Date :

 27, 30 March 2009

Place :

 27 March: Room 312, Department of Physics, National Taiwan University, Taipei

 30 March: 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

 Miss Chun-Ling Chang (Assistant of LSCP, Institute of Physics, Academia Sinica)

 Tel: +886-2-27898362; FAX: (886)-2-2782-2467; E-mail: labthpp@phys.sinica.edu.tw

Speakers :

Dr. Rita P.-Y. Chen
Institute of Biological Chemistry, Academia Sinica, Taipei, TAIWAN
E-mail: pyc@gate.sinica.edu.tw

Protein Aggregation Problem: Ab and Prion

    Amyloid plaques formed of amyloid b (Ab) peptides, is one of the pathological characterization.  In order to study the structural plasticity of the Ab peptid, the residue immediately preceding each glycine in the 40 amino acid Ab40 peptide (S8, V24, I32, and V36) was individually replaced by D-form proline (^DPro).  The resulting ^DP-G sequence (the ^DPro residue and the following Gly residue) was designed as a “structural clip” to force the formation of a bend in the peptide, as this sequence has been reported to be a strong promoter of b-hairpin formation.  The mutated peptides (V24, I32, and V36) no longer formed an amyloid fibril structure, although they still went through a coil-to-b structural conversion.  Interestingly, Thioflavin T and Congo red, the dyes usually employed in amyloid detection and quantification, were able to bind to this converted b-sheet structure.  We concluded that these Ab mutants form a new amyloid-like aggregate.  Moreover, the mutant peptide V24P, when mixed with Ab40, can attenuate the cytotoxicity of Ab40.   

    Prion disease is one famous, transmissible, neurodegenerative diseases.  A special protein aggregate called prion is involved in the culprit of the diseases.  We are interested in knowing how the structural conversion can happen and lead to the amyloid formation.  We found that the conformational properties of prion peptide can be affected by post-translational modification, especially glycosylation.  This effect is site-specific and sugar-specific.  Adding a sugar moiety at Ser-132 promotes amyloidogenesis whereas adding the same sugar at Ser-135 inhibits it.  The glycosidic linkage at a-anomeric position has a more dramatic effect than that at b-anomeric position. 

Prof. Shan-Tarng Chen

Department of Physics, National Chung-Hsing University, TAIWAN

E-mail: sywang@aptg.net

A Further Study on the Dynamics of Kauffman Networks

    Random Boolean Networks are also known as Kauffman Networks. The Networks are now widely used as models for complex systems, such as neuronal networks, protein networks and social networks, etc. In 1969 S.A. Kauffman first investigated the model of a genetic regulatory system. His research discovered for the complex network systems the dynamic behavior with two features: (1) the systems have three kinds of phases: frozen, critical and chaos. This is quite similar to “percolation” of statistical physics; (2) in the critical phase for connection number k=2 the mean attractor lengths and numbers of the system exhibit the behavior of. This is similar to that discovered in biology that if N denotes the number of genes then the kinds of cell and the time of reproduction are proportional to. The above two discoveries immediately gave rise to high interests of biologists and statisticians.

    In recent ten years following the increasing capacity of computer operational ability the theoretical investigation of the behavior of network dynamics gradually become mature. Authors gradually began to query about the behavior of of the network attractors. We have also tried in these years using three different numerical simulation to study the dynamics behavior of the critical k=2 random Boolean networks. Based on our research results the mean attractor lengths and numbers for the critical k=2 random Boolean networks do not show the behavior. We think that our new results could have far reaching effects and could further improve the Kauffman model.

Prof. Chin-Kun Hu

Institute of Physics, Academia Sinica, TAIWAN
E-mail: huck@phys.sinica.edu.tw

Game Models for Public Traffic Networks

Dr. Hsien-Kuei Hwang

Institute of Statistical Science, Academia Sinica, TAIWAN
E-mail: hkhwang@stat.sinica.edu.tw

Stochastic Behaviors of Random Trees of Logarithmic Height

  Random trees are ubiquitous in many scientific disciplines. Most random trees in the applied probability literature can be classified into two categories depending on their height (the size of the longest path from the root) being of logarithmic or of square-root in the tree size. A survey of random trees of the first category will be given, focusing on the diverse stochastic properties exhibited. Connections to some statistical physical models will also be indicated.

Prof. Doochul Kim

Department of Physics and Astronomy, Seoul National University, KOREA

E-mail: dkim@snu.ac.kr

1. Renormalization and Self-similarity in Scale-Free Networks

    In this talk, the fractal scaling and self-similar connectivity behaviors of scale-free (SF) networks are reviewed. The renormalization transformation is achieved by the so-called random sequential box-covering algorithm that is useful and easy to implement in SF networks. To understand the origin of the fractal scaling, fractal networks are viewed as comprising of a skeleton and shortcuts. The skeleton, embedded underneath the original network, is a spanning tree specifically based on the edge-betweenness centrality or load. We show that the skeleton is a non-causal tree, either critical or supercritical. We also study the self-similarity, manifested as the scale-invariance of the degree distribution under coarse-graining of vertices by the box-covering method. We obtain the condition for self-similarity, which turns out to be independent of the fractality, and find that some non-fractal networks are self-similar. Therefore, fractality and self-similarity are disparate notions in SF networks.

