Development of polarizable embedding coupled to static and dynamic QM/MM simulations

This PhD thesis details on the theoretical advancements in polarizable embedding within quantum mechanical/molecular mechanical (QM/MM) static calculations and multiscale dynamics. It also delves into the implementation details of these theoretical models within modular software frameworks for high-performance computing (HPC) applications. Thus, the work documented in the thesis spans from foundational theories to practical implementations.
Central to the thesis is the development and implementation of the Polarizable Embedding with Minimum Image Convention (PE-MIC) model, which mitigates the artificial boundary polarization that other models suffer from. Additionally, we present a novel multiscale model integration of Kohn-Sham Density Functional Theory (KS-DFT) with plane waves used in combination with the AMOEBA polarizable force field, which is also extended to the multiscale dynamics by deriving and implementing the analytical gradients. These methodologies provide more accurate and scalable simulations of complex molecular systems, particularly for molecules with electronic charge density sensitive to environment charge distribution changes.
Much of the work focuses on developing the MiMiC framework, which aims to enable computationally scalable polarizable embedding multiscale simulations in HPC environments.
The future perspectives of these robust theoretical models include their application to a broad range of complex biomolecular systems, thus enhancing multiscale computational simulations in the exascale computing era.