Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Simulations of Biological Systems: From Understanding to Control
During the last years, we have developed nonadiabatic excited state dynamics methods based on Trajectory Surface Hopping/Linear Response Time-Dependent Density Functional Theory (TSH/LR-TDDFT)  and real time propagation TDDFT (PT-TDDFT) based Ehrenfest dynamics  and have combined them with mixed quantum mechanical/ molecular mechanical (QM/MM) simulations to study nonadiabatic processes in complex environments. We have also implemented the presence of external electromagnetic fields  in combination with local control theory for an on-the-fly pulse shaping to control population transfer between electronic states . We have used these QM/MM simulations in ground and excited states to study photoactive proteins [5-7] and photoinduced protein and DNA damage.
In this talk, I will present our results on the structural, dynamical and optical properties of the visual pigment rhodopsin along the photocycle [5-7]. We performed a systematic study of the size and sampling dependence of the optical properties and assessed the performance of a variety of different electronic structure methods in describing the photoabsorption spectra . By applying feature selection and causality inference algorithms, we were able to identify the main factors that influence the color tuning in this system . We have applied similar techniques to identify photoprotection mechanisms in proteins by studying the photodynamics of the highly abundant cation-π motif, Lys+ – Trp.
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