dc.contributor.advisor | Grubmüller, Helmut Prof. Dr. | de |
dc.contributor.author | Burmeister, Carl Friedrich | de |
dc.date.accessioned | 2013-06-27T08:12:33Z | de |
dc.date.available | 2013-06-27T08:12:33Z | de |
dc.date.issued | 2013-06-27 | de |
dc.identifier.uri | http://hdl.handle.net/11858/00-1735-0000-0001-B984-D | de |
dc.identifier.uri | http://dx.doi.org/10.53846/goediss-3899 | |
dc.language.iso | eng | de |
dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/3.0/ | |
dc.subject.ddc | 530 | de |
dc.title | Primary Effects of X-ray and Photo-Absorption Induced Excitations in Biomolecules | de |
dc.type | doctoralThesis | de |
dc.contributor.referee | Grubmüller, Helmut Prof. Dr. | de |
dc.date.examination | 2013-04-11 | de |
dc.subject.gok | Physik (PPN621336750) | de |
dc.description.abstracteng | To see whether single molecule scattering experiments can yield atomic resolution
structures of biomolecules, it is necessary to understand the physics underlying the radiation damage processes induced by the X-ray radiation. The first part of this
work is concerned with the electron dynamics during the Auger decay as part of
the radiation damage processes in single molecule scattering experiments. To test
if Hartree-Fock theory suffices to describe auto-ionization processes like the Auger
decay, we simulated the electron dynamics in a one-dimensional model system and a beryllium atom after instantaneous core-shell ionization using time-dependent
Hartree-Fock theory. The simulations employed both numerical grids as well as
B-splines. In a model system containing six particles the initially created core-hole
is refilled during the electron dynamics. But no clear emission of a particle into the
continuum occurred. During the electron dynamics in a beryllium atom, however,
neither a refilling of the initially created core-hole nor the emission of a particle
was observed. As two different, flexible basis sets were used it is likely to be
the limitation of Hartree-Fock theory causing the absence of the Auger process in
the simulations. In addition, we used the approach described above to simulate the
electron dynamics after instantaneous valence-shell ionization in two small organic
molecules. The electron dynamics exhibit a diffusion-like behavior of the valence
hole. These dynamics, however, do not reproduce the charge migration dynamics
predicted by correlated ab-initio methods.
To compare different hopping algorithms and to validate previous simulation
results, excited state molecular dynamics simulations of the photo-isomerization
dynamics of a small retinal model and the photo-active yellow protein were per-
formed in the second part of this thesis. In the retinal model small differences in the
excited state lifetimes and quantum yields are observed among the different hop-
ping algorithms. The simulations of the photo-active yellow protein chromophore
yield a photo-isomerization pathway that agrees with the isomerization pathway
previously predicted. There is, however, a large difference in the excited state life-
times among the hopping algorithms. Additionally, the excited state molecular
dynamics simulations are used to study the molecular dynamics induced excita-
tion energy transfer in a small bi-chromophoric molecule. The molecular dynamics
simulations together with ab-initio calculations indicate that molecular dynamics
on different nonadiabatically coupled potential energy surfaces can explain the ex-
citation energy transfer from one chromophore to another. This offers a different
explanation of excitation energy transfer processes in small molecules compared
to Förster and Dexter theory. | de |
dc.contributor.coReferee | Salditt, Tim Prof. Dr. | de |
dc.subject.eng | electron dynamics | de |
dc.subject.eng | time-dependent hartree-fock | de |
dc.subject.eng | molecular dynamics | de |
dc.subject.eng | surface hopping | de |
dc.subject.eng | photo-active yellow protein | de |
dc.subject.eng | excitation energy transfer | de |
dc.identifier.urn | urn:nbn:de:gbv:7-11858/00-1735-0000-0001-B984-D-2 | de |
dc.affiliation.institute | Fakultät für Physik | de |
dc.identifier.ppn | 750586435 | de |