Michael Kuron

From ICPWiki
Revision as of 15:04, 27 March 2015 by Mkuron (talk | contribs)
Jump to: navigation, search
Michael kuron.jpg
Michael Kuron
Master 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 am a master student in Christian Holm's group, working with Joost de Graaf and Georg Rempfer on electrokinetics and active colloids. My master's project includes implementing the necessary models in waLBerla, a highly-scalable grid framework for applications such as lattice-Boltzmann and solving partial differential equations. This shall then be used to study self-propelled particles.


Bachelor Thesis

application_pdf.png"Like-Charge Attraction in DNA" (2.3 MB)Info circle.png, 2013, Institute for Computational Physics, Stuttgart

For this thesis, 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.