Institute of Advanced Studies

Institute of Advanced Studies 南洋理工大学|高等研究所简讯|第六期 | 二零零八年七月 Newsletter of Institute of Advanced Studies | Issue 6 | July 2008 Editor-in-Chief: Profess...
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Institute of Advanced Studies 南洋理工大学|高等研究所简讯|第六期 | 二零零八年七月 Newsletter of Institute of Advanced Studies | Issue 6 | July 2008

Editor-in-Chief: Professor Kok-Khoo Phua, Founding Director, Institute of Advanced Studies, NTU

IAS Research Activities

Protein Folding Medicinal Orchid

IAS Short Course

Fluid Dynamics and Multi-Scale Problems

IAS Upcoming Events

Graduate Lecture Series PAQFT08 Les Houches School of Physics International Science Camp

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Mont-Blanc and the village of Les Houches, viewed from Les Houches School of Physics at Chamonix Valley.

IAS Research Activities

A Stochastic Approach to the Problem of Protein Folding The problem of protein folding is one of the biggest unsolved mysteries in mankind. It is stated that the sequence of amino acid residues, which form the basic units of a polypeptide chain, shall determine the final native structure of a protein, and hence its biological function. Recently, Professor Kerson Huang, an Emeritus Professor of Physics from the Massachusetts Institute of Technology (MIT) has collaborated with Dr. Lock-Yue Chew from the School of Physical and Mathematical Sciences (SPMS), Nanyang Technological University (NTU), to search for a solution to this problem through the approach of stochastic processes.

the protein folding problem since 2006. Other researchers working in the same team with Professor Kerson Huang include Dr. Jin-Zhi Lei and Dr. Wei-Tao Sun from the Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University. During the early stages of the research, the protein is being modeled by backbone molecules only. With the consideration of hydrophobic interaction alone, CSAW is able to fold the protein such that the hydrophobic amino acid residues are being shielded by the hydrophilic amino acid residues, demonstrating the hydrophobic effect. Subsequently, by adding the hydrogen bonding interaction into the model, CSAW then accomplishes the folding of the secondary α-helix protein structure.

At the Zhou Pei-Yuan Center for Applied Mathematics in Tsinghua University, Beijing. From left: Dr. Jin-Zhi Lei, Dr. Lock-Yue Chew, Prof. Kerson Huang, Mr Yee-Woon Lim. The backbone molecular configuration of a protein with an α-helix structure. Professor Kerson Huang envisages that a more efficient way to fold a protein is to put it under the action of random forces. He has developed a theoretical model based on the concept of Conditioned Self-Avoiding Walk (CSAW). In this model, the initial unfolded protein chain is being treated as a random coil, which then proceeds to fold by performing a Self-Avoiding Walk (SAW) in configuration space, under the conditions of intra- and inter-molecular interactions such as the hydrophobic forces, the hydrogen bonding effects, and electrostatic interaction. Mathematically, CSAW can be formulated as a generalized Langevin equation. In practice, the model is implemented on a computer by combining SAW with Monte Carlo simulation. CSAW is a paradigm initiated by Professor Kerson Huang, which has been further enhanced in later stages through collaborative work with other researchers. Being a regular visiting professor to the Institute of Advanced Studies (IAS) in NTU, Professor Kerson Huang has started the collaborative research with Dr. Chew on

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Just before Dr. Chew’s visit to Beijing in June 2007 together with his graduate student Mr. Yee-Woon Lim, a further improvement on the CSAW model has been achieved by Dr. Sun through the addition of the electrostatic interaction. Dr. Sun has developed an allatom model in CSAW, and with the use of the amino acid sequence obtained from the Protein Data Bank, he has successfully folded the secondary β-sheet protein structure of the 3AIT protein for the first time. This is an important progress for the research team as the folding of a β-sheet is a very challenging task computationally. The research on the problem of protein folding at IAS is still growing, and is believed to have a large potential in solving the mystery of protein folding, judging from the results obtained so far. New researchers are constantly being recruited into the team, to further develop and enhance the CSAW model. Hon-Wai Leong PhD student Physics and Applied Physics School of Physical and Mathematical Science

