Date :

 12 August 2011

Place :

 12 August: 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. Yevgeni Mamasakhlisov

Yerevan State University

E-mail: y.mamasakhlisov@gmail.com

Charged Macromolecule in the Entropic Trap: The Effect of the Surface Roughness

  We consider a dsDNA as a charged long semiflexible chain and estimate its free energy in the entropic trap. The chain entropy in both the deep and the shallow slits, the electric energy and the elastic energy of the chain have been taken into account. From the obtained free energy, the kinetics and scaling behavior of the chain escaping from the entropic trap have been investigated. We find that the process of the escape occurs in two kinetic stages with different scalings. We also discuss the possible influence of the roughness of the surface.

Mr. Nguyen Truong Co

Saigon Inst Computat Sci & Technol, Thanh Pho Ho Chi Minh, Vietnam

E-mail: truongcophysics@gmail.com

Study of Fibril Formation Using Lattice Model

ß-structure fibrils, which occur due to protein misfolding proteins, associated with many prion diseases like Alzheimer, Parkinson, type II diabetes etc [1]. So the understanding mechanisms of their formation plays the important role in developing

effective drugs to treat them. All-atom simulations are a good way to solve this problem but they are rather expensive and can not be used to monitor the aggregation of many polypeptide chains. Therefore, to explore the universal physics principles gov-

erning fibril formation we use lattice models [2]. It is shown that the fibril formation time depends on intrinsic factors of polypeptide chains such as charge, hydrophobic interactions and the population of the fibril prone conformation in monomer state [3, 4]. We have also demonstrated the usefulness of lattice models in studying the crowding effect on oligomerization dynamics.

References:

[1] Protein Misfolding, Functional Amyloid, and Human Disease Fabrizio Chiti and Christopher M.Dobson   

     Annu.Rev.Biochem.2006.75:333-336

[2] Mai Suan Li, D. K. Klimov, J.E. Straub, and D. Thirumalai J. Chem. Phys.129,175101 (2008)

[3] H.B. Nam, M. Kouza, H. Zung, and Mai Suan Li, Relationship between population of the fibril-prone conformation in the 

     monomeric state and oligomer formation times of peptides: Insights from all-atom simulations J. Chem. Phys. 132, 165104

[4] Mai Suan Li, N.T. Co, G. Reddy, C-K Hu, J.E. Straub and D. Thirumalai Phys. Rev. Lett,105, 3218101(2010)

Miss Nguyen Truc Trang

Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam

E-mail: tructrang27@gmail.com

Estimation of Binding Free Energy by Different Force Fields

  Binding free energy estimation of a ligand to receptor DGbind, which is one of the most important subject in drug design has been studied by continually improved methods to achieve an estimation as much accurate as possible. Beside calculation methods, force fields used for modeling a ligand-receptor complex are expected to correlate the final binding results. This paper, thus figures out the influence of four main force fields, AMBER99SB, CHARMM27, OPLS-AA/L, and GROMOS96 43a1 on the binding affinity of Oseltamivir carboxylate to the wild-type and Y252H, N294S and H274Y mutants of glycoprotein neuraminidase from the pandemic A/H5N1 virus. Having used the Molecular Mechanic-Poisson Boltzmann Surface Area method, we have shown that DGbind, obtained by AMBER99SB, OPLS-AA/L, and CHARMM27 shows the high correlation level with available experimental data. They correctly capture the binding ranking Y252H-->WT-->N294S-->H274Y observed in experiments (P.J. Collins et al, Nature 453, 1258 (2008)). However, in term of absolute values of binding scores, results obtained by GROMOS96 43a1 are in the nearest range with experiments, while AMBER99SB and CHARMM27 are almost similar. OPLS-AA/L, which is applied to study binding of Oseltamivir to the influenza virus for the first time,gives rather big negative values for ΔG_bind.Our study suggests that force fields have pronounced influence on theoretical estimations of binding free energy of a ligand to receptor. The effect of all-atom models on dynamics of the binding pocket as well as on the hydrogen bond network between Oseltamivir and receptors is studied in detail.

Prof. Lei Wang

Department of Physics, Renmin University of China, Beijing, China

E-mail: phywanglei@ruc.edu.cn

Functional Heat Control in Microscopic Scale - from Thermal Diode, Thermal Transistor to Phononics

  Heat conduction and electric conduction are two fundamental energy transport phenomena with comparable importance in nature. However, they have never been treated equally by scientists. Electronics, which is based on the inventions of electronic transistor and other relevant devices that control electric flow, has led to an impressive technological development that has greatly changed our lives. But similar devices that allow the flow of heat to be controlled are still not available, despite many decades of research. Is ‘phononics’, the counterpart of electronics, which provides useful functions by microscopic heat controlling and thermal information processing, always a dream?

  The rapid developments that have taken place in the recent years are turning the phononics from a dream into reality. In this talk I will introduce those recently research progresses, mainly focus on the most important building blocks of phononics that realize various functions of heat flow control, including thermal diode that rectifies heat flow [1], thermal transistor that switches and modulates heat flow [2], thermal logic gates that perform basic logic operations by heat [3], and thermal memory that stores information by heat [4]. Although at this time those models are basically toy models, which have not been fully realized in experiment yet, we believe the light on the long way to phononics has already been turned on [5].

References:

[1] M. Terraneo, M. Peyrard, and G. Casati, Phys. Rev. Lett. 88, 094302 (2002);

     B. Li, L. Wang, and G. Casati, Phys. Rev. Lett. 93, 184301 (2004);

     B. Li, J. Lan, and L. Wang, Phys. Rev. Lett. 95, 104302 (2005).

[2] B. Li, L. Wang, and G. Casati, Appl. Phys. Lett. 88, 143501 (2006)

[3] L. Wang and B. Li, Phys. Rev. Lett. 99, 177208 (2007)

[4] L. Wang and B. Li, Phys. Rev. Lett. 101, 267203 (2008)

[5] L. Wang and B. Li, Physics World 21, no.3, 27 (2008)

Mr. Shih-Chieh Wang

Department of Physics, National Chung-Hsing University, Taichung, Taiwan

E-mail: scwang1979@gmail.com

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.

Dr. Johannes Voit

Director of Internal Models, German Savings Banks Association, Berlin, Germany

E-mail:johannes.voit@ekit.com

The Financial Crisis 2007 – 2009: How Did It Come? Will It Happen Again?

  I will give a biased overview of the events of the 2007 – 2009 financial crisis, and of bank and risk management issues related to it. The bias is due to my training as a physicist and my activity as a model builder both in physics and in finance.

  I will introduce the underwriting of prime and subprime loans, credit risk management, and loan securitization. I then discuss to what extent the packaging of loans into tradable “asset backed securities” is responsible for the crisis, and/or what else contributed to it.