Conferences / Workshops ( 2000~2011 ) / Seminars and Group Meetings
2006 NCTS Spring Workshop on Critical Phenomena and Complex Systems
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Date : |
30 March - 1 April 2006 [ Announcement ] |
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Place : |
Department of Physics, Chinese Culture University, Taipei 30 March - 31 March: at the Fei-Hwa Building (菲華樓) 1 April : at the restaurant of the International Hotel
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| Organized by : |
National Center for Theoretical Sciences (Critical Phenomena and Complex Systems focus group) Institute of Physics of Academia Sinica (Taipei) Department of Physics, Chinese Culture University
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| Contact Info. : |
Miss Chia-Chi Liu (Secretary,
Physics Division, NCTS)
Mr. Lee-Min Chang (鄭立明) (Department of Physics, Chinese Culture University)
Tel:(886)-2-28610511 ext.
25205; Fax(886)-2-28610577; E-mail:
crsspy@staff.pccu.edu.tw
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Hotel Info. : |
International Hotel (陽明山國際大旅館) Address: 台北市陽明山湖山路一段7號 Tel: (886)-2-28617100 Website: http://www.ihhotel.com.tw
If you need to reserve a room, please contact with Mr. Lee-Min Chang (鄭立明, Tel:(886)-2-28610511 ext. 25205 ). Hotel expense will be paid by yourself ($2,100NT for a single room with a twin bed, $2,500NT for a room with two beds).
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Speaker : |
Dr. Bidhan Chandra Bag Institute of Physics, Academia Sinica, TAIWAN
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| Title: |
Escape through a fluctuating energy barrier: resonant activation |
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| Abstract: |
In this presentation first I summarize the processes of noise driven escape of particle over a potential barrier, i.e., the well known Kramers’ problem [1], which is ubiquitous in a wide variety of physical, chemical and biological contexts [2]. Over the several decades the model and many of its variants have served as standard paradigms in various problems of physical and chemical kinetics to understand the decay rate of meta- stable system in the over-damped and under-damped limits [3] , the signature of non-Markovian effect [4], quantum and semi-classical corrections [5] to classical rate and related similar aspects. However, a surge of fresh interest in this topic wag triggered, not long ago, by Doering and Gadoua [6] who studied how the inter-well mean-first-passage time (MFPT) of a Brownian particle in a bi-stable potential depends on the correlation time t of the barrier fluctuations. They observed that this dependency may be non-monotonous and it has been termed "resonant activation" (RA). In many complex biological and physical systems fluctuations in activation energy is found to occur, e.g., in molecular dissociation dynamics [7], the binding of ATP and the release of ADP serve to randomly modulate the activation energy experienced by the motor protein as it travels along the biopolymer backbone [8], relaxation in glasses [9] etc. Very recently we have studied [10] the MFPT for a Brownian particle which is in an harmonic potential and escape through an unstable limit cycle from an attractor basin in presence of multiplicative colored and additive white noises. Our study shows that the MFPT first decreases and then increases after passing through a minimum as the noise correlation time is varied for a given variance of the colored multiplicative noise. The essential behavior is due to strange behavior of limit cycle since in the present model the concerned potential is linear. We have also shown that the MFPT increases linearly with t for a fixed value of the noise strength. It is in sharp contrast to what we observe in the calculation of the same in the case of fluctuations of nonlinear potentials. In the later situation the MFPT first increases nonlinearly then reaches to a limiting value. Our present study also demonstrates how the active Brownian parcels extracts energy from internal thermal fluctuations as well as external fluctuations.
References: J. Chem. Phys. 111, 10852 (1999); D. Banerjee, B. C. Bag, S. K. Banik and D. S. Ray, Phys. Rev. E 65,
021109
(2002).
