Theory and Simulation of Soft Matter, Hydrodynamics, and Biophysics Joost de Graaf

Bachelor's and Master's Student Projects

Below I list a few ideas for students projects, which I am eager to work on. The list is by no means exhaustive and I welcome you to come by to discuss opportunities for Bachelor's and Master's thesis projects relating to the theory and simulation of soft matter, hydrodynamics, and biophysics. All the projects below can be done at the Bachelor's and Master's level. We can tailor the focus and ambition of the project to best suit your expertise and curricular needs.

If you are a student interested in project work and are not currently enrolled within the Master's level theoretical physics program at Utrecht University, please ensure that your qualifications are comparable to those required for this program. This will help to avoid any disappointments in requesting project work. In contacting me, please provide a detailed CV (including a list of your marks and accreditation transfer information), details of the content of the courses your have taken in the direction of my research, a statement of financial support, and a motivation letter (maximum 1A4) indicating your reasons for wanting to run a project in my group, your relevant skill set, and your expectations concerning the nature of the project you are interested in.

Flow and Dynamics of Epithelial Tissues

In this project, Voronoi-based numerical methods are developed and subsequently used to investigate the properties of an epithelial tissue in its confluent state. Of specific interest are the nature of the topological transitions that take place in such a tissue and how these ultimately characterize the large length- and time-scale flow of the tissue as a whole.

Structure and Development Bacterial Communities

Bacteria form colonies by cell division. This process is inherrently complex and the various factors that go into the formation of the bacterial community are not well understood. In this project, you will develop simple simulation algorithms to investigate the process of the growth and development of a bacterial community and how its structure changes as a function of the interaction between bacteria.

Gravitational Sedimentation of Colloidal Helices

In this project, you will use theoretical and numerical approaches to investigate the behavior of colloidal helices sedimenting in a viscous liquid. Describing falling objects in vacuum is one of the first things covered in any mechanics course. But things become quite counterintuitive when small objects fall in a liquid: a rod will fall at a constant angle with respect to gravity. You can expect to learn about hydrodynamic theory, as well as a range of numerical and analytic approaches to solve the Stokes equations. N.B. This project has connections to the activities of Prof. dr. A. Morozov of the University of Edinburgh.

Translation and Rotation in Non-Newtonian Fluids

Asymmetric objects moving through a regular fluid, like water, can experience a coupling between rotation and translation, as is the case for a helix. However, when the properties of the fluid are non-linear, i.e., when the fluid is non-Newtonian (think corn starch or a polymer solution), things change. Even a shape as simple as a sphere can experience coupling between translation and rotation. This project will explore the analytics behind this coupling. You can expect to learn about hydrodynamic theory and how to perform perturbative analysis on the equations for Newtonian flow in order to study particles in non-Newtonian fluids.

The Gravitational Collapse of Colloidal Gels

Colloidal gels are everywhere: shaving cream, toothpaste, clays, cement, ... Any consumer is happy when the gel is stable, but not so pleased when they open their toothpaste tube to find a bunch of mint-flavored water and a clump of scouring agent. Understanding the processes that underlie the shelf life of colloidal gels is key to the performance of many household and industrial products. Currently, much is understood of the dynamics of gels using simulations. However, there is a need to develop theoretical models that complement the simulations. This project sets out to develop this theory and compare it to the results of hydrodynamic simulations, as well as explore the further application of this theory beyond the realm of gelation and gel collapse. You can expect to learn about hydrodynamic equations, the way to couple colloid density distributions to the body force acting on the fluid, and much more.