Date :

 09-11 June 2011

Place :

 09-11 June: The auditorium on 1st floor, 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

Speakers :

Prof. Chi-Ning Chen

Department of Physics, National Dong-Hwa University, Taiwan

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

Partition Function Zeros and the Foldability of HP Chains in the Cubic Lattice

  The loci of partition function zeros of the three-dimensional HP model are used to set up a criterion that determines the foldability of HP chains in the cubic lattice. The sequence space of a fixed chain length N is exhaustively explored, and kinetic Monte Carlo simulation is preformed to measure the folding times for all sequences with a unique sround state. The kinetic accessibility of the ground state is found to fit the criterion in which only equilibrium properties of HP chains are checked.

Prof. Joseph Jen-Tse Huang

Institute of Chemistry, Academia Sinica, Taiwan

E-mail:jthuang@chem.sinica.edu.tw

Induction of Amyloid Fibrils by the TDP-43 Fragments in Amyotrophic Lateral Sclerosis

  TAR DNA-binding protein 43 (TDP-43) has been identified as the major ubiquitinated aggregates in the inclusion bodies in the patients of amyotrophic lateral sclerosis (ALS) since 2006 and become a crucial culprit for ALS and related motor neuron diseases. Recent literature has further indicated that the major components of these aggregates are hyper-phosphorylated TDP-43 C-terminus. In an effort to clarify the conformational and physical properties of its disordered C-terminal domain, we have synthesized several peptide fragments and shown that only D1 within D1−4 can form twisted fibrils with cross-section approximately 11 nm in width under the incubation of phosphate buffer. In contrast, the D2−4 peptides all formed amorphous aggregates, showing different aggregation propensity. In addition to D1, two pathological mutant peptides, A315T and G294A, can also form fibrils that share similar shape and morphology with neuronal cytoplasmic inclusions. We propose that the residues with this region (287−322), which contains myriads of glycine repeats, may contribute significantly to the fiber formation as well as aggregation propensity. Moreover, from the spectroscopic properties in G294A including CD, fluorescence, and UV spectra, we found that this mutant peptide underwent random coil to β-sheet transformation and formed amyloid structure, providing insights into the nature of its aggregation vis a vis the other peptides.

Dr. Yao-Chen Hung

Department of Physics, National Chung Cheng University, Taiwan

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

Noise as a Potential Controller in Antagonist Inter-reacting Systems

  Noise has been recognized as an important factor in a range of physical and informational systems, including the elementary physics of life, such as cellular developments and functions. Here we use a stochastic differential equation to study the effects of noise on a typical system of antagonist actors, the Schlögl model. The phenomena of noise-induced bifurcation are observed. Detailed analysis demonstrates that the region revealing bistability can be modulated by the intensity of noise. This suggests that an external noise source can serve as an engineering tool for controlling antagonist inter-reacting systems in general, and in particular, for manipulating biochemical pathways.

Prof. Satoru G. Itoh

Research Center for Computational Science, Institute for Molecular Science, Okazaki, JAPAN

E-mail: itoh@ims.ac.jp

Replica-Exchange Methods and Comparison of their Sampling Eefficiency

  Effective samplings in the conformational space are necessary to predict the native structures of proteins. The replica-exchange method is one of the most well-known methods among the generalized-ensemble algorithms which realize effective samplings in the conformational space for biomolecular systems. However, the replica-exchange method (REM) has a difficulty for large systems that many replicas are needed to realize such effective samplings. In other words, huge amount of computation time is required in the replica-exchange method for the large systems. In order to overcome this difficulty, we proposed new Hamiltonian replica-exchange methods, recently. One of them is the van der Waals REM (VWREM) where the van der Waals radius parameters are exchanged between replicas although the temperatures are exchanged in conventional replica-exchange method. Other of them is the Coulomb REM (CREM) where the electrostatic charges are exchanged. I will introduce these two REMs and compare the efficiency of conformational samplings with the three methods, the conventional REM, VWREM, and CREM.

