Difference between revisions of "Advanced Simulation Methods SS 2015"

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:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Jens Smiatek]]</b>}}
 
:{{Infobox|<b> A preliminary registration for this course is mandatory. Interested students write an Email to [[Jens Smiatek]]</b>}}
 +
 +
== Module 1: [[Christian Holm]], Electrostatics and Lattice Boltzmann ==
 +
=== Description ===
 +
 +
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 presentation
 +
and hand in one report per group. It consists of three parts.
 +
 +
=== Contact ===
 +
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 ===
 +
==== Description ====
 +
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. Give the presentation to [[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.
 +
 +
==== Literature ====
 +
<bibentry>deserno98a,arnold13b,arnold05a</bibentry>
 +
 +
=== Part 2: Slit Pore ===
 +
==== Description ====
 +
[[File:Slitpore.png|550px|right|Electroosmotic flow in a 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 [http://espressomd.org 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.
 +
 +
==== Literature ====
 +
Georg Rempfer, {{Download|BSc_thesis_rempfer.pdf|"Lattice-Boltzmann Simulations in Complex Geometries"}}, 2010, Institute for Computational Physics, Stuttgart
 +
<bibentry>grass09c</bibentry>
 +
 +
=== Part 3: Electrophoresis of Polyelectrolytes ===
 +
==== Description ====
 +
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).
 +
 +
==== Literature ====
 +
<bibentry>grass08a, grass09c</bibentry>
 +
 +
 +
=== Report ===
 +
Please write a report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.

Revision as of 17:22, 4 May 2015

Overview

Type
Lecture and Tutorials (2 SWS in total)
Lecturer
The group leaders of the ICP
Course language
English (German if possible)
Location
ICP, Allmandring 3; Room: tba.
Time
tba.

The course will consist out of a lecture and a tutorial in weekly turns.

Information icon-40x40.png A preliminary registration for this course is mandatory. Interested students write an Email to Jens Smiatek

Module 1: Christian Holm, Electrostatics and Lattice Boltzmann

Description

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 presentation and hand in one report per group. It consists of three parts.

Contact

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

Description

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. Give the presentation to 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.

Literature

  • Markus Deserno, Christian Holm.
    How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines.
    The Journal of Chemical Physics 109:7678, 1998.
    [PDF] (307 KB) [DOI]
  • Axel Arnold, Florian Fahrenberger, Christian Holm, Olaf Lenz, Matthias Bolten, Holger Dachsel, Rene Halver, Ivo Kabadshow, Franz Gähler, Frederik Heber, Julian Iseringhausen, Michael Hofmann, Michael Pippig, Daniel Potts, Godehard Sutmann.
    Comparison of scalable fast methods for long-range interactions.
    Physical Review E 88(6):063308, 2013.
    [PDF] (2.3 MB) [DOI]
  • Axel Arnold, Christian Holm.
    Efficient methods to compute long range interactions for soft matter systems.
    In Advanced Computer Simulation Approaches for Soft Matter Sciences II, pages 59–109. Edited by C. Holm, K. Kremer. Part of Advances in Polymer Science.
    Springer, Berlin, 2005. ISBN: 9783540260912.
    [PDF] (1.1 MB) [DOI]


Part 2: Slit Pore

Description

Electroosmotic flow in a 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.

Literature

Georg Rempfer, application_pdf.png"Lattice-Boltzmann Simulations in Complex Geometries" (1.36 MB)Info circle.png, 2010, Institute for Computational Physics, Stuttgart

  • Kai Christian Grass.
    Towards realistic modelling of free solution electrophoresis: a case study on charged macromolecules.
    PhD thesis, Goethe-Universität Frankfurt am Main, 2008.
    [PDF] (5.3 MB)


Part 3: Electrophoresis of Polyelectrolytes

Description

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).

Literature

  • Kai Grass, Ute Böhme, Ulrich Scheler, Hervé Cottet, Christian Holm.
    Importance of Hydrodynamic Shielding for the Dynamic Behavior of Short Polyelectrolyte Chains.
    Physical Review Letters 100(9):096104, 2008.
    [PDF] (115 KB) [DOI]
  • Kai Christian Grass.
    Towards realistic modelling of free solution electrophoresis: a case study on charged macromolecules.
    PhD thesis, Goethe-Universität Frankfurt am Main, 2008.
    [PDF] (5.3 MB)


Report

Please write a report of 5 to 10 pages containing and discussing your simulation results from part 2 and 3.

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