Ab Initio Molecular Dynamics Thesis

In this dissertation, I simulate and disentangle excitation dynamics in the presence of complex vibrational environments for a light-harvesting protein and a synthetic dimer, both of which are controversial.

A periodic box, consisting of 288 carbon atoms is chosen for the simulations.

After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees.

" We performed, for the first time to our knowledge, fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions.

We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm.

The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation.

We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier. CO adsorption is modeled using a 4 × 4 cell, while a 2 × 2 cell is used both for methoxy and H adsorption.

We describe the foundations of the method and present in some detail the practical performance of an ab-initio molecular dynamics simulation.

accuracy, and prediction of a new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations.

I obtain the first-ever quantitative reproduction of experimental linear spectra from first principles for a pigment-protein complex and find that stronger than expected environmental vibrations control the pathways of excitation transport.

I generalize my findings using a model vibronic dimer, defining regimes of vibronic transport and demonstrating that biological systems are outside of the coherent regime.


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