Syllabus for Molecular and Statistical Mechanics

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. On completion of 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.

Content

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.

Instruction

The schedule comprises lectures, classroom exercises och computer practicals.

Assessment

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.

If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.