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濃度制御に基づくDNAコンピューティング

研究報告コード R040000093
掲載日 2007年5月18日
研究者
  • 山本 雅人
研究者所属機関
  • 北海道大学大学院工学研究科
研究機関
  • 北海道大学
報告名称 濃度制御に基づくDNAコンピューティング
報告概要 本研究では、これまでのDNAコンピューティングが抱える問題のブレークスルーとなりうる濃度制御手法を提案する。本手法は、DNAの本来持つ性質の一つである溶液性(水の中で数多くの分子が存在すること)に焦点をあて、DNA分子の濃度を制御することで、目的とするDNA配列(ターゲットDNA)の生成濃度を高くすることを期待するものである。具体的な例として、最短経路問題を取り上げ、DNAコンピューティングの実験過程について、シミュレーションによる分析、分子化学的実験とともに本手法の確立を目指す。ここでの狙いは、新しい濃度という概念を計算に持ち込むと同時に、対象とする問題のサイズを大きくすることを目的とし、個々の実験操作それぞれについて、計算精度や計算時間といった観点から見直しを行うことである。現在の技術における限界的な規模の問題を扱うことで、現在の技術の問題点や限界が見え、それらを解決していくことで最終的なスケールアップを狙う。
研究分野
  • 理論生物学一般
  • 分子遺伝学一般
  • 遺伝子の構造と化学
関連発表論文 (1) Masashi Nakatsugawa, Masahito Yamamoto and Azuma Ohuchi: Study of the Effircient Parameter Setting based on Mahalanobis-Taguchi Strategy, Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03), pp.640-643 (2003)
(2) Satoshi Kashiwamura, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: Two Step Search for DNA Sequence Design, Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03), pp.1815-1818 (2003)
(3) Fumiaki Tanaka. Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: The Effect on a Bonding Strength by the Freedom of Movement of a DNA strand on a Solid Support in DNA Computing, Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03), pp.1901-1904 (2003)
(4) Keisuke Hashimoto, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: State Transition Model Based on DNA Polymerization, Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03), pp.1889-1892 (2003)
(5) Naoto Takahashi, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: Construction of DNA Hairpin based RAM, Proceedings of the International Technical Conference on Circuits/Systems, Computers and Communications (ITC-CSCC03), pp.1897-1900 (2003)
(6) Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: Nearest-Neighbor Thermodynamics of DNA Sequences with Single Bulge Loop, Proceedings of 9th International Meetings on DNA Based Computers (DNA9), pp.150-159 (2003)
(7) Atsushi Kameda, Masahito Yamamoto, Hiroki Uejima, Masami Hagiya, Kensaku Sakamoto and Azuma Ohuchi: Conformational Addressing using the Hairpin Structure of Single-strand DNA, Proceedings of 9th International Meetings on DNA Based Computers (DNA9), pp.197-201 (2003)
(8) Fumiaki Tanaka, Atsushi Kameda, Masahito Yamamoto and Azuma Ohuchi: The Effect of the Bulge Loop upon the Hybridization Process in DNA Computing, Evolvable Systems: From Biology to Hardware, 5th International Conference (ICES 2003), LNCS 2606, pp.446-456 (2003)
(9) Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba and Azuma Ohuchi: Hierarchical DNA Memory Based on Nested PCR, DNA Computing, 8th International Workshop on DNA-based Computers. LNCS 2568, Springer-Verlag, pp.112-123 (2003)
(10) Masahito Yamamoto, Atsushi Kameda, Nobuo Matsuura, Toshikazu Shiba, Yumi Kawazoe and Azuma Ohuchi: Local Search by Concentration Controlled DNA Computing, The International Journal of Computational Intelligence and Applications (IJCIA), Vol.2, No.4, pp.447-456 (2002)
(11) Masashi Nakatsugawa, Satoshi Kashiwamura, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Towards a High Reliability of the PCR Amplification Process in DNA Computing, The International Journal of Computational Intelligence and Applications (IJCIA), Vol.2, No.4, pp.423-432 (2002)
(12) Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto and Azuma Ohuchi: A Security System for Personal Genome Information at DNA level, Proceedings of IEEE Computer Society Bioinformatics Conference, pp.314-320 (2002)
(13) Atsushi Kameda, Nobuo Matsuura, Masahito Yamamoto and Azuma Ohuchi: An Analysis of Computational Efficiency on DNA Computing, Proceedings of 3rd International Conference on Unconventional Models of Computation (UMC' 02), pp.191-198 (2002)
(14) Masahito Yamamoto, Atsushi Kameda, Nobuo Matsuura, Toshikazu Shiha, Yumi Kawazoe and Azuma Ohuchi: A Separation Method for DNA Computing Based on Concentration Control, New Generation Computing, Vol.20, pp.249-259 (2002)
