In this course you will learn how the structure and function of proteins can be explained from fundamental physical properties of amino acids and their structure. You will learn how to develop simplified models and reasoning based on physics and free energy to determine what processes are likely to happen, and why proteins look the way they do, and we will apply this while looking at a number of different proteins and systems both inside cells and in their membranes.

If you haven't started yet, it's time to look at hand-in task1! Soft deadline Friday Sep 13, hard one Sunday evening!

Add this ICS link to get all the events (and possible updates) in your calendar app:

https://canvas.kth.se/feeds/calendars/user_mDWhwCqyV1VBHsgiZnMNWGvMj7HaUFu3DyZI48ub.ics

Since spring 2020, this entire class has been converted to use a flipped-classroom setup. This means that after the first kick-off meeting, you will be asked to view a recorded lecture before we meet for each seminar, at which we will discuss tasks such as a scientific paper or brainstorming problem.

We have converted the lectures from the usual 2*45 min continuous sessions to instead be split into 20-30 smaller "concepts" that each take a few minutes to explain. This can appear a bit scattered until you get used to it, but the feedback from previous years is that your peer students really liked it, since it makes it much easier to check off items you know you understand and just repeat the difficult ones (which you can do at 150% playback speed).

This year (2023) we are also going to introduce some new concepts by applying modern scientific theories and statistical analysis of learning outcomes to the whole class concept for the first time (after all, we are scientists!).

In particular, it is well known that short tests are an excellent method for learning, in particular when the testing is slightly delayed from the learning part. We will experiment with designing short quiz sessions in Canvas that you will use to test your knowledge of facts.

For the classroom sessions, we will instead focus on the higher levels of learning, meaning analysis, synthesis and critical thinking - in particular by introducing a handful of concepts we discuss at each session.

Let us know how you like this format, and/or if there is anything else we should change. After having watched lecture 3 you should also be in good shape to start working on the first hand-in task!

After having taken the course, you should be able to

Explain the physical basis of structure and dynamics in proteins, lipids, and nucleic acids
Use thermodynamics and molecular interactions to explain protein folding and molecular properties of amino acids
Describe and practically use methods to model, simulate and calculate how proteins interact with other molecules
Assess the quality and precision of theoretical and experimental physical methods used to study biomolecular structure and dynamics
Have a basic knowledge of modern bioinformatics tools, and how the informatics approach relates to physics
Combine theory and experimental results in biophysics to draw conclusions about biological processes, and use advanced computational tools in your work

You can view the formal course syllabus including eligibility criteria at the course's KTH student page.

The teaching consists of a series of 13 lectures combined with discussions of the previous lecture, three hand-in tasks, and two lab events. The hand-in tasks have been planned so you have roughly two weeks to complete each of them from the lecture where we cover the concept.

There is no mandatory presence at the lectures, but you must register yourself on the course in LADOK within a week - after that the registration closes. If you have any problems with the registration, talk to the physics student front desk - unfortunately I do not have access to that system as a teacher.
However, remember that this freedom comes with responsibility: If you cannot participate in a lecture you are free to download all material, study both slides and the literature yourself - but the teachers won't be able to give you one-on-one assistance to repeat material covered in lectures you decided not to attend.
The hand-in tasks must be submitted on time. This is important both so we have a chance to correct them and give you feedback on time - so it in turn helps you understand the course better.
You have to be present at the computer lab, but when you are present the teachers present will approve your work right there - no need to submit any report. If you absolutely cannot attend, you will be allowed to do it on your own, but then the requirement will be a written report instead.

Ready to begin? You can find a little info about your teachers at the getting started module, and then it's time for lecture 1.

Teacher information

Erik Lindahl: erik@kth.se

Nandan Haloi: nandan.haloi@scilifelab.se