Summary of Research Project Results Under the JSPS FY2000
"Research for the future Program"



1.Research Institution University of Tokyo
 
2.Research Area Integrated Fields
 
3.Research Field Information on Life Systems
 
4.Term of Project FY1996〜FY2000
 
5.Project Number 96I00101
 
6.Title of Project Theory and Construction of Molecular Computers

7.Projetct Leader
Name Institution,Department Title of Position
Masami Hagiya University of Tokyo, Department of Science Information, Graduate School of Science Professor

8.Core Members

Names Institution,Department Title of Position
Yuzuru Husimi University of Saitama, Department of Functional Materials Science Professor
Akira Suyama University of Tokyo, Institute of Physics, Graduate School of Arts and Sciences Associate Professor
Kensaku Sakamoto University of Tokyo, Department of Biophysics and Biochemistry, Graduate School of Science Research Associate

9.Cooperating Researchers

Names Institution,Department Title of Position
Masayuki Yamamura Tokyo Institute of Technology, Department of Computational Intelligence and System Science, Graduate School of Science and Engineering Associate Professor
Masanori Arita Electrotechnical Laboratory, Supermolecular Science Division Research Scientist
Akio Nishikawa Osaka Electro-Communication Junior College, Department of Electronics and Information Technology Associate Professor

10.Summary of Research Results

Yokomori's group studied (1) multi-tube model (2) design and prediction of reactions (3) molecular computation and learning Boolean expressions (4) application of DNA computing to gene expression analysis.
Arita and Nishikawa tried to apply the m-balance index to the design and analysis of DNA sequences. Rose designed sequences for DNA chips according to computational incoherency. He also proposed and analyzed the use of anti-sense PNA to improve Whiplash PCR.
Suyama's group developed the DNA computer that automates DNA computation reactions, and succeeded in solving a 6-variable 10-clause 3-SAT problem. They also developed the universal DNA chip using DNA-coded numbers based on the DNA computer.
Sakamoto's group continued to develop Hairpin Engines. As for the DNA state machine (Whiplash PCR), they succeeded in realizing 8 successive state transitions autonomously.
Hagiya tried computational analysis of the SAT Engine
Sakamoto tried to artificially engineer the specificity of the enzymes involved in genetic code translation.
Yamamura's group continues to develop the aqueous computer, and made reliability experiments on the newly proposed implementation by PNA invading into double-strand DNA.
Husimi's group analyzed the mechanism of autonomous evolution of amplification from 3SR to RNA-Z-like hairpin or CATCH within the natural selection evolutionary reactor. They also proposed the use of anti-sense DNA of the promoter sequence for inhibiting the hairpin amplification, and tried to solve the problem of learning binary DNFs.
Nishikawa proposed the DNA nanotechnology that combines the top-down structure formation with AFM and the bottom-up structure formation by self-assembly of DNA, and began realizability experiments.

11.Key Words

(1)DNA computing、(2)molecular computing、(3)computational model
(4)formal language、(5)theory of computing、(6)simulation
(7)DNA chip、(8)gene expression analysis、(9)nanotechnology

12.References

[Reference Articles]
Author Title of Article
T. Aita, Y. Husimi Fitness landcape of biopolymers and efficient optimization strategy in evolutionary molecular engineering
Journal Volume Year Pages Concerned
Proc. of 6th Int. Sympo. on A-life and Robotics Vol.6 2001 365-368

Author Title of Article
T. Aita, Y. Husimi Theory of an Evolutionary Molecular Engineering using Simultaneous Accumulation of Advantageous Mutations
Journal Volume Year Pages Concerned
J. Theoret. Biol. Vol.207 2000 543-556

Author Title of Article
T. Aita, Y. Husimi Adaptive walks by the fittest among finite random mutants on the Mt. Fuji-type fitness Landscape II The effect of small nonadditivity
Journal Volume Year Pages Concerned
J. Math. Biol. Vol.41 2000 207-231

Author Title of Article
T. Aita, S. Urata, Y. Husimi From amino acid Landscape to protein landscape: Analysis of genetic codes in terms of fitness landscape
Journal Volume Year Pages Concerned
J. Mol. Evol. Vol.50 2000 313-323

Author Title of Article
T. Aita, H. Uchiyama, T. Inaoka, M. Nakajima, Y. Husimi Analysis of local fitness landscapes with a model of the rough Mt. Fuji-type Landscape:Application to prolyl endopeptidase and thermolysin.
Journal Volume Year Pages Concerned
Biopolymers Vol.54 2000 64-79

Author Title of Article
M. Arita, A. Nishikawa, M. Hagiya, K. Komiya, H. Gouzu, K. Sakamoto Improving Sequence Design for DNA Computing
Journal Volume Year Pages Concerned
Proceedings of the Genetic and Evolutionary Computation Conference(GECCO 2000)   2000 875-882

Author Title of Article
M. Arita, K. Asai, T. Nishioka Reconstructing Metabolic Pathways with New Enzyme Classification
Journal Volume Year Pages Concerned
German Conference in Bioinformatics(GCB'00)   2000 99-106

Author Title of Article
M. Arita Metabolic Reconstruction using Shortest Paths
Journal Volume Year Pages Concerned
Simulation Practice and Theory Vol.8 No.2 2000 109-125

