Development of a Polarizable Force Field for DNA Based on the Block Model
| Project/Area Number |
15K00410
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Life / Health / Medical informatics
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| Research Institution | Kinjo Gakuin University |
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Principal Investigator |
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| Co-Investigator(Renkei-kenkyūsha) |
MARIAN Christel M Heinrich Heine University, Institute of Theoretical and Computational Chemistry, 教授
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| Research Collaborator |
WEINGART Oliver Heinrich Heine University, Institute of Theoretical and Computational Chemistry, 研究員
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Project Status |
Completed (Fiscal Year 2017)
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| Budget Amount *help |
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2017: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2016: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
Fiscal Year 2015: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
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| Keywords | 分極力場 / 分極率 / 誘起双極子 / 点電荷 / 核酸 / ブロック分子 / ブロックモデル / DNA |
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| Outline of Final Research Achievements |
Molecular dynamics simulation is a powerful method for studying the dynamic structure of biopolymers such as proteins and nucleic acids. In heterogeneous systems with a large number of charges like biological systems, it is necessary to increase the calculation accuracy by using the polarizable force field incorporating the polarization effect. However, in a system containing a large number of phosphate ions like DNA, it is difficult to set the charge and the polarizability on atom separately, so it is not possible to construct a polarizable force field with high accuracy. Therefore, a practical method adaptable for DNA is proposed by obtaining charges and polarizabilities in block units. The method was verified using A, B, and Z type trinucleotide duplexes, and a polarized block model potential with sufficient accuracy was developed.
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Report
(4 results)
Research Products
(6 results)