Prof. Nikolay Izmailyan

Yerevan Physics Institute, Yerevan, ARMENIA

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

Bijection between Spin S=(P^M-1)/2 and a Cluster of M Spins σ  = (P-1)/2

  We propose a general method by which a spin-S is decomposed into spins less than S. We have obtain the exact mapping between spin S=(P^M-1)/2 and a cluster of M spins σ = (P-1)/2. We have discuss the possible applications of such transformations. In particular we have show how a general d+1 dimensional spin-(P-1)/2 model with general interactions can be reduced to d-dimensional spin-S model with S=(P^M-1)/2.

Dr. Yuki Izumida

Department of Applied Physics, the University of Tokyo, JAPAN

E-mail: izumida@serow.t.u-tokyo.ac.jp

Efficiency of Finite-Time Carnot Cycle Working at Maximum Power: Molecular Dynamics Computer Simulations and Theoretical Upper Bound

  Although it is widely known that the Carnot cycle gives the upper bound of the efficiency of the heat engines, its power, the work output per unit time becomes 0 since it takes infinite time to do a finite amount of work. In 1975, Curzon and Ahlborn suggested a formula for giving the efficiency at the maximum power of the heat engines, which is determined only by the temperatures of the heat  reservoirs like the Carnot efficiency [1].
  In this talk, we show results obtained by performing molecular dynamics computer simulations of the finite-time Carnot cycle whose working substance is hard-sphere particles to confirm the prediction by Curzon and Ahlborn. The simulation data reveal that the Curzon-Ahlborn efficiency is always confirmed in the limit of the small temperature difference, which is consistent with the Onsager's linear irreversible thermodynamics [2]. But it can be violated when the temperature difference becomes larger.

  We also propose a new theory for describing the efficiency of the heat engines by extending the linear irreversible  thermodynamics [3]. It can explain the overall behavior of the simulation data and gives a general theoretical upper bound of the efficiency at the maximum power.

References:

[1] F. Curzon and B. Ahlborn, Am. J. Phys, 43, 22 (1975).

[2] C. Van den Broeck, Phys. Rev. Lett. 95, 190602 (2005).

[3] Y. Izumida and K. Okuda, arXiv: 1104.1542.

Prof. Wen-Tau, Juan

Institute of Physics, Academia Sinica, TAIWAN

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

Prof. Chai-Yu Lin

Department of Physics, National Chung Cheng University, Taiwan

E-mail: lincy@phy.ccu.edu.tw

Monte Carlo Studies for Ising Model through Several Ensembles

  Metadynamics (Wang-Landau algorithm) is based on the ensemble, called the metadynamics (Wang-Landau) ensemble, that every free energy (energy) corresponds to the same probability. For calculating the free energy of a LxL Ising model, we apply the canonical, Wang-Landau, metadynamics, and well-tempered ensembles to the sampling of the Monte Carlo procedure. We find that every ensemble leads to the accurate free energy landscape except for canonical ensemble. Finally, the comparison of efficiency for these ensembles is discussed.

Prof. Hisashi Okumura

Research Center for Computational Science, Institute for Molecular Science, Okazaki, JAPAN

E-mail:hokumura@ims.ac.jp

Multibaric-Multithermal Molecular Dynamics Simulations of Alanine Dipeptide and Chignolin

  Biomolecules such as proteins have complicated free energy surfaces with many local minima. Conventional molecular dynamics (MD) and Monte Carlo (MC) simulations in physical ensembles, such as the canonical and isobaric-isothermal ensemble, tend to get trapped in these local-minimum states. One of the powerful techniques to avoid this difficulty is generalized-ensemble algorithms such as the multicanonical algorithm. However, because the multicanonical simulation is performed in a fixed volume, neither the pressure dependence nor temperature dependence at certain pressure can be investigated as in experiments. To overcome this difficulty, the author recently proposed multibaric-multithermal MC [1-3] and MD [4-6] algorithms. In this ensemble, two-dimensional random walks in the potential-energy space and in the volume space are realized. I applied the multibaric-multithermal MD algorithm to an alanine dipeptide and a mini-protein, chignolin in explicit water [6, 7].

References:

[1] H. Okumura and Y. Okamoto: Chem. Phys. Lett. 383 (2004) 391-396.

[2] H. Okumura and Y. Okamoto: Phys. Rev. E 70 (2004) 026702 (14pages).

[3] H. Okumura and Y. Okamoto: J. Phys. Soc. Jpn. 73 (2004) 3304-3311.