IAS Research Activities

Chinese Orchid (Gastrodia elata Blume) as a Medicinal Herb The use of orchids as herbal medicine has a long history in China . Gastrodia is one of the three orchids listed in the earliest known Chinese Materia Medica (Shennon bencaojing) [ca, 100AD]. In China, the Gastrodia elata tubers are commonly used to treat various nerve related symptoms, include epilepsy. However, there is rather limited knowledge about these potentially life-saving bioactive compounds, their interaction characteristics, and the molecular mechanism of their purported actions in these medicinal orchids.

as Chih Chien (red arrow) or “Tienma” (literal translation: “heavenly hemp”). Based on scientific studies, the bioactive compounds in GE are gastrodin (GA), 4-hydroxybenzyl alcohol (4HBA) and vanillyl alcohol (VA), with GA being the major active component. These compounds are pharmacologically active which possess anti-inflammatory, anti-coagulation, anti-angiogenic and anti-convulsive properties. Our research group had improved upon the isolation method to extract GA and VA with pressurized liquid extraction at room temperature and also with two green-solvent extraction methods, namely Pressurized Hot Water Extraction (PHWE) and Microwave-Assisted Extraction (MAE). As a substitute for the usage of organic solvent, water was used as the extraction solvent for extraction works. The advantages of using water include its cheaper cost, availability and more environment-friendly disposal. The marker compounds present in the plant extracts were determined by a reversed-phase High Performance Liquid Chromatography*. This is a collaborative research between National Institute of Education and Institute of Advanced Studies, NTU.

The Gastrodia elata flower. Gastrodia elata Blume (GE) is a chlorophyll-free orchid found in tropical Asia, Japan and China. A photograph of the orchid is shown above. Flowers are brownish. The sepals and petals are united, forming a cylindrical tube about 1.25cm long. The growth and maturity of this orchid rely on a special relationship with two fungi: Mycena osmundicola, which provides nutrients to the seed during germination, and Armillaria mellea, which invades the sprouted tuber and provides nutrients and energy. Matured rhizomes or tubers are oblong, slightly curved and about 10-17 cm in length as shown in the photographs below. In Chinese medicinal practice, this orchid is known

Gastrodia elata grown in 3 different culture media.

Chin-Chye Teo Research Associate Institute of Advanced Studies

*A list of publications: (1) ES Ong, MY Heng, SN Tan, JWH Yong, HJ Koh, CC Teo, CS Hew Determination of gastrodin and vanillyl alcohol in Gastrodia elata Blume by pressurized liquid extraction at room temperature J. Sep. Sci. 2007, 30, 2130-2137 (2) CC Teo, SN Tan, JWH Yong, CS Hew, ES Ong Evaluation of the extraction efficiency of thermally labile bioactive compounds in Gastrodia elata Blume by pressurized hot water extraction and microwaveassisted extraction J.Chromatogr. A 2008, 1182, 34-40

Photograph of dried tuber of Gastrodia elata. 3

IAS Short Course

Intensive Graduate Course on Computational Methods for Fluid Dynamics and Multi-Scale Problems An intensive graduate course on Computational Methods for Fluid Dynamics and Multi-Scale Problems, jointly organized by the Institute of Advanced Studies (IAS) and the School of Physical and Mathematical Sciences (SPMS) in Nanyang Technological University (NTU), was successfully held at the Nanyang Executive Centre from 5 to 10 May 2008.

and awards including the Computational and Applied Sciences award from USACM (United States Association for Computational Mechanics) and SIAM (Society for Industrial and Applied Mathematics) Wilkinson Prize. He is also the founding Editor-in-Chief of the SIAM interdisciplinary Journal “Multi-scale Modeling and Simulation” from 2002 to 2007.

The course aimed to introduce efficient computational tools applicable to a broad range of science and engineering problems, such as fluid dynamics, image processing, porous media and composite materials. The methodologies and techniques for algorithm design, numerical analysis and realizations of some fundamental methods focused in this course are essential for exploring and inventing computational apparatuses for various complicated and challenging applications. Some recent advances and frontiers in applied mathematics, together with emerging engineering applications, were also reported during the lectures.

