Entry requirements

Alternative 1: 120 credits within the Master's Programme in Molecular Biotechnology Engineering including Probability and Statistics, Structural Bioinformatics, Chemical Thermodynamics, and Introductory Organic Chemistry or Organic Chemistry I. Proficiency in English equivalent to the Swedish upper secondary course English 6.

Alternative 2: 15 credits within the Master's (120 credits) programme in Biophysics including Introduction to Statistics for Life Sciences and participation in Introduction to Modern Physics. Proficiency in English equivalent to the Swedish upper secondary course English 6.

Alternative 3: 15 credits within the Master's (120 credits) programme in Biophysics including Introduction to Biochemistry and participation in Introduction to Molecular Biology. Proficiency in English equivalent to the Swedish upper secondary course English 6.

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, interactions and energetics of macromolecules.

On completing 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 descriptions 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 implementations in computational methods such as molecular dynamics simulations, protein-ligand and protein-protein docking, energy optimisations, Monte Carlo and free energy calculations based on thermodynamics cycles
• use computer modelling methods for analysing biomolecular structure, function and dynamics
• critically understand and rationally use modern molecular simulation metods in biochemistry and pharmacology
• use the aforementioned computational techniques in the framework of structure-based ligand design within pharmaceutical applications, including protein-ligand docking, chemical data mining and optimization of protein-ligand interactions

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. The 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, force field parametrization, energy optimisation, Monte Carlo methods, molecular dynamics simulation and molecular dynamics algorithms, thermodynamics cycles and free energy calculations, advanced molecular computational methods, automated docking and virtual screening, chemical data mining and machine learning methods, and methodology and applications in computer-aided drug design.

Instruction

The schedule comprises lectures, classroom exercises and computer practicals.

Assessment

Written exam (8 credits) at the end of the course and passed written reports from computer practicals (2 credits). 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.