Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules
Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules
复制标题
对扩展生物分子电子和分子动力学模拟先进方法开发的贡献
DOI：
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发表时间：
2018
期刊：
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通讯作者：
Xiaojing Wu
中科院分区：
文献类型：
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作者：
Xiaojing Wu
本论文涉及两个项目，致力于发展先进的方法来模拟扩展生物分子中的分子和电子动力学。第一个项目旨在通过数值模拟显著提高蛋白质氧化还原电位的准确性。一个复杂的力场依赖于静电相互作用（AMOEBA）的多极描述，用于对血红素蛋白进行分子动力学模拟。我们推导了阿米巴的参数，以准确地描述与血红蛋白的静电相互作用，包括铁态和铁态。与标准力场相比，得到了非常令人鼓舞的改进。第二个项目旨在开发原始方法来模拟与极化环境接触的生物分子中的超快电子动力学。我们设计了实时时变密度泛函理论（RT-TDDFT）和极化分子力学（MMpol）的结合。该方法在deMon2k软件中实现了高效、稳健的实现。密度拟合技术允许降低RT-TDDFT/MMpol传播的计算成本。该方法应用于了解激光脉冲激发肽的能量耗散机制。
This thesis involves two projects devoted to the development of advanced approaches for simulating molecular and electron dynamics in extended biomolecules. The first project aims at significantly improving the accuracy of redox potentials of proteins by numerical simulations. A sophisticated force field relying on a multipolar description of electrostartic interactions (AMOEBA) is used to perform molecular dynamics simulations onheme proteins. We derived parameters for AMOEBA to accurately describe electrostatic interactions with hemein both ferrous and ferric states. Very encouraging improvements are obtained compared to the standard force fields. The second project aims at developing original approaches for simulating ultrafast electron dynamics in biomolecules in contact to polarizable environments. We devised acombination of Real-time Time-Dependent Density Functional Theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol). An efficient and robust implementation of this method has been realized in deMon2k software. Density fitting techniques allow to reduce the computational cost of RT-TDDFT/MMpol propagations. The methodology is applied to understand the mechanisms of energy dissipation of a peptide excited by a laser pulse.