2. Spectral Density of Complex Networks

    The spectral density, also called the density of states, is the density of eigenvalues averaged over an appropriate ensemble of graph. In this work, we study the spectral densities of several types of matrices associated with a scale-free network, which has a power-law tail in the distribution of the number of incoming links to a node. The matrices include the Laplacian of weighted graphs, the weighted adjacency and Laplacian, and random walk matrix. The spectral densities in the thermodynamic limit are expressed in terms of solutions of corresponding nonlinear functional equations using the replica method and are solved analytically in the limit where the average incoming links per node are large. The link weights are parametrized by a weight exponent β and explicit results are obtained for arbitrary degree exponent γ and β. Implications of our results on the synchronizability of coupled non-linear oscillator systems are discussed.

Prof. D. Y. Lando

Belarus National Academy of Sciences, BELARUS

E-mail: dmitrilando@yahoo.com

Temporal Behavior of DNA Stability and Renaturation in the Presence of Cisplatin and Transplatin

    As shown in our previous study, a negative shift of DNA melting temperature (Tm) caused by antitumor compound cisplatin is strongly increased if melting experiment is carried out in alkaline medium (E.N. Galyuk et al. J. Biomol. Struct. Dynam. 25, 407-418 (2008)). Transplatin also decreases T_m at pH>10 but the decrease is lower than for cisplatin. This result allowed us to increase sensitivity of melting measurements for DNA complexes with platinum compounds. Using it, we have demonstrated in the present study that the development of platination is stopped in alkaline medium (0.1 M NaCl, pH 10.5-10.8). All these findings gave an opportunity to measure kinetics of DNA stability under platination in 0.01M NaClO₄ at various temperatures and compare these results with other properties of DNA complexes with platinum compounds. We have found that, in the presence cisplatin, DNA stability is monotonously decreased with the time of incubation in 0.01 M NaClO₄. The beginning of the effect of cisplatin on the melting temperature was registered in 2 minutes. At 37^oC, the time of a half of the maximal decrease of T_m is ~1 h. The reaction is four-fold slower and four-fold faster at 25^oC and 50^oC, respectively. At 25 and 37^oC, the maximal decrease in the melting temperature is almost the same but the maximal shift value is lower under a 50^oC incubation. In contrast to cisplatin, kinetics is not monotonous for transplatin. A decrease in T_m during 3 h incubation at 37^oC is changed by an increase. However, the melting temperature does not reach the value corresponding to control unplatinated DNA even after a 48 hour incubation. To evaluate kinetics of DNA interstrand crosslinking by cis- and transplatin, platination was stopped after various time interval of incubation, and then DNA was subjected to denaturation by heating to 100^oC followed by quick cooling or by freeze-thaw procedure in alkaline medium. The second type of denaturation was found recently (E.N. Galyuk et al. J. Biomol. Struct. Dynam. 26, 517-524 (2009)).  It was shown that a weak interstrand crosslinking appears after a 15 minute incubation but it becomes sufficiently effective to restore the double helix after a 24 hour incubation.

Dr. Koryun B. Oganesyan

Yerevan Physics Institute, Yerevan, ARMENIA

E-mail: koryunoganesyan@yahoo.com

1. Induced Smith-Purcell Radiation in the Absence of Resonator

    A Smith-Purcell instability of 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 solution of dispersion equation is the mirror case, when the electron beam propagates above plane metal surface (mirror). The condition of the Thompson or Raman regimes of excitation does not depend on beam current and depends on the height of the beam above grating surface.

2. The Threshold Conditions for FELWI

    According to the main idea of Ref [1], a possibility of FELWI realization is strongly related to a deviation of electrons from their original direction of motion owing to interaction with the fields of undulator and co-propagating light wave. The deviation angle appears to be proportional to energy gained or lost by an electron during its passage through the undulator. Owing to this, the subsequent regrouping of electrons over angles provides regrouping over energies. In principle, a proper insallation of magnetic lenses and turning magnets after the first undulator in FELWI can be used in this case for making faster electrons running over a longer trajectory than the slower ones [2]. This is the negative dispersion condition, which is necessary for getting amplification without inversion [3].  It's clear that the described mechanism can work only if the interaction-induced deviation of electrons (with a characteristic angle a ) is lager than the natural angular width a_beam of the electron beam, a>a_beam (1).  As the energy gained/lost by electrons in the undulator and the deviation angle are proportional to the field strength amplitude of the light wave to be amplified, the condition (1) determines the threshold light intensity, only above which amplification without inversion can become possible. This threshold intensity is estimated below.

[Reference]

[1] D. E. Nikonov, M. O. Scully and G. Kuritski, Phys. Rev. E 54, 6780, (1996).

[2] A. I. Artemiev, M. V. Fedorov, Yu. V. Rostovtsev, G. Kuritski and M. O. Scully, Phys. Rev. Lett. 85, 4510, (2000).

