Date :

 28-29 January 2010

Place :

Lecture Room 4A of NCTS, 4F, General 3rd Building, National Tsing Hua University, Hsinchu

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

 Institute of Physics, Academia Sinica (Taipei)

 Miss 施玫如 (Secretary, NCTS)
 TEL: (886)-3-5731265; E-mail: mrshi@phys.cts.nthu.edu.tw

http://phys.cts.nthu.edu.tw/actnews/actnews.php?Sn=388270

Speakers :

Prof. Chi-Ning Chen

Department of Physics, National Dong-Hwa University, TAIWAN

Email: cnchen@mail.ndhu.edu.tw

Maximum Degree Distribution in Complex Networks

Prof. Chun-Jung Chen

Physics Department, National Tsing Hua University, TAIWAN

Email: cjchen@nsrrc.org.tw

Dr. Nan-Yow Chen

Institute of Physics, Academia Sinica, TAIWAN

Email: nanyow@phys.sinica.edu.tw

Guiding Proteins through Folding Pathways by Dynamical Contact Map

    A novel optimization method, Dynamical Contact Map Guiding method, that can retrieve the major folding pathway is purposed.  To prevent from trapping in the local minimum, this method use the information of contact map in the previous generation(s) as the guiding functions to guide the protein fold into the native state efficiently.  Meanwhile, without depicting the energy landscape, the method also can provide the information of key contacts and initiation sites during the folding process.  The different folding dynamics for two wild-type sequences of protein G and protein L can be shown via this method.

Dr. Yun-Ru Chen

The Genomics Research Center, Academia Sinica, TAIWAN

Email:yrchen@gate.sinica.edu.tw

Introduction of Amyloids-Emphasis on Amyloid Beta in Alzheimer’s Disease

    Amyloidosis is a protein misfolding event occurs in more than 40 diseases in which many of them of age-related especially neurodegenerative diseases.  The diseases, such as Alzheimer’s, Parkinson’s, Huntington’s, Prion diseases, harbor specific pathogenic amyloid proteins, Amyloid b (Ab), a-synuclein, polyQ, PrP, respectively, that undergo protein misfolding and from insoluble amyloid fibrils.  Despite they have different primary protein sequences, their fibril morphology are strikingly similar. The fibrils all contain cross-b structures, stretch to a length up to µm.  Those proteins undergo fibrillization that initiate either with natively unfolded structure or partially unfolded structure and extend the assembly to oligomers and to mature fibrils. The fibrillization process is suggested to follow either nucleation-elongation polymerization or monomer addition polymerization.

    Among all amyloidosis, Alzheimer disease (AD) is the most devastating and prevail neurodegenerative disease and accounts for ~70% of the dementia cases.  In 2009, there are more than 20 million AD patients world wide.  The prevalence of AD occurs dominantly in the elderly over 65 of age (sporadic AD) with a minor percentage of AD occurs in younger adults due to genetic mutations (familial AD).  In AD brain, Ab aggregation is a causative factor for neuron loss.  It is the main composition of senile plagues found in the AD brains.  Ab has been the biggest target in the AD therapeutic development.  Here, our laboratory studies the fundamental mechanism of Ab folding and aggregation. We would discuss different folding and aggregation behaviors of familial AD mutants, effect of metal ions, as well as effect of different Ab42/40 ratios using biochemical and biophysical methods.

Prof. Lin-Ni Hau

Institute of Space Science, National Central University, TAIWAN

Email: lnhau@jupiter.ss.ncu.edu.tw

Statistics and Thermodynamics of Inhomogeneous Charged Particle and Field Systems

    Plasma constitutes 99% of the matter in the Universe and has important applications in the laboratory and industry.  A system of plasmas comprises many charged particles interacting with electromagnetic and or gravitational fields in a self-consistent manner.  One of the major challenges in the study of plasma physics lies on the fact that on the macroscopic scale the system is spatially inhomogeneous and in most circumstances in nontherrmal equilibrium due to the lack of sufficient short-range collisions (referred to as collisionless plasma).  The statistics and thermodynamics of an inhomogeneous nonthermal system involves close interplay between kinetic and fluid theories describing microscopic and macroscopic physics of charged particle and field system, respectively.  In this talk an overview is presented of the issues and challenges in the study of many elementary particles interacting with electromagnetic and or gravitational fields which include the nonthermal characteristics and energy closure associated with collisionless plasmas.

Introduction to Models of Phase Transitions and Critical Phenomena

Prof. Ming-Chang Huang
Center for Nonlinear and Complex Systems and Department of Physics, Chung-Yuan Christian University, TAIWAN
E-mail: ming@phys.cycu.edu.tw

Majority Rule, Steady States, and Noise in Scale-Free Networks

Prof. Tzay-Ming Hong

Physics Department, National Tsing Hua University, TAIWAN

E-mail: ming@phys.nthu.edu.tw

What’s Common between a Crumpled Aluminum Foil and Liquid Crystals?

