Modern Computational Science - Summer School

Modern Computational Science 2011 - Lecture Materials

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:
  • 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):
  • 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:
  • Alexander K. Hartmanns's Lecture and Tutorial on Sampling of Extreme Sequence Alignments:
  • Christoph Dobler's Lecture and Practical Demonstration on Simulation of Extreme Traffic Events: