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 of a cell (plasma membrane, cytoskeleton, nucleus). Most of this is covered in the course ”Fysica van Leven” in the first 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. We will have one programming exercise in Python.
The class is taught in English.
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.
Course objectives
At the end of the course you will be able to:
- Analyze biological processes to identify where (statistical) physics comes into play.
- Conceptualize biological processes such, that they get tracktable by physics concepts and methods.
- Understand how physics dictates how the cellular machinery functions.
- Understand that life descibes systems far from equilibrium.
Specifically, five cellular/molecular processes will be treated:
Self-assembly of lipids and proteins; chemical reactions => chemical potential, grand canonical ensemble
DNA elasticity, helix-coil transition => Ising model, freely jointed chain
Allostery, cooperative binding => phase transitions
Molecular motors => Brownian ratchet, Michaelis-Menten kinetics
Action potentials in neurons => electrodiffusion
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
The background knowledge is aquired in self-study by reading the book and following the online video clips on BS. The interactive sessions are meant to reflect on that knowledge, place the knowledge into a biology or physics perspective, and joinedly solve extended problems.
Each topic is discussed in two sessions. In total there will be ten sessions. Before the session you are supposed to aquire the respective background knowledge through reading the book and working through the video clips on BS. In class there will be a brief recap on the topic before we will consolidate our knowledge in solving questions that highlight the underlying principles just learned. Exercise problems will be solved in order to deepen our understandig and apply the new knowledge.
Every week there will be a homework problem issued, which the student may use as self-assessment and preparation for the exam. One of those will be a 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 determines the final grade.
Reading list
Philip Nelson, "Biological Physics: Energy, Information, Life".
We will cover chapters 8-12.
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