Modern Computational Science - Summer School
Here you will find material that the lecturers provide for your convenience (slides of the classes, supplementary material relevant to the different topics of the Summer School, etc). This area is expected to grow continuously before, during and (maybe) even after the School. All downloads are password-protected.
Material that may be useful in order to prepare yourself for the Summer School
- All participants are strongly advised
to read and (work over) the script
which is an excerpt from the book A Practical Guide to Computer Simulations by A.K.Hartmann. It is expected that each participant has a basic working knowledge of the C programming language, which is required to follow the hands-on tutorials in the PC labs. Every participant will obtain a free copy of the book upon registration, thus there is no need to bring this C course for the Summer School. - Elementary introduction into the UNIX
and Linux OS:
Learning the UNIX Operating System by Jerry Peek, Grace Todino, and John Strang.
It is recommended that participants take a look at this book before the School starts, in particular if they are not very familiar with the UNIX/Linux OS.
First week: Fundamentals of Scientific Computing and Large Deviations / Rare-event Theory
- Frauke Liers' Lectures and Tutorials
on Advanced Programming Techniques:
- Slides of the classes
- Exercise Sheet, source codes of sample programs, and solutions of the exercises
- All example programs (Python scripts) of Oliver Melchert's introduction to Basic Data Analysis.
- Thomas Schuster's introductory Lectures on Numerical Methods: Integration and Interpolation.
- Slides of Hugo Touchette's lectures on Large Deviation Theory (Theory, applications, and simulations).
- Slides of Andreas Engel's Lecture on Large Deviations in Thermodynamics.
Second week: Special Topics
- Thomas Prellberg's Lectures and Tutorials
on Rare-event sampling with stochastic growth algorithms
(with applications to Extreme Polymer Conformations):
- Lecture Notes (not contained in the "official" volume!) and Slides of the Lectures.
- Exercise Sheet.
- Source codes of programs.
- Slides of Christoph Dellago's Lectures on
Transition Path Sampling: Parts I-II [11 MB] and
Parts III-IV [8 MB].
Selection of review articles on the subject matter:- Peter G. Bolhuis and Christoph Dellago, Trajectory based rare event simulations, Reviews of Computational Chemistry 27, 111-210 (2010).
- Christoph Dellago and Peter G. Bolhuis, Transition Path Sampling and other Advanced Simulation Techniques for Rare Events, Advances in Polymer Science Vol. 221, Eds. C. Holm and K. Kremer, pp. 167-233, Springer (2008).
- Christoph Dellago and Peter G. Bolhuis, Transition Path Sampling Simulations of Biological Systems, Atomistic Approaches in Modern Biology - From quantum chemistry to molecular simulation, Topics in Current Chemistry Vol. 268:291-317, Springer (2007).
- Christoph Dellago, Transition Path Sampling and the Calculation of Free Energies, Free Energy Calculations, Springer Series in Chemical Physics Vol. 86, Ch. Chipot and A. Pohorille (Eds.), pp. 249-276, Springer-Verlag Berlin Heidelberg (2007).
- Christoph Dellago, Peter G. Bolhuis, and Phillip L. Geissler, Transition Path Sampling Methods, Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Vol. 1, Eds. M. Ferrario, G. Ciccotti, and K. Binder, pp.349-391, Springer-Verlag Berlin Heidelberg (2006).
- Christoph Dellago, Peter G. Bolhuis, and Phillip L. Geissler, Transition Path Sampling, Advances in Chemical Physics 123, 1 (2002).
- Slides of Joachim Peinke's Lectures on Extreme Events in Weather and Stock Market Phenomena (and other systems): Part 1 [12 MB] and Part 2 [7.2 MB].
- Ryan Woodard's Lectures on
Analysis of Stock Market Crashes:
- Slides: Part 1 [32 MB] and Part 2 [9 MB].
- Python code to analyse financial data, and sample data.
- Please check this website where the newest version of the code including fixes/improvements is available. It is preferred that you download the code (and other, useful material) from there.
- Olaf R.P. Bininda-Emonds' Lecture
and Tutorial on Molecular homology and sequence alignment:
- Slides of the Lecture.
- Practical on multiple sequence alignment.
- Data files needed for the Practical.
- Alexander K. Hartmanns's Lecture
and Tutorial on Sampling of Extreme Sequence Alignments:
- Lecture Notes (not contained in the "official" volume, but a printed copy was handed out to each participant at the beginning of the Summer School) and Slides of the Lecture.
- Exercise Sheet.
- Source codes of programs.
- Christoph Dobler's Lecture and Practical Demonstration on Simulation of Extreme Traffic Events: