Ab Initio Molecular Dynamics Thesis
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.
" 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.
I then investigate three controversial synthetic fluorescein heterodimers that were engineered with the goal of providing a model system for understanding coherent energy transfer in multichromophoric systems.
I extract Hamiltonians and spectral densities using AIMD and find electronic couplings an order of magnitude larger than previously thought.
The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package.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. CO adsorption is modeled using a 4 × 4 cell, while a 2 × 2 cell is used both for methoxy and H adsorption.In the case of H, the most favorable adsorption is obtained by considering two atoms per cell, both at three-fold sites.In 2007, Engel’s proposal of long-lived coherence in photosynthesis precipitated substantial efforts to understand the role of quantum effects in biology.While much progress has been made in the last decade, the timescale, type, and functional importance of coherence coupled to thermal vibrations remains poorly understood.I calculate coherence dynamics and a trajectory of 2D spectra and demonstrate that electronic coherence persists for just 100-150 femtoseconds, after which long-lived vibrationally driven coherences persist for hundreds of femtoseconds.Thus, I resolve the controversy and confirm that while electronic coherence can be engineered in artificial molecular systems, it will not persist for a picosecond, as previously claimed.In the present work, this method is employed to study the low energy recoil events in Gd disordering.The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ∼0.15, ∼0.11 to 0.27 and ∼0.1 to 0.13 |e| for Gd, Zr (or Ti), and O, respectively.