Advanced Simulation Methods SS 2015
- Lecture and Tutorials (2 SWS in total)
- C. Holm, J. de Graaf, J. Smiatek, M. Fyta
- Course language
- English or German
- ICP, Allmandring 3; Room: tba.
The course will consist of four modules supervised by C. Holm, J. de Graaf, J. Smiatek, and M. Fyta, that contain exercises, presentations, discussion meetings, and written reports, worked out in groups of up to four people.
A preliminary registration for this course is mandatory. Interested students write an Email to Jens Smiatek
Module 1: Christian Holm, Electrostatics and Lattice Boltzmann
This module focuses on charged matter with electrostatic and hydrodynamic interactions. It should be taken in groups of three people. It consists of simulations, theory, a presentation and a short report on the simulation results. You only have to give one common presentation and hand in one report per group. It consists of three parts.
If you have any questions regarding the organisation or content of this module please do not hesitate to contact Florian Weik, Owen Hickey or Christian Holm. For questions regarding the practical part of the module and technical help contact Florian Weik or Owen Hickey.
Part 1: Electrostatics
This part is about the theory of electrostatic algorithms for molecular dynamics simulations. It is concerned with state of the art algorithms beyond the Ewald sum, especially mesh Ewald methods. To this end the students should read the referenced literature and prepare a 20 minutes presentation. Hold the presentation with Christian Holm and discuss the content and open questions with him. The presentation should contain the students understanding of the P3M method as well as a discussion of its performance compared to other modern electrostatics methods.
Part 2: Slit Pore
This part is practical. It is concerned with the movement of ions in an charged slit pore. It is similar to the systems that are discussed in the Bachelors thesis of Georg Rempfer which is recommended reading. A slit pore consists of two infinite charge walls as shown in the figure to the right. In this exercise you should simulate such a system with ESPResSo. You are supposed too use a Lattice Boltzmann fluid coupled to explicit ions which are represented by charge Week-Chandler-Anderson spheres. In addition to the charge on the walls, the ions are also subject to an external electrical field parallel to the walls. Electrostatics should be handled by the P3M algorithm. A set of realistic parameters and an more in detail description of the system can be found in the thesis. You should measure the flow profile of the fluid and the density and velocity profiles of the ions. The case of the slit pore can be solved analytically either in the case of only counter ions (the so called salt free case) or in the high salt limit (Debye-Hueckel-Limit). Calculate the ion profiles in one or both of these cases and compare the results with the simulation.
Georg Rempfer, "Lattice-Boltzmann Simulations in Complex Geometries" (1.36 MB), 2010, Institute for Computational Physics, Stuttgart
Part 3: Electrophoresis of Polyelectrolytes
In this part you simulate the movement of a charged polymer under the influence of an external electrical field and hydrodynamic interactions. Set up a system consisting of a charge polymer, ions with the opposite charge to make the system neutral and an Lattice Boltzmann fluid coupled the the ions and polymer. Apply an external field and measure the center of mass velocity of the polymer as a function of the length of the polymer for polymers of one to 20 monomers. Make sure the system is in equilibrium before you start the sampling. Compare your result to theory and experimental results (see literature).
Please write together one report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.