Date :

 2-3 March 2007

Place :

 2 March: Room 312, Department of Physics, National Taiwan university, Taipei

 3 March: The first meeting room on the 5th floor, Institute of Physics, Academia Sinica, Taipei

 National Center for Theoretical Sciences (Critical Phenomena and Complex Systems focus group)

 Institute of Physics of Academia Sinica (Taipei)

 Department of Physics, National Taiwan university (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

1. Bath-Assisted Cooling of Spins

    Cooling, i.e., obtaining relatively pure states from mixed ones, is of central importance in fields dealing with quantum features of matter.  Recently it got renewed attention due to realizations of setups for quantum computers.  Here we demonstrate that a suitable sequence of sharp pulses applied to a spin coupled to a bosonic bath can cool its state, i.e., increase its polarization or ground state occupation probability. Starting from an unpolarized state of the spin in equilibrium with the bath, one can reach very low temperatures or sizable polarizations within a time shorter than the decoherence time. Both the bath and external fields are necessary for the effect, which comes from the backreaction of the spin on the bath. This method can be applied to cool at once a completely disordered ensemble of spins.

2. Minimal Work Principle and its Limits

    The minimal work principle is one of formulations of the second law.  It was recently strengthened via the fluctuation theorems, and is nowadays regarded as the cornerstone of the thermodynamics of small (nanoscale) systems.  In this talk I shall derive the minimal work principle from the classical Hamiltonian mechanics. It will be shown that the principle is valid for a system of which the observable of work is an ergodic function. For non-ergodic systems the principle may or may not hold, depending on additional conditions. Examples displaying the limits of the principle are presented and their direct experimental realizations are discussed.

3. Statistical networks emerging from link-node interactions

    Statistical mechanics of networks is a growing field with a wide range of applications from physics and mathematics to biology and sociology.  Normally networks are modeled either via passive nodes with a given distribution of links, or with a given dynamics of link formation.  Here we present a network model, where the nodes and links are active variables influencing each other. Thus network's  structure is not given a priori, but rather emerges due to the spins located at its nodes and interacting via its links. Network's structure is determined by an effective potential generated by the quickly relaxing nodes, and is measurable via the statistical features of the nodes. For low temperatures the nodes get spontaneously ordered inducing the connectivity enhancement, link-link correlations and clustering. The giant component of the network does appear via a first-order percolation transition leading to bistability and hysteresis.

Dr. Chung-ke Chang

Institute of Biomedical Science, Academia Sinica, TAIWAN

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

Biophysical and biochemical methods in protein research: Hemoglobin as a case study

    Proteins are the major constituents of all organisms, ranging from humans to the simplest bacterium. The advent of novel biophysical and biochemical methodologies has greatly sped up research in the biological sciences, including protein research. However, proteins are complex entities consisted of polymeric chain(s) of amino acids, which manifests in a large number of three-dimensional structures.  Since the structure of proteins is closely coupled to its physiological function, elucidation of the protein structure and its correlation to the function of the protein are of immense interest to biologists. The complexity of a protein makes it impossible to explore these aspects with any single experimental method, thus necessitating the employment of various approaches. In this lecture, I will present some common biophysical and biochemical methods in protein research by using hemoglobin as a model.  More importantly, I hope to convey the mentality driving modern protein research, and discuss facets which can benefit from input by physicists.

Dr. D. B. Saakian

Yerevan Physics Institute, ARMENIA

E-mail: saakian@mail.yerphi.am

1. Exact results for finite population size quasispecies theory

    We solved exactly both Kimura and Eigen model in case finite, but large population. For the Single peak fitness case our results are well confirmed numerically. For the Kimura model with general population we derived a functional euations. Our results are valid even for the case of finite genome. After 40 years we derive exact probability distributio for the Muller Ratchet.

2. Exact solution of diploid evolution models with general fitness

    We find the exact mean fitness and steady state distribution, using the Hamilton-Jakobi equation method.

