Admission Requirements
You should know the basic concepts from statistical physics (such as: the laws of thermodynamics, random walks, equipartition theorem, entropy, free energies, partition functions, Boltzmann distribution, Ising model, fluctuation-dissipation theorem) and the main structures in a cell (plasma membrane, cytoskeleton, nucleus). Most of this is covered in the course ”Fysica van Leven” in the second semester, and the "Statistical Physics" courses of the study program. If you are missing part of this background, you may want to study chapters 1-7 of the book “Biological physics: energy, information, life” by Philip Nelson prior to entering this course.
Description
In "Physics of Life - From Motors to Nerve Pulses" we explore how the dazzling complexity of life at the nanoscale is understood through key concepts of physics. We will see that entropy plays an essential role. We will discover how molecular machines can carry out diverse tasks in the cell, and understand how brain cells communicate through electrical impulses.
Five cellular/molecular processes will be covered:
1. Biological process: self-assembly of lipids and proteins; chemical reactions.
Physics concepts: chemical potential; grand canonical ensemble.
2. Biological process: DNA elasticity, helix-coil transition.
Physics concepts: Ising model, freely jointed chain.
3. Biological process: allostery, cooperative binding.
Physics concepts: phase transitions.
4. Biological process: molecular motors.
Physics concepts: Brownian ratchet, Michaelis-Menten kinetics.
6. Biological process: action potentials in neurons.
Physics concepts: electrodiffusion.
Course objectives
At the end of the course you will be able to:
1. Analyze biological processes to identify where (statistical) physics comes into play.
2. Conceptualize biological processes such, that they get tracktable by physics concepts and methods.
3. Understand how physics dictates the function of cellular machinery.
4. Understand that life descibes systems far from equilibrium.
Timetable
Schedule
For detailed information go to Timetable in Brightspace
You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.
MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).
For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.
Mode of instruction
In this year (2023/24) the course is organized as self-study module, complemented with weekly interactive sessions which are compulsory to attend. It is expected from the participants that they acquire knowledge on the topics by study of the respective book-chapter and/or study of the video clips prepared. The interactive sessions will be led by one of the participants, in which exercises are solved and further discussed. The exercises concern biological/biophysical observations, which can be understood in terms of the concepts prior learned in self-study.
Each of the five topics is discussed in two sessions. There will be one computational problem that fits into the "Python Leerlijn" of the study program.
Assessment method
An exam will be held at the end of the course. The format (written/oral) will be decided on after the first sessions. The exam result fully determines the final grade.
Reading list
Philip Nelson, "Biological Physics: Energy, Information, Life".
We will cover chapters 8-12. Knowledge of chapters 1-7 is a prerequisit to follow this course.
Registration
From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.
Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.
Extensive FAQ's on MyStudymap can be found here.
Contact
Contact details lecturer: Prof.dr. T. Schmidt
Remarks
none