DNA 8 – Preliminary Program


Monday, June 10 –Tutorials


  9:00-10:00                           Registration/Coffee


Morning Tutorials*


10:00-12:00 (Session A)                              Takashi Yokomori - Introduction to Natural Computing

10:00-12:00 (Session B)                              John A. Rose  - Nucleic Acid Sequence Design


*Tutorials are concurrent. Coffee break at 10:50-11:10.


12:00-14:00                          Lunch


Afternoon Tutorials**


14:00-16:00 (Session A)                              Toshikazu Shiba - Introduction to Biotechnology

14:00-16:00 (Session B)                              Nadrian C. Seeman - DNA Self-Assembly


**Tutorials are concurrent. Coffee break at 14:50-15:10.


Tuesday, June 11 – Conference


  9:00-  9:20                              Registration/Coffee

  9:20-  9:25                              Masami Hagiya        Opening Address


Session I --                          Molecular Evolution


Session Chair:    Yuzuru Husimi


  9:25-10:25                              Willem P. C. Stemmer (Invited Plenary Lecture)  - Expanded Natural

                                                 Computing: exploring many variations of directed molecular computing in



10:25-10:50                              John A. Rose, Mitsunori Takano, and Akira Suyama - A PNA-mediated

                                                 Whiplash PCR-based program for in vitro protein evolution

10:50-11:15                              K Wickiser, S. Chalamish-Cohen, S. Narashimhan, B. Sawichi, D. C.

                                                 Ward, and R. R. Breaker: Oligonucleotide sensitive hammerhead

                                                 ribozymes as logic gates


11:15-11:35                              Coffee Break and Poster Viewing

Session II --                         Computing by Self-assembly


Session Chair:    (Thomas H. LaBean)


11:35-12:00                              Phiset Sa-Ardyen, Natasa Jonoska, and Nadrian C. Seeman –

                                                 Self-assembling DNA Graphs

12:00-12:25                               Alessandra Carbone and Nadrian C. Seeman - Circuits and Programmable

                                                 Self-Assembling DNA Structures


12:25-14:00                              Lunch


Session III --                         DNA Computing and Nanotechnology


Session Chair:    (Nadrian C. Seeman)


14:00-15:00                              Tomoji Kawai (Invited Plenary Lecture) –DNA Nanotechnology:  Toward

                                                 Bio-Molecular Electronics


15:00-15:25                              Dage Liu, John H. Reif, and Thomas H. LaBean - DNA Nanotubes:

                                                 Construction and Characterization of Filaments Composed of TX –tile


15:25-15:50                              Elizaveta Kossoy, Michal Soreni, Yuval Shoham, and Ehud Keinan –

                                                 A Nanoscale Programmable Computing Machine with Molecular Input,

                                                 Molecular Software and Bio-Functional Output


15:50-16:20                              Coffee Break and Poster Viewing


Session IV --                          Applications to Graph Problems


Session Chair:    Masahito Yamamoto


16:20-16:45                              Ji Youn Lee, Soo-Yong Shin, Sirk June Augh, Tai Hyun Park, and

                                                 Byoung Tak Zhang - Temperature Gradient-Based DNA Computing for

                                                 Graph Problems with Weighted Edges       

16:45-17:10                              Takenaka Yoichi and Hashimoto Akihiro - Shortening the Computational

                                                 Time of the Fluorescent DNA Computing 

17:10-17:35                              Pilar de la Torre - How Efficiently Can Room at the Bottom Be Traded

                                                 Away for Speed at the Top?


18:00-20:00                              Reception



Wednesday, June 12-Conference


  9:00-  9:15                              Registration/Coffee


Session V --                         Applications to Biotechnology and Engineering


Session Chair:    (John McCaskill)


  9:15-  9:40                              Nao Nishida, Masatoshi Wakui, Yoko Ohashi, Katsushi Tokunaga, and

                                                 Akira Suyama: Highly specific and quantitative gene expression profiling

                                                 based on DNA computing

  9:40-10:05                              Subhayu Basu, David Karig, and Ron Weiss - Engineering Signal

                                                 Processing in Cells: Towards Molecular Concentration Band Detection      

10:05-10:30                              Dipankar Sen and Richard P. Fahlman - DNA Conformational Switches as

                                                 Sensitive Electronic Sensors of Analytes and as Components for Logic Gates


10:30-11:00                              Coffee Break and Poster Viewing 


11:00-12:00                              Akira Suyama (Invited Plenary Lecture)  -  Programmable DNA computer


12:00-14:00                              Lunch


Session VI --                           Nucleic Acid Sequence Design 


Session Chair:    (John A. Rose)


14:00-14:25                              Mirela Andronescu, Danielle Dees, Laura Slaybaugh, Yinglei Zhao,

                                                 Anne Condon, Barry Cohen, and Steven Skiena - Algorithms for testing

                                                  that DNA word designs avoid unwanted secondary structure 

14:25-14:50                              Russel Deaton, Junghuei Chen, Hong Bi, Max Garzon, Harvey Rubin,

                                                 and David Harlan Wood - A PCR-based Protocol for In Vitro Selection of

                                                 Non-Crosshybridizing Oligonucleotides

14:50-15:15                              Satoshi Kobayashi, Tomohiro Kondo, and Masanori Arita - On Template

                                                 Method for DNA Sequence Design

15:15-15:40                              Christine E. Heitsch, Anne E. Condon and Holger H. Hoos - From RNA

                                                 Secondary Structure to Coding Theory: A Combinatorial Approach


15:40-16:10                              Coffee Break and Poster Viewing

16:30-19:00                              Excursion

19:30-22:00                              Conference Dinner




Thursday, June 13 – Conference


  9:00- 9:15                              Registration/Coffee


Session VII --                         Theory


Session Chair:    (Giancarlo Mauri)


  9:15-  9:40                              Akihiro Takahara and Takashi Yokomori - On the Computational

                                                 Powers of  Insertion-Deletion Systems

  9:40-10:05                              Mihai Ionescu, Carlos Martin-Vide, Andrei Paun, and Gheorghe Paun –

                                                 Membrane Systems with Symport/Antiport: (Unexpected) Universality


10:05-10:30                              Pierluigi Frisco and Sungchul Ji -
                                                 Info-energy P Systems

10:30-10:55                              Daniela Besozzi, Claudio Ferretti, Giancarlo Mauri, and Claudio

                                                 Zandron - Parallel Rewriting P Systems with Deadlock


10:55-11:25                              Coffee Break and Poster Viewing


11:25-12:25                              Tom Head (Invited Plenary Lecture)  -  Splicing Systems:  Regular

                                                 Languages and Below


12:25-14:00                              Lunch


Session VIII --                          Autonomous Molecular Computation


Session Chair:    (Masayuki Yamamura)


14:00-15:00                              Bernard Yurke (Invited Plenary Lecture)  -  DNA based molecular motors


15:00-15:30                              Coffee Break/Poster Session


15:30-15:55                              John Reif - The Design of Autonomous DNA Nanomechanical Devices:

                                                 Walking and Rolling DNA

15:55-16:20                              Yaakov Benenson, Rivka Adar, Tamar Paz-Elizur, Zvi Livneh & Ehud

                                                 Shapiro - Molecular computing machine uses its DNA input as fuel

16:20-16:45                              Ken Komiya, Kensaku Sakamoto, Daisuke Kiga, and Shigeyuki

                                                 Yokoyama – Evaluation of the potential of an autonomous DNA computer

                                                 on the basis  of  molecular biology experiments


16:45-17:15                              Steering Committee – Closing Session