Ursula Roethlisberger
(EPFL, Switzerland)
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) [1] and real time propagation TDDFT (PT-TDDFT) based Ehrenfest dynamics [2] 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 [3] in combination with local control theory for an on-the-fly pulse shaping to control population transfer between electronic states [4]. 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 [7]. By applying feature selection and causality inference algorithms, we were able to identify the main factors that influence the color tuning in this system [5]. We have applied similar techniques to identify photoprotection mechanisms in proteins by studying the photodynamics of the highly abundant cation-π motif, Lys+ – Trp.
References:
1. E. Tapavicza, I. Tavernelli and U. Rothlisberger, Phys Rev Lett, 2007, 98, No.023001.
2. I. Tavernelli, U. F. Rohrig and U. Rothlisberger, Mol Phys, 2005, 103, 963.
3. I. Tavernelli, B. F. E. Curchod and U. Rothlisberger, Phys Rev A, 2010, 81.
4. B. F. E. Curchod, T. J. Penfold, U. Rothlisberger and I. Tavernelli, Phys Rev A, 2011, 84.
5. P. Campomanes , Neri M, Vanni S, Tavernelli I and Rothlisberger U, J Am Chem Soc, 2014, 136, 3842.
6. M. Neri, S. Vanni, I. Tavernelli and U. Rothlisberger, Biochemistry-Us, 2010, 49, 4827.
7. P. C. O. Valsson, I. Tavernelli, U. Rothlisberger, and C. Filippi, J. Chem. Theor. Comp., 2013, 9, 244.