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Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules

Abstract : 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.
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  • HAL Id : tel-02094795, version 1

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Xiaojing Wu. Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules. Theoretical and/or physical chemistry. Université Paris Saclay (COmUE), 2018. English. ⟨NNT : 2018SACLS252⟩. ⟨tel-02094795⟩

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