S-114.250 Course outline

1) Basic physics background

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

2) many particle simulation

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

3) Optimisation of free particle simulation algorithms

Box subdivisions, linked list of neighbors, image particles, verlet table, bitwise decomposition

4) toy model of a polymer

Polymer bond potential, efficient simulation method for inclusion of bonds, Hybridisation of MC with MD: pivot moves

5) Parallelization of MD simulation code

basics of parallel programming, Geometric parallelization

6) Advanced topics (Time permitting, and dependent on class interest)

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

Assignments and evaluation

  • 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%


  • Comments/questions/suggestions? Mail to bunker@lce.hut.fi
    Last updated Feb. 15, 2005