The course attracted more than 40 graduate and undergraduate students, research staff and faculty members from the College of Engineering and the College of Science, of whom 19 registered for credit. Participants were actively engaged in the discussions. They had not only gained a better and deeper understanding of the topics covered, but also a broader appreciation of the applications of the computational methods which provided them with a useful tool for future research.

The course was conducted by Professor Thomas Hou, Charles Lee Powell Professor of Applied and Computational Mathematics, from California Institute of Technology (Caltech), USA. Professor Hou is a leading applied mathematician with research interests centered around developing analytic tools and effective numerical methods for vortex dynamics, interfacial flows, and multiscale problems. He has received numerous honours

At the end of the course, there is no doubt that the participants benefited a lot from what Professor Hou had taught and shared. Professor Hou’s visit certainly enhanced our research capability in the field of computational methods for fluid dynamics and multiscale problems. Li-Lian Wang Assistant Professor Division of Mathematical Sciences School of Physical and Mathematical Sciences

Professor Thomas Hou (standing, eighth from the left) and students who attended the graduate course on “Computational Methods for Fluid Dynamics and Multi-scale Problems”.

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IAS Upcoming Events

Graduate Lecture Series by Invited Speakers: Prof Anthony Leggett, Prof Kerson Huang & Prof N P Chang Date: 28 – 30 July 2008 Venue: Nanyang Executive Centre Lecture Room 1 Invited Speaker

Topic

Prof Anthony Leggett

“Introduction to Superconducting Qubits” 

Prof Kerson Huang

“Pure Mathematics and the Real World” • Prime Numbers and Bose-Einstein Condensation • Partitio Numerorum, the Fourth Law of Thermodynamics, and Precursor to String Theory • Renormalization: Why Truth is Beauty

Prof N P Chang

“Topics in Quantum Physics” • Topology & Quantization • Symmetry Principles in Physics • Cosmic Questions in Physics” Sir Anthony James Leggett is John D. and Catherine T. MacArthur Chair and Center for Advanced Study Professor of Physics at the University of Illinois at Urbana-Champaign. He is widely recognized as a world leader in the theory of low-temperature physics, and his pioneering work on superfluidity was recognized by the 2003 Nobel Prize in Physics. He has shaped the theoretical understanding of normal and superfluid helium liquids and strongly coupled superfluids. He set directions for research in the quantum physics of macroscopic dissipative systems and use of condensed systems to test the foundations of quantum mechanics.



His current research focuses on cuprate superconductivity, conceptual issues in the foundations of quantum mechanics and superfluidity in highly degenerate atomic gases.



(Adapted from Wikipedia)

Kerson Huang, Emeritus Professor of Physics, at M.I.T., was born in 1928 in Nanning, China. He received his S.B. (1950) and Ph.D. (1953) at MIT. After a brief stint at the Institute of Advanced Study, Princeton, he joined the Physics Faculty at MIT in 1957. His research in Theoretical Physics included works on Bose-Einstein Condensation and Quantum Field Theory. Professor Huang devotes his time to research on Biophysics. He is a Fellow of the American Physical Society and the American Academy of Arts and Sciences, and is the author of a number of textbooks in Statistical Mechanics, Quantum Field Theory and Statistical Physics. Other works include an English translation of the I Ching (“Yi Jing” in Mandarin), and a translation of the Rubaiyat of Omar Khayyam into Chinese classical quantrains. Professor Huang is currently Senior Fellow of the Institute of Advanced Studies, NTU. Ngee-Pong Chang is Professor of Physics at City College of New York, CUNY. He received his Ph.D. in Physics from Columbia University, specializing in Theoretical High-Energy Physics. Professor Chang is also a Fellow of the American Physical Society, and a Fellow of the Japan Society for Promotion of Science. Professor Chang is currently appointed as Nanyang Professor at Nanyang Technological University and Senior Fellow, Institute of Advanced Studies, NTU.

