Date :

 25-26,29 November 2010

Place :

 25 November: P101 meeting room on 1st floor, Institute of Physics, Academia Sinica, Taipei

 26,29 November: The auditorium 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. Chi Keung Chan

Institute of Physics, Academia Sinica, TAIWAN

E-mail:ckchan@gate.sinica.edu.tw

Dr. Chien-Hsiun Chen

Institute of Biomedical Sciences, Academia Sinica, TAIWAN

E-mail: chchen@ibms.sinica.edu.tw

Mapping Human Genetic Diversity in Asia

  Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Porf. Arthur Chiou

Institute of Biophotonics, Biophotonics Interdisciplinary Research Center, National Yang-Ming University, Taiwan

E-mail:aechiou@ym.edu.tw

Optical Tweezers Based Bio-Micro-Rheology

  Bio-Micro-Rheology (BMR) refers to the study of the viscoelastic properties of biological samples, such as bio-fluids, cells, nucleic acids and proteins, at the micron or sub-micron scale. Viscoelastic properties of a myriad of biological cells and bio-fluids are strongly correlated to their physiological functions; a change in their viscoelastic properties, even at a very small fraction on the order of a few percents, is often concomitant with related diseases. A classical example is the red blood cells (RBCs) whose deformability is critical to their oxgen-carrying and delivery function through veins and arteries. In the case of biological fluids, the viscosity of blood is closely related to cerebral vascular disease and coronary artery disease, and the liquefaction of vitreous humor can lead to retinal detachment. The relation of viscoelastic alterations of cerebral-spinal fluid and hydrocephalus has also been reported. Accurate measurement of the viscoelastic properties of biological samples at either single cell resolution (for the case of biological cells) or with sample volume on the order of micro-liter (for the case of biological fluids) may hence shed light on clinically-relevant mechano-biology at the molecular level. From the practical point of view, the requirement of only a very small amount of sample is particularly important since many biological fluids such as synovial fluid and vitreous humor are available only in very limited amount.

  Optical-Tweezers Based Micro-Rheology has emerged in recent years as one of the critical techniques capable of fulfilling the needs elucidated above. In this talk I will introduce 4 complementary approaches for bio-microrheology, namely (1) dynamic light scattering (or diffuse wave spectroscopy); (2) blinking optical tweezers based single-particle tracking; (3) oscillatory optical tweezers based biomicrorheology; (4) jumping optical tweezers based biomicrorheology. Applications of these techniques to a wide range of samples including individual human red blood cells; macrophage cells, DNA, synovial fluid, and polymer solutions such as polysodium styrene sulfonate (NaPSS), sodium hyaluronate (NaHA) and hyaluronic acids will be highlighted in this talk.

Porf. Chia-Fu Chou

Institute of Physics, Academia Sinica, TAIWAN

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

Dr. Yao-Chen Hung

Department of Physics, National Chung Cheng University, Taiwan

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

Noise, a Potential Controller in Biochemical Reaction Systems

  Noise in biochemical reaction systems nowadays has been recognized as an important factor in cellular developments and functions. Here we study its effects on a simple system, the SchlÖgl model, based on a stochastic differential equation. The phenomena of noise-induced bifurcation are observed both numerically and analytically.  Detailed analysis demonstrates that the region revealing bistability can be modulated under the manipulation of noise intensity.  The results suggest that an external noise source can be potentially served as an engineered controller in biochemical pathways.

Prof. Satoru G. Itoh

Research Center for Computational Science, Institute for Molecular Science, Okazaki, JAPAN

E-mail: itoh@ims.ac.jp

Dimerization of Amyloid Beta-Peptides Studied by the Multicanonical-Multioverlap Algorithm
  Amyloid β-peptide (Aβ) is comprised of 39 to 43 amino-acid residues and has tendency to form amyloid fibrils, which are associated with Alzheimer's disease. In these amyloid fibrils, Aβ has an intermolecular beta-sheet structure. Furthermore, Aβ(29-42) peptides, which are comprised of the residues 29-42 of Aβ, have intermolecular beta-sheet structures in aqueous solution by themselves.
  The multicanonical-multioverlap algorithm has advantages of both of the multicanonical algorithm and the multioverlap algorithm. Namely, the multicanonical-multioverlap simulations can sample effectively the conformational space including specific configurations. Applying this method to protein systems, therefore, we can obtain effectively the accurate free-energy landscapes of these systems including specific configurations.
  I will show the results of applying the multicanonical-multioverlap algorithm to Abeta(29-42) dimer with implicit water in my talk.
　

Dr. Tomoaki NOGAWA

Department of Applied Physics, the University of Tokyo, JAPAN

E-mail: nogawa@serow.t.u-tokyo.ac.jp

Numerical Study of the Metastable Structure in the Free Energy Landscape of the Three Dimensional Ising Model

  We investigate the density of states and the equilibrium free energy of the Ising model on cubic lattice by extensive parallel Monte-Carlo simulations using the flat histogram method. When the free energy is plotted as a function of macroscopic quantity, such as internal energy and magnetization, a local minimum state is observed for certain range of temperature in addition to the global minimum, which corresponds to the equilibrium state. The width of the hysteresis region, however, becomes narrower to disappear as the system size increases, which imply that there is no metastable state in the thermodynamic limit within the framework of equilibrium statistics.

