Lecturer | Prof. Petros Koumoutsakos |
Class Times | |
Assistants |
Wim van Rees, CAB F84, wvanrees_AT_inf.ethz.ch Rajdeep Deb, CAB H83.1, debr_AT_student.ethz.ch Mattia Gazzola, CAB F84, mgazzola_AT_inf.ethz.ch Eduardo Cruz-Chu, CAB F84, eduardo.cruz_AT_inf.ethz.ch |
week | Monday | Thursday |
1 (19/09) | – | Introduction (slides) |
2 (26/09) | Multipoles I | homework class (slides) |
3 (03/10) | Multipoles II (FMM boxes: slides) | homework class |
4 (10/10) | Multigrid I | Multigrid II |
5 (17/10) | homework class (slides) | Multigrid III (slides) |
6 (24/10) | homework class | Multigrid IV |
7 (31/10) | homework class | Wavelets I |
8 (07/11) | homework class (slides) | Wavelets II |
9 (14/11) | Stochastics I | homework class |
10 (21/11) | homework class | Stochastics II (slides) |
11 (28/11) | homework class (slides) (white bg) | Stochastics III (slides: see week 10) |
12 (05/12) | homework class | Equation Free |
13 (12/12) | homework class | HMM I |
14 (19/12) | homework class | EXAM |
Course notes:
NOTES
Homework:
Homework 1 – Multipoles (due October 17th): pdf.
How to visualize particles using Paraview: pdf
Homework 1 – Solution code: zip
Homework 2 – Multigrid (due November 7th): pdf, code: zip
Homework 2 – Solution: pdf, code: zip
Homework 3 – Wavelets (due November 24th): pdf, code: zip, images: zip
Homework 3 – Solution: pdf, code: zip
Homework 4 – Stochastics (due December 8th): pdf, code: zip
Homework 4 – Solution: pdf, code: zip
Literature:
– R-leaping: Accelerating the stochastic simulation algorithm by reaction leaps. A. Auger, P. Chatelain, P. Koumoutsakos., JCP 2006 (pdf)
– Approximate accelerated stochastic simulation of chemically reacting systems, Gillespie, D.T., JCP 2001 (pdf)
– Exact stochastic simulation of coupled chemical reactions, Gillespie, D.T., JPC 1977 (pdf)
– A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Gillespie, D.T., JCP 1976 (pdf)
– A new algorithm for Monte Carlo simulation of Ising spin systems, Bortz, A.B., Kalos, M.H. and Lebowitz, J.L., JCP 1975 (pdf)
– The Master Equation, Hizanidis, J. (2002): pdf
– Factoring Wavelet Transforms into Lifting Steps, Daubechies, I. and Sweldens, W.: pdf
– Building your own wavelets at home, Schröder, P. and Sweldens, W.: pdf
– Wavelets for Computer Graphics: a Primer, Stollnitz, E. et. al.: pdf
– A Multigrid Tutorial, slides. Briggs, W.L., Henson, V.E. and McCormick, S.: pdf
Software:
– Netlogo, a multi-agent programmable modeling environment: link
Visualization:
– Paraview
– VMD
– Grace
– POVray
– DataTank