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Prof. Chi-Ming Chen Department of Physics, National Taiwan Normal University, TAIWAN
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| Title: |
Structure Prediction and Folding Dynamics of Membrane Proteins
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| Abstract: |
Membrane proteins play a crucial role in many cellular and physiological
processes, but the knowledge of their high resolution structures and
folding mechanism is very limited due to the difficulties in
experiments. Recent advances in computer simulations now offer a
convenient tool to study these problems. Here we propose a three-step
process to predict the native structures of membrane proteins by
combining coarse-grained Monte-Carlo simulations and all-atom molecular
dynamics simulations. In particular, we have applied this approach to
obtain the structures of retinal proteins found in Halobacterium
salinarium membranes. The overall root mean square deviation in
coordinates of backbone atoms from the X-ray structure is 1.89 Å
for halorhodopsin, 1.92 Å for sensory rhodopsin II, and 2.64 Å
for bacteriorhodopsin. |
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Dr. Hueih Min Chen Institute of BioAgricultural Science, Academia Sinica
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| Title: |
Local stability in protein folding
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Dr. Nan-Yow Chen Institute of Physics, Academia Sinica
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| Title: |
Effective potentials for Folding Proteins
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| Abstract: |
The
problem of predicting the native structure of a protein for a given
sequence has been of great interest due to its relevancy to many fields
in biology. In this talk, a coarse-grained off-lattice model that is not
biased in any way to the native state is proposed to fold proteins. To
predict the native structure in a reasonable time, the model has
included the essential effects of water in an effective potential. Two
new ingredients, the dipole-dipole interaction and the local hydrophobic
interaction, are introduced and are shown to be as crucial as the
hydrogen bonding. This model has been tested successfully on more than
16 small proteins, of sizes from 12 to 56 amino acids and allows
successful folding of the wild-type sequence of protein G. |
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Dr. Yeng-Long Chen Institute of Physics, Academia Sinica
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| Title: |
Migration dynamics of DNA molecules under oscillatory microfluidic flow
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| Abstract: |
The
conformation and dynamics of DNA molecules in microchannels from 10-40
microns are investigated using dynamics simulation. Pressure-driven
oscillatory flow is applied in the channel. This results in the
stretching of the molecule due to shear, and surprisingly, induces DNA
migration towards the channel center. We developed a theoretical
understanding of this behavior. It has potential application in DNA
separation and analysis. |
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Dr. Shura Hayryan Institute of Physics, Academia Sinica
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| Title: |
Efficient Combination of Wang-Landau and Transition Matrix Monte Carlo Methods for Protein Simulations
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| Abstract: |
An efficient combination of the Wang-Landau and transition matrix Monte Carlo methods for protein and peptide simulations is described. At the initial stage of simulation the algorithm behaves like the Wang-Landau algorithm, allowing to sample the entire interval of energies, and at the later stages, it behaves like transition matrix Monte Carlo method and has significantly lower statistical errors. This combination allows to achieve fast convergence to the correct values of density of states. We propose that the violation of TTT identities may serve as a qualitative criterion to check the convergence of density of states. The simulation process can be parallelized by cutting the entire interval of simulation into subintervals. The violation of ergodicity in this case is discussed. We test the algorithm on a set of peptides of different lengths and observe good statistical convergent properties for the density of states. We believe that the method is of general nature and can be used for simulations of other systems with either discrete or continuous energy spectrum.
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Dr. Tai-Huang Huang Institute of Biomedical Science, Academia Sinica
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| Title: |
Challenges for Physicists in NMR-based structural Biology
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| Abstract: |
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Prof. Hoong-Chien Lee Department of Physics and Institute for Systems Biology and Bioinformatics, National Central University
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| Title: |
Emergence and spontaneous symmetry breaking in genome evolution by Cellular Automata
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| Abstract: |
How does a code emerge in a genome? Or, generally, how does a genome transform from a state of "nothingness" to a state of having something? Here we use the emergence of the DNA uptake signal sequence possessed by some competent human pathogens as a prototypical case study of the emergence problem in biology. We use the method of cellular automata to show that the emergence of USS in genomes may be expressed in terms of a first order transition, in which an invariance is spontaneously broken.