    In collaboration with Dr. Yeukuang Hwu of Academia Sinica, we performed X-ray tomography to acquire 3D images of crumpled aluminum foils. Ordered domains appear near the crust, similar to the lamellae phase mixed by the amorphous portion in lyotropic liquid crystals. The size and density of these domains grow with further compaction and their orientation favors either perpendicular or parallel to the radial directions. Ordering is also identified near the core with an arbitrary orientation. Our most recent finding of a second power-law behavior for the force-size relation will also be presented. The nature of phase transition between these two power-law regimes is yet to be explored.

Conceptions of "Ideal Crosslinking" and "Ideal Uncrosslinking" and Their Use for Evaluation of Local Distortions Caused in DNA by Some Antitumor Compounds

Prof. Hsiu-Hau Lin

Physics Department, National Tsing Hua University, TAIWAN

E-mail: hsiuhau@phys.nthu.edu.tw

Discreteness of Population Erodes Biodiversity in Evolution

    It is generally believed that cyclic competition among three species leads to a delicate dynamical balance and thus promotes biodiversity in the ecological system. We show that this belief is in doubt due to the presence of very general intrinsic fluctuations that will lead to dissipative dynamics and definite extinction. These fluctuations come from the discreteness of number we use to characterize the size of each species, which play the same role as the Brownian forces that cause the damping to a harmonic oscillator. As a result, the variety of species will eventually dwindle behind the common rise and fall of their numbers. Useful lessons can be learned from the laws of thermodynamics and the fluctuation-dissipation theorem in physics, which provide an intuitive explanation of the sure destiny and its related properties. Since our arguments are general, we urge that cares be taken whenever one conveniently approximates an intrinsically discrete variable by a continuous parameter.
　

Non Maxwell-Boltzmann Properties Induced by Backbone Dynamical Anisotropy in Model of Polymer Melt

    Using molecular dynamics simulation, we explore how well-defined velocity distributions of monomers in systems of non-equilibrium polymer chains deviate from standard Maxwell-Boltzmann description, caused by chain connectivity. We study systems of polymer chains with nearby monomers along each chain connected by rigid bonds or springs for the nearest and by bending as well as torsion potentials for the subsequent neighboring, in mixing with Lennard-Jones molecules. The velocity distributions are described by Tsallis q-statistics, with the value of q deviating and larger than unity in increasing the strength of the springs. We analyze the corresponding distributions for velocity orientation correlations along the chains and find that the enhanced anisotropy follows the deviation of q from unity, the Maxwell-Boltzmann type. Such anisotropy may also be responsible for the reduction in the effective number degrees of freedom in consideration of the condition of reaching equilibration between polymer and fluid. Our results suggest, the analysis of dynamic anisotropy along the backbones is useful in classifying the collective dynamic properties in various complex systems of polymers.

1. Introduction to the Application of Statistical Mechanics to Evolution

    We introduce the main biological problems and models.  The Crow-Kiumra and Eigen models are defined. We consider the error threshold problem, the evolution with neutral and lethal mutants. In this introduction lecture we give minimum mathematics.

2.The Hamilton Jacobi Equation  Method and the Optimization in Evolution Dynamics
    We introduce the Hamilton Jacobi Equation(HJE) method, the most powerful method for solution of evolution models. We apply it to the solution of optimization problems in evolution. We consider the optimal dynamics in the infinite population evolution models with general symmetric fitness landscape.  The search of optimal evolution trajectories are complicated due to sharp transitions (like shock waves) in evolution dynamics.

3. Investigation of Recombination Phenomenon in Evolution

    We consider first exact dynamics in case of selection-free and single-peak fitness models, then later the statics of recombination. We solve the recombination in case of robust fitness landscapes and apply our results to HIV evolution.

Prof. Zhigang Zheng

E-mail: zgzheng@bnu.edu.cn

1. Synchronization and Topology Identification of Complex Networks

    In recent years, there has been a growing interest in the synchronization of spatiotemporal systems, especially in synchronous dynamics on networks. Network topology plays an important role in governing the collective dynamics. Synchronization, as a universal cooperative behavior and a fundamental mechanism in nature, has been extensively studied in relating to numerous phenomena in physics, chemistry, and biology. Synchronizations on typical complex networks, e.g., on small-world networks or scale-free networks, have been investigated recently.

