Courses in the Master´s program in Molecular Biophysics
All courses are given in English and most of them as block courses meaning that the student concentrates on one topic at a time. Each block is typically 5 or 10 weeks. A study year has 40 weeks.
First four courses (30 ECTS credits, 20 weeks)
The amount of available data in life sciences is rapidly increasing, and to use this data in the best possible way is rapidly becoming one of the cornerstones in all biological research. In this course we will cover the basic bioinformatical methods to analyze protein sequence and protein structure. The goals are that after this course you should be able to use state of the art methods to predict the function and structure of an unknown protein sequence.You will learn to use and understand the basic tools in bioinformatics, including tools for: sequence searching, sequence alignments, secondary structure, fold recognition, homology modeling.
- Bioinformatics (scroll down the page to see course information)
Arne Elofsson, KB7004, 7.5 ECTS credits, 5 weeks, Aug-Sept
The course gives an introduction to biological molecules (water, amino acids, proteins, nucleic acids, DNA, RNA) and biological systems (cells, membranes). Teaching is done in form of lectures and literature seminars. The course also teaches the fundamental chemical and physical principles that underly reactions of biological molecules. These include classical thermodynamics, chemical equilibrium, kinetics of chemical reactions, and molecular orbital theory. The course is a self-study course with provided material.
- or Biomolecules and the physical principles of their reactions
Andreas Barth, KB7006, 7.5 ECTS credits, 5 weeks, Aug-Sept or any other time
The field dealing with protein structure at atomic resolution, structural biochemistry, has had a great impact on our understanding of the details in important processes that occur with high precision in the cell. This course deals with concepts in structural biochemistry, both in terms of understanding the most important protein structures on a molecular level, as well as the most important techniques for determining three-dimensional structure at atomic resolution. The important relationship between structure and function is illustrated with examples of how three-dimensional structures have provided us with molecular details of important reactions in the cell. The two main techniques for determining protein structure at atomic resolution are X-ray crystallography and nuclear magnetic resonance. These two techniques are covered in the course, which also gives an introduction to other important methods, such as electron microscopy.
- Structural biochemistry (scroll down the page to see course information)
Martin Högbom, KB7002, 7.5 ECTS credits, 5 weeks, Sept-Oct
This course gives a thorough background in spectroscopic methods and illustrates their application in the life sciences. Content: UV/vis, Circular dichroism, fluorescence, infrared, Raman, EPR, light and neutron scattering, small angle X-ray diffraction. There is no overlap with the structural biochemistry course
- Spectroscopy of biological molecules (scroll down the page to see course information)
Andreas Barth, KB7007 7.5 ECTS credits, 5 weeks, Oct-Nov
- Molecular modeling (scroll down the page to see course information)
Jens Carlsson, KB8005, 7.5 ECTS credits, 5 weeks, Nov-Jan
Modeling of biological systems at the molecular level is becoming increasingly important. In this course we will provide an introduction to methods that are used in molecular modeling. Both quantum mechanical and classical methods will be discussed, including Hartree-Fock, basis sets, semi-empirical methods, density functional theory, molecular mechanics, energy minimization, molecular dynamics simulations, Monte Carlo methods,sequence alignments.
Profile courses (15 - 30 ECTS credits)
Profile courses are subdivided here into experimental and theoretical courses for the sake of clarity. You can choose amongst all of these courses and combine experimental and theoretical courses..
Experimental profile courses
This course introduces you in a comprehensive way to the exciting and rapidly developing field of biochemical and biophysical methods. You will become acquainted with a flurry of state-of-the-art techniques such as DNA and protein arrays, laser spectroscopy, protein over-expression and purification, crystallogenesis, high-resolution NMR, 2D-gel electrophoresis, mass spectrometry, proteomics and structure-based drug design. You will not only gain in-depth knowledge of the different methods, but you will also learn how to combine them to solve complex and challenging biochemical questions.
