Quantum/Classical Dynamics

In general, the size and complexity of biomolecular systems necessitates the use of classical mechanics in conjunction with so called empirical force fields. However, in cases where there are changes in covalent interactions, such as during chemical reactions or photochemical processes, we have no choice but to turn to a quantum mechanical description of at least those parts of the system involved in the reaction. The group has incorporated time-dependent Density Functional Theory (DFT) into MD simulations. We have also used an excited state force field to study the process of photoactivation and the subsequent relaxation pathway in the photoactive yellow protein (PYP) and other photo-activated systems. Results on PYP indicate that the protein stabilises the transition-state during the isomerisation process. It has also been shown that the isomerisation of the chromophore in PYP does not in itself destabilise the protein, nor does it lead to the conformational changes that are characteristic of the latter steps in the photocycle. Instead, isomerisation leads to a proton being transferred from the protein to the chromophore and the associated change in charge distribution is what drives partial unfolding. This finding is supported by recent independent experimental studies. Together, this work has led to a detailed description of the events that occur on a nanosecond time scale in PYP after the photo-excitation, which accounts for many of the experimental findings. Work is now focused on applying the same approach to other systems. In particular, in collaboration with the group of Prof. Ben Feringa (RUG), we have modeled a series of small light activated molecular motors in order to understand how it might be possible to modulate their speed and efficiency.

This page was last updated on July the 10th, 2017.

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