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. 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 and energetics of macromolecules.

On completing of the course, the student should be able to

• account for the basic principles and concepts of quantum mechanics
• 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 quantum mechanics calculations, molecular dynamics simulations, energy optimisations, Monte Carlo and free energy calculations based on thermodynamics cycles
• use computer modelling methods (outlined above) for analysing biomolecular structure, function and dynamics.
• Use the aforementioned computational techniques in the framework of pharmaceutical structure-based ligand design, including protein-ligand docking and optimization of protein-ligand interactions.

Content

The course gives an introduction to quantum mechanical and 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:

Quantum mechanics relevance within biochemistry, the formalism of quantum mechanics, the Schrödinger equation, the Born-Oppenheimer approximation, particle in a box, molecular vibrations and the harmonic oscillator, wave function and density functional theory methods, 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, the application of quantum mechanics in biomolecular simulations, force field parametrization and quantum chemistry calculations, energy optimisation, Monte Carlo methods, molecular dynamics simulation and algorithms, thermodynamics cycles and free energy calculations, automated docking and virtual screening, 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.