Case Study Topics of the course Advanced Soft Matter

1. Superhydrophobic surfaces or the lotus leaf effect

In recent years soft matter scientists have had a strong interest in so-called superhydrophobic surfaces, surfaces which are extremely water repellant. These surfaces are inspired by nature, the best known example being the leaf of the lotus plant, to which water shows almost no adherence (see left picture).  If one would be able to produce man-made variants of these surface, preferably in a cheap and facile manner, this would offer interesting perspectives for coating applications, for example to make the windshield of your car, or the lenses in your eyeglasses extremely water repelling.

It is now known that these high contact angles can be reached by a combination of a hydrophobic material and a specific microstructure (an electronmicroscopy picture of the microstructure of lotus leaf is shown in the central figure). Flat, unstructured surfaces of a hydrophobic material or microstructured surfaces of a hydrophilic material do not give these extreme contact angles, hence it is essential to combine these two properties. More and more articles appear each week to describe new ways to fabricate these (see middle and right picture).

In this project, you will study the physical principles that underlie superhydrophobicity. You will also design, prepare and test your own superhydrophobic surfaces. Techniques: microscopy / AFM / contact angle measurements.

Some hints:

  • Silica, or glass, which is very hydrophilic, can be made hydrophobic easily, by placing the glass object, or surface structure, in a closed box in the vapor of hexadimethyl silazane, which will spontaneously form covalent bonds with the SiOH groups at the surface of the glass.
  • Nanoparticles are an interesting, cheap and versatile route towards creating rough surfaces (should these particles be monodisperse?)
  • Make sure that the structured layer is properly fixed to the underlying substrate, so that the layer does not release or disperse into the water droplet.

2. Microgels for drug delivery

There is an increasing demand for effective encapsulation systems consisting of natural polymers, in which the active compounds are well-protected, and can be released at the time and place where they are needed. A novel biocompatible and biodegradable microgel system consisting of oxidized starch has been developed for controlled uptake and release of proteins. Microgels are soft cross-linked polymer particles that can absorb large amounts of water. The physical chemical properties of the microgel particles have been characterized, so it is time to test their potential for controlled drug release applications. We will choose fluorescently labeled proteins (e.g. FITC-Lysozyme) as our “model drug”.  In this project, you will investigate the protein distribution and mobility inside the microgel particles and test whether they can be released on demand by some external trigger. The techniques that will be used are CLSM (confocal laser scanning microscopy) to image the protein distribution in the gel particles, and FRAP (Florescence recovery after photo bleaching) to measure the mobility inside the gel particles.

 Left: Schematic picture of drug delivery particle Right: Fluorescent microgel particles
Left: Schematic picture of drug delivery particle Right: Fluorescent microgel particles

3. Particles as local probes in gelling systems

Gels and gelling agents are used in numerous applications, such as foods and cosmetic products. The best-known example is gelatin. However, because gelatin (which is animal-derived) is easily contaminated with prions or viruses, there is a strong desire to find alternative gelators. A recent development is the design of artificial protein polymers (with modern biotechnology tools) that can self-assemble into gel-like networks. An example of this is a triblock copolymer which has a random-coil like middle part and two end-blocks that have a sequence very similar to the associating groups in gelatin. Upon cooling, these polymers form a physical gel with triple helices as cross-links (see left picture).  In order to test the potential of this system as a gelling agent, the rheological properties and the kinetics of gel formation must be studied.

In this case study you will study gelation of these polymers using a relatively new experimental tool: microrheology.  Particles will be added to the system (see right picture) and their dynamics (i.e. their Brownian motion) will be followed using dynamic light scattering or microscopy. Because the particle dynamics are directly related to the viscous and elastic properties of the medium, this technique can be used to probe the local rheological properties of the system. It therefore seems an ideal technique to study gelation. To test whether this is true, you will also compare your results on local rheology to the macroscopic bulk-rheology of the same system.

4. How to pack large DNA molecules in small cells


Every human cell contains roughly 2 meters of DNA that must be fitted into a nucleus with a diameter on the order of several microns. The same packing problem occurs in bacteria, as shown in the figure below: after lysis of the cell, the DNA leaks from the cell and occupies a volume much larger than the bacterium size. To achieve such a strong confinement, the DNA must be condensed into a compact structure. In this case study, you will consider different strategies to compact DNA and you will test these ideas experimentally.

5. Soft matter with biological polymers

In the course Advanced Soft Matter, you learn about polymers and their properties.  The models and theories that we discuss are based on experimental evidence using synthetic polymers. Because these synthetic polymers are too small to be seen directly, this evidence is always indirect. In living cells, however, we can find polymers that are much larger. Actin filaments are supra-molecular protein filaments with a diameter of several nanometers and a length of many micrometers. This makes it possible to see them under a microscope, so that the concepts and models of polymer physics can be tested directly.
Left: Labeled actin filaments in a living cell Right: polymerized actin filaments in vitro
Left: Labeled actin filaments in a living cell Right: polymerized actin filaments in vitro

Actin is a globular protein that can polymerize into long semiflexible polymers under the right conditions (high salt, ATP). In living cells, these filaments form a gel-like network that gives the cell rigidity. Active growth of polymers can also generate forces that can push cells forward or push objects (vesicles, organelles, bacteria) around within the cell. Understanding how actin filaments achieve all these tasks is an important goal in modern polymer science and soft matter physics.

In this project you can test some of the concepts of polymer physics using actin as a model system. This will also tell us something about the biological function of this polymer. Some possibilities for your project:

  • How stiff are actin filaments ? Can we indeed see individual actin filaments under the microscope and observe their conformations? Alternatively, we may use an atomic force microscope to look at the filaments.
  • How do filaments move?  The model for motion of polymers in a concentrated solution is the reptation model. Can we see reptating actin filaments in action?
  • How viscous or elastic are actin solutions and networks? An important role of actin in cells is to provide stiffness. Can we measure the stiffness of actin networks or solutions with a rheometer, or using microrheology? And does it agree with models discussed in the lecture?
  • How do cells move? How can actin filaments push things forward?  We can use an in-vitro assay for actin-based movement in which plastic particles are pushed by a growing actin network.