Date :

 2-3 May 2008

Place :

 2 May, The auditorium on 1st floor, institute of Physics of Academia Sinica, Taipei

 3 May, Room 312, Department of Physics, National Taiwan University, Taipei

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems Focus Group)

 Institute of Physics of 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

 Miss Shu-Min Yang (Assistant of LSCP, Institute of Physics, Academia Sinica)

 Tel: (886)-2-2782-2467, or (886)-2-27880058 ext. 6012; FAX: (886)-2-2782-2467; E-mail: shumin@phys.sinica.edu.tw

Speakers :

Dr. Armen E. Allahverdyan

Yerevan Physics Institute, ARMENIA

E-mail: aarmen@yerphi.am

Employing Feedback in Adiabatic Quantum Dynamics

    We study quantum adiabatic dynamics, where the external field moves slowly in time and is influenced by system's state
(feedback). The information for the feedback is gained from non-disturbating measurements done on an ensemble of identical non-interacting systems.  This situation without feedback is governed by the adiabatic theorem: adiabatic energy level populations stay constant, while the adiabatic eigenvectors get a specific phase contribution (Berry phase).  Under feedback the adiabatic theorem does not hold: the adiabatic populations satisfy a closed equation of motion that coincides with the replicator dynamics well-known by its applications in evolutionary game theory. The feedback generates a new gauge-invariant adiabatic phase, which is free of the constraints on the Berry phase (e.g., the new phase is non-zero even for real adiabatic eigenfunctions).

Comment: submitted to Phys. Rev. Lett.; this a continuation of the work published in Europhys. Lett. 81, 30003 (2008).

Structure and Function of Quantum Heat Engines

    We consider a class of quantum heat engines consisting of two subsystems interacting with a work-source and coupled to two separate baths at different temperatures. The purpose of the engine is to extract work due to the temperature difference. Its dynamics is not restricted to the near equilibrium regime. The engine structure is determined by maximizing the extracted work under various constraints. When this maximization is carried out at finite power, the engine dynamics is described by well-defined temperatures and satisfies the local version of the second law. In addition, its efficiency is bounded from below by the Curzon-Ahlborn value and from above by the Carnot value. The latter is reached--at finite power--for a macroscopic engine, while the former is achieved in the equilibrium limit. The efficiency that maximizes the power is strictly larger than the Curzon-Ahloborn value. When the work is maximized at a zero power, even a small (few-level) engine extracts work right at the Carnot efficiency.

Comment: accepted for publication in Phys. Rev. E
　

Kinetics of Helix-Coil Transition

    We study the kinetics of the temperature-driven helix-coil transition of a long polymer chain modeled via the one-dimensional Ising system.  The cooperative helix-coil transition induced by a finite-rate change of the temperature differs significantly from its equilibrium counterpart. There is an assymetry between the coil->helix and helix->coil transition: the latter is well-displayed already for finite rates of heating, and takes much shorther time than the former. A finite-rate cooling induces a kinetic helix phase with the cooperative unit longer than the one in the vicinity of the equilibrium helix-coil transition. The temperature of the kinetic transition scales as a logarithm of the cooling-reheating rate.  In the kinetic helix phase the non-equilibrium specific heat is negative under reheating.  Our findings are in a qualitative agreement with experiments.

Comment: submitted to Phys. Rev. Lett.

Replicators in Time-Periodic Environment: A Model for Polymorphism

    We study the two-player replicator dynamics in a time-periodic environment. For sufficiently fast environmental changes, this dynamics is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms arise due to the adaptation of the morphs to their varying environment.  The multi-player (adaptive) terms can induces a stable polymorphism, though they do not spoil any polymorphism that exists already without them. The establishment of the polymorphism in parthnership games [genetic selection] is accompanied by decreasing mean fitness of the population.
　

Dr. Chung-Ke Chang

IBMS, Academia Sinica, TAIWAN

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

Probing Protein Unfolding With NMR

    The problem of protein folding is one of the key themes in structural biology and has attracted a tremendous amount of attention from other disciplines, especially those from the physical sciences.  Various techniques have been developed to study this problem, ranging from theoretical simulations to experimental methods such as circular dichroism (CD).  Nuclear magnetic resonance (NMR) is a particularly powerful experimental tool since it can provide structural information at the residue and atomic level.  This presentation will focus on how NMR techniques are used to study protein folding/unfolding and the principles behind them.  We will also briefly discuss how instrinsically unstructured proteins, a class of proteins that share features common to unfolded proteins, can be studied with these same NMR methods.

