Soft Matter
Concepts, Phenomena, and Applications
9. Active Matter
The additional material is organized according to book sections and it includes links to (review) papers mentioned in the book, videos of different phenomena we discuss (experiments and simulations), as well as links to online lectures that address certain topics in more details.
The workshop Active mechanics, from single cells to cell layers, tissues and developments, held in 2023 at the Isaac Newton Institute, has many videos of lectures relevant to the chapter on active matter.
Several talks at the Kavli workshops Physical Principles Shaping Biomolecular Condensates, Active Solids: From Metamaterials to Biological Tissue, and The Many Faces of Active Mechanics are relevant to the material of chapter 9.
9.1 Hydrodynamic theories of active media
A general introductory lecture on active matter
by Cristina Marchetti.
From AspenPhysics.
Four lectures on collective motion by Ajay Gopinathan at the Umass summer school.
Lecture 1, Lecture 2, Lecture 3, Lecture 4.
A lecture on active field theories part I
by Mike Cates.
From Ecole de Physique des Houches.
A lecture on active field theories part II
by Mike Cates
From Ecole de Physique des Houches.
A lecture on active filed theories part III
by Mike Cates.
From Ecole de Physique des Houches.
- Link to the lecture notes by Mike Cates accompanying videos Active Field Theories I, II and II given at the Les Houches Summer School 2018.
The link does require institutional access. - A thematic issue on Active Matter in Europhysics News (vol. 55(3) 2024) contains a number of interesting short articles covering several aspects of Active Matter.
9.2 Flocking
The original lecture by John Toner in Les Houches that inspired this section.
From Ecole de Physique des Houches.
A lecture by Hai Tasaki on Hohenberg-Mermin-Wagner type theorems for flocking.
From Hal Tasaki.
An introductory lecture by Rob Phillips on the Toner-Tu model.
From Physical Biology of the Cell.
A Python-based simulation of the Vicsek model with 10k particles. From Galen Seilis.
9.3 Motility induced phase separation
A simulation of active brownian particles.
From Active Brownian Particles.
9.4 Bacterial suspensions
Video of swarming E. Coli bacteria.
From Amin Khanchezar.
9.5 Active Nematics
Lecture by Julia Yeomans on active nematics.
From FLUIDOS.
Active nematics with the moving defects labeled from Hagan lab at Brandeis. From Brandeis Science.
9.6 Active Solids
A lecture by Nikta Fakhri on “Nonreciprocal matter: living chiral crystals”. From Harvard CMSA.
9.9 Applications to biological problems
Experimental observation of an active gel.
From The Wu Lab.
Lectures by Kinneret Keren on hydra morphogenesis.
From Institut Curie (left) and ICTS (right).
A lecture by Luca Giomi on active matter and discussion of multi-scale order in epithelia using vertex models. From Harvard CMSA.
A lecture by Michael Moshe on geometrical aspects of epithelial mechanics. From IIPTV.
A talk by Jean-François Joanny on
“Cell deformation and mechanics of epithelial tissues“.Talk starts at 23.12 minutes.
Problems
Coding Problems
Below you can find links to several coding problems formatted as jupyter notebooks that can be easily opened for example in Google Colaboratory. These notebooks have embedded images. If these do not appear when you open the file, you can use the link from the markdown cell directly in your browser to view them.
1. Vicsek model Download jupyter notebook
2. Flocking and the Mermin-Wagner theorem Download jupyter notebook
3. Vertex model A very nice tutorial on the vertex model can be found on Sknepnek lab github. The basic implementation is described here (students can try to implement themselves or they can use the code offered by the Sknepnek lab) and examples of what can be measured can be found here. Jupyter notebooks are provided on the lab’s github as well.
4. Active brownian particles A very nice tutorial on the active brownian particle model can be found on Sknepnek lab github. This was created as a part of a KITP ACTIVE20 workshop. Links to video tutorials, codes and example jupyter notebooks are all available on the lab’s github.