[4] H. Okumura and Y. Okamoto: Chem. Phys. Lett. 391 (2004) 248-253.

[5] H. Okumura and Y. Okamoto: J. Comput. Chem. 27 (2006) 379-395

[6] H. Okumura and Y. Okamoto: Bull. Chem. Soc. Jpn. 80 (2007) 1114-1123.

[7] H. Okumura and Y. Okamoto: J. Phys. Chem. B 112 (2008) 12038-12049.
　

Prof. Chun-Wei Pao

Research Center for Applied Sciences, Academia Sinica, Taiwan

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

Prof. Michele Parrinello

Department of Chemistry and Applied Biosciences, ETH Zürich, Switzerland

E-mail: parrinello@phys.chem.ethz.ch

Through Mountains and Valleys* with Metadynamics

  Computer simulation methods based on empirical potentials or on an ab-initio approach over the years have made invaluable contributions to our understanding of many complex chemical and biochemical processes. However, in spite of amazing progress in software and hardware, severe limitations restrict the impact that these simulations might otherwise have. Such limits are evident, for instance, when it comes to study problems in nanosciences or in biochemistry. In either cases both the system size and the time scale of the process typically exceed present say capabilities. The time scale problem is particularly challenging and will be addressed here. The severity of the problem is witnessed by the plethora of methods proposed. We describe here metadynamics which has been introduced in our group [A. Laio and M. Parrinello, PNAS 99, 12562 (2002)]. We  also present recent progress which now allow very complex problems to be solved. We illustrate these capabilities with studies of large protein motions and of homogeneous and non homogeneous solid nucleation from the liquid.

* Rough translation of  the words  “per montagne e per valloni”  from  the air  “Non più andrai, farfallone amoroso“  of  “Le nozze di Figaro” of W.A Mozart and L. da Ponte

Prof. Davit Sahakyan

Yerevan Physics Institute, Yerevan, ARMENIA

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

Error Threshold, Extinction Threshold, and the Origin of Life

Prof. Manish Dev Shrimali

The LNM Institute of Information Technology, Jaipur, India

E-mail: m.shrimali@gmail.com

Phase-Flip Transition in the Absence of Time Delays in Coupled Oscillators

  We study the dynamics of relay coupled nonlinear oscillators. We observed that this form of relay coupling leads to a synchronization and phase-flip transition in chaotic as well as in periodic regime even in the absence of time-delay. The phase–flip transition from in- to anti- phase synchronous or vise-versa behavior is analyzed in the parameter plane by numerical studies of specific case of Rössler oscillator. The behavior of the dynamical systems is characterized using various indices such as average phase difference, frequency, and Lyapunov exponents.

Prof. Takashi SHIMADA

Dept. of Applied Physics, Graduate School of Engineering, The University of Tokyo. Japan

E-mail: shimada@ap.t.u-tokyo.ac.jp

Swimming in Sand

  One of the properties of granular materials that makes them unique and leads to striking and unexpected behaviors is their ability to act either as a solid, supporting a load like sand on a beach, or as a fluid, flowing freely as in avalanches. Inspired by the fact that some lizards living in deserts swim in sand, we here tackle a new problem: How a self-propelling object moves in granular bed? We studied this by an event-driven simulation with a simple model swimmer.
From the systematic analysis, we found that there exist two different optimum swimming frequencies for given parameters. One is the frequency which gives the fastest translational velocity. Another optimum frequency is for the efficiency of the swimming.

Prof. Kaito Takahashi

Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan

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

Can Water Catalyze Overtone Induced Reaction?: Simulation Study on Hydrate Fluoromethanol Clusters

Prof. Tina Yu

Department of Computer Science, Memorial University, Canada

E-mail:tinayu@cs.mun.ca

Program Evolvability Under Environmental Variations and Neutrality

  Biological organisms employ various mechanisms to cope with the dynamic environments they live in. One recent research reported that depending on the rates of environmental variation, populations evolve toward genotypes in different regions of the neutral networks to adapt to the changes. Inspired by that work, we used a genetic programming system to study the evolution of computer programs under environmental variation. Similar to biological evolution, the genetic programming populations exploit neutrality to cope with environmental fluctuations and evolve evolvability. We hope this work sheds new light on the design of open-ended evolutionary systems which are able to provide consistent evolvability under variable conditions.