247 citations · 1.4k across the 37 of their papers we have counts for
38 papers
Cell Competition Driven by Secreted Ligands: Modeling Liver Metastasis of Colorectal Cancer
Hossein Nemati, Saskia Jacoba Elisabeth Suijkerbuijk, Joost de Graaf
Cell competition in multicellular organisms has been shown to play a critical role during the development of organisms, cancer progression, and in the establishment and maintenance…
Projection-Based Solver for Viscoelastic Stokes Flow using FFTs
Georg Rempfer, Mae Nesenberend, Chengkai Zhu +3
Understanding the flow of complex media is relevant for a wide range of research fields and industrial applications. Several numerical approaches exist by which approximate solutio…
Fluid-Derived Lattices for Unbiased Modeling of Bacterial Colony Growth
Bryan Verhoef, Rutger Hermsen, Joost de Graaf
Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and…
Delayed Gravitational Collapse of Attractive Colloidal Suspensions
Kim William Torre, Joost de Graaf
Colloidal gels have strong industrial relevance as they can behave liquid- and solid-like. The latter allows them to support the buoyant weight against gravity. However, the system…
The Cellular Potts Model on Disordered Lattices
Hossein Nemati, Joost de Graaf
The Cellular Potts model, also known as the Glazier-Graner-Hogeweg model, is a lattice-based approach by which biological tissues at the level of individual cells can be numericall…
Hydrodynamic Lubrication in Colloidal Gels
Kim William Torre, Joost de Graaf
Colloidal gels are elasto-plastic materials composed of an out-of-equilibrium, self-assembled network of micron-sized (solid) particles suspended in a fluid. Recent work has shown…
Hydrodynamic Stability Criterion for Colloidal Gelation under Gravity
Joost de Graaf, Kim William Torre, Wilson C. K. Poon +1
Attractive colloids diffuse and aggregate to form gels, solid-like particle networks suspended in a fluid. Gravity is known to strongly impact the stability of gels once they are f…
Amphibious Transport of Fluids and Solids by Soft Magnetic Carpets
Ahmet F. Demirörs, Sümeyye Aykut, Sophia Ganzeboom +8
One of the major challenges in modern robotics is controlling micromanipulation by active and adaptive materials. In the respiratory system, such actuation enables pathogen clearan…
Activity-induced microswimmer interactions and cooperation in one-dimensional environments
Stefania Ketzetzi, Melissa Rinaldin, Pim Dröge +2
Cooperative motion in biological microswimmers is crucial for their survival as it facilitates adhesion to surfaces, formation of hierarchical colonies, efficient motion, and enhan…
Autonomously Probing Viscoelasticity in Disordered Suspensions
Clara Abaurrea-Velasco, Celia Lozano, Clemens Bechinger +1
Recent experiments show a strong rotational-diffusion enhancement for self-propelled microrheological probes in colloidal glasses. Here, we provide microscopic understanding using…
Height Distribution and Orientation of Colloidal Dumbbells Near a Wall
Ruben W. Verweij, Stefania Ketzetzi, Joost de Graaf +1
Geometric confinement strongly influences the behavior of microparticles in liquid environments. However, to date, nonspherical particle behaviors close to confining boundaries, ev…
An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids
Michael Kuron, Cameron Stewart, Joost de Graaf +1
Most biological fluids are viscoelastic, meaning that they have elastic properties in addition to the dissipative properties found in Newtonian fluids. Computational models can hel…
Hydrodynamic Mobility Reversal of Squirmers near Flat and Curved Surfaces
Michael Kuron, Philipp Stärk, Christian Holm +1
Self-propelled particles have been experimentally shown to orbit spherical obstacles and move along surfaces. Here, we theoretically and numerically investigate this behavior for a…
A Lattice Boltzmann Model for Squirmers
Michael Kuron, Philipp Stärk, Christian Burkard +2
The squirmer is a simple yet instructive model for microswimmers, which employs an effective slip velocity on the surface of a spherical swimmer to describe its self-propulsion. We…
Slip length dependent propulsion speed of catalytic colloidal swimmers near walls
Stefania Ketzetzi, Joost de Graaf, Rachel P. Doherty +1
Catalytic colloidal swimmers that propel due to self-generated fluid flows exhibit strong affinity for surfaces. We here report experimental measurements of significantly different…
ESPResSo 4.0 -- An Extensible Software Package for Simulating Soft Matter Systems
Florian Weik, Rudolf Weeber, Kai Szuttor +7
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of c…
Hydrodynamics strongly affect the dynamics of colloidal gelation but not gel structure
Joost de Graaf, Wilson C. K. Poon, Magnus J. Haughey +1
Colloidal particles with strong, short-ranged attractions can form a gel. We simulate this process without and with hydrodynamic interactions (HI), using the lattice-Boltzmann meth…
Microfluidic Pumping by Micromolar Salt Concentrations
Ran Niu, Patrick Kreissl, Aidan T. Brown +5
An ion-exchange-resin-based microfluidic pump is introduced that utilizes trace amounts of ions to generate fluid flows. We show experimentally that our pump operates in almost dei…
Lattice-Boltzmann Simulations of Microswimmer-Tracer Interactions
Joost de Graaf, Joakim Stenhammar
Hydrodynamic interactions in systems comprised of self-propelled particles, such as swimming microorganisms, and passive tracers have a significant impact on the tracer dynamics co…
Moving Charged Particles in Lattice Boltzmann-Based Electrokinetics
Michael Kuron, Georg Rempfer, Florian Schornbaum +4
The motion of ionic solutes and charged particles under the influence of an electric field and the ensuing hydrodynamic flow of the underlying solvent is ubiquitous in aqueous coll…
Stirring by Periodic Arrays of Microswimmers
Joost de Graaf, Joakim Stenhammar
The interaction between swimming microorganisms or artificial self-propelled colloids and passive (tracer) particles in a fluid leads to enhanced diffusion of the tracers. This enh…
Selective Trapping of DNA using Glass Microcapillaries
Georg Rempfer, Sascha Ehrhardt, Nadanai Laohakunakorn +4
We show experimentally that a cheap glass microcapillary can accumulate λ-phage DNA at its tip and deliver the DNA into the capillary using a combination of electro-osmotic flow, p…
Understanding the Onset of Oscillatory Swimming in Microchannels
Joost de Graaf, Arnold J. T. M. Mathijssen, Marc Fabritius +3
Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interact…
Limiting Spurious Flow in Simulations of Electrokinetic Phenomena
Georg Rempfer, Gary B. Davies, Christian Holm +1
Electrokinetic transport phenomena can strongly influence the behaviour of macromolecules and colloidal particles in solution, with applications in, e.g., DNA translocation through…