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Dr. Wen-Tau Juan Institute of Physics, Academia Sinica
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| Title: |
Single Molecule Studies of DNA Brushes
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| Abstract: |
Polymer brushes are widely applied to colloidal stabilization and surface lubrication. Studies of polymer coating on surfaces also have biological significance. Polysaccharide polymer coatings have been found on extremely malignant cancer cells, neural cells, and in some fetal cells. However, the physical properties of these polymer coatings and the reason for their existence are still generally little known. In this study, we introduce a novel technique to construct high density end-tethered DNA brushes at grafting density about 25 DNA/Rg2. Through the confocal and fluorescence microscopy techniques, static and dynamic behaviors of polymer brushes are studied both at the single molecule and mesoscopic levels for the first time. The entropy driven DNA swelling up to 7 micrometers has been demonstrated. The parabolic monomer density distribution along the swelling direction, which was proposed by S.T. Milner in 1988, has also been confirmed. High frequency thermal motions around the DNA backbone superposed by the low frequency collective modes are also observed at the single molecule level.
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Prof. Jung-Hsin Lin School of Pharmacy, National Taiwan University, and Institute of Biomedical Sciences, Academia Sinica, Taipei, TAIWAN
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| Title: |
On the Design of Global Optimization Algorithms for Prediction of Protein-Ligand Interactions
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| Abstract: |
One of the most important characteristics of the biological complex
problems is the rugged nature of the potential energy functions and the
spin glass-like “frustration” of conflicting interactions. Among these
complex global optimization problems, the protein-ligand docking
problems constitute an important subclass with a myriad of biochemical
and pharmaceutical applications. The potential energy surface of such
complex problems along a one-dimensional reaction coordinate is usually
high asymmetric and the true global minimum is often surrounded by many
deceptive local minima. Many computational strategies directly dealing
with such global optimization problem have been applied for the protein-ligand
interaction. However, comparison of these algorithms is difficult,
partly due to their widely varied implementations, the scoring
functions, and the choice of biological systems. In order to compare the
efficiency of different global optimization algorithms on a universal
ground, artificial potential energy functions that can capture the major
features of complex biological problems are needed. In the past, there
have been many benchmark functions proposed for evaluating different
global optimization algorithms, but few of them can really represent the
realistic situations of biological complex problems. In addition, the
complexity usually increases dramatically with dimensionality, whose
effect on the efficiency of the optimization algorithms should also be
investigated systematically. |
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Prof. Yuko Okamoto Department of Physics, School of Science, Nagoya University, JAPAN
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| Title: |
Generalized-ensemble algorithms for protein folding
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| Abstract: |
The difficulty in protein folding simulations comes from the fact that there exist an astronomically large number of local minima in the energy function of the protein systems, forcing any simulation to get trapped in one of the energy local minima. Novel algorithms that can alleviate this multiple-minima problem are thus in urgent demand.�We have been advocating the uses of generalized-ensemble algorithms.�WWith these algorithms we can explore wide range of the configurational space. The advantage of generalized-ensemble algorithms such as multicanonical algorithm and replica-exchange method lies in the fact that from only one simulation run, one can obtain not only the global-minimum state in energy but also various thermodynamic quantities as a function of temperature (for reviews, see Refs. [1,2]). In this talk, I will give details of generalized-ensemble algorithms including the latest examples [3-10].
References: [7] H. Okumura and Y. Okamoto, Chem. Phys. Lett. 391, 248-253 (2004). [8] H. Okumura and Y. Okamoto, Phys. Rev. E70, 026702 (2004). [9] H. Okumura and Y. Okamoto, J. Phys. Soc. Jpn. 73, 3304-3311 (2004). [10] H. Okumura and Y. Okamoto, J. Comput. Chem. 27, 379-395 (2006).
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| Title: |
Force fields for all-atom protein models
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| Abstract: |
With powerful simulation algorithms such as generalized-ensemble algorithms, we can make detailed comparisons of existing force fields, potential energy functions for the protein system. Six well-known versions of protein force fields, namely, AMBER94, AMBER96, AMBER99, CHARMM22, OPLS-AA/L, and GROMOS96, have been compared by generalized-ensemble MD simulations of two short peptides in aqueous solution [1,2].?We found large differences mong various force fields.�WWe then tried to optimize the force-field parameters so that they are most consistent with the Protein Data Bank [3-5].�WWe further proposed a new force-field function [6]. In this talk, I will present these results. References: [1] T. Yoda,Y. Sugita, and Y. Okamoto, Chem. Phys. Lett. 386, 460-467 (2004). [2] T. Yoda, Y. Sugita, and Y. Okamoto, Chem. Phys. 307, 269-283 (2004). [3] Y. Sakae and Y. Okamoto, Chem. Phys. Lett. 382, 626-636 (2003). [4] Y. Sakae and Y. Okamoto, J. Theor. Comput. Chem. 3, 339-358 (2004). [5] Y. Sakae and Y. Okamoto, J. Theor. Comput. Chem. 3, 359-378 (2004).
