DNA-Computing

Date: 2nd December 2004

Time: 13:30PM --16:30PM

Venue: Malacca Room, Traders Hotel

Admission: No registration charges are due for this tutorial, it is on a first come first serve basis.

Tutorial Abstract and Content

PART I - Introduction to DNA Computing, and DNA Computing-based Robotics

Speaker: Professor Osamu Ono (Electrical Engineering, Meiji University)

This Introductory segment of the Tutorial on DNA-based Computing (DNAC) will provide participants with the basic tools necessary to understand current research in DNAC, along with a discussion of potential applications to Robotics and Smart Machines. Following a brief review of DNA structure, an overview of the basic tools from molecular biology utilized for DNAC (e.g., DNA annealing, ligation, polymerization, restriction, PCR, etc.) will be undertaken. A discussion of the major, basic computational architectures of BMC (e.g., Adleman's algorithm for HPP, DNA Chip-based SAT) will then be provided, in each case presenting an animation detailing execution of a

simple example. Finally, attention will turn to advanced topics related to robotics and artificial intelligence in DNAC. In particular, a new robotics and smart machine will be presented, which implements a DNAC-inspired semantic model. A discussion of the model and implementation will be undertaken, with attention to both theoretical and chemical points of view.

PART II - ADVANCED TOPICS

Speaker: Professor Masami Hagiya, (Computer Science, University of Tokyo)

We survey the current directions of molecular computing research. The survey includes research on DNA self-assembly, in particular, computation by self-assembly of DNA tiles as advocated by Seeman and Winfree. Research on self-assembly has led to research on nanorobotics, i.e., research efforts to implement dynamic molecular devices. We then summarize future perspectives in the field, including self-assembly and nanorobotics. We also emphasize the importance of establishing systematic design principles for molecules and reactions, since the field still relies on ad-hoc trial-and-error for designing and implementing molecular systems. We call these systematic design principles "molecular programming". We also briefly touch on some contributions of our research group. Just as proteins fold into three-dimensional structures through interactions among their amino bases, DNA molecules can also take various forms other than the ordinary double helix through hybridization between complementary base sequences, including hairpins, bulges, and various junctions and tiles. Our group has been studying the computational power of simple hairpin DNA structures, and implementing various computational models based on hairpins. More concretely, we will explain computational models based on hairpin formation, hairpin dissociation, and iterated hairpin formation and dissociation. They have revealed that even hairpins have interesting computational applications and suggests that more complex structures will allow more powerful computation.

Presenters Contact Information, and Brief Biography:

Osamu Ono

Professor, Director, Institute of Applied DNA Computing

Faculty of Science and Technology

Meiji University

1-1-1, Higashimita, Tamaku, Kawasaki, Kanagawa, 214-8571 JAPAN

Email: ono@isc.meiji.ac.jp

• 1974, Bachelor of Engineering, Electrical Engineering, Waseda University.

• 1976, Master of Engineering, Electrical Engineering, Waseda University.

• 1979, Doctor of Engineering, Electrical Engineering, Waseda University.

• 1979-1986, Research Assistant/Lecturer, Department of Electrical Engineering, Meiji University.

• 1986-1991, Associate Professor, Department of Electrical Engineering, Meiji University.

• 1991-present, Professor, Department of Electrical Engineering, Meiji University.

• 2003-present, Director, Institute of Applied DNA Computing, Meiji University.

Masami Hagiya

Professor, Department of Computer Science

Graduate School of Information Science and Technology

University of Tokyo.

Email: hagiya@is.s.u-tokyo.ac.jp

• March 1980, B.Sc. from Department of Information Science, Faculty of Science, University of Tokyo.

• March 1982, M.Sc. from Department of Information Science, Graduate School of Science, University of Tokyo.

• April 1982, Research Associate,

• Research Institute for Mathematical Sciences, Kyoto University.

• March 1988, Doctor of Science from Kyoto University.

• October 1988, Associate Professor,

• Research Institute for Mathematical Sciences, Kyoto University.

• April 1992, Associate Professor, Department of Information Science, Faculty of Science, University of Tokyo.

• April 1993, Associate Professor, Department of Information Science, Graduate School of Science, University of Tokyo.

• November 1995, Professor, Department of Information Science, Graduate School of Science, University of Tokyo.

• April 2001, Professor, Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo.