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

Featured Research Goblet cell interactions reorient bundled mucus strands for efficient airway clearance

In this PNAS Nexus, my PhD student Meike Bos provides a model, by which she can explain experimental work carried out by Anna Ermund and Gunnar Hansson from the University of Gothenburg. Our simulations reveal that goblet-cell interactions can reorient the bundled strands within 10 mm of release—making reorientation on the length scale of the tracheal tube feasible—and can stabilize the orthogonal orientation. Our model also reproduces other experimental observations such as strong velocity fluctuations and significant slow-down of the bundled strand with respect to the cilia-mediated flow.

Peer-Reviewed Publications

  1. H. Nemati and J. de Graaf, The cellular Potts model on disordered lattices, Soft Matter advance article (2024)
  2. M. Bos, A. Ermund, G. Hansson, and J. de Graaf, Goblet cell interactions reorient bundled mucus strands for efficient airway clearance, PNAS Nexus 2, pgad388 (2023)
  3. K. Torre and J. de Graaf, Hydrodynamic Lubrication in Colloidal Gels, Soft Matter 19, 7388 (2023)
  4. J. de Graaf, K. Torre, W. Poon, and M. Hermes, Hydrodynamic stability criterion for colloidal gelation under gravity, Phys. Rev. E 107, 034608 (2023)
  5. K. Torre and J. de Graaf, Structuring Colloidal Gels via Micro-Bubble Oscillations, Soft Matter 19, 2771 (2023)
  6. T. Welling, A. Grau-Carbonell, K. Watanabe, D. Nagao, J. de Graaf, M. van Huis, and A. van Blaaderen, Frequency-controlled electrophoretic mobility of a particle within a porous, hollow shell, J. Colloid Interface Sci. 627, 761 (2022)
  7. N. Narinder, M. Bos, C. Abaurrea-Velasco, J. de Graaf, and C. Bechinger, Understanding enhanced rotational dynamics of active probes in rod suspensions, Soft Matter 18, 6246 (2022)
  8. S. Ketzetzi, M. Rinaldin, P. Dröge, J. de Graaf, D. Kraft, Activity-induced microswimmer interactions and cooperation in one-dimensional environments, Nat. Commun. 13, 1772 (2022)
  9. A. Demirörs, S. Aykut, S. Ganzeboom, Y. Meier, R. Hardeman, J. de Graaf, A. Mathijssen, E. Poloni, J. Carpenter, C. Ünlü, and D. Zenhäusern, Amphibious Transport of Fluids and Solids by Soft Magnetic Carpets, Sci. Adv. 8, 2102510 (2021)
  10. T. Welling, K. Watanabe, A. Grau-Carbonell, J. de Graaf, D. Nagao, A. Imhof, M. van Huis, and A. van Blaaderen, Tunability of interactions between the core and shell in rattle-type particles studied with liquid-cell electron microscopy, ACS Nano 15, 11137 (2021)
  11. T. Huang, B. Ibarlucea, A. Caspari, A. Synytska, G. Cuniberti, J. de Graaf, and L. Baraban, Impact of surface charge on the motion of light-activated Janus micromotors, Euro. Phys. J. E 44, 39 (2021)
  12. M. Kuron, C. Stewart, J. de Graaf, C. Holm, An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids, Euro. Phys. J. E 44, 1 (2021)
