Molecular Dynamics, 2011
Department of Physics
(site in Finnish, the English site is broken) @
University of Helsinki
Course #: 533633, Fall 2011
FINAL EXAM: Thu 15.12.2011 at 10-14, in Exactum D122
Prerequisites
Some knowledge of programming will be immensely helpful during the course, preferably in Unix/Linux environment. In addition, the students should have basic knowledge of the structure of matter and thermodynamics. The course is a part of the MoMoNano Master's programme. The teaching is hence given in English.
Summary
| Lecturers: | Docent Jani Kotakoski (Ph.D.) | <jani.kotakoski(-at-)iki.fi> |
| Dr. Olli Pakarinen | <olli.pakarinen(-at-)helsinki.fi> | |
| Assistant: | M.Sc. Eero Holmström | <eero.holmstrom(-at-)helsinki.fi> |
This course is a 10 ECTS credit points course on atomistic simulations. We will concentrate on molecular dynamics simulations (MD) which enable following the evolution of a system of point-like objects over time. During the course, students will write in a supervised manner their own MD code which can be used to model atomic motion in simple metals. The course will also cover genetic algorithm and conjugent gradient energy minimization as well as the nudged elastic band (NEB) method for migration energy barrier calculations. Quantum mechanical and classical atomic interaction models will be covered, main stress being on classical methods.
Scope: 10 ECTS points
Schedule (tentative)
| Tue 12-14 @ D104 | Thu 12-14 @ D104 | ||
| 06.09.2011 Lecture #1 | 08.09.2011 Hands-on (10-12 @ D221) | ||
| 13.09.2011 Lecture #2 | 15.09.2011 Exercise #1 | ||
| 20.09.2011 Lecture #3 | 22.09.2011 Exercise #2 | ||
| 27.09.2011 Lecture #4 | 29.09.2011 Exercise #3 | ||
| 04.10.2011 Lecture #5 | 06.10.2011 Exercise #4 | ||
| 11.10.2011 FREE | 13.10.2011 Exercise #5 | ||
| 18.11.2011 Lecture #6 | 20.11.2011 Exercise #6 | ||
| 25.10.2011 BREAK | 27.10.2011 BREAK | ||
| 01.11.2011 Lecture #7 | 03.11.2011 Exercise #7 | ||
| 08.11.2011 Lecture #8 | 10.11.2011 Exercise #8 | ||
| 15.11.2011 Lecture #9 | 17.11.2011 Exercise #9 | ||
| 22.11.2011 Lecture #10 | 24.11.2011 Exercise #10 | ||
| 29.11.2011 Lecture #11 | 01.12.2011 Exercise #11 | ||
| 06.12.2011 FREE | 08.12.2011 Lecture #12 | ||
| 13.12.2011 FREE | 15.12.2011 EXAM (10-14) |
Lecture Notes
- Lecture #1: Introduction, Download: Notes (pdf)
- Lecture #2: MD Basics, Download: Notes (pdf)
- Lecture #3: Solving the Equations of Motion, Download: Notes (pdf)
- Lecture #4: Pair potentials and force calculations, Download: Notes (pdf)
- Lecture #5: Equilibrium thermodynamics, Download: Notes (pdf)
- Lecture #6: Ab Initio MD, Download: Notes (pdf)
- Lecture #7: Interaction models for metals, Download: Notes (pdf)
- Lecture #8: Covalent interaction models, Download: Notes (pdf)
- Lecture #9: Molecular Mechanics / ReaxFF, Download: Notes (pdf)
- Lecture #10: Ionic Interactions, Download: Notes (pdf)
- Lecture #11: Energy Minimization, Download: Notes (pdf)
- Lecture #12: Path Optimization Calculations, Download: Notes (pdf)
Exercises
- Exercise #1: Download: pdf
- Exercise #2: Download: pdf
- Exercise #3: Download: pdf
- Exercise #4: Download: pdf
- Exercise #5: Download: pdf
- Exercise #6: Download: pdf
- Exercise #7: Download: pdf
- Exercise #8: Download: pdf
- Exercise #9: Download: pdf
- Exercise #10: Download: pdf
- Exercise #11: Download: pdf
Presentation schedule
- Tuesday 13.9. H. Åhlgren: "TBA"
- Tuesday 20.9. M. Ullah: "TBA"
- Thursday 22.9. T. Pinomaa: "TBA"
- Tuesday 27.9. A. Ruzibaev: "TBA"
- Thursday 29.9. A. Ilinov: "TBA"
- Tuesday 4.10. M. Mehine: "TBA"
- Thursday 6.10. M. Utkin: "TBA"
- Tuesday 1.11. D. Du: "TBA"
- Tuesday 8.11. W. Ren: "TBA"
- Thursday 24.11. V. Haikola:"Introduction to nonadiabatic molecular dynamics"
- Tuesday 29.11. D. Landau: "High-performance MD"
- Thursday 1.12. M. Korpinen: "MD simulations of nanoparticles"
- Thursday 8.12. K. Viisanen: "MD of biomolecules"
Ideas for presentation
- Early MD (first few publications on the method and on its use)
- Molecular dynamics for stars and galaxies, see f.ex.
- Annu. Rev. Astron. Astrophys. 25, 151
- New J. Phys. 10, 125002 (2008)
- Monthly Notices of the Royal Astronomical Society 364, 1105 (2005)
- MD for protein folding (f.ex. Annu. Rev. Phys. Chem. 58, 57-83 (2007)
- MD of biomolecules (f.ex. Nature Structural Biology 9, 646 (2002)
- MD of brittle fracture in Si (Nature 455 (30), 1224 (2008))
- Self-diffusion in Si (Nuclear Instruments and Methods in Physics Research B 102, 247–255 (1995))
- Pattern formation by energetic particle irradiation (Nature Communications 2, 276 (2011))