Prof. Hueih Min Chen

Agricultural Biotechnology Research Center, Academia Sinica, TAIWAN

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

Compact dimension of denatured states of staphylococcal nuclease

    Fluorescence and CD stopped-flow have been widely used to determine the kinetics of protein folding including the rates and possible pathways.  However, these measurements are not able to provide the spatial information of protein folding/unfolding. Especially, the denatured state conformation cannot be elaborated in detail. In this study, we apply a method of fluorescence energy transfer with stopped-flow technique by following global structural changes during folding of a staphylococcal nuclease mutant K45C, where lysine 45 was replaced by cysteine. We labeled the thiol group of cysteine with TNB (5,5’-dithiobis-2-nitrobenzoic acid) as an energy acceptor and a tryptophan at position 140 as a donor. Distance changes between acceptor and donor during folding and unfolding were measured due to the efficiency of energy transfer. Results indicated that the denatured state of SNase is highly compact regardless of which unfolded states (pH-induced or GdmCl-induced) are induced since the scope of distance changes between donor and acceptor is within between 22Å and 26Å as compared with 20.4 Å in native state. Furthermore, the folding reaction consists of three kinetic phases and the unfolding reaction is a single phase. These observations agree with our previous sequential model: N_o D D₁D D₂ DD₃. The efficiency of protein folding therefore may be counted by initiating the folding process from these compact denatured proteins. 

Dr. N.Sh. Izmailian

Yerevan Physics Institute, ARMENIA

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

Finite - Size Effects for Ising Model on Helical Tori

    We analyze the exact partition functions of the Ising model on the square lattice under helical boundary conditions obtained by Liaw et.al. [Phys. Rev. E 73, 055101(R), (2006)]. Based on such expression, we then extend the algorithm of Ivashkevich, Izmailian and Hu [J. Phys. A 35, 5543 (2002)] to derive the exact asymptotic expansion of the logarithm of the partition function and his derivatives in the critical point. We found that the shift exponent for the specific heat is λ= 1, except for special case of the infinitely long helical torus, in which case pseudocritical specific-heat scaling behavior was found to be of the form N^{-2} \ln N.

Prof. C.-Y. D. Lu

Departments of Chemistry and Physics, National Taiwan University, TAIWAN

E-mail: cydlu@ntu.edu.tw

The dielectric spectrum of the polyelectrolyte solutions

    We extend the double layer polarization theory to the flexible polyelectrolyte solutions. The low frequency dielectric spectrum is calculated theoretically. The two major ingredients in the theory are that the salt-electric field coupling induced by the double layer around the polyelectrolyte chains, and the free energy formulation to calculate the dielectric function. We find that the low frequency dielectric function can be expressed as the convolution of the salt diffusion kernel and the tensorial chain structure factor. We calculate explicitly the spectrums of the dilute polyelectrolyte solution, and the concentrated solution.

Dr. Yu-Pin Luo

Center for Nonlinear and Complex Systems and Department of Physics, Chung-Yuan Christian University, TAIWAN

E-mail: pin@phys.cycu.edu.tw

Master Equation Approach to Folding Kinetics of Lattice Polymers Based on Conformation Networks

    Based on master equation with the inherent structure of conformation-network, we investigate some important issues in the folding kinetics of lattice polymers. Firstly, the topologies of conformation networks are discussed. Moreover, a new scheme of implementing Metropolis algorithm, which fulfills the condition of detailed balance, is proposed. Then, upon incorporating this new schem into the geometric structure of conformation network we provide a theorem which can be used to place an upper bound on relaxation time. To effectively identify the kinetic traps of folding, we also introduce a new quantity, which is employed from the continuous time Monte Carlo method and called rigidity-factor. Throughout the discussions, we analyze the results for different move sets to demonstrate the methods and to study the features of the kinetics of folding.

Dr. K.G. Petrosyan

Yerevan Physics Institute, ARMENIA

E-mail: pkaren@yerphi.am

Globally connected rotors with random couplings

    We consider a system of rotors (rotational oscillators) which are globally connected via random couplings. We assume that we have two subsystems with diRerent time scales. One subsystem consists of the rotors (fast subsystem) and the other one is a set of links (slow subsystem) which connect the rotors. First we investigate the equilibrium case of the subsystems having equal temper-atures (not assuming diRerent time scales for that case). Then we consider the non-equilibrium case of subsystems having diRerent temperatures. Taking the adiabatic limit and applying the replica method we investigate the non-equilibrium thermodynamics and various statistical properties of the model.

Prof. Fa-Yueh Wu

Department of Physics, Northeastern University, USA

E-mail: fywu@lepton.neu.edu

1. Theory of impedance networks: A new formulation of the Kirchhoff  law

2. Recent results in dimer statistics