding elastic constant.

In this lecture structural changes in FNs based on LCs such as  8CB, 6CHBT and MBBA doped with various MNPs i.e. nearly spherical, rod-like and chain-like will be  presented. The obtained results have shown that sensitivity of 8CB based FNs doped by nearly spherical MNPs was decreased in comparison with pure LC while in MBBA and 6CHBT based FNs the sensitivity was increased. The shape of MNPs significantly increases the sensitivity of magnetic Fredericksz transition.  For all studied systems the anchoring energies as well as parameters w were estimated from experimental data. All results were discussed in frame of Burylov-Raikher theory [3]. The  effect of induction of isotropic nematic transition in ferronematics in the presence of external magnetic field will be presented also  and discussed in frame of  Landau de Gennes theory and  simple thermodynamical model .

This work was supported within the projects No. 26220120033, in frame of Structural Funds of European Union, Centre of Excellence of SAS NANOFLUID, APVV 0509-07 and VEGA 0077.

References:

[1] F. Brochard, P. G. de Gennes., J. Phys. (Paris) 31,691(1970).

[2] S.V. Burylov, Y.L. Raikher, Phys. Lett. A. 149, 279 (1990).

[3] P. Kopcansky et.al., Phys Rev E 78, 011702 (2008).

Dr. Tibor Kozar
Slovak Academy of Sciences, Slovak Republic

E-mail: tibor@suske.sk

Clusters, Grids and Molecules: HTC and HPC Computing

  High-performance parallel computing (HPC) is a prerequisite for efficient molecular modeling of large systems such as solvated biological macromolecules. Considering discrete solvation models, the number of atoms in a simulation increases considerably. For realistic molecular modeling the simulation should be long enough to monitor conformational transitions appearing under real experimental conditions. Accordingly, the time scale of the simulation (in nanoseconds) is an additional factor, requiring powerful computational resources. There are two options to speed up the simulations: development and use of new methodologies (e.g. coarse-grained or mesoscopic simulations) or utilize new hardware and software technologies such as GPU (Graphics Processing Unit) CUDA (Compute Unified Device Architecture) computing. High-throughput computing (HTC), one the other hand, is more typical for inhibitor design. Screening hundreds of thousands of small molecules against a well-defined protein target is a common task for inhibitor design. The routinely used docking methods have empirical background and run fast on recent computers. The docking results can be significantly improved by utilization of more robust quantum chemical protocols in order to gain a more precise atomic charge set. The QPLD method developed at Schrodinger LLC thus reflects changes in protein charge distribution initiated by ligand binding into the proteinâs active site. Our presentation is focusing on discussion of some of these high-performance modeling tools together with the discussion of the HTC methods available for docking.

Dr. Karen Petrosyan

Institute of Physics of Academia Sinica, Taipei, Taiwan

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

Oscillations in probability distribution for biochemical reactions involving small number of molecule

  We consider biochemical reactions that involve small number of interacting molecules. In order to analytically treat the case we apply the Poisson representation approach to the models described by the master equation. The method allows for derivation of stochastic differential equations with exact diffusion matrices without the system size expansion approximation. Using the Poisson representation technique we derived the equations and then via linearization around steady states obtained spectra for temporal and spatiotemporal fluctuations. In addition to that, we derived stationary probability distribution function for the number of molecules. A remarkable result is the existence of oscillations in the molecular distribution for biochemical reactions involving small number of molecules. 
　

Porf. David B. Saakian
Yerevan Physics Institute, Armenia

 E-mail: saakian@jerewan1.yerphi.am