For more information and registration. please visit http://www.ntu.edu.sg/ias. 5

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IAS Upcoming Events

About Les Houches School of Physics The theoretical physics summer school was founded in 1951 by a young theoretical physicist, Cecile DeWitt. Her goal was to provide the young students with a training that was not available at their university, owing to the destitute condition of French science at that time.

weeks, help stimulate exchanges among the international community. A special feature of the Les Houches School is that its students and professors share a life in common: everyone stays in close proximity and partakes in academic and recreational activities throughout the entire school period.

Scattered in distant centres, trainee physicists had little access to original publications and a huge gap separated them from physics specialists. Thus was born the concept of a summer school: for 8 weeks, twenty students, French or foreigners, could meet specialists that were known internationally both for their scientific and for their teaching ability.

Each summer school at Les Houches attracts roughly 50 young PhDs students or postdocs, together with fifteen or so professors of world reputation who teach them high level courses. The length of these sessions allows in-depth work in which formal lectures are backed up by study groups under the supervision of a tutor.

The Les Houches School of Physics is currently located in the Chamonix Valley, above the village of Les Houches. Facing Mont-Blanc, the school aims to train physicists of all levels, in close connection with related sciences such as biology, chemistry, mathematics and engineering or economy. It is a non-profit organization run by University Joseph Fourier and the Institut National Polytechnique de Grenoble in France. Sessions, lasting from one to five

Bonds forged among participants are long lasting and each class persists as a scientific community for years. Lectures delivered during these sessions are published in the following year and often become basic references. These form a corpus of fundamental courses in developing research areas, which owing to the almost inevitable division into disciplines, no ordinary university program can offer.

Les Houches School of Physics in Singapore Les Houches is a very successful and prestigious program in Europe since many years. However, not many of the participants come from Asian countries. Students and young researchers in Asia generally find it difficult and expensive to travel and stay for a long period in Europe for the summer schools or the advanced schools at Les Houches. Motivated by the original purpose of the Les Houches establishment, which is to provide high level scientific training for those who lack the opportunity in their own

institutions, a special session of the Les Houches School of Physics will be held from 29 June to 24 July 2009 at Nanyang Executive Centre, Nanyang Technological University. Based on Singapore’s good connectivity to foreign countries, neighbouring and beyond, participants from Asian countries will be able to meet fellow participants flying in from France and other European countries in a unique blend of cultural and scientific interactions, facilitating future links between these distant parts of the world.

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IAS Upcoming Events

International Science Camp: Interaction with Nobel Laureates

Following the successful running of the Science Education Symposium held in conjunction with the Conference in Honour of CN Yang’s 85th Birthday in November 2007, an International Science Camp for the international students and teachers will be jointly organized by IAS, Ministry of Education and Hwa Chong Institution in January 2009. With attendance of several invited Nobel Laureates, it is proposed that the camp be held annually. The camp will be externally funded by MOE. Designed for students aged 16-17, the camp aims to develop in them a deeper

understanding of the scientific inquiry approach and scientific mindset of curiosity, questioning, postulating and verifying. Being a residential camp, local and overseas participants will have the opportunity to interact with Nobel Prize Winners at a more personal and informal level, enabling them to appreciate the personal qualities of great scientists, including broad-based knowledge, diverse interests, deep passion and tenacity. The focused on Physics and emerging technologies may hopefully nurture an interest in the students to pursue a course of study and career in the fields.

Editorial Board

Contact Information

Editor-in-Chief Kok-Khoo Phua

Institute of Advanced Studies Nanyang Executive Centre 60 Nanyang View #02-18 Singapore 639673

Members Ngee-Pong Chang Choy-Sin Hew Kerson Huang Leong-Chuan Kwek Shuyan Xu Wuan-Suan Ang Toh-Miang Ng Chris Ong Shirley Seet

Tel: (65) 6790 6491 Fax: (65) 6794 4941 Email: [email protected] Website http//www.ntu.edu.sg/ias

ISSN: 1793 5687