Date :

 23-24, 26 March 2007

Place :

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

 24, 26 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

Anomalous latent heat in non-equilibrium phase transitions

Dr. Shura Hayryan

Institute of Physics, Academia of Sinica, TAIWAN

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

Enveloping Triangulation Method for Detection and Quantitation of Internal Cavities in Proteins

Dr. Yao-Chen Hung

Institute of Physics, Academia of Sinica, TAIWAN

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

Transitions form Partially to Globally Generalized Synchronization in Scale-free Networks of Chaotic Oscillators

    We investigate collective behaviors, especially synchronization, in scale-free networks consisting of symmetrically (bi-directionally) coupled chaotic oscillators.  Nevertheless complete synchronization (CS) and phase synchronization (PS) have been observed and well studied in networks with such a topology, to our knowledge, other levels of synchrony are still not found. Applying the auxiliary-system approach, generalized synchronization (GS) in scale-free networks is first explored, including the transitions from partial GS to global GS.  Our investigation reveals some dynamical importance. Besides a few specified coupling strategies, typically, CS is regarded as the form of synchronization proper of identical systems, while GS is expected to be achieved in coupled nonidentical systems. However, the present work shows that GS is realizable in a network of identical oscillators.  The counterintuitive outcome results from the heterogeneity of the degree (connectivity) of each node.  Notwithstanding the coupling is symmetry, numerical experiments show GS of each node is not achieved simultaneously. Generally the oscillator with a larger degree is entrained by a relatively smaller criterion of coupling strength. Such results not only give us an insight into the self-synchronization process, but also provide a potential application to estimate the essential nodes in a complex network. Moreover,  the intermittent behavior near the synchronization threshold is demonstrated to be the typical on-off intermittency  which obeys the -3/2 power law.

Prof. Jooyoung Lee

School of Computational Sciences, Korea Institute for Advanced Study, KOREA
E-mail: jlee@kias.re.kr

1. Unbiased Global Optimization of Lennard-Jones Clusters for N <= 201 Using the Conformational Space Annealing Method
    We apply the conformational space annealing method to the Lennard-Jones clusters and find all known lowest energy configurations up to 201 atoms, without using extra information of the problem such as the structures of the known global energy minima.  In addition, the robustness of the algorithm with respect to the randomness of initial conditions of the problem is demonstrated by ten successful independent runs up to 183 atoms.  Our results indicate that this method is a general and yet efficient global optimization algorithm applicable to many systems.

2. Folding of Small Proteins Using a Single Continuous Potential

    Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single continuous potential (united-residue force field). In all cases, collapse occurs at a very early stage, and proteins fold into their native-like conformations at appropriate temperatures. We also observe that glassy transitions occur at low temperatures. The simulation results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.
　

3. Multiple Sequence Alignment Using the Conformational Space Annealing
    We present a new method for multiple sequence alignment (MSA), which we call MSACSA.
The method is based on the direct and rigorous application of the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences.  The MSACSA is applied to two simple alignment sets as well as to a couple of MSA databases, the 82 families from the Balibase reference set 1 and the 366 families from the Homstrad set.  In all 450 cases, the energy of the lowest energy alignment by MSACSA is always less than or equal to the energy of the existing alignments.  In addition, when the accuracy of an alignment is measured on the reference alignment provided by the databases, MSACSA provides better alignments on average than the current top methods based on the progressive alignment.  Another major advantage of MSACSA is that it provides not just the global minimum alignment but also many distinct low-lying sub-optimal alignments for a given objective function.  This is due to the fact that CSA  can maintain the conformational diversity while searching low-energy conformational space.  This characteristics can help us to alleviate the problem arising from using an inaccurate score function.
　

Prof. Jung-Hsin Lin

Research Center for Applied Sciences & Institute of Biomedical Sciences, Academia Sinica, TAIWAN
E-mail: jlin@ntu.edu.tw

Targeting Loop Flexibility in Avian Influenza N1 for Drug Design

Prof. Yuo-Hsien Shiau

Department of Physics, National Dong-Hwa University, TAIWAN

E-mail: yhshiau@mail.ndhu.edu.tw

Nonlinear Analysis on Cardiac Dynamics: A Clinical Tool or a Research Toy?