  13. A. Demirörs, A. Stauffer, C. Lauener, J. Cossu, S. Ramakrishna, J. de Graaf, C. Alcantara, S. Pané, N. Spencer, A. Studart, Magnetic propulsion of colloidal microrollers controlled by electrically modulated friction, Soft Matter 17, 1037 (2021)
  14. R. Verweij, S. Ketzetzi, J. de Graaf, and D. Kraft, Height distribution and orientation of colloidal dumbbells near a wall, Phys. Rev. E 102, 062608 (2020)
  15. C. Abaurrea-Velasco, C. Lozano, C. Bechinger, and J. de Graaf, Autonomously Probing Viscoelasticity in Disordered Suspensions, Phys. Rev. Lett. 125, 258002 (2020)
  16. S. Ketzetzi, J. de Graaf, and D. Kraft, Diffusion-based height analysis reveals robust microswimmer-wall separation, Phys. Rev. Lett. 125, 238001 (2020)
  17. S. Ketzetzi, J. de Graaf, R. Doherty, and D. Kraft, Slip length dependent propulsion speed of catalytic colloidal swimmers near walls, Phys. Rev. Lett. 124, 048002 (2020)
  18. Z. Zhang, J. de Graaf, and S. Faez, Regulating the aggregation of colloidal particles in an electro-osmotic micropump, Soft Matter 16, 10707 (2020)
  19. J. de Graaf and S. Samin, Self-Thermoelectrophoresis at Low Salinity, Soft Matter 15, 7219 (2019)
  20. M. Kuron, P. Stärk, C. Holm, and J. de Graaf, Hydrodynamic mobility reversal of squirmers near flat and curved surfaces, Soft Matter 15, 5908 (2019)
  21. M. Kuron, P. Stärk, C. Burkard, J. de Graaf, and C. Holm, A Lattice Boltzmann Model for Squirmers, J. Chem. Phys. 150, 144110 (2019)
  22. J. de Graaf, W.C.K. Poon, M.J. Haughey, and M. Hermes, Hydrodynamics strongly affect the dynamics of colloidal gelation but not gel structure, Soft Matter 15, 10 (2019)
  23. F. Weik, R. Weeber, K. Szuttor, K. Breitsprecher, J. de Graaf, M. Kuron, J. Landsgesell, H. Menke, D. Sean, and C. Holm, ESPResSo 4.0 -- An Extensible Software Package for Simulating Soft Matter Systems, Eur. Phys. J. S.T. 227, 1789 (2019)
  24. M. Palusa, J. de Graaf, A. Brown, and A. Morozov, Sedimentation of a rigid helix in viscous media, Phys. Rev. Fluids 3, 124301 (2018)
  25. A. Castelli, J. de Graaf, S. Marras, R. Brescia, L. Goldoni, L. Manna, and M. Arciniegas, Understanding and Tailoring Ligand Interactions in the Self-Assembly of Branched Colloidal Nanocrystals into Planar Superlattices, Nat. Commun. 9, 1141 (2018)
  26. R. Niu, P. Kreissl, A. Brown, G. Rempfer, D. Botin, C. Holm, T. Palberg, and J. de Graaf, Microfluidic Pumping by Micromolar Salt Concentrations, Soft Matter 13, 1505 (2017)
  27. A. Brown, W. Poon, C. Holm, and J. de Graaf, Ionic Screening and Dissociation are Crucial for Understanding Chemical Self-Propulsion in Polar Solvents, Soft Matter 13, 1200 (2017)
  28. G. Rempfer, S. Ehrhardt, C. Holm, and J. de Graaf, Nanoparticle Translocation through Conical Nanopores: A Finite Element Study of Electrokinetic Transport, Macromol. Theor. Simul. 26, 1600051 (2017)
  29. J. de Graaf and J. Stenhammar, Lattice-Boltzmann Simulations of Microswimmer-Tracer Interactions, Phys. Rev. E 95, 023302 (2017)
