Difference between revisions of "Simulation Techniques for Soft Matter Sciences (SS 2007)"
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−  +  == Overview ==  
−  
;Type  ;Type  
:Lecture (2 SWS) and Tutorials (2 SWS)  :Lecture (2 SWS) and Tutorials (2 SWS)  
;Lecturer  ;Lecturer  
−  :PD Dr. Christian Holm (Lecture) and  +  :PD Dr. [[Christian Holm]] (Lecture) and working group (Tutorials) 
;Course language  ;Course language  
:English  :English  
;Time and Room  ;Time and Room  
−  :Lecture: Thu 12:  +  :Lecture: Thu 12:15  13:45, Phys 1.114<br/>Tutorials: Thu 14:0016:00, 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.  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 ===  
+  {  
+  valign="top"  
+  !Date !! Subject  
+  
+  valign="top"  
+  ! 19.4.  
+   MonteCarlo integration/simulation (Simple vs. Importance sampling)  
+  
+  Look at Zuse's Z3 computer from 1941: [http://upload.wikimedia.org/wikipedia/de/4/4c/Z3_Deutsches_Museum.JPG Z3] and  
+  read something about the first big US computer at Los Alamos [http://www.lanl.gov/history/atomicbomb/computers.shtml Evolving from Calculators to Computers]  
+  
+  valign="top"  
+  ! 26.4.  
+   2D Random walks (RW) and Selfavoiding random walks (SAW)Ising model I (Phase transitions, Critical phenomena, Finite size scaling)  
+  
+  valign="top"  
+  ! 3.5.  
+   2D Ising model II (Reweighting, Cluster Algorithm)  
+  
+  valign="top"  
+  ! 10.5.  
+   Error Analysis (Binning, Jackknife, ...)  
+  
+  valign="top"  
+  ! 17.5.  
+   '''Holiday'''  
+  
+  valign="top"  
+  ! 24.5.  
+   Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields)  
+  
+  valign="top"  
+  ! 31.5.  
+   Molecular Dynamics II  
+  
+  valign="top"  
+  ! 7.6.  
+   '''Holiday'''  
+  
+  valign="top"  
+  ! 14.6.  
+   Long range interactions (Direct sum, Ewald summation, P3M, Fast Multipole method)  
+  This pdf file {{Downloadlong_range_lecture.pdflong_range_lecture.pdf}} 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 ({{Downloadarnold05a.pdfarnold05a.pdf}})  
+  
+  valign="top"  
+  ! 21.6.  
+   Continuation of long range lecture, beginning of ''How to simulate Polymers and Polyelectrolytes''.  
+  
+  valign="top"  
+  ! 28.6.  
+   12:15 Tutorial14:30 Talk by Prof. Binder in Seminar room 2.116,  
+  
+  Afterwards we meet in the Computer room: Continuation on ''How to simulate Polymers and Polyelectrolytes'' and background of PoissonBoltzmann Theory.  
+  valign="top"  
+  ! 5.7.  
+   Introduction to the Project work: charged infinite rods in ionic solutioncomparison to PB theory. {{DownloadCompMethods.pdfCompMethods.pdf}}  
+  
+  A good background reading is the thesis of M. Deserno {{Downloaddeserno00b.pdfthesis_deserno.pdf}}  
+  
+  valign="top"  
+  ! 12.7.  
+   Extended tutorial I: project work  
+  
+  valign="top"  
+  ! 19.7.  
+   Extended tutorial II: project work  
+  
+  valign="top"  
+  ! 23.7.  
+   <span style="color:black;border: solid red"> On this Monday from 10:00 on we will have the oral examination in my office 01.218! </span>.  
+  
+  }  
+  
+  === Tutorials ===  
+  Materials on the tutorials can be found behind the links!  
+  
+  {  
+  
+  valign="top"  
+  !Date !! Subject !! Tutors  
+  
+  valign="top"  
+  ! 19.4.  
+   [[/IntroductionIntroductory tutorial]]  
+   [[Kai Grass]]  
+  
+  valign="top"  
+  ! 26.4.  
+   [[/Random walksRandom walks]]  
+   [[Kai Grass]]  
+  
+  valign="top"  
+  ! 3.5.  
+   [[/Ising 1Monte Carlo: The Ising model I]]  
+   [[Marcello Sega]]  
+  
+  valign="top"  
+  ! 10.5.  
+   [[/Ising 2Monte Carlo: The Ising model II]]  
+   [[Marcello Sega]]  
+  
+  valign="top"  
+  ! 17.5.  
+   '''Holiday'''  
+  
+  valign="top"  
+  ! 24.5.  
+   [[/Error analysisError analysis]]  
+   [[Joan Josep Cerdà]]  
−  =  +  valign="top" 
−  +  ! 31.5.  
+   [[/Molecular DynamicsMolecular Dynamics: LennardJones liquid]]  
+   [[Qiao Baofu]]  
−  +  valign="top"  
+  ! 7.6.  
+   '''Holiday'''  
−  =  +  valign="top" 
−  +  ! 14.6.  
+   [[/ESPResSoIntroduction to MD simulations with ESPResSo]]  
+   [[Mehmet Süzen]]  
−  =  +  valign="top" 
−  +  ! 21.6.  
−  +   [[/Ewald summationLong range interactions: Direct sum and Ewald summation]]  
−  +   [[Joan Josep Cerdà]]  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  
−  =  +  valign="top" 
−  +  ! 28.6.  
+   [[/VMDVisualisation of MD simulations with VMD]]  
+   [[Olaf Lenz]]  
−  +  valign="top"  
+  ! 5.7.  
+   [[/Simulating polymersSimulation of polymers and polyeletrolytes]]  
+   [[Qiao Baofu]]  
−  +  valign="top"  
+  ! 12.7.  
+   [[/ProjectExtended tutorial I: project work]]  
+   [[Olaf Lenz]] and [[Mehmet Süzen]]  
−  +  valign="top"  
−  +  ! 19.7.  
−  +   [[/ProjectExtended tutorial II: project work]]  
−  +   [[Olaf Lenz]] and [[Mehmet Süzen]]  
−  
−  
−  
−  
−  
−  
−  
−  
−  +  }  
−  +  == Recommended literature ==  
+  <bibentry>frenkel02b,allen87a,rapaport04a,landau05a,newman99a</bibentry> 
Latest revision as of 11:47, 16 July 2007
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 12:15  13:45, Phys 1.114
Tutorials: Thu 14:0016:00, 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 

