Ab Initio Molecular Dynamics Thesis

The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band.

The calculated bandgap, as expected is close to 0 e V.

Neglecting the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.

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DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations.

The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package.

I examine phycobiliprotein PC645, a light-harvesting complex found in cryptophyte algae and, contrary to previous literature, I show that the protein’s key function proceeds via an incoherent mechanism.

For the first time, I extract spectral densities from ab initio molecular dynamics (AIMD) combined with density functional theory excited state calculations.

The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K.

The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms.


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