Prof. Zbigniew Struzik

Graduate School of Education, The University of Tokyo, JAPAN

E-mail: zbigniew.struzik@gmail.com

1. On the Recurrence Time of Earthquakes: Insight from Vrancea (Romania) Intermediate-depth Events

    Although earthquakes are an extremely complex spatio-temporal phenomenon, certain simple general laws govern the statistics of their occurrence. The decay of aftershock activity after a large event is well described by a simple power-law, known as the Omori law. Moreover, the interoccurence times of earthquakes over wide areas have recently been described by universal scaling laws [Corral04]. However, in both cases, notable exceptions seem to occur. Intermediate and deep earthquakes may provide the key insight into why this is so, since due to the scarcity of aftershocks, these events are very suitable for analysis of earthquake interoccurrence times. In the talk, we will show that the interoccurrence time of (Vrancea) intermediate-depth earthquakes can be well explained using an exponential model. This sharply contrasts with the 'universal scaling law' recently proposed ([Bak02, Corral04]), and suggests that deviations from the exponential model characteristic of the scaling law result primarily from aftershocks in the case of intermediate-depth earthquakes, while reduced heterogeneity at depth compared to the shallow crust may be the main reason why Corral's model may be inadequate to describe intermediate-depth and deep seismic activity worldwide.

References:
[1] B. Enescu, Z.R. Struzik, K. Kiyono, On the Recurrence Time of Earthquakes: Insight from Vrancea (Romania) Intermediate-depth Events, preprint (2007), to appear.
[2] P. Bak, K. Christensen, L. Danon and T. Scanlon, Unified scaling law for earthquakes, Phys. Rev. Lett., 88, 178501 (2002).
[3] A. Corral, Long-term clustering, scaling and universality in the temporal occurrence of earthquakes, Phys. Rev. Lett., 92, 108501 (2004).
　

2. Statistical Physics of Human Heart Rate in Health and Disease

    Complex phenomena know several benchmarks, or 'hard' and to date unsatisfactorily understood problems. Human heart rate control is such a complexity benchmark in biophysics, consistently defying full explanation. Over the past thirty years, fluctuations in heart rate, often referred to as heart rate variability (HRV), have become a central topic in physiological signal analysis, serving as a vital non-invasive indicator of cardiovascular and autonomic system function. A Medline search reveals more than 8,000 papers to date, on different aspects of HRV - this in a discipline which is subject to
continued controversy and rapidly growing interest and scientific effort [Point:Counterpoint, 2006], closely following the exponential growth rate of the available computing power. In our recent work, heart rate regulation by the autonomic nervous system has been shown to display remarkable fundamental properties of scale-invariance of extreme value statistics [Kiyono et al, 2004] in healthy heart rate fluctuations, ubiquitously observed in physical systems at criticality, and to undergo a second order phase transition as a result of altered neuro-regulatory balance [Kiyono et al, 2005]. Most recently, we have shown this behaviour to depart from the critical scale invariance in the case of life-threatening CHF. Our new index, derived from the non-Gaussianity characteristic, has proved to be the only meaningful one among all known HRV based mortality predictors and to be independent of plasma brain natriuretic peptide concentration, another potent mortality predictor for CHF. We will speculate on possible mechanisms for the increased variability and complexity of heart rate for life-threatening CHF, as reflected in the intermittent large deviations, forming non-Gaussian 'fat' tails in the probability density function of heart rate increments and breaking the critical scale invariance observed in healthy heart rate, both in model and real life [Kiyono et al, 2004, 2005, Kotani et al 2005].

References:

[1] K. Kiyono, Z. R. Struzik, N. Aoyagi, F. Togo and Y. Yamamoto, Phase Transition in Healthy Human Heart Rate, Phys. Rev. Lett., 95, 058101 (2005).
[2] K. Kotani, Z. R. Struzik, K. Takamasu, H. E. Stanley and Y. Yamamoto, Model for Complex Heart Rate Dynamics in Health and Diseases, Phys. Rev. E, 72, 041904 (2005).
[3] Z. R. Struzik, J. Hayano, S. Sakata, S. Kwak and Y. Yamamoto, 1/f Scaling in Heart Rate Requires Antagonistic Autonomic Control, Rapid Communication, Phys. Rev. E, 70, 050901(R) (2004).
[4] K. Kiyono, Z. R. Struzik, N. Aoyagi, S. Sakata, J. Hayano and Y. Yamamoto, Critical Scale-invariance in Healthy Human Heart Rate, Phys. Rev. Lett., 93, 178103 (2004).
[5] K. Kiyono, J. Hayano, E. Watanabe, Z. R. Struzik, I. Kodama, H. Hishida and Y. Yamamoto, Non-Gaussian heart rate as an independent predictor of mortality of chronic heart failure patients, to appear.
[6] A. Malliani, C. Julien, G. E. Billman, S. Cerutti, M. F. Piepoli, L. Bernardi, P. Sleight, M. A. Cohen, C. O. Tan, D. Laude, M. Elstad, K. Toska, J. M. Evans and D. L. Eckberg, Cardiovascular variability is/is not an index of autonomic control of circulation, J. Appl. Physiol., 101(2), 684, (2006).

