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

Dynamics of Lung Clearance

We are interested in the way the upper airways are cleared of large particles in mammals. Recent experiments have shown that bundled strands sweeping along the airway surface are crucial to this clearance. These bundled strands can be millimetric in length and consist of the MUC5B mucin. They are produced by submucosal glands and upon emerging from these glands, the long axis of the bundled strand is oriented along the cilia-mediated flow toward the oral cavity. However, after release, the bundled strands turn orthogonal to the flow, which maximizes their clearance potential. How this unexpected reorientation is accomplished is presently not understood.

Theory and Numerics of Growing and Living Systems

My group studies a wide range growing, developing, and living systems using computational and theoretical techniques. We also develop new softwares for studying such systems, which enable the characterization of living processes involving millions of discete participants. Currently we are interested in antimicrobial resistance development and how the structure of a bacterial colony impacts this. Additionally, we are working toward a new computational tissue model that more accurately accounts for the cell cycle.

Hydrodynamics of Colloidal Gel Collapse

We are interested in the effect of hydrodynamics on the formation and collapse of colloidal gels, where we model the effect of fluid flows using the lattice-Boltzmann algorithm coupled to an explicit-colloid molecular dynamics simulation. My group is also exploring more analytic means to investigate these systems. The above figure shows the difference between the evolution of a system, for which hydrodynamics are (top) and are not (bottom) taken into account.

Theory and Numerics of Thermo(di)electrokinetics

My group studies a wide range of electrokinetic phenomena, ranging from self-propulsion of chemically and thermophoretically powered colloidal swimmers, to rectification in nanopores, and to ion-exchange-resin based microfluidic pumping. Here, we employ analytic approaches, the finite-element method, and lattice-Boltzmann-based solvers. The picture is reproduced from this Soft Matter publication and shows the thermal and flow fields around a hot swimmer in a monovalent electrolyte, as well as the match between theory and numerics for the swim speed over the entire range of solvent ionic strength.

(Non‑)​Newtonian Hydrodynamics

We are also interested in the dynamics of particles in (non-)Newtonian flow, such as sedimenting spheres, helices, etc., as well as the motion of particles under the influence of external flow. The picture is reproduced from a Bachelor student project that led to a J. Chem. Phys. publication and shows a simple bead-like model for the coupling of shape-anisotropic particles to a lattice-Boltzmann fluid.

Anisotropic Particle Self-Assembly

My group also investigates the self-assembly of octapod-shaped colloidal nanoparticles, for which the experiments are carried out in the group of Prof. Dr. L. Manna at the Istituto Italiano di Technologia in Genova. We use both Molecular Dynamics and Monte Carlo methods, in addition to theoretically considering the relevant inter-octapod potentials. The picture is reproduced from this ACS Nano publication and shows how a combination of ligand exchange and particle shape can be used to create intercalated sphere-octapod lattices, which are also predicted by a simple simulation model.