| 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 |
| 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
| 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 | |