(15) Satoshi Kashiwamura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba and Azuma Ohuchi: Hierarchical DNA Memory based on Nested PCR, Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8), pp.231-240 (2002)
(16) Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Improvement of the Reliability of Experiments in DNA Computing, Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8), p.333 (2002)
(17) Yumi Kawazoe, Toshikazu Shiba, Masahito Yamamoto and Azuma Ohuchi: Constructions of Security System for Information Encoded by DNA, Preliminary Proceedings of Eighth International Meeting on DNA Based Computers (DNA8), p.337 (2002)
(18) Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Towards a General-Purpose Sequence Design System in DNA Computing, Proceedings of 2002 Congress on Evolutionary Computation (CEC2002), pp.73-78 (2002)
(19) Masahito Yamamoto, Atsushi Kameda, Nobuo Matsuura, Toshikazu Shiba and Azuma Ohuchi: Simulation Analysis of Hybridization Process for DNA Computing with Concentration Control, Proceedings of 2002 Congress on Evolutionary Computation (CEC2002), pp.85-90 (2002)
(20) Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Design of a PCR Protocol for Improving Reliability of PCR in DNA Computing, Proceedings of 2002 Congress on Evolutionary Computation (CEC2002), pp.91-96 (2002)
(21) Nobuo Matsuura, Masahito Yamamoto, Atsushi Kameda, Toshikazu Shiba and Azuma Ohuchi: The Efficiency of Computation by using DNA Concentration, Proceedings of The Seventh International Symposium on Artificial Life and Robotics (A-Reb 7th '02), Oita (Japan), Vol.2, pp.681-684 (2002)
(22) Nobuo Matsuura, Masahito Yamamoto, Toshikazu Shiba, Yumi Kawazoe and Azuma Ohuchi: Solutions of Shortest Path Problems by Concentration Control, Proceedings of 7th International Meeting on DNA Based Computers, pp.231-240 (2001)
(23) Satoshi Kashiwamura, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Towards Optimization of PCR Protocol in DNA Computing, Proceedings of 7th International Meeting on DNA Based Computers, pp.283-292 (2001)
(24) Fumiaki Tanaka, Masashi Nakatsugawa, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Developing Support System for Sequence Design in DNA Computing, Proceedings of 7th International Meeting on DNA Based Computers, pp.340-349 (2001)
(25) Masashi Nakatsugawa, Satoshi Kashiwamura, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: Towards a High Reliability of the PCR Amplification Process in DNA Computing, Proceedings of Fourth International Conference on Computational Intelligence and Multimedia Applications (ICCIMA '0l), pp.158-162 (2001)
(26) Masahito Yamamoto, Nobuo Matsuura, Toshikazu Shiba, Yumi Kawazoe and Azuma Ohuchi: Local Search by Concentration Controlled DNA Computing, Proceedings of Fourth International Conference on Computational Intelligence and Multimedia Applications (ICCIMA '01), pp.167-171 (2001)
(27) Kentaro Matsuno, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: An in vivo approach to molecular computation, Proceedings of The Sixth International Symposium on Artificial Life and Robotics, pp.532-535 (2001)
(28) Nobuo Matsuura, Masahito Yamamoto, Toshikazu Shiba and Azuma Ohuchi: DNA computing for shortest path problem, Proceedings of The Sixth International Symposium on Artificial Life and Robotics, pp.81-84 (2001).
(29) Masahito Yamamoto, Jin Yamashita, Toshikazu Shiba, Takuo Hirayama, Shigeharu Takiya, Keiji Suzuki, Masanobu Munekata and Azuma Ohuchi: A Study on the Hybridization Process in DNA Computing, DNA Based Computers 5, DIMACS Series 54 in Discrete Mathematics and Theoretical Computer Science, pp.101-110 (2000)
(30) Masahito Yamamoto, Nobuo Matsuura, Toshikazu Shiba and Azuma Ohuchi: DNA Solution of the Shortest Path Problem by Concentration Control, Genome Informatics 2000, pp.466-467 (2000)
研究制度
  • さきがけタイプ 「協調と制御」領域
研究報告資料
  • 山本 雅人. 濃度制御に基づくDNAコンピューティング. 「さきがけタイプ」「協調と制御」領域 研究報告会講演要旨集(研究期間2000-2003),2003. p.108 - 117.

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