3. Time Series Analysis of Complex Systems Data at the Physiology Lab of the Faculty of Education, Tokyo University

    An overview of problems recently addressed within our group will be presented, with particular attention being paid to the methodological approaches used. The problems have as a common denominator complex dynamics, in particular of physiological origin, and range from the assessment of car drivers' alertness to the prediction of fatigue levels and panic attacks. The main types of analysis methods will be discussed, highlighting their general applicability.

Prof. Takahisa Yamato

Graduate School of Science, Nagoya University, JAPAN

E-mail: yamato@phys.nagoya-u.ac.jp

1. Signal Transduction of Photoreceptor Proteins.  I. Color Tuning Mechanism

    The peak in the solar spectral intensity at ground level occurs in the visible region (at 500 nm), where human vision has maximal sensitivity, determined by the optical property of the visual pigment. In general living organism adapt to a diverse range of environments by modulating the optical absorption spectra upon mutations via the protein-chromophore interaction. For example, the λ_max of different visual pigments cover a broad range of wavelength from 360 to 560 nm.
    Various theoretical studies have been carried out on the spectral  tuning mechanism of photosensory receptors. The theoretical prediction of the λ_max is a challenging problem for number of reasons: (a) the complexity of the system (b) involvement of the electronic excited state, and (c) the existence of multiple minium energy conformations. To overcome these difficulties, we developed a self-consistent hierarchical approach, called the Multi-Layer Self-Consistent Molecular Orbital (MLSCMO) method.  By using this method, we found a linear correlation between the theoretically predicted shifts and experimentally observed absorption spectra for various mutants of photoactive yellow protein, a small photosensory receptor. Excitation energies of mutants were evaluated by the combination of the high level ab initio calculation for the chromophore inside and the low level ab initio calculation for the surrounding protein environment. Importantly, the electronic states of these two regions were treated both as variables and they are solved consistently to each other. The protein-chromophore interaction has been accurately reproduced by this method.

References:

[1] T. Yamato, T. Ishikura, T. Kakitani, K. Kawaguchi, H. Watanabe, Spectral tuning of photoactive yellow protein, Photochemistry and Photobiology, in press.
[2] S. Yokoyama, T. Tada, T. Yamato, Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus, Photochemistry and Photobiology, in press.
[3] K. Kawaguchi, T. Yamato, Theoretical prediction of optical absorption peaks for photosensory
receptor mutants, Chem. Phys. Lett., 430, 386 (2006).

2. Signal Transduction of Photoreceptor Proteins.  II. Excited-State Dynamics

    In living organisms the excited-state properties of photosensory receptors are optimized to realize efficient photosignal transduction. For instance, the photoisomerization reaction of the 13-cis retinal to the all-trans form takes place within 200 fs in the rhodopsin environment. Computational techniques are useful to study the reaction-control mechanism of photosensory receptors at the atomic level. We show the unexpectedly important role of the protein environment in the primary step of the photoreaction of the yellow protein after light illumination. The driving force of the trans-tocis isomerization reaction was analyzed by a computational method. The force was separated into two different components: the term due to the protein-chromophore interaction and the intrinsic term of the chromophore itself. As a result, we found that the contribution from the interaction term was much greater than that coming from the intrinsic term. This accounts for the efficiency of the isomerization reaction in the protein environment in contrast to that in solution environments. We then analyzed the relaxation process of the chromophore on the excited-state energy surface and compared the process in the protein environment and that in a vacuum. Based on this analysis, we found that the bond-selectivity of the isomerization reaction also comes from the interaction between the chromophore and the protein environment.
References:

[1] A. Yamada, T. Ishikura, T. Yamato,  Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: Application to photoisomerization reaction. PROTEINS: Structure, Function and Bioinformatics, 55, 1070 (2004).
[2] A. Yamada, T. Ishikura, T. Yamato,  Role of protein in the primary step of the photoreaction of yellow protein. PROTEINS: Structure, Function and Bioinformatics, 55, 1063 (2004).
[3] A. Yamada, T. Yamato, T. Kakitani, S. Yamamoto,  Torsion potential works in rhodopsin, Photochemistry and Photobiology, 79, 476 (2004).
　

3. Signal Transduction of Photoreceptor Proteins.  III. Long-Range Intramolecular Signaling

    We report a theoretical/computational analysis of the energy flow relevant to the long-range intramolecular crosstalk between different regions in a photosensory receptor, photoactive yellow protein (PYP).  To analyze the energy flow in atomic detail, we derived a theoretical expression for the interresidue energy conductivity in terms of the time-correlation function of the interatomic energy flux. The values of energy conductivities were numerically evaluated by using a long molecular dynamics simulation trajectory of the PYP molecule in the aqueous solution environment. As a result, we detected several pathways for energy transfer relevant for the long-range intramolecular signalling of PYP.
References:

[1] T. Ishikura, T. Yamato, Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis. Chem. Phys. Lett., 432, 533 (2006).