[6] Y.
Sakae and Y. Okamoto, J. Phys. Soc. Jpn. 75 (2006), in press. |
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| Title: |
Prediction of membrane protein structures by molecular simulations
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| Abstract: |
We have applied the replica-exchange Monte Carlo method to the prediction of transmembrane helix configurations of membrane proteins [1-4].𤪻Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing WWW servers such as SOSUI. In the second part, we perform a replica-exchange simulation of these transmembrane helices with some constraints and identify the predicted structure as the global-minimum-energy state. We have tested the method with the dimeric transmembrane domain of glycophorin A [1-3] and bacteriorhodopsin [4]. In this talk, I will present these results. References: [1] H. Kokubo and Y. Okamoto, Chem. Phys. Lett. 383, 397-402 (2004).
[2] H. Kokubo and Y.
Okamoto, J. Chem. Phys. 120, 10837-10847 (2004).
[4] H. Kokubo and Y.
Okamoto, Chem. Phys. Lett. 392, 168-175 (2004). |
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Prof. Zbigniew Struzik Graduate School of Education, The University of Tokyo, JAPAN Zbigniew.Struzik(a)p.u-tokyo.ac.jp
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| Title: |
Recent Progress and Unsolved Problems in Heart Rate Variability Analysis |
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Recent results in the analysis of human heart rate variability (HRV) will be discussed. Special attention will be paid to the contrast between the Criticality versus Cascade description of HRV complexity. Also will be addressed the insights obtained through modelling a physiologically sound control, analysing the effects of disease and ageing, and through controlled physiological experiments.
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| Title: |
Phase transition in S&P500: Is Statistical Analysis of Stock Prices useful ? |
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The recent discovery of phase transition and criticality in stock market fluctuations will be presented. The unexpected similarities and known differences from HRV (human heart rate variability) criticality will be addressed, as well as the issue of the predictability of critical events. The context of information cascade and analogies with hydrodynamic turbulence will also be discussed, together with a possibility of modelling the critical behaviour.
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| Title: |
Methodology Perspective on Time Series Analysis of Complex Systems Data |
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An overview of methodological approaches used for the analysis of time series data arising in complex systems, in particular of physiological origin, will be presented and accompanied by a brief introduction of the data currently available. Multiscale-type detrending approaches, including the continuous wavelet transformation, continuous detrended fluctuation analysis and multiscale probability density estimation will be among the techniques discussed. Future possibilities of physiological data acquisition using an intelligent Mobile Nurse platform will be suggested.
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Dr. Chih-Yuan Tseng Computational Biology Laboratory, Department of Physics, National Central University |
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| Title: |
Study of PrPC to PrPSc conversion of prion protein by MD simulation |
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| Abstract: |
In template-assistance model, normal prion protein (PrPC), the pathogenic cause of prion diseases such as Creutzfeldt-Jakob (CJD) in human, Bovine Spongiform Encephalopathy (BSE) in cow, and scrapie in sheep, converts to infectious prion (PrPSc) through an autocatalytic process triggered by a transient interaction between PrPC and PrPSc. Conventional studies suggest the S1-H1-S2 region in PrPC to be the template of S1-S2 -sheet in PrPSc, and the conformational conversion of PrPC into PrPSc may involve an unfolding of H1 in PrPC and its refolding into the -sheet in PrPSc. We have conducted a series of simulation experiments to test the idea of transient interaction of the template-assistance model. We found that the integrity of H1 in PrPC is vulnerable to a transient interaction that would alter the native dihedral angles at residue Asn143, which connects the S1 flank to H1, but not to interactions that alter the internal structure of the S1 flank, nor to those that alter the relative orientation between H1 and the S2 flank.
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Dr. Ming-Chya Wu Institute of Physics, Academia Sinica
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| Title: |
The Hilbert-Huang method and its applications to the analyses of physiologic and financial time series |
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