@phdthesis{NarayananNair2006,
  author    = {Narayanan Nair, Arun Kumar},
  title     = {Molecular dynamics simulations of polyelectrolyte brushes},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-7005},
  school      = {Universit{\"a}t Potsdam},
  year      = {2006},
  abstract  = {This thesis studies strong, completely charged polyelectrolyte brushes. Extensive molecular dynamics simulations are performed on different polyelectrolyte brush systems using local compute servers and massively parallel supercomputers. The full Coulomb interaction of charged monomers, counterions, and salt ions is treated explicitly. The polymer chains are anchored by one of their ends to a uncharged planar surface. The chains are treated under good solvent conditions. Monovalent salt ions (1:1 type) are modelled same as counterions. The studies concentrate on three different brush systems at constant temperature and moderate Coulomb interaction strength (Bjerrum length equal to bond length): The first system consists of a single polyelectrolyte brush anchored with varying grafting density to a plane. Results show that chains are extended up to about 2/3 of their contour length. The brush thickness slightly grows with increasing anchoring density. This slight dependence of the brush height on grafting density is in contrast to the well known scaling result for the osmotic brush regime. That is why the result obtained by simulations has stimulated further development of theory as well as new experimental investigations on polyelectrolyte brushes. This observation can be understood on a semi-quantitative level using a simple scaling model that incorporates excluded volume effects in a free-volume formulation where an effective cross section is assigned to the polymer chain from where couterions are excluded. The resulting regime is called nonlinear osmotic brush regime. Recently this regime was also obtained in experiments. The second system studied consists of polyelectrolyte brushes with added salt in the nonlinear osmotic regime. Varying salt is an important parameter to tune the structure and properties of polyelectrolytes. Further motivation is due to a theoretical scaling prediction by Pincus for the salt dependence of brush thickness. In the high salt limit (salt concentration much larger than counterion concentration) the brush height is predicted to decrease with increasing external salt, but with a relatively weak power law showing an exponent -1/3. There is some experimental and theoretical work that confirms this prediction, but there are other results that are in contradiction. In such a situation simulations are performed to validate the theoretical prediction. The simulation result shows that brush thickness decreases with added salt, and indeed is in quite good agreement with the scaling prediction by Pincus. The relation between buffer concentration and the effective ion strength inside the brush at varying salt concentration is of interest both from theoretical as well as experimental point of view. The simulation result shows that mobile ions (counterions as well as salt) distribute nonhomogeneously inside and outside of the brush. To explain the relation between the internal ion concentration with the buffer concentration a Donnan equilibrium approach is employed. Modifying the Donnan approach by taking into account the self-volume of polyelectrolyte chains as indicated above, the simulation result can be explained using the same effective cross section for the polymer chains. The extended Donnan equilibrium relation represents a interesting theoretical prediction that should be checked by experimental data. The third system consist of two interacting polyelectrolyte brushes that are grafted to two parallel surfaces. The interactions between brushes are important, for instance, in stabilization of dispersions against flocculation. In the simulations pressure is evaluated as a function of separation D between the two grafting planes. The pressure behavior shows different regimes for decreasing separation. This behavior is in qualitative agreement with experimental data. At relatively weak compression the pressure behavior obtained in the simulation agrees with a 1/D power law predicted by scaling theory. Beyond that the present study could supply new insight for understanding the interaction between polyelectrolyte brushes.},
  subject      = {Molekulardynamik},
  language  = {en}
}
@phdthesis{Kav2019,
  author    = {Kav, Batuhan},
  title     = {Membrane adhesion mediated via lipid-anchored saccharides},
  doi       = {10.25932/publishup-42879},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428790},
  school      = {Universit{\"a}t Potsdam},
  pages     = {125},
  year      = {2019},
