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S-114.250 Course outline

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1) Basic physics background
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Newtons laws, energy, two body dynamics, classical models of intermolecular interactions,
review of statistical mechanics and thermodynamics, single polymer chain in a good solution,
Monte Carlo methods

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2) many particle simulation
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The unsolvable three body problem, numerical solution to differential equations, boundary
conditions, MC vs. MD simulation of many particle simulations, energy minimisation
techniques, NVT and NPT ensembles

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3) Optimisation of free particle simulation algorithms
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Box subdivisions, linked list of neighbors, image particles, verlet table, bitwise
decomposition

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4) toy model of a polymer
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Polymer bond potential, efficient simulation method for inclusion of bonds, Hybridisation
of MC with MD: pivot moves

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5) Parallelization of MD simulation code
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basics of parallel programming, Geometric parallelization

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6) Advanced topics (Time permitting, and dependent on class interest)
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Possible topics include: dissipative particle dynamics simulation, Atomistic model
simulations ( MC MD hybridisation and/or an introduction to the GROMAX MD package),
Simulation of complex fluids under shear, applications to problems in physical chemistry
and computational systems biology

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Assignments and evaluation
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1 individual assignment on material covered in part 1
3 team projects each one covering one of chapters 2 - 4
Oral exam covering whole course but mostly focussed on parts 5 and 6
each component 20%
Grades:

- 0-50: 0 (failed)
- 50-60: 1
- 60-70: 2
- 70-80: 3
- 80-90: 4
- 90-100: 5

Comments/questions/suggestions? Mail to
*bunker@lce.hut.fi
*

Last updated Feb. 15, 2005