# Difference between revisions of "Georg Rempfer"

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Electrokinetic phemonena comprise three distinct physical effects: hydrodynamics, electrostatics, and diffusion. Their complicated interplay gives rise to a multitude of interesting consequences, important for example in DNA electrophoresis and electroosmotic flow. What makes such systems hard to simulate is the fact that effects on very different time and length scales are involved. Typically, the dynamics of ions involved happen on the scale of picoseconds and nanometers, while the dynamics of macromolecules such as DNA can easily exceed time scales of milliseconds or even minutes for the folding of some proteins, and length scales of micrometers. | Electrokinetic phemonena comprise three distinct physical effects: hydrodynamics, electrostatics, and diffusion. Their complicated interplay gives rise to a multitude of interesting consequences, important for example in DNA electrophoresis and electroosmotic flow. What makes such systems hard to simulate is the fact that effects on very different time and length scales are involved. Typically, the dynamics of ions involved happen on the scale of picoseconds and nanometers, while the dynamics of macromolecules such as DNA can easily exceed time scales of milliseconds or even minutes for the folding of some proteins, and length scales of micrometers. | ||

− | Previously, the molecular dynamics simulation software ESPResSo ([http://www.espressomd.org www.espressomd.org]), developed mainly by the Institute for Computational Physics in Stuttgart, was able to treat the diffusive effects only by using explicit particles in simulations like the ones carried out as part of my {{Download|BSc_thesis_rempfer.pdf|bachelor's thesis}}. | + | Previously, the molecular dynamics simulation software ESPResSo ([http://www.espressomd.org www.espressomd.org]), developed mainly by the Institute for Computational Physics in Stuttgart, was able to treat the diffusive effects only by using explicit particles in simulations like the ones carried out as part of my {{Download|BSc_thesis_rempfer.pdf|bachelor's thesis}}. To overcome the limitations imposed by the excessive requirements in computational power of this approach, I implemented an algorithm to treat the neutral and ionic species in such a simulation using a continuum mechanical model as proposed by Capuani et. al. in 2004 (http://arxiv.org/pdf/cond-mat/0404289.pdf). I did so, relying on NVIDIA's CUDA framework for GPU computing to implement it as a module in [http://www.espressomd.org ESPResSo]. |

=== Bachelor's Thesis === | === Bachelor's Thesis === |

## Revision as of 16:44, 11 March 2013

**Georg Rempfer**

PhD student

Office: | 1.035 |
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Phone: | +49 711 685-67702 |

Fax: | +49 711 685-63658 |

Email: | georg _at_ icp.uni-stuttgart.de |

Address: | Georg Rempfer Institute for Computational Physics Universität Stuttgart Allmandring 3 70569 Stuttgart Germany |

### Master Thesis

"A Lattice Model for Electrokinetics" (2.23 MB), 2013, Institute for Computational Physics, Stuttgart

Electrokinetic phemonena comprise three distinct physical effects: hydrodynamics, electrostatics, and diffusion. Their complicated interplay gives rise to a multitude of interesting consequences, important for example in DNA electrophoresis and electroosmotic flow. What makes such systems hard to simulate is the fact that effects on very different time and length scales are involved. Typically, the dynamics of ions involved happen on the scale of picoseconds and nanometers, while the dynamics of macromolecules such as DNA can easily exceed time scales of milliseconds or even minutes for the folding of some proteins, and length scales of micrometers.

Previously, the molecular dynamics simulation software ESPResSo (www.espressomd.org), developed mainly by the Institute for Computational Physics in Stuttgart, was able to treat the diffusive effects only by using explicit particles in simulations like the ones carried out as part of my bachelor's thesis (1.36 MB). To overcome the limitations imposed by the excessive requirements in computational power of this approach, I implemented an algorithm to treat the neutral and ionic species in such a simulation using a continuum mechanical model as proposed by Capuani et. al. in 2004 (http://arxiv.org/pdf/cond-mat/0404289.pdf). I did so, relying on NVIDIA's CUDA framework for GPU computing to implement it as a module in ESPResSo.

### Bachelor's Thesis

"Lattice-Boltzmann Simulations in Complex Geometries" (1.36 MB), 2010, Institute for Computational Physics, Stuttgart

The focus of this thesis lies on the simulation of processes in molecular dynamics that are governed by electrostatic and hydrodynamic interactions in volumes with boundaries. The first objective was to change the existing implementation of the Lattice-Boltzmann-Method in ESPResSo so that it can handle systems with arbitrarily complex boundary geometries.

Additionally, a scenario involving the fluid-boundary interaction and the fluid-particle interaction was supposed to be developed for which analytical results can be obtained, so that the correctness of the implementation could be verified. This system consists of an electro-osmotic flow in an infinite slit pore. The analytical treatment was conducted by means of the electrokinetic equations.

## Teaching

- Simulation Methods in Physics II (SS 12)
- Mathematische Methoden der Physik (WS 11/12)
- Höhere Mathematik 3 für Ingenieure (WS 10/11)