19.4.  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 
26.4.  2D Random walks (RW) and Selfavoiding random walks (SAW)Ising model I (Phase transitions, Critical phenomena, Finite size scaling) 
3.5.  2D Ising model II (Reweighting, Cluster Algorithm) 
10.5.  Error Analysis (Binning, Jackknife, ...) 
17.5.  Holiday 
24.5.  Molecular Dynamics I (Velocity Verlet algorithm, Reduced units, Langevin thermostat, Potentials, Forces, Atomistic force fields) 
31.5.  Molecular Dynamics II 
7.6.  Holiday 
14.6.  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!)) 
21.6.  Continuation of long range lecture, beginning of How to simulate Polymers and Polyelectrolytes. 
28.6.  12:15 Tutorial14:30 Talk by Prof. Binder in Seminar room 2.116,
Afterwards we meet in the Computer room: Continuation on How to simulate Polymers and Polyelectrolytes and background of PoissonBoltzmann Theory. 
5.7.  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) 
12.7.  Extended tutorial I: project work 
19.7.  Extended tutorial II: project work 
23.7.  On this Monday from 10:00 on we will have the oral examination in my office 01.218! . 
Tutorials
Materials on the tutorials can be found behind the links!
Date  Subject  Tutors 

19.4.  Introductory tutorial  Kai Grass 
26.4.  Random walks  Kai Grass 
3.5.  Monte Carlo: The Ising model I  Marcello Sega 
10.5.  Monte Carlo: The Ising model II  Marcello Sega 
17.5.  Holiday  
24.5.  Error analysis  Joan Josep Cerdà 
31.5.  Molecular Dynamics: LennardJones liquid  Qiao Baofu 
7.6.  Holiday  
14.6.  Introduction to MD simulations with ESPResSo  Mehmet Süzen 
21.6.  Long range interactions: Direct sum and Ewald summation  Joan Josep Cerdà 
28.6.  Visualisation of MD simulations with VMD  Olaf Lenz 
5.7.  Simulation of polymers and polyeletrolytes  Qiao Baofu 
12.7.  Extended tutorial I: project work  Olaf Lenz and Mehmet Süzen 
19.7.  Extended tutorial II: project work  Olaf Lenz and Mehmet Süzen 
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.

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