Author Title of Article
M. Arita Graph Modeling of Metabolism
Journal Volume Year Pages Concerned
Journal of Japanese Society for Artificial Intelligence (JSAI) Vol.15 No.4 2000 703-710

Author Title of Article
M. Hagiya From Molecular Computing to Molecular Programming
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers, Lecture Notes in Computer Science (DNA6)   2001  

Author Title of Article
T. Higuchi, S. Tsutsui M. Yamamura Theoretical Analysis of Simplex Crossover for Real-Coded Genetic Algorithms
Journal Volume Year Pages Concerned
Proc PPSN VI   2000 365-374

Author Title of Article
Y. Ito, M. Suzuki, Y. Husimi A novel T-vector using green fluorescent protein as an indicator
Journal Volume Year Pages Concerned
Gene Vol.245 2000 67-77

Author Title of Article
S. Kobayashi, V. Mitrana Gh. Paun, G. Rozenberg Formal Properties of PA-Matching
Journal Volume Year Pages Concerned
Theoretical Computer Science   2001  

Author Title of Article
S. Kobayashi, Y. Sakakibara Multiple Splicing Systems and the Universal Computability
Journal Volume Year Pages Concerned
Theoretical Computer Science   2001  

Author Title of Article
S. Kobayashi Concentration Prediction of Pattern Reaction Systems
Journal Volume Year Pages Concerned
Pre-Proc. of Workshop on Multiset Processing CDMTS Research Report Series 140   2000 112-123

Author Title of Article
K. Komiya, K. Sakamoto, H. Gouzu, M. Arita, S. Yokoyama, A. Niashikawa, M. Hagiya Successive State Transitions with I/O Interface by Molecules
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers, Lecture Notes in Computer Science(DNA6)   2001  

Author Title of Article
K. Komiya, K. Sakamoto, H. Gouzu, M. Arita, S. Yokoyama, A. Niashikawa, M. Hagiya Successive State Transitions with I/O Interface by Molecules
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers, Preliminary Proceedings(DNA6)   2000 21-30

Author Title of Article
A. Nishikawa, M. Yamamura M. Hagiya DNA Computation Simulator Based on Abstract Bases
Journal Volume Year Pages Concerned
Soft Computing   2001  

Author Title of Article
S. J. Park, M. Yamamura Using Genetic Algorithm to Detect Structural Similarities in Proteins
Journal Volume Year Pages Concerned
Proc. BRGS2000 Vol.2 2000 201-203

Author Title of Article
G. Paun, T. Yokomori Simulating H systems by P systems
Journal Volume Year Pages Concerned
Journal of Universal Computer Science Vol.6 No.1 2000 178-193

Author Title of Article
J. A. Rose, A. Suyama M. Hagiya, R. J. Deaton An Antisense Antidote for Whiplash PCR
Journal Volume Year Pages Concerned
IPSJ Symposium Series Vol.2000 No.16 2000 101-108

Author Title of Article
J. A. Rose, R. J. Deaton The fidelity of annealing-ligation: A theoretical analysis
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers(DNA6), Preliminary Proceedings   2000 207-221

Author Title of Article
Y. Sakakibara Solving computational learning problems of Boolean formulae on DNA computers
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers(DNA6), Lecture Notes in Computer Science   2001  

Author Title of Article
Y. Sakakibara, S. Kobayashi Sticker System with Complex Structures
Journal Volume Year Pages Concerned
Soft Computing   2001  

Author Title of Article
Y. Sakakibara, A. Suyama Intelligent DNA Chips : Logical operation of gene expression profiles on DNA computers
Journal Volume Year Pages Concerned
Genome Inforematics 2000, Genome Inforematics Series No.11 2000 33-42

Author Title of Article
Y. Sakakibara Solving computational learning problems of Boolean formulae on DNA computers
Journal Volume Year Pages Concerned
Sixth International Meeting on DNA Based Computers(DNA6), Preliminary Proceedings   2000 193-204

Author Title of Article
K. Sakamoto, H. Gouzu, K. Komiya, D. Kiga, S. Yokoyama, T. Yokomori, M. Hagiya Molecular Computation by DNA hairpin formaion
Journal Volume Year Pages Concerned
Science Vol.288 2000 1223-1226

Author Title of Article
A. Suyama, N. Nishida, K. Kurata, K. Omagari Gene Expression Analysis by DNA computing
Journal Volume Year Pages Concerned
Currents in Computational Molecular Biology   2000 12-13

Author Title of Article
Y. Yamamoto, S. Komiya, Y. Husimi Stabilized 3SR against evolutionary instability
Journal Volume Year Pages Concerned
Chem. Lett   2001  

Author Title of Article
Y. Yamamoto, M. Suzuki, Y. Husimi Dynamics in a 3SR evolution reactor and its applications
Journal Volume Year Pages Concerned
DIMACS Series in Discrete Mathematics and Theoretical Computer Science   2001  

Author Title of Article
C. Ferretti, G. Mauri, S. Kobayashi, T. Yokomori On the Universality of Post and Splicing Systems
Journal Volume Year Pages Concerned
Theoretical Computer Science Vol.231 2000 157-170

Author Title of Article
H. Yoshida, A. Suyama Solution to 3-SAT by breadth first search
Journal Volume Year Pages Concerned
DIMACS Series in Discrete Mathematics and Theoretical Computer Science Vol.54 2000 9-22


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