nl en

Soft and Biomatter Theory


Admission Requirements

No special requirements for those admitted to the MSc programme Research in Physics


In soft matter physics we study physical constituents – particles or complex molecules - whose relevant interactions are small enough (often of order kT) that the matter is easily deformed, hence soft. Many soft matter materials and concepts are relevant for biology, and we will specifically also consider active materials which are internally driven. In this course you will get an introduction to several basic soft matter systems and phases, and to the most important concepts to describe and analyze them. Attention is paid to biological applications, but we aim to pay due attention to general applicability of the techniques and concepts, and to connections with other areas of physics.

We will start the course with an elementary introduction to fluid dynamics, elasticity and fluctuation phenomena like Brownian motion as well as the notion of active driving. After this we will study several important examples of soft matter including colloids, liquid crystals, jammed and glassy systems and finally and cells & biological tissues.

The core of the course is formed by 11 lectures of two hours. For the course we will follow the syllabus which is provided, and which contains essentially all the material covered. Six additional exercise classes will deepen your understanding and train you how to do practical calculations or estimates yourself.

Topics covered:
Basics of fluid mechanics and of elasticity theory
The Reynolds number; small Reynolds number hydrodynamics in biomatter
Brownian motion of particles in a fluid, active Brownian motion
Use of the fluctuation-dissipation theorem to measure stiffness-constants in biomatter
Introduction to Colloids; forces between colloidal particles; active colloids
Elements of liquid crystals and Frank free energy
Introduction to the phenomenology of jammed and glassy materials, overview of theoretical approaches
Cells and tissues as soft active materials

Course objectives

After completion of the course you will be able to

  • critically discuss the concepts and material treated in the course using a blackboard or whiteboard.

  • explain intermediate steps in a line of reasoning in a research paper in the field.

  • explain intermediate steps in the reasoning leading to a Landau-type coarse grained description of a soft matter or biophysical problem, and use the approach to analyse a problem.

  • perform or critically follow a simple linear stability calculation.

  • explain the difference between equilibrium and nonequilbrium systems in the context of active matter


Physics 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

See Brightspace

Lecture and tutorials (6 mandatory exercise sets); a syllabus is provided. For each lecture we will provide a videoclip of about 15-20 minutes with either a summary of what was treated the week before, or an introduction to the new topic. The students are asked to watch this clip before the scheduled lecture.

For the exercises, the students are asked to form teams of maximum three students, who will work on the exercises together. How the teams do this is up to them, last year some teams worked closely together on the exercises, others mostly compared noted after each team member worked on the exercises individually. Once a team has finished the exercises, the team sends the solution to the Teaching Assistant, who then discusses the solutions with the team in an online or physical meeting of about half an hour.

Assessment method

The assessment is based on two parts:
1. Active participation in the class and exercise class (on an overall pass/fail basis).
2. After the course, students will take an oral exam, at a mutually agreeable date in December or January that fits the student's schedule and preferences. The oral exam will be in person and will take about an hour, and is in the spirit of an informed discussion in front of a traditional blackboard about the course material.

The aim of the oral exam is to test whether you have studied and grasped the material covered in the syllabus. This does not mean, of course, that you need to memorize everything in the syllabus – in fact, you should feel free to take the syllabus or any notes with you to the exam. Think of the exam more as an intelligent discussion about the concepts that were treated in the course. We will use a blackboard or whiteboard, and I might show you some experimental data to discuss these with you in the light of the material that I covered. The exam is in a relaxed atmosphere and we hope that you will actually learn from the oral exam. A soft matter colleague will also be present at the exam as a second examiner. The final mark for the course is determined by the oral exam.

PhD students who take the course only for pass/fail do not have to do the exercises.

Reading list

The course material will be covered in a syllabus which the students can obtain online in Brightspace. An additional reader with figures and certain additional material is also provided.

Students are not expected to buy a book, but will in fact receive a pdf of the draft of the book Soft Matter - Concept, Phenomena, Applications which the previous lecturer Wim van Saarloos is presently writing with two colleagues (V. Vitelli and Z. Zeravcic) and which will be published by Princeton University Press in 2022 (to be confirmed). This book contains much background material for the course, with the exception of the active matter and glassy physics components.


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.


Lecturer: Dr. S.E. Henkes


Transferable skills

After completion of the course you have gained enough background to independently learn about these topics from the specialized literature.