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

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=== Lecture ===
 
=== Lecture ===
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Materials on the tutorials will be sent to students by tutors via mail!
 
Materials on the tutorials will be sent to students by tutors via mail!
  
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! 17.4.
 
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| /Introduction|Introductory tutorial, random walks
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| Introductory tutorial, random walks
 
| [[Nadezhda Gribova]]
 
| [[Nadezhda Gribova]]
  
 
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! 24.4.
 
! 24.4.
| /Ising 1|Monte Carlo: The Ising model I
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| Monte Carlo: The Ising model I {{Download|T2_ss08.tar.gz|Ising I|tar}}
 
| [[Marcello Sega]]
 
| [[Marcello Sega]]
  
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! 8.5.
 
! 8.5.
| /Ising 2|Monte Carlo: The Ising model II
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| Monte Carlo: The Ising model II {{Download|T3_ss08.pdf|Ising II|pdf}}
 
| [[Marcello Sega]]
 
| [[Marcello Sega]]
  
 
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! 15.5.
 
! 15.5.
| /Error analysis|Error analysis
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| Error analysis
 
| [[Joan Josep Cerdà]]
 
| [[Joan Josep Cerdà]]
  
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! 29.5.
 
! 29.5.
| /Molecular Dynamics|Molecular Dynamics: Lennard-Jones liquid
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| Molecular Dynamics: {{Download|t6-sose08.tar.gz|Lennard-Jones liquid|tar}}
 
| [[Florian Dommert]]
 
| [[Florian Dommert]]
  
 
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! 5.6.
 
! 5.6.
| /ESPResSo|Introduction to MD simulations with ESPResSo
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| Introduction to MD simulations with ESPResSo
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{{Download|espresso_tutorial_summer_2008.tar‎.bz2|Handout and sources|tar}}
 
| [[Mehmet Süzen]]
 
| [[Mehmet Süzen]]
  
 
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! 12.6.
 
! 12.6.
| /Ewald summation|Long range interactions: Direct sum and Ewald summation
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| Long range interactions: Direct sum and Ewald summation: {{Download|T6_long_range_interaction.tar‎|Long range interactions|tar}}
 
| [[Kai Grass]]
 
| [[Kai Grass]]
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! 19.6.
 
! 19.6.
| /VMD|Visualisation of MD simulations with VMD
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| Simulation of polymers and polyeletrolytes; Project work
| [[Olaf Lenz]]
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{{Download|Project_SoSe_summer_2008.tar.bz2|Handout and sources|tar}}
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Further References:
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{{Download|Deserno00b.pdf|Deserno Thesis}}
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{{Download|Deserno00a.pdf|Fraction of Condensed Counterions around a Charge Rod: Comparison of Poisson-Boltzmann Theory and Computer Simulations}}
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{{Download|Deserno01c.pdf|Cell Model and Poisson-Boltzmann Theory: A Brief Introduction}}
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| [[Mehmet Süzen]]
  
 
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! 26.6.
 
! 26.6.
| /Simulating polymers|Simulation of polymers and polyeletrolytes; Project work
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| Visualisation of MD simulations with VMD
 
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| [[Olaf Lenz]]
  
 
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Latest revision as of 12:37, 12 August 2008

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 16:00-18:00, 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 Monte-Carlo (MC) and Molecular dynamics (MD) simulations (on- and off-lattice) and Poisson-Boltzmann 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 hands-on-tutorials 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. Monte-Carlo 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 Self-avoiding 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 application_pdf.pnglong_range_lecture.pdf (216 KB)Info circle.png 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 Poisson-Boltzmann Theory.
26.6. Introduction to the Project work: charged infinite rods in ionic solution-comparison to PB theory. application_pdf.pngCompMethods.pdf (1.65 MB)Info circle.png

A good background reading is the thesis of M. Deserno application_pdf.pngthesis_deserno.pdf (3.57 MB)Info circle.png

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 tar.pngIsing I (90 KB)Info circle.png Marcello Sega
1.5. Holiday
8.5. Monte Carlo: The Ising model II pdf.pngIsing II (28 KB)Info circle.png Marcello Sega
15.5. Error analysis Joan Josep Cerdà
22.5. Holiday
29.5. Molecular Dynamics: tar.pngLennard-Jones liquid (687 KB)Info circle.png Florian Dommert
5.6. Introduction to MD simulations with ESPResSo

tar.pngHandout and sources (314 KB)Info circle.png

Mehmet Süzen
12.6. Long range interactions: Direct sum and Ewald summation: tar.pngLong range interactions (40 KB)Info circle.png Kai Grass


19.6. Simulation of polymers and polyeletrolytes; Project work

tar.pngHandout and sources (138 KB)Info circle.png

Further References:

application_pdf.pngDeserno Thesis (3.57 MB)Info circle.png

Fraction of Condensed Counterions around a Charge Rod: Comparison of Poisson-Boltzmann Theory and Computer Simulations (file does not exist!)

application_pdf.pngCell Model and Poisson-Boltzmann Theory: A Brief Introduction (262 KB)Info circle.png

Mehmet Süzen
26.6. Visualisation of MD simulations with VMD Olaf Lenz

Recommended literature