Prof. Chi-Ning Chen 

Physics Department, National Dong-Hwa University, TAIWAN

E-mail: cnchen@mail.ndhu.edu.tw     

Complex Networks in Linux Kernel

Dr. Mei-Chu Chung

Institute of Plant and Microbiology, Academia Sinica, TAIWAN

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

Chromosomal Polymorphism of rDNAs in the Genus Oryza

    We used the coding region of 45S rRNA gene (rDNA) as probe in fluorescent in situ hybridization to localize rDNAs on chromosomes of 15 accessions representing ten Oryza species. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci are various in one to eight among Oryza species. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution.

Prof. Wen-Tau Juan

Institute of Physics, Academia Sinica, TAIWAN

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

DNA- A Model System for Single Molecule Studies of Polymer Physics

    Polymer science is an interdisciplinary field involving the material sciences, physics, chemistry, biology, and chemical engineering. The non-Newtonian fluid properties of polymeric solutions have been widely applied in various industries. Due to the limitation of experimental techniques, the underlying physics of such a complex fluid, especially at the molecular level, has not been fully understood. The fluorescent microscopy is a powerful tool to visualize the dynamics of individual dye labeled DNA in solutions. It sheds light on how the fluid interacts with this model polymer molecule in the microscopic scale. The talk will be focused on the recent progress of the DNA based single molecule polymer physics studies.

Mr. Chi-Ching Lin

Department of Physics, National Sun Yet-Sen University, TAIWAN

E-mail: valentineph@gmail.com

Experimental Observations of Dual-Polarization Oscillations in Laser-Diode-Pumped Wide-Aperture Thin-Slice Nd:GdVO4 Lasers

    Dual-polarization oscillations have been observed in a mirror-coated thin-slice Nd:GdVO4 laser. We study the oscillation spectra, input-output characteristics, pump-dependent pattern formations and noise power spectra. Simultaneous oscillations of orthogonally-polarized different transverse modes and the resultant violation of inherent anti-phase dynamics in multimode lasers are demonstrated. We explained the results in terms of the reduced three-dimensional cross-saturation of population inversions among orthogonally-polarized modes.

Dr. Yu-Pin Luo

Institute of Physics, Academia Sinica, TAIWAN; Physics Division, National Center for Theoretical Science, TAIWAN

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

System-Wide Coordination for Tunable Scale-Free Networks

Prof. Sheau-Yann Shieh

Institute of Biomedical Sciences, Academia Sinica, TAIWAN

E-mail: sy88@ibms.sinica.edu.tw

    Progression of cell cycle is safeguarded by an intricate network of checkpoints, so that cells with incompletely replicated or damaged DNA will be either eliminated or repaired before the continuation of cell cycle. In the past few years, my lab has been focusing on mainly two lines of research, one involves regulation of the tumor suppressor protein p53 by DNA damage, in particular in the aspect of post-translational modification; the other concerns the checkpoint kinases CHK1 and CHK2, specifically their roles in DNA damage induced signal transduction.

    The tumor suppressor protein p53 plays pivotal roles in maintaining genome stability by inducing growth arrest or apoptosis upon genotoxic assaults. The significance of its presence is manifested by its mutation in over 50% of cancers. Under unstressed condition, p53 is a latent transcription factor with a half-life of about 30 min. However, stress such as DNA damage, hypoxia, and nucleotide depletion significantly increases p53 stability and at the same time leads to its activation. As a result, several p53 downstream target genes are activated. Among them, p21/Waf1 is known to mediate p53-dependent G1 arrest, while genes such as AIP1 and PUMA are involved in p53-mediated apoptosis. Aside from these downstream events, the molecular basis leading to p53 stabilization and activation is equally intriguing. Evidence suggests that post-translational modification of p53, in particular, phosphorylation and acetylation, contribute to stabilization and activation of the protein. Some of these modifications are stress-inducible, suggesting they may participate in the regulation of the p53 response.

    Based on our understanding of the tumor suppressor protein, several chemotherapeutic approaches have been taken, which target cancer cells carrying functionally compromised p53.

Prof. Hiroshi Watanabe

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

E-mail: hwatanabe@is.nagoya-u.ac.jp

1. Ergodicity of Isothermal Molecular Dynamics Method
    A condition for equations of motion for isothermal dynamics is derived, and the Nosé--Hoover method is generalized on the basis of this condition.  The ergodicity of the one-variable thermostats are studied, and it is shown that the one-variable thermostat coupled with the one-dimensional harmonic oscillator loses its ergodicity with large enough relaxation time.  A stochastic process of the Nosé--Hoover method is also discussed based on the Markovian approximation.

2. Dynamic Monte Carlo Rejection-Free Method for Particle Systems

    We construct asymptotic arguments for the relative efficiency of rejection-free Monte Carlo (RFMC) methods compared to the standard MC method.  We investigated the efficiency in the particles systems as well as spin systems, and confirmed the RFMC has a greater computational efficiency at high densities, and the density dependence of the efficiency is as predicted by our arguments.