- Advanced biochemical methods
Jan Willem deGier, KB8002, 15 ECTS credits, 10 weeks, Aug-Oct
(for students with biochemistry/chemistry background)
The course consists of lectures, tutorials, problem solving sessions, project based practicals, student presentations and biotech site visits/demonstrations.
The course is applicable for research focussed students, students oriented towards entering industry, and for students who want and/or need practical working knowledge of novel biochemical methods and advanced problem solving techniques
The course covers nuclear magnetic resonance (NMR), the chemists' most important spectroscopic tool. We explain the basic principles of NMR experiments, for example those used to determine molecular structure and to make three-dimensional pictures of organs inside the human body. Selected chemical applications are also presented. Laboratory exercises, covering the liquid and the solid-state NMR, are included and we make a study visit at a clinical "NMR-Imaging" facility.
- Biomolecular NMR
Lena Mäler, KB7005, 15 ECTS credits, 10 weeks, Jan-March
- NMR in materials chemistry
Mattias Edén, KZ8005, 7.5 ECTS credits, 5 weeks, Feb-March
Biological membrane and membrane proteins are central elements in all living organisms. The course topics include the three-dimensional structure and properties of membranes, the structure, function, expression, biogenesis, methods for purification, structural determination and functional studies of membrane proteins, and transport processes across biological membranes. In addition, recent developments within the research area are discussed where the recent advancements in structural determination of membrane proteins have led to understanding of basic mechanisms, e.g. of signal transduction, at the molecular level. The course is closely associated with the research activities at the Department, where several groups are in the frontline at the international level. A number of one-week projects, done within these research groups, provide practical insights into the topics discussed in the lectures.
- Structure and dynamics of biological membranes
Åke Wieslander, KB8001, 15 ECTS credits, 10 weeks, Jan-March
(for students with biochemistry/chemistry background)
Theoretical profile courses
This course will increase the student's ability to write efficient larger codes by using existing program libraries. The course contains sections such as : Solution of linear algebraic equations, Interpolation and extrapolation, Integration of functions, Evaluations of functions, Special functions, Random numbers, Sorting, Root finding and nonlinear sets of equations, Minimization or maximization of functions, Eigenstates, Fourier transform spectral methods, Statistical description of data, Modeling of data, Integration of ordinary differential equations, Two point boundary value problems, Partial differential equations.
- Computational physics
Eva Lindroth, FK8002, 15 ECTS credits, 10 weeks, March-June
(for students with a physics background)
This is an advance level course in collaboration between Stockholm University and KTH that covers structure, self-organization, and function of the biological macromolecules of life - primarily proteins. It will cover biophysical chemistry of proteins folding, Protein structure, Protein Folding and Protein structure prediction.
- Protein physics
Erik Lindahl, KB8011, 7.5 ECTS credits, half speed, 10 weeks, Jan-March
The goal of the course is to give a deeper knowledge about molecular orbital theory and how to use it. The theories behind the basic quantum chemistry methods are discussed. An important part of the course are computer exercises. They are intended to give a practical knowledge of quantum chemical methods, in particular DFT (density functional theory), and also to give some experience in studying chemical reactions by quantum chemical methods, i.e. how to determine structures, activation energies,solvent effects etc. Furthermore, a review of modern quantum chemical methods and their applications is given.
- Quantum chemistry
Michael Odelius, FK7009, 15 ECTS credits, half speed, 20 weeks, Aug-Jan
Computer simulations are today an indispensable tool in essentially all branches of chemistry. In particular, quantum chemistry has proven very valuable in the fields of organic and organometallic chemistry, where it has had a major impact. The course involves both quantitative and qualitative aspects of quantum chemistry, with focus on applications. Practical computer exercises are an important part of the course contents.
- Theoretical organic chemistry
Fahmi Himo, KO7007, 15 ECTS credits, March-June 2014
Free-choice courses (15 - 30 ECTS credits)
You can choose any university course, for which you fulfill the requirements.