Difference between revisions of "Simulation Techniques for Soft Matter Sciences (SS 2008)"
(→Tutorials) 
(→Tutorials) 

Line 155:  Line 155:  
 Simulation of polymers and polyeletrolytes; Project work   Simulation of polymers and polyeletrolytes; Project work  
{{DownloadProject_SoSe_summer_2008.tar.bz2Handout and sourcestar}}  {{DownloadProject_SoSe_summer_2008.tar.bz2Handout and sourcestar}}  
+  
+  Further References:  
+  
+  {{DownloadDeserno00b.pdfDeserno Thesis}}  
+  
+  {{DownloadDeserno00a.pdfFraction of Condensed Counterions around a Charge Rod: Comparison of PoissonBoltzmann Theory and Computer Simulations}}  
+  
+  {{DownloadDeserno01c.pdfCell Model and PoissonBoltzmann Theory: A Brief Introduction}}  
+  
 [[Mehmet Süzen]]   [[Mehmet Süzen]]  
Revision as of 12:22, 12 August 2008
Contents
Overview
 Type
 Lecture (2 SWS) and Tutorials (2 SWS)
 Lecturer
 PD Dr. Christian Holm (Lecture) and working group (Tutorials)
 Course language
 English
 Time and Room
 Lecture: Thu special appointment, FIAS Room 200
Tutorials: Thu 16:0018:00, Phys 1.120
Soft matter science is the science of "soft" materials, like polymers, liquid crystals, colloidal suspensions, ionic solutions, hydrogels and most biological matter. The phenomena that define the properties of these materials occur on mesoscopic length and time scales, where thermal fluctuations play a major role. These scales are hard to tackle both experimentally and theoretically. Instead, computer simulations and other computational techniques play a major role.
The course will give an introduction to the computational tools that are used in soft matter science, like MonteCarlo (MC) and Molecular dynamics (MD) simulations (on and offlattice) and PoissonBoltzmann theory (and extensions).
Prerequisites
The course is intended for participants in the Master Program "Computational Science", but should also be useful for FIGSS students and for other interested science students.
We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).
Lecture and tutorials
The lecture is accompanied by handsontutorials which will be held in the computer room (Physics, 1.120). They consist of practical excercises at the computer, like small programming tasks, simulations, visualisation and data analysis.
The tutorials build on each other, therefore continous attendance is expected.
The dates of the tutorials will be scheduled in the first lecture.
Lecture
Date  Subject 

10.4.  MonteCarlo integration/simulation (Simple vs. Importance sampling)
Look at Zuse's Z3 computer from 1941: Z3 and read something about the first big US computer at Los Alamos Evolving from Calculators to Computers 
17.4.  2D Random walks (RW) and Selfavoiding random walks (SAW)Ising model I (Phase transitions, Critical phenomena, Finite size scaling) 
24.4.  2D Ising model II (Reweighting, Cluster Algorithm) 
1.5.  Holiday 
08.5.  Error Analysis (Binning, Jackknife, ...)

15.5.  Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields) 
22.5.  Holiday 
29.5.  Molecular Dynamics II

5.6.  Long range interactions (Direct sum, Ewald summation, P3M, Fast Multipole method)
This pdf file long_range_lecture.pdf (216 KB) contains surely too many details, but I will walk you through in class. In case you like to have some more background material, here is a review article by A. Arnold and me about this topic (arnold05a.pdf (file does not exist!)) 
12.6.  Continuation of long range lecture, beginning of How to simulate Polymers and Polyelectrolytes. 
19.6.  Continuation on How to simulate Polymers and Polyelectrolytes and background of PoissonBoltzmann Theory. 
26.6.  Introduction to the Project work: charged infinite rods in ionic solutioncomparison to PB theory. CompMethods.pdf (1.65 MB)
A good background reading is the thesis of M. Deserno thesis_deserno.pdf (3.57 MB) 
03.7.  Extended tutorial: project work 
July.  Oral examination in my office FIAS 02.301, date to be fixed . 
Tutorials
Materials on the tutorials will be sent to students by tutors via mail!
Date  Subject  Tutors  

17.4.  Introductory tutorial, random walks  Nadezhda Gribova  
24.4.  Monte Carlo: The Ising model I Ising I (90 KB)  Florian Dommert  Marcello Sega 
1.5.  Holiday  
8.5.  Monte Carlo: The Ising model II Ising II (28 KB)  Marcello Sega  
15.5.  Error analysis  Joan Josep Cerdà  
22.5.  Holiday  
29.5.  Molecular Dynamics: LennardJones liquid (687 KB)  Florian Dommert  
5.6.  Introduction to MD simulations with ESPResSo
Handout and sources (314 KB) 
Mehmet Süzen  
12.6.  Long range interactions: Direct sum and Ewald summation: Long range interactions (40 KB)  Kai Grass
 
19.6.  Simulation of polymers and polyeletrolytes; Project work
Handout and sources (138 KB) Further References: Deserno Thesis (3.57 MB) Fraction of Condensed Counterions around a Charge Rod: Comparison of PoissonBoltzmann Theory and Computer Simulations (file does not exist!) Cell Model and PoissonBoltzmann Theory: A Brief Introduction (262 KB) 
Mehmet Süzen  
26.6.  Visualisation of MD simulations with VMD  Olaf Lenz 
Recommended literature

Daan Frenkel and Berend Smit.
"Understanding Molecular Simulation".
Academic Press, San Diego, 2002.
[DOI] 
Mike P. Allen and Dominik J. Tildesley.
"Computer Simulation of Liquids".
Oxford Science Publications, Clarendon Press, Oxford, 1987.

D. C. Rapaport.
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.

D. P. Landau and K. Binder.
"A guide to Monte Carlo Simulations in Statistical Physics".
Cambridge, 2005.

M. E. J. Newman and G. T. Barkema.
"Monte Carlo Methods in Statistical Physics".
Oxford University Press, 1999.