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Soft and Biomatter Theory

Vak
2024-2025

Admission Requirements

There are no special requirements for those admitted to the MSc programme Research in Physics. We however expect you to have taken statistical mechanis and classical mechanics courses, and be comfortable with tensor notation, partial differential equations and Fourier transforms. You should also have basic programming skills.

Description

Overview
In soft matter physics we study physical constituents with interactions that are weak enough (often of the order kT) that the matter is easily deformed, hence soft or squishy, and at scales from about a micron and up where quantum mechanics is irrelevant. Many soft matter materials and concepts are relevant for biology, and we will specifically also consider active materials which are internally driven.
This course will provide an introduction to several key soft and biological materials and phases, and to the most important concepts to describe and analyze them. In addition, we focus on the general applicability of techniques and concepts, and to connections with other areas of physics.

The core of the course is formed by 11 lectures of two hours. Weekly additional exercise classes will deepen your understanding and train you how to do practical calculations or estimates yourself.

The course broadly follows 'Soft Matter: Concepts, Phenomena, and Applications', by Wim van Saarloos, Vincenzo Vitelli and Zorana Zeravcic. Additional material and slides for the whole course as well as exercises and solutions will also be provided.

Topics covered:
An introduction to fluid mechanics and to elasticity theory
Life at low Reynolds numbers and application to cells, colloids and microfluidics
Brownian motion of particles in a fluid, leading to the Langevin equation, fluctuation-dissipation theorem, and the Smoluchowski equation.
Introduction to Colloids; forces between colloidal particles. Active Brownian particles and active colloids.
Introduction to the physics of jammed and glassy materials.
The physics of polymers, and application to biopolymers.
Liquid crystals, including the Frank free energy, topological defects, and active nematic materials

Course objectives

After completion of the course you will be able to

  • gain a broad overview of the existing soft and biological materials and what the focus of ongoing research is.

  • understand the context and line of reasoning in a research paper in the field.

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

  • be able to apply the concepts and techniques introduced in the course to your own research problems

  • derive intermediate steps in a line of reasoning and carry out theoretical calculations with the broad range of techniques introduced in the course and exercises

Timetable

Physics Schedule
For detailed information go to Timetable in Brightspace

In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.

Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.

Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.

Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.

Mode of instruction

See Brightspace

Lecture and tutorials (5 mandatory exercise sets); a text book, slides and additional materials are provided.

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 the exercise class. Specifically, we ask that students attend the weekly tutorials and hand in a minimum 4 out of 5 exercise sets, and show that they have made a credible effort at solving those sets. This will count for 30% of the grade.
2. After the course, students will take an oral exam, at a mutually agreeable date in May 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. This will count for 70% of the grade.

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.

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 slides and additional notes, homework and solutions as well as programs which the students can obtain online in Brightspace.
We will broadly follow 'Soft Matter: Concepts, Phenomena, and Applications', by Wim van Saarloos, Vincenzo Vitelli and Zorana Zeravcic, to be published by Princeton University Press in early 2024.

Registration

As a student, you are responsible for enrolling on time through MyStudyMap.

In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.

There are two enrolment periods per year:

  • Enrolment for the fall opens in July

  • Enrolment for the spring opens in December

See this page for more information about deadlines and enrolling for courses and exams.

Note:

  • It is mandatory to enrol for all activities of a course that you are going to follow.

  • Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.

  • Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.

Contact

Lecturer: Dr. S.E. Henkes

Remarks

Transferable skills

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

Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.