  30. M. Kuron, G. Rempfer, F. Schornbaum, M. Bauer, C. Godenschwager, C. Holm, and J. de Graaf, Moving Charged Particles in Lattice Boltzmann-Based Electrokinetics, J. Chem. Phys. 145, 214102 (2016)
  31. J. de Graaf and J. Stenhammar, Stirring by Periodic Arrays of Microswimmers, J. Fluid Mech. 811, 487 (2016)
  32. S. Ilse, C. Holm, and J. de Graaf, Surface Roughness Stabilizes the Clustering of Self-Propelled Triangles, J. Chem. Phys. 145, 134904 (2016)
  33. G. Rempfer, S. Ehrhardt, N. Laohakunakorn, G. Davies, U. Keyser, C. Holm, and J. de Graaf, Selective Trapping of DNA Using Glass Microcapillaries, Langmuir 32, 8525 (2016)
  34. G. Rempfer, G. Davies, C. Holm, and J. de Graaf, Reducing Spurious Flow in Simulations of Electrokinetic Phenomena, J. Chem. Phys. 145, 044901 (2016)
  35. P. Kreissl, C. Holm, and J. de Graaf, The Efficiency of Self-Phoretic Propulsion Mechanisms with Surface Reaction Heterogeneity, J. Chem. Phys. 144, 204902 (2016)
  36. J. de Graaf, A. Mathijssen, M. Fabritius, H. Menke, C. Holm, and T. Shendruk, Understanding the Onset of Oscillatory Swimming in Microchannels, Soft Matter 12, 4704 (2016)
  37. J. de Graaf, H. Menke, A. Mathijssen, M. Fabritius, C. Holm, and T. Shendruk, Lattice-Boltzmann Hydrodynamics of Anisotropic Active Matter, J. Chem. Phys. 144, 134106 (2016)
  38. A. Castelli, J. de Graaf, M. Prato, L. Manna, and M. Arciniegas, Tic-Tac-Toe Binary Lattices from the Interfacial Self-Assembly of Branched and Spherical Nanocrystals, ACS Nano 10, 4345 (2016)
  39. E. Sutter, P. Sutter, A. Tkachenko, R. Krahne, J. de Graaf, M. Arciniegas, and L. Manna, In Situ Microscopy of the Self-Assembly of Branched Nanocrystals in Solution, Nat. Commun. 7, 11213 (2016)
  40. J. de Graaf, T. Peter, L. Fischer, and C. Holm, The Raspberry Model for Hydrodynamic Interactions Revisited. II. The Effect of Confinement, J. Chem. Phys. 143, 084108 (2015)
  41. L. Fischer, T. Peter, C. Holm, and J. de Graaf, The Raspberry Model for Hydrodynamic Interactions Revisited. I. Periodic Arrays of Spheres and Dumbbells, J. Chem. Phys. 143, 084107 (2015)
  42. J. de Graaf, G. Rempfer, and C. Holm, Diffusiophoretic Self-Propulsion for Partially Catalytic Spherical Colloids, IEEE Trans. Nanobiosci. 14, 272 (2015)
  43. A. Gantapara, J. de Graaf, R. van Roij, and M. Dijkstra, Phase Behavior of a Family of Truncated Hard Cubes, J. Chem. Phys. 142, 054904 (2015)
  44. B. Peng, G. Soligno, M. Kamp, B. de Nijs, J. de Graaf, M. Dijkstra, R. van Roij, A. van Blaaderen, and A. Imhof, Site-Specific Growth of Polymers on Silica Rods, Soft Matter 10, 9644 (2014)
  45. M. Arciniegas, M. Kim, J. de Graaf, R. Brescia, S. Marras, K. Miszta, M. Dijkstra, R. van Roij, and L. Manna, Self-Assembly of Octapod-Shaped Colloidal Nanocrystals into a Hexagonal Ballerina Network Embedded in a Thin Polymer Film, Nano Lett. 14, 1056 (2014)
