Extraction of dynamical hidden order of water by mining simulation data

• Project/Area Number: 24700145
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Intelligent informatics
• Research Institution: Japan Advanced Institute of Science and Technology
• Principal Investigator: DAM Hieu Chi 北陸先端科学技術大学院大学, 知識科学研究科, 准教授 (70397230)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2015: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000); Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: データマイニング / 動的振る舞い / 水素結合ネットワーク / 機械学習 / 第一原理計算 / シミュレーション

Outline of Final Research Achievements

Water molecules with their electrostatic dipole moments and characteristic hydrogen bond network have tight interaction to each other as well as to proteins in solutions. The water molecules are moving under the interactions with the surrounding water molecules and information about the local chemical environment is implicitly included in their dynamical behaviors. By applying data mining techniques to the simulation data of protein solution, we have constructed an analysis system for analyzing the dynamical behavior of water molecules for extracting the hidden dynamical structure of protein solution.

Research Products

• [Journal Article] Data mining for materials design: A computational study of single molecule magnet (2014)
  • Author(s): Hieu Chi Dam, Tien Lam Pham, Tu Bao Ho, Anh Tuan Nguyen, and Viet Cuong Nguyen
  • Journal Title: The Journal of Chemical Physics Volume: 140 Issue: 4 Pages: 44101-44101
  • DOI: 10.1063/1.4862156
  • Peer Reviewed
• [Presentation] Sparse Modeling for Materials Design (2015)
  • Author(s): H.C. Dam, T.L. Pham, and V.C. Nguyen
  • Organizer: Pacifichem2015
  • Place of Presentation: USA, Honolulu
  • Year and Date: 2015-12-14
  • Int'l Joint Research
• [Presentation] Sparse Modeling for Materials Design (2015)
  • Author(s): H.C. Dam, T.L. Pham, and V.C. Nguyen
  • Organizer: The 8th Conference of the Asian Consortium on Computational Materials Science (ACCMS-8)
  • Place of Presentation: Taipei, Taiwan
  • Year and Date: 2015-06-12
  • Int'l Joint Research / Invited
• [Presentation] Combination of Gaussian mixture model and linear regression for estimating potential energy surfaces (2015)
  • Author(s): Pham Tien Lam and Dam Hieu Chi
  • Organizer: The 9th International Conference on Computational Physics
  • Place of Presentation: Singapore
  • Year and Date: 2015-01-07 – 2015-01-11
• [Presentation] Data mining of quantum mechanical calculations for designing materials (2014)
  • Author(s): Dam Hieu Chi, Tien Lam Pham, Tu Bao Ho, Anh Tuan Nguyen, and Viet Cuong Nguyen
  • Organizer: 7th International Workshop on Advanced Materials Science and Nanotechnology, IWAMSN 2014
  • Place of Presentation: Halong City, Vietnam
  • Year and Date: 2014-11-02 – 2014-11-06
  • Invited
• [Presentation] Linear model for estimating potential energy surface of silicon hydride systems (2014)
  • Author(s): Pham Tien Lam and Dam Hieu Chi
  • Organizer: 7th International Workshop on Advanced Materials Science and Nanotechnology, IWAMSN 2014
  • Place of Presentation: Halong City, Vietnam
  • Year and Date: 2014-11-02 – 2014-11-06
• [Presentation] Designing Single Molecule Magnet with Data Mining (2014)
  • Author(s): Dam Hieu Chi, Tien Lam Pham, Tu Bao Ho, Anh Tuan Nguyen, and Viet Cuong Nguyen
  • Organizer: The IUMRS International Conference in Asia 2014
  • Place of Presentation: 福岡大学（福岡県，福岡市）
  • Year and Date: 2014-08-24 – 2014-08-30
  • Invited
• [Presentation] A Novel Category of Protein Hydration Water Classified by Simulated Data Mining (2013)
  • Author(s): Taku Mizukami, Ayumu Sugiyama, Dam Hieu Chi
  • Organizer: The 7th Conference of the Asian Consortium on Computational Materials Science (ACCMS-7)
  • Place of Presentation: Nakhon Ratchasima, Thailand
• [Presentation] Data Mining for Materials Design: A Computational Study of Single Molecule Magnet (2013)
  • Author(s): Dam Hieu Chi, Nguyen Anh Tuan, Pham Tien Lam, and Ho Tu Bao
  • Organizer: The 7th Conference of the Asian Consortium on Computational Materials Science (ACCMS-7)
  • Place of Presentation: Nakhon Ratchasima, Thailand
  • Invited
• [Presentation] データマイニングによる塩水濃度と水溶液の動的構造に関する研究 (2012)
  • Author(s): 杉山 歩，中村 大城，山口 和宏，水上 卓，Dam Hieu Chi, Ho Tu Bao
  • Organizer: 第6回分子科学討論会
  • Place of Presentation: 東京大学本郷キャンパス
• [Presentation] 混合分布モデルをもちいた水分子のマイニング-ダイナミックス (2012)
  • Author(s): 水上卓、杉山歩、山口和宏、Dam Hieu Chi、Ho Tu Bao
  • Organizer: 第6回分子科学討論会
  • Place of Presentation: 東京大学本郷キャンパス
• [Presentation] シミュレーション・データマイニングアプローチによる蛋白質ドッキング過程における水和水ダイナミクス
  • Author(s): 水上 卓, 杉山 歩, ホー・ツー・バオ, ダム・ヒョウ・チ
  • Organizer: 生物物理学会 第51回年会
  • Place of Presentation: 京都国際会議場
• [Presentation] L1型正則化線形回帰モデルを用いたシミュレーションデータからの二元合金の物性予測
  • Author(s): 鈴木 大輔，川崎 隆史,水上 卓, 杉山 歩, ホー・ツー・バオ, ダム・ヒョウ・チ
  • Organizer: 分子科学討論会 第7回
  • Place of Presentation: 京都テルサ
• [Presentation] スパースモデルによる水溶液構造の解析
  • Author(s): 水上 卓, 杉山 歩, 川崎 隆史, 高木 啓行, ホー・ツー・バオ, ダム・ヒョウ・チ
  • Organizer: 分子科学討論会 第7回
  • Place of Presentation: 京都テルサ