Entry requirements

120 credits inclusive Algebra and geometry. Calculus. Mechanics. Chemical thermodynamics. Organic chemistry. Quantum mechanics and chemical bonding.

Learning outcomes

The course covers statistical mechanical theory and its applications to molecular systems as well as modern computer simulation methods for studying the dynamics and energetics of macromolecules. After completing the course the student should be able to

• explain the foundations and concepts of statistical mechanics such as canonical distributions, ensembles and partition functions
• account for the statistical mechanical description of ideal and non-ideal gases and simple liquids as well as the molecular mechanical description of force fields for intereacting systems
• use computational methods such as molecular dynamics simulations, energy optimisation, Monte Carlo and free energy calculations based on thermodynamics cycles
• use an integrated computer modelling environment for analysing biomolecular structure, function and dynamics

Content

The course is oriented both towards statistical mechanical theory and computer simulations of biomolecular dynamics and energetics. It covers the following elements:

Maxwell-Boltzmann distributions, ensembles, molecular and canonical partition functions, kinetic theory of gases, transition state theory, configurational distributions, non-ideal gases, simple liquids, analytical force fields for interacting systems, energy optimisation, Monte Carlo methods, molecular dynamics simulation and algorithms, thermodynamics cycles and free energy calculations, methodology and applications in computer-aided drug design.

Instruction

The schedule comprises lectures, classroom exercises och computer practicals.

Assessment

Written exam at the end of the course and passed written reports from computer practicals. Credits are only awarded for the completely passed course.