Date :

 25, 28 September 2009

Place :

 25 September: Room 312, Department of Physics, National Taiwan University, Taipei

 28 September: 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 :

Dr. Paul Wei-Che Hsu

Institute of Molecular Biology, Academia Sinica, TAIWAN

E-mail: paul@imb.sinica.edu.tw

Discovering MicroRNA's Role in Cancer

    MicroRNAs (miRNAs) are small non-coding RNA molecules of ~22 nt sequences that have an important role in the translational inhibition and degradation of mRNA to downregulate gene expression. Recent work supports miRNAs downregulate gene expression during various crucial cell processes such as apoptosis, differentiation and development. Those studies have suggested that oncogenesis may be link with aberrant expression of miRNAs, but in most case it is still not clear what mechanism of miRNA leads to cancer formation. In our study, more than 200 miRNAs which are aberrantly expressed in tumor cells have been analyzed, and the tissue specificity has been tested by the miRNA expression among normal tissues. We are investigating the transcription factor binding sites (TFBS) in miRNA promoter and identified miRNA targets which are tumour suppressors or oncogenes. Those analyses are integrated for miRNA regulatory network construction in certain cancers, and we hope our achievements can support cancer research and clinical trial.

Dr. Dmitry Nikolaevich Klochkov

A.M. Prokhorov General Physics Institute RAS, Moscow, RUSSIA

E-mail: klochkoff@tula.net

Raman and Thompson Regimes of Amplification in A Wiggler with Noncollinear Laser and Electron Beams

    The collective and single-electron amplification regimes of a non-collinear free electron laser (FEL) are studied within the framework of dispersion equations. In the limit of small-signal gain the growth rates and the conditions for self-amplified excitations are found for the collective (Raman) and single-electron (Thompson) regimes. Raman regime is shown to be preferable for the coherent spontaneous second harmonic generation by ultra-relativistic electron beams. Raman excitations in a non-collinear FEL, e.g., in an FEL without inversion, are favored by the non-collinear geometry of the electron and the laser beams, and by the relativity of the beam electrons.

Induced Smith-Purcell Radiation: Free Electron Laser in Open System

    Generation of induced Smith-Purcell (SP) radiation by relativistic electron beam in the absence of the resonator is considered within frame work of dispersion equation. We have found that zero-order approximation for the solution of dispersion equation corresponds to the mirror boundary case, when the electron beam propagates above plane metal surface (mirror). The ``mirror'' boundary condition gives discrete spectrum, modes of which contain two coupled frequencies: ``high'' frequency with ω=ω_n+Ω_bn and ``low'' frequency with ω=ω_n-Ω_bn, where ω_n=nиu/1-βcosθ, Ω_bn=ω_nγ₀^-2(Δ_bω_n(1-e^{-2(ωnb)/(uγ0)})/2u)^1/2. 

Here β=u/c, u is a velocity of electrons, θ is an angle between wave vector of radiation and direction of beam propagation.
    The growth rates for both The Thompson (single-particle approximation) and The Raman (collective regime) types of waves excitation are proportional to the Langmuir frequency ω_b or square root of the beam current I_b^1/2. The conditions of excitations for both The Thompson and The Raman types do not depend on the Langmuir beam frequency (or the beam current), but depend on the beam height b above the grating. It is essential distinction between the Cherenkov and The SP instabilities for the generation problem.

Miss Chung-Fan Lee

Institute of Molecular Medicine, National Taiwan University, TAIWAN

E-mail: kettylee113@gmail.com

Prof. Chai-Yu Lin
Physics Department, National Chung Cheng University, TAIWAN
E-mail: lincy@phys.sinica.edu.tw

Scalings and Renormalization-Group studies of the Manna Model

    1. The dissipation mechanism of a Manna model with open boundary condition is responsible for the boundary dissipation. We investigate a modified Manna model with both the boundary and bulk dissipations. We find that the bulk dissipation dominates the scaling behaviors but the total dissipation or the boundary dissipation do not.
    2. A renormalization group (RG) scheme for the q-state Manna model is proposed, based on the stochastic feature and the similarity of topplings at different scales. Full enumerations of the RG evolution events inside a 2*2 RG cell for q=2, 3, and 4 are calculated. Fixed point analysis shows that the resulting height probabilities and the toppling number exponent are very close to the results obtained from the numerical simulations.

Prof. Olga S. Rozanova

Mechanics and Mathematics Dept., Moscow State University, RUSSIA

E-mail: rozanova@mech.math.msu.su

Probabilistic Model Associated with A Simplest Model of Rarified Medium

    Using a method of stochastic perturbation of a Langevin system associated with the non-viscous Burgers equation we construct a solution to the Riemann problem for the pressureless gas dynamics describing sticky particles. As a bridging step we consider a medium consisting of noninteracting particles. We analyze the difference in the behavior of discontinuous solutions for these two models and the relations between them. In our framework we obtain a unique entropy solution to the Riemann problem in 1D case. Moreover, we describe how starting from smooth data a δ- singularity arises in one component of the solution.