    In spite of these efforts, a lot of efforts have been made on the relation between network topology and collective dynamics. First, much less was explored for the collective behaviors prior to the global synchronization. A good understanding of this issue should be relevant to many collective behaviors in spatiotemporal systems, especially in complex networks. Second, it is still an open issue to infer information of network topology from the output dynamics, even though the inverse problem has been extensively explored.

    In this talk, I will discuss the partial synchronization (PaS) on regular networks with a few non-local links. Different PaS patterns out of the symmetry breaking are observed for different ways of non-local couplings. We give the criterion for the emergence of PaS. Theoretical and numerical analysis indicate that non-local coupling may drastically change the dynamical feature of the network, emphasizing the important topological dependence of collective dynamics on complex networks. We further apply the the criterion of PaS to the studies of synchronizations between spatiotemporal systems with sparse couplings. The identification of the topological structures of complex networks from dynamical information is an inverse and significant problem. We present a method in revealing network connectivity from transient dynamics. By applying the transient dynamical signals as a periodic drive, the adjacent matrix can be determined in terms of the modified adaptive feedback scheme. This improved scheme is found to be very useful in the presence of global or local synchronization, where the transient drive can be obtained by perturbing the system to an asynchronous state.

Acknowledgments

    Project supported by this work is supported in part by the National Natural Science Foundation of China, the 973 project, and the Foundation of Doctoral Training from Ministry of Education.

2. Coupled Ratchets: Cooperative Directed Transport and Locomotion

    In recent years, much effort has been devoted to understanding the nonequilibrium mechanism of the emergence of net currents by the rectification of thermal fluctuations in the presence of various drivings with temporally, spatially, and statistically zero mean. These explorations helped us to get a deeper understanding of the mechanism of many phenomena in molecular motors, flux dynamics in superconductors, Josephson junctions arrays, ladders, and lines, transport in quantum dots, nano-device design, particle separation, and solid surfaces treatment.

    Things become very different when one considers the interaction among particles or motors. In physical systems, it has been found that interactions among particles may strikingly dominate the directed transport. In recent years there have been a number of explorations on directed transport in coupled systems. Biological experiments have revealed that numerous biological motors such as kinesin, Myosin, and dynein, are all bipedal motors with coordinated activity between two strongly coupled motor domains. It is very important to explore the relation between the structure of motors and locomotion, and the classical single-particle scenario of Brownian motors is inadequate for modelling biological motor systems. Furthermore, manual designing mechanisms in coordinating the motion between multiple domains of the motor to bias random thermal motion has become a great challenge in engineering molecular motors. Very recently it was claimed that the autonomous DNA bipedal walker has been proposed.

    In this talk, we review recent explorations on coupled ratchets and molecular motors. We will discuss the rocking overdamped ratchet lattice with harmonic couplings, ratchet motion of particles with hard-core interactions, asymmetrically coupled lattice in symmetric potentials without external forces, ratchet motion by breaking the spatiotemporal symmetries, and so on. We also propose a mechanism that cooperative directional transport can be achieved in one direction through the zero-mean drivings in the other direction. The energy inputted by the external drivings can be translated to the work for directional motion only by mutual couplings of individual elements. This mechanism can be applied to understanding the transport of polymers in microtubules.

Acknowledgments

    Project supported by This work is supported in part by the key NNSF of China, the FANEDD, the TRAPOYT in Higher Education Institutions of MOE, and the Foundation of Doctoral Training.

Conformal and Mechanical Properties of Filaments and Its Application to Biopolymers

    In this talk I will present some of our recent works on the conformal and mechanical properties of filaments and its application to biopolymers.

    We derived the shape equations in terms of Euler angles for a uniform elastic filament with finite intrinsic curvatures and torsion, and study elasticity and stability of the helical filament under uniaxial force and torque. We showed analytically that the extension of a helix may undergo a one-step sharp transition when we fix the torque. This agrees quantitatively with experimental observations for a stretched helix in a chemically defined lipid concentrate.

    We studied the mechanical properties of a two-dimensional filament with finite intrinsic curvature and under uniaxial applied force. We obtained closed-form expressions on the force-extension relation for a filament at low force and for a long filament under strong stretching force. Our results showed that the effect of a nonvanishing intrinsic curvature may become important when the intrinsic radius is comparable to the persistence length of the filament.

    We studied the effects of sequence-dependent intrinsic curvatures and torsion on a semiflexible biopolymer with short-range correlation in intrinsic curvatures and torsion. We showed exactly that if we perform the disorder average in intrinsic quantities over all samples first, the system is equivalent to a biopolymer with well-defined (i.e., without randomness) intrinsic curvature and torsion as well as renormalized persistence lengths. However, we showed further that if we perform the configuration average in an individual sample first, 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.