Prof. Koryun Oganesyan

Yerevan Physics Institute, Yerevan, Armenia

E-mail:koryunoganesyan@yahoo.com

Threshold Characteristics of Free Electron Lasers Without Inversion

  The interaction between noncolinear laser and relativistic electron beams in static magnetic un-dulator has been studied within the framework of dispersion equations. In the limit of small signal gain the spatial growth rates are found for the collective (Raman) and single-electron (Thompson) regimes. For a free-electron laser without inversion (FELWI), estimates of the threshold laser power are found. The large-amplification regime should be used to bring an FELWI above the threshold laser power.

Prof. Hisashi Okumura

Research Center for Computational Science, Institute for Molecular Science, Okazaki, JAPAN

E-mail:hokumura@ims.ac.jp

New Generalized-Ensemble Algorithms for Alanine Dipeptide and Polyalanine Simulations

  Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics (MD) and Monte Carlo (MC) simulations in physical ensembles, such as the canonical and isobaric-isothermal ensemble, tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is generalized-ensemble algorithms such as the multicanonical algorithm.
  However, because the multicanonical simulation is performed in a fixed volume, neither the pressure dependence nor temperature dependence at certain pressure can be investigated as in experiments. To overcome this difficulty, the author recently proposed multibaric-multithermal MC[1-3] and MD[4-6] algorithms. In this ensemble, two-dimensional random walks in the potential-energy space and in the volume space are realized. I applied the multibaric-multithermal MD algorithm to an alanine dipeptide and ployalanine in explicit water[6,7].

References:

[1] H. Okumura and Y. Okamoto: Chem. Phys. Lett. 383, 391(2004).
[2] H. Okumura and Y. Okamoto: Phys. Rev. E 70, 026702 (2004)  (14pages).
[3] H. Okumura and Y. Okamoto: J. Phys. Soc. Jpn. 73, 3304 (2004).
[4] H. Okumura and Y. Okamoto: Chem. Phys. Lett. 391, 248 (2004).
[5] H. Okumura and Y. Okamoto: J. Comput. Chem. 27, 379 (2006).
[6] H. Okumura and Y. Okamoto: Bull. Chem. Soc. Jpn. 80, 1114 (2007).
[7] H. Okumura and Y. Okamoto: J. Phys. Chem. B 112, 12038 (2008).

Dr. Karen Petrosyan

Institute of Physics, Academia Sinica, TAIWAN

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

Transition to Coherence in a Network of Phase Oscillators
  We consider a system of phase oscillators which are connected in a network with fluctuating links. The network has the plasticity property such as it favors connection of oscillators with close values of phases. We investigate the equilibrium properties of the system and reveal a phenomenon of stepwise transition to high degrees of coherence as the system goes through a series of second-order phase transitions for the order parameters.

Prof. Davit Sahakyan

Yerevan Physics Institute, Yerevan, Armenia

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

Hamilton-Jacobi Equation Method for the Investigation of the Master Equation in Evolution and Chemistry

Prof. Sujit Sarkar

PoornaPrajna Institute of Scientific Research, India

E-mail:sujit_mpi@yahoo.co.uk

Non-Universal Tunneling Resistance at the Quantum Critical Point of Mesoscopic SQUIDs Array

Prof. Zbigniew Struzik

Graduate School of Education, The University of Tokyo, JAPAN

E-mail: zbigniew.struzik(at)gmail.com

Is Our Life Complex?

  To anyone facing the challenges of everyday life, this question may appear to be out of touch. However, for the scientist, a second thought raises the essential questions: what exactly is 'complex' and what characterize 'life'? An exhaustive answer to these is still beyond the current capability of science, as is the very question raised in the talks' title, that of life's complexity. Far from attempting to be complete, I will review some areas of 'life' through the paradigm of human and animal behavioral and neural dynamics, and in particular, through domains such as human activity, conscious decision-making and creativity, generally assumed to be highly unpredictable and complex. Such areas, hitherto considered to be inherently intractable for the exact sciences, have recently been becoming more accessible to rigorous methodology. In contrast to the widely assumed belief of inherent randomness, a surprising, dominant pattern of consistent burstiness, intermittency and strongly non-Gaussian behavior emerges within these domains. Perhaps counter-intuitively, such dynamics does not necessarily correspond with a high degree of unpredictability or originality. But is it still 'complex'?

Dr. Fumiko TAKAGI

Department of Applied Physics, the University of Tokyo, JAPAN

E-mail: takagi@serow.t.u-tokyo.ac.jp

Toward the Simulation of Virus Capsid Formation

  Virus is, roughly speaking, constituted of genome and protein shells (called "capsid"). They are replicated and synthesized in infected cells, and reassemble into the virus particle in the intracellular crowded condition. We are interested in this virus capsid assembly in the cell. To understand the kinetics and the statistical mechanics of the capsid assembly, we are now constructing a coarse-grained capsomer model for molecular dynamics simulation in which 5- and 6-fold protein multimers are represented as pentagonal or hexagonal molecules. There is no concrete result yet, so I'll show you some prototype simulations.

Dr. Chia-Hei Yang

Institute of Physics, Academia Sinica, TAIWAN

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

Temporal Dynamics of Site Percolation in Nanoparticle Assemblies

  Dynamics of the formation of self-assembled sub-monolayer networks of colloidal nanoparticles is studied in the two-dimensional lattice gas model by Monte Carlo simulation. The site-percolation threshold (p_c) is studied for various temperatures and chemical potentials. Our numerical results show that p_c is greatly reduced due to the evaporation-driving self-organization. The results are qualitatively consistent with our experimental observation.