Michael Kuron

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Michael Kuron
PhD student
Phone:+49 711 685-67715
Fax:+49 711 685-63658
Email:mkuron _at_ icp.uni-stuttgart.de
Address:Michael Kuron
Institute for Computational Physics
Universität Stuttgart
Allmandring 3
70569 Stuttgart



I wrote this dissertation as a PhD student of Christian Holm under co-supervision of Joost de Graaf. It contains material from some of the above publications, but covers many things in more depth and provides additional results and insight that were obtained after the papers had been published.

Master's Thesis

For this thesis, supervised by Joost de Graaf and Georg Rempfer, waLBerla, a highly-scalable grid framework for applications such as lattice-Boltzmann and solving partial differential equations, was extended so that it can be used for simulating the electrokinetics of active colloids.

Bachelor Thesis

For this thesis, supervised by Axel Arnold, the MMM1D algorithm was ported to GPGPU. This resulted in a 40-fold performance increase over the previous implementation in ESPResSo and now allows for Molecular Dynamics simulations with electrostatic interactions in 1D-periodic geometries with several thousand particles.

Using this, simulations with various simple DNA models were performed. These simulations show that charge discretization and phase shifts between DNA molecules, modeled as rods, have a significant influence on their attractive properties, an effect that previous works disregarded as it was computationally too expensive, even though it turns out to be too large to neglect for realistic results. Curling up the discretely charged rods into helices, thus making the most accurate model of DNA that could be simulated with the limits of time and resources for this thesis, reveals further geometry dependencies and again a strong influence of a phase shift between the two helices. For phase shifts of 180°, the results for the continuous rods are mostly recovered for large Bjerrum lengths, but for any other phase shift, the forces are weaker, albeit still attractive.



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