  abstract  = {Membrane adhesion is a fundamental biological process in which membranes are attached to neighboring membranes or surfaces. Membrane adhesion emerges from a complex interplay between the binding of membrane-anchored receptors/ligands and the membrane properties. In this work, we study membrane adhesion mediated by lipid-anchored saccharides using microsecond-long full-atomistic molecular dynamics simulations. Motivated by neutron scattering experiments on membrane adhesion via lipid-anchored saccharides, we investigate the role of LeX, Lac1, and Lac2 saccharides and membrane fluctuations in membrane adhesion. We study the binding of saccharides in three different systems: for saccharides in water, for saccharides anchored to essentially planar membranes at fixed separations, and for saccharides anchored to apposing fluctuating membranes. Our simulations of two saccharides in water indicate that the saccharides engage in weak interactions to form dimers. We find that the binding occurs in a continuum of bound states instead of a certain number of well-defined bound structures, which we term as "diffuse binding". The binding of saccharides anchored to essentially planar membranes strongly depends on separation of the membranes, which is fixed in our simulation system. We show that the binding constants for trans-interactions of two lipid-anchored saccharides monotonically decrease with increasing separation. Saccharides anchored to the same membrane leaflet engage in cis-interactions with binding constants comparable to the trans-binding constants at the smallest membrane separations. The interplay of cis- and trans-binding can be investigated in simulation systems with many lipid-anchored saccharides. For Lac2, our simulation results indicate a positive cooperativity of trans- and cis-binding. In this cooperative binding the trans-binding constant is enhanced by the cis-interactions. For LeX, in contrast, we observe no cooperativity between trans- and cis-binding. In addition, we determine the forces generated by trans-binding of lipid-anchored saccharides in planar membranes from the binding-induced deviations of the lipid-anchors. We find that the forces acting on trans-bound saccharides increase with increasing membrane separation to values of the order of 10 pN. The binding of saccharides anchored to the fluctuating membranes results from an interplay between the binding properties of the lipid-anchored saccharides and membrane fluctuations. Our simulations, which have the same average separation of the membranes as obtained from the neutron scattering experiments, yield a binding constant larger than in planar membranes with the same separation. This result demonstrates that membrane fluctuations play an important role at average membrane separations which are seemingly too large for effective binding. We further show that the probability distribution of the local separation can be well approximated by a Gaussian distribution. We calculate the relative membrane roughness and show that our results are in good agreement with the roughness values reported from the neutron scattering experiments.},
  language  = {en}
}
@phdthesis{Lever2022,
  author    = {Lever, Fabiano},
  title     = {Probing the ultrafast dynamics of 2-Thiouracil with soft x-rays},
  doi       = {10.25932/publishup-55523},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-555230},
  school      = {Universit{\"a}t Potsdam},
  pages     = {129},
  year      = {2022},
  abstract  = {Understanding the changes that follow UV-excitation in thionucleobases is of great importance for the study of light-induced DNA lesions and, in a broader context, for their applications in medicine and biochemistry. Their ultrafast photophysical reactions can alter the chemical structure of DNA - leading to damages to the genetic code - as proven by the increased skin cancer risk observed for patients treated with thiouracil for its immunosuppressant properties. In this thesis, I present four research papers that result from an investigation of the ultrafast dynamics of 2-thiouracil by means of ultrafast x-ray probing combined with electron spectroscopy. A molecular jet in the gas phase is excited with a uv pulse and then ionized with x-ray radiation from a Free Electron Laser. The kinetic energy of the emitted electrons is measured in a magnetic bottle spectrometer. The spectra of the measured photo and Auger electrons are used to derive a picture of the changes in the geometrical and electronic configurations. The results allow us to look at the dynamical processes from a new perspective, thanks to the element- and site- sensitivity of x-rays. The custom-built URSA-PQ apparatus used in the experiment is described. It has been commissioned and used at the FL24 beamline of the FLASH2 FEL, showing an electron kinetic energy resolution of ∆E/E ~ 40 and a pump-probe timing resolution of 190 f s. X-ray only photoelectron and Auger spectra of 2-thiouracil are extracted from the data and used as reference. Photoelectrons following the formation a 2p core hole are identified, as well as resonant and non-resonant Auger electrons. At the L 1 edge, Coster-Kronig decay is observed from the 2s core hole. The UV-induced changes in the 2p photoline allow the study the electronic-state dynamics. With the use of an Excited-State Chemical Shift (ESCS) model, we observe a ultrafast ground-state relaxation within 250 f s. Furthermore, an oscillation with a 250 f s period is observed in the 2p binding energy, showing a coherent population exchange between electronic states. Auger electrons from the 2p core hole are analyzed and used to deduce a ultrafast C -S bond expansion on a sub 100 f s scale. A simple Coulomb-model, coupled to quantum chemical calculations, can be used to infer the geometrical changes in the molecular structure.},
  language  = {en}
}