Typhoon Eye Trajectory Based on A Mathematical Model

    We propose a model based on the primitive system of the Navier-Stokes equations in a bidimensional framework as the 1-plane approximation, which allows us to explain the variety of tracks of tropical cyclones. Also, we compare our theoretical trajectories based on initial conditions from the flow with tracks obtained from the observational database.

Dr. D. B. Saakian
Yerevan Physics Institute, ARMENIA
E-mail: saakian@mail.yerphi.am

The Statistical Mechanics and Financial Markets: An Attempt to Understand the Crisis and Describe the Stock Fluctuations

    The economics highly resembles the thermodynamics with the 0-th and second law. The self-regulating market is deeply equivalent to the  thermodynamic systems with 0-th and second law, and the concept of self-regulating market is quite reasonable hypothesis for the financial (without derivatives), like the application of Gibbs statistical mechanics instead of Hamilton equations.  The situation drastically change in case of derivatives: the corresponding statistical mechanics systems could not go to equilibrium according to 0-th and second laws.  Therefore there is no any basis for the hypothesis of self-regulation of market in this case.
    We consider also the problem of stock fluctuations in market, described by mitiscaling random walks. These models are exactly mapped into Random Energy Model by Derrida and  special renormalization group equation. The market state corresponds to the Lee-Yang Fisher phase.
　

The Role of Sex and Recombination in Evolution

    We investigated the combined effect of neutrality and recombination for virus evolution. We checked that the combined action of recombination and neutrality could be stronger as an evolution factor, than the neutrality alone, negative epistasis or finite population size effects with recombination.  The recombination increases mean fitness about 4-10 times more than the increase of mean fitness due to neutrality alone. The increase of mean fitness could be much stronger  than the change of mean fitness due to epistasis.  In the dynamics the recombination distinguishes clearly the mean-field like evolution factors (phenotype, robustness) from the fluctuation like factors. While the mutations affect in the same way both the mean field like and fluctuation like factors, the recombination could accelerate the non mean field (fluctuation) type dynamics without touching the mean-field like factors. We suggest an anti-viral strategy in case of HIV.
　

Mr. Jui-Chih Wang

Institute of Biomedical Engineering, National Taiwan University, TAIWAN

E-mail: f93548056@ntu.edu.tw

Applying An Extended Relaxed Complex Scheme for Discovery of New Neuraminidase Inhibitors

    There are two important glycoproteins on the membrane of influenza virus, haemagglutinin and neuraminidase. HA mediates cell-surface sialic acid receptor binding to initiate virus infection. NA removes sialic acid from virus to facilitate virus release and spread. There have been two famous drugs targeting to neuraminidase, relenza (zanamivir) and tamiflu (oseltamivir). In 2006, Russell et al. crystallized neuraminidase structures with oseltamivir binding, they found that there is a larger cavity adjacent to oseltamivir binding site called 150 loop. In 2007, Amaro et al. found that there are more remarkable loop flexibility in N1 by molecular dynamics (MD) simulations. Besides, there is another cavity called 430 loop. MD helps to obtain more wide-open and nearly closed structures in these cavities.

    Therefore, it should be possible to design new inhibitors for neuraminidases that are for the open 150-loop or 430-loop conformation and would have the potential to bind more strongly than oseltamivir or zanamivir. We developed and applied an extended relax complex scheme to discovery new neuraminidase inhibitors. First, not only the typical explicit MD simulation was completed but also the efficient implicit MD simulation with generalized born solvent. We investigated the dynamics and relation of three important pockets in neuraminidase. Subsequently, several clustering methods were utilized to reduce computation largely for docking process of RCS. The precise rank of binding affinity of compounds which matched with experimented result was obtained via analysis of the energy spectrum of RCS.

Prof. Zicong Zhou

Department of Physics, Tamkang University, TAIWAN

E-mail: zzhou@mail.tku.edu.tw

Conformal and Mechanical Properties of Inhomogeneous Semiflexible Biopolymers

    We study the properties of inhomogeneous semiflexible biopolymers. We show exactly that when free of external force, a semiflexible biopolymer with short range correlations in the sequence-disorder intrinsic curvatures and torsions is equivalent to a biopolymer with well-defined (i.e., without randomness) intrinsic curvature and torsion as well as renormalized persistence lengths. We find an exact expression for the distribution function of a two-dimensional inhomogeneous semiflexible biopolymer and use it to evaluate the bending profile. Our results agree well with bending profiles of dsDNA with long-range correlation in base pairs. However, we show that an “equivalent system” does not always exist for the biopolymer under external force. We find that under an external force, the effect of sequence-disorder depends upon the averaging order, the degree of disorder, and the experimental conditions.