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

practice

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

Lattice

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

Results

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