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, as well as the statistical mechanical description of ideal and non-ideal gases and simple liquids
account for the molecular mechanical description for interacting systems , including the theoretical basis behind force fields, intramolecular and intermolecular interactions
connect the theoretical basis with its implementation in computational methods such as molecular dynamics simulations, energy optimisation, Monte Carlo and free energy calculations based on thermodynamics cycles
use computer modelling methods (outlined above) for analysing biomolecular structure, function and dynamics.
The course gives an introduction to statistical mechanical theory, and connects it with the foundation of computer simulations of biomolecular dynamics and energetics, methods which are then covered extensively from a theoretical and practical perspective. Tthe following elements are covered in this course:
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.
The schedule comprises lectures, classroom exercises och computer practicals.
Written exam (4 credits) at the end of the course and passed written reports from computer practicals (1 credit). Credits are only awarded for the completely passed course.