  46. A. Gantapara, J. de Graaf, R. van Roij, and M. Dijkstra, Phase Diagram and Structural Diversity of a Family of Truncated Cubes: Degenerate Close-Packed Structures and Vacancy-Rich States, Phys. Rev. Lett. 111, 015501 (2013)
  47. W. Qi, J. de Graaf, F. Qiao, S. Marras, L. Manna, and M. Dijkstra, Phase Diagram of Octapod-shaped Nanocrystals in a Quasi-Two-Dimensional Planar Geometry, J. Chem. Phys. 138, 154504 (2013)
  48. J. de Graaf, L. Filion, M. Marechal, M. Dijkstra, and R. van Roij, Crystal-structure prediction via the Floppy-Box Monte Carlo algorithm: Method and application to hard (non)convex particles, J. Chem. Phys. 137, 214101 (2012)
  49. W. Evers, B. Goris, S. Bals, M. Casavola, J. de Graaf, R. van Roij, M. Dijkstra, and D. Vanmaekelbergh, Low-Dimensional Semiconductor Superlattices Formed by Geometric Control over Nanocrystal Attachment, Nano Lett. 13, 2317 (2012)
  50. J. de Graaf, N. Boon, M. Dijkstra, and R. van Roij, Electrostatic Interactions between Janus Particles, J. Chem. Phys. 137, 104910 (2012)
  51. W. Qi, J. de Graaf, F. Qiao, S. Marras, L. Manna, and M. Dijkstra, Ordered Two-Dimensional Superstructures of Colloidal Octapod-Shaped Nanocrystals on Flat Substrates, Nano Lett. 12, 5299 (2012)
  52. R. Ni, A. Gantapara, J. de Graaf, R. van Roij, and M. Dijkstra, Phase Diagram of Colloidal Hard Superballs: from Cubes via Spheres to Octahedra, Soft Matter 8, 8826 (2012)
  53. J. de Graaf, R. van Roij, and M. Dijkstra, Dense Regular Packings of Irregular Nonconvex Particles, Phys. Rev. Lett. 107, 155501 (2011)
  54. K. Miszta, J. de Graaf, G. Bertoni, D. Dorfs, R. Brescia, S. Marras, L. Ceseracciu, R. Cingolani, R. van Roij, M. Dijkstra, and L. Manna, Hierarchical Self-Assembly of Suspended Branched Colloidal Nanocrystals into Superlattice Structures, Nat. Mater. 10, 872 (2011)
  55. J. de Graaf, M. Dijkstra, and R. van Roij, Adsorption Trajectories and Free-Energy Separatrices for Colloidal Particles in Contact with a Liquid-Liquid Interface, J. Chem. Phys. 132, 164902 (2010)
  56. J. de Graaf, M. Dijkstra, and R. van Roij, Triangular Tessellation Scheme for the Adsorption Free Energy at the Liquid-Liquid Interface: Towards Nonconvex Patterned Colloids, Phys. Rev. E 80, 051405 (2009)
  57. M. Bier, J. de Graaf, J. Zwanikken, and R. van Roij, Curvature Dependence of the Electrolytic Liquid-Liquid Interfacial Tension, J. Chem. Phys. 130, 024703 (2009)
  58. J. de Graaf, J. Zwanikken, M. Bier, A. Baarsma, Y. Oloumi, M. Spelt and R. van Roij, Spontaneous Charging and Crystallization of Water Droplets in Oil, J. Chem. Phys. 129, 194701 (2008)
  59. J. Zwanikken, J. de Graaf, M. Bier, and R. van Roij, Stability of Additive-Free Water-in-Oil Emulsions, J. Phys.: Condens. Matter 20, 494238 (2008)
Scientific publication is unfortunately prone to errors. The responsible course of action is to report these and provide transparency, such that these do not affect other researchers. Here, I list those issues that I am aware of for the papers listed above.