[3] G. Kuritski, M. O. Scully and C. Keitel, Phys. Rev. Lett. 70, 1433, (1993); B. Sherman, G. Kuritski, D. E. Nikonov and M. O. Scully, Phys. Rev. Lett. 75, 4602, (1995).

Prof. George S Wang

Retired from Department of Physics, National Tsing-Hua University, TAIWAN

E-mail:

A Kind of Innovative Table Form of Analyzing Chinese Medicine Prescription

    The characteristics of a Chinese herbal medicine can be described as the four properties, the five flavours and the meridians.  By four properties we mean the four kinds: cold, hot, warm or cool.  The five flavours are the five kinds of taste: pungent (numbness, hot), sweet, sour (astringent), bitter (burnt) and salty.  By the meridians we mean, through the function of the meridians, the characteristics of a Chinese herbal medicine will affect the five internal organs (including the six collateral internal organs). Since the five flavours are closely related with the meridians, the tart flavor entering the liver for instance, we will only discuss the four properties and the meridians.

    The four properties of a Chinese herbal medicine, cold, hot, warm or cool are now quantitatively defined by cold-hot indexes. For ordinary Chinese medicines the cold-hot indexes are numerically defined as: - 2 for extreme cold, - 1 for cold, - 0.5 for little cold, 0 for neutral (neither cold nor hot), 0.5 for little hot or warm, 1 for hot, and 2 for extreme hot. The cold-hot value of a medicine is determined as the product of the cold-hot index of the medicine and the amount of this medicine used in the prescription in unit of Chinese Chans (CCn) (1 CCn = 3.75 grams).  The distribution and overall effects of cold-hot values of all medicines in the prescription are presented in a table form (Excel of Microsoft Office) according to meridians of the five internal organs of heart, liver, kidney, lung, and spleen ( including the six internal collateral bowels) as shown in the attached Excel form). 

    The academic value of this table-form analysis lies in the innovative ideas of scientifically applying cold-hot indexes and meridians to Chinese medicines and thus significantly expanding the scope of traditional pure characters prescription way used for thousands of years on Chinese medicine.  Its practical value, because of its ability to provide detail and actual information of cold-hot indexes and meridians of medicines used in a prescription, is to offer feasible practical advantages to both the doctor and the patient. Abundant examples will be given to illustrate.

Prof. Sun-Chong Wang

Institute of Systems Biology and Bioinformatics, National Central University, TAIWAN

E-mail: scwang@ncu.edu.tw

DNA Methylation Profiles in Monozygotic and Dizygotic Twins

    Twin studies have provided the basis for genetic and epidemiological studies in human complex traits. As epigenetic factors can contribute to phenotypic outcomes, we conducted a DNA methylation analysis in white blood cells (WBC), buccal epithelial cells and gut biopsies of 114 monozygotic (MZ) twins as well as WBC and buccal epithelial cells of 80 dizygotic (DZ) twins using 12K CpG island microarrays. Here we provide the first annotation of epigenetic metastability of 6,000 unique genomic regions in MZ twins. An intraclass correlation (ICC)-based comparison of matched MZ and DZ twins showed significantly higher epigenetic difference in buccal cells of DZ co-twins (P = 1.2 x 10^-294). Although such higher epigenetic discordance in DZ twins can result from DNA sequence differences, our in silico SNP analyses and animal studies favor the hypothesis that it is due to epigenomic differences in the zygotes, suggesting that molecular mechanisms of heritability may not be limited to DNA sequence differences.

Prof. Fa-Yueh Wu
Department of Physics, Northeastern University, USA
E-mail: fywu@lepton.neu.edu

    This talk begins with a review of known results on exact critical point of the q-state standard Potts model. The Potts model on kagome-type lattices is then considered. We show that the consideration of a duality relation for Potts models with multi-spin interactions leads to a conjectured determination of the critical point for kagome-type lattices. In the case of q = 1 the conjectured results agree extremely well with the recent highly accurate determination of bond percolation thresholds by Ziff and co-workers.

Prof. Jui-Ling Yu

Department of Applied Mathematics, Providence University, TAIWAN

E-mail: jlyu@pu.edu.tw

An Adaptive Optimal m-stage Runge-Kutta Methods for Solving Chemotaxis Systems 

    In this talk, we present a class of numerical methods for the reaction-diffusion-chemotaxis system which is significant for biological and chemistry pattern formation problems. It also has intrinsic merit as a non-linear parabolic model that admits highly nonlinear reaction terms and requires long term observations that pose challenges to conventional numerical methods. Along with the implementation of the method of lines, implicit or semi-implicit schemes are typical time stepping solvers to reduce the effect on time step constrains due to the stability condition. However, these two schemes are usually difficult to employ. In this talk, we propose an adaptive optimal time stepping strategy for the explicit m-stage Runge-Kutta method to solve reaction-diffusion-chemotaxis systems. Instead of relying on empirical approaches to control the time step size, variable time step sizes are given explicitly. Yet, theorems about stability and convergence of the algorithm are
provided in analyzing robustness and efficiency. Numerical experiment results on a testing problem and a real application problem are shown.