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

I am proud to have contributed to the following publications. However, it should be noted that scientific publication is prone to errors. Not all these merit retractions or the issuing of an erratum. However, in my honest opinion, it would benefit research if we were to collectively use such tools more often. Lowering the barrier for error reporting and providing transparency would help us take the responsible course of action in clearing up issues, such that these do not affect other researchers. Here, I list those issues that I am aware of in my own publishing presently. Please let me know if you find any other issues, then I would be happy to update this page.

  1. J. de Graaf, The Geometry behind the Glass Transition and Frictional Jamming in Systems of Two-Dimensional Hard Disks, under revision (2026)
    The original version that was prepared for submission late 2024, was rough in several aspects. Since that time, I have refined my analysis and conclusions substantially. These are presented in the 2nd version of the arxiv paper.
  2. H. Nemati, S. Suijkerbuijk, and J. de Graaf, Cell Competition Driven by Secreted Ligands: Modeling Liver Metastasis of Colorectal Cancer, submitted (2025)
  3. L. Eij, J. de Graaf, M. Haase, and J. Steenhoff, Phase-Field Models for Particle-Stabilized Emulsions, under revision (2025)
    A open-access version of this text will be made available as soon as possible, please be patient.
  4. G. Rempfer, C. Zhu, B. Stam, M. Nesenberend, D. Panja, and J. de Graaf, Projection-Based Solver for Viscoelastic Stokes Flow using FFTs, under revision (2025)
    The version on arxiv presently contains several oversights, which include a non-trivial compressibility