- In [W.H. Evers et al., Nano Lett. 13, 2317 (2012)] the proposed argument for the orientation of the nanocrystals is overly simplified, this model was subsequently improved upon in [G. Soligno, M. Dijkstra, and R. van Roij, Phys. Rev. Lett. 116, 258001 (2016)].

- Both papers on the raspberry-particle method for fluid coupling [J. de Graaf et al., J. Chem. Phys. 143, 084108 (2015) and L. Fischer et al., J. Chem. Phys. 143, 084107 (2015)] contain minor oversights that are corrected and identified in the latest arXiv versions of the manuscripts in bold face. The most significant of these is an incorrect ordering of table entries.

- In [M. Kuron et al., J. Chem. Phys. 150, 144110 (2019)] we report lattice artefacts for a moving squimer. I suspect that the origin of these is a bug/inconsistency in the way boundary conditions are handled in the lattice-Boltzmann (LB) algorithm of WaLBerLa, rather than something intrinsically wrong with implementing squimers in LB. This is because both for the electrokinetic version [M. Kuron et al., J. Chem. Phys. 145, 214102 (2016)] and the viscoelastic version of the LB method [M. Kuron et al., Euro. Phys. J. E 44, 1 (2021)], we were unable to get self-propelled particles or squimers to work properly. In fact, for the latter, there was a clear artefact, which depended sensitively on the direction in which the squirmer traversed the simulation box. In addition, snow-man-like swimmers in a viscoelastic LB medium came to a halt, rather than that they continued to move with a constant velocity. That is, the behavior is indicative of a momentum leak. My current understanding is that there is a small bug in the working of the moving boundary conditions in WaLBerLa, which is obscured by putting an external force on the object. Whenever the forces on the fluid are self-generated, as is the case with squirmers or snow-man particles, this effect is much more noticeable. Squirmer particles in LB likely do not require the diameters that we report in [M. Kuron et al., J. Chem. Phys. 150, 144110 (2019)].

- Finally, for [C. Abaurrea-Velasco et al., Phys. Rev. Lett. 125, 258002 (2020)] there was an oversight in terms of the referencing, which has been corrected via an erratum. In addition, it is my current understanding that the model that we used does not have a glass transition in the sense of the experimental system by the Bechinger group. That is, we misidentified the jamming transition as a glass transition. Nonetheless, the major elements of the paper hold, as can be appreciated from the follow-up study [N. Narinder et al., Soft Matter 18, 6246 (2022)].

Other Publications

  1. M. Kuron, P. Kreissl, and C. Holm, Toward Understanding of Self-Electrophoretic Propulsion under Realistic Conditions : From Bulk Reactions to Confinement Effects, Acc. Chem. Res. 51, 2998 (2018)*
  2. J. de Graaf and L. Manna, A Roadmap for the Assembly of Polyhedral Particles, Science 337, 417 (2012)**
  3. J. de Graaf, Anisotropic Nanocolloids: self-assembly, interfacial adsorption, and electrostatic screening, PhD Thesis, Utrecht University (2012)
  4. M. Dijkstra, J. de Graaf, D. Vanmaekelbergh, and R. van Roij, Orde uit wanorde: Van plantensex via Einstein naar zelf-assemblage van nanodeeltjes, Nederlands Tijdschrift voor Natuurkunde 78(7), 258 (2012)
  5. J. de Graaf, Ions Near Curved Oil-Water Interfaces: Towards a Microscopic Theory for Pickering Emulsions, Master's Thesis, Utrecht University (2008)
  6. J. de Graaf, Bidisperse Mixtures Of Colloidal Rods In A Dipolar External Field, Bachelor's Thesis, Utrecht University (2006)
*For the Accounts in Chemical Research, I wrote most of the SPP1726 grant, I co-supervised the research, wrote the conspectus, and reviewed part of the writing before submission. Unfortunately, I was forced to pull my name off the article, due to the way in which the writing of this manuscript was managed. For example, upon submission of the paper, the research that A. Brown had initiated on ionic screening for microswimmers and with which I was involved for the numerical aspects [A. Brown et al., Soft Matter 13, 1200 (2017)], was significantly misrepresented: trends that are due to swimmer size were attributed to bulk ionic reactions. This issue could have been easily avoided if the principles and practices of good scientific conduct had been respected. I have however had the involved PhD candidates fix this issue post peer-review, against the wishes of the management. Please do not blame the PhDs for the clear misrepresentation of involvement or way the research came about.

** The Science publication is an editorial perspective on the work by the group of S. Glotzer. The vast majority of the writing was carried out by L. Manna.