骨骼组织中纤维内胶原蛋白矿化的分子生物学机理任务书

 2021-10-23 09:10

1. 毕业设计（论文）的内容和要求

本课题通过研究受限空间中不同密度的水溶液中Ca和HPO4的成核过程，探索生物的早期成核和能量机理。

1. 理解分子模拟的基本概念、原理、模拟软件； 2.掌握受限空间胶原蛋白成核理论及研究最新进展； 3.熟悉分子动力学模拟软件gromacs的基本知识，操作步骤，并学会使用； 4.合理安排实验进程，工作时间不迟到早退；5.实验认真仔细，对实验现象进行详细的记录，定期对实验数据进行总结，及时调整实验方案；6. 工作积极主动，勤于思考，做好实验室安全卫生工作。

2. 参考文献

[1] Xu, ZJ; Yang, Y; Zhao, WL; Wang, ZQ ; Landis, WJ; Cui, Q; Sahai, N ,Molecular mechanisms for intrafibrillar collagen mineralization in skeletal tissues,Biomaterials 2015, 1, 59-66.[2] How does Bone Sialoprotein promote the nucleation of hydroxyapatie?A molecular dynamics study using model peptides of different conformations, Langmuir 2010, 26, 12, 9848-9859 [3] Du, L.-W.; Bian, S.; Gou, B.-D.; Jiang, Y.; Huang, J.; Gao, Y.-X.; Zhao, Y.-D.; Wen, W.; Zhang, T.-L.; Wang, K. Structure of Clusters and Formation of Amorphous Calcium Phosphate and Hydroxyapatite: From the Perspective of Coordination Chemistry. Cryst. Growth Des. 2013, 13, 31033109. [4] Zhang, Q.; Jiang, Y.; Gou, B. D.; Huang, J.; Gao, Y. X.; Zhao, J. T.; Zheng, L.; Zhao, Y. D.; Zhang, T. L.; Wang, K. In Situ Detection of Calcium Phosphate Clusters in Solution and Wet Amorphous Phase by Synchrotron X-ray Absorption Near-Edge Spectroscopy at Calcium K-Edge. Cryst. Growth Des. 2015, 15, 22042210. [5] Hu, Q.; Nielsen, M. H.; Freeman, C. L.; Hamm, L. M.; Tao, J.; Lee, J. R. I.; Han, T. Y. J.; Becker, U.; Harding, J. H.; Dove, P. M.; De Yoreo, J. J. The thermodynamics of calcite nucleation at organic interfaces: Classical vs. non-classical pathways. Faraday Discuss. 2012, 159, 509.[6] Torrie, G.; Valleau, J. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling. J. Comput. Phys. 1977, 23, 187199.[7] Kastner, J. Umbrella sampling. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2011, 1, 932942. [8] Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. THE weighted histogram analysis method for freeenergy calculations on biomolecules. I. The method. J. Comput. Chem. 1992, 13, 10111021. [9] Weilong Zhao; Zhijun Xu; Qiang Cui; Nita Sahai, Predicting the Structure-Activity Relationship of Hydroxyaoatite-Binding Peptides by Enhanced-Sampling Molecular Simulation, Langmuir 2016, 32, 27, 7009-7022[10] Roux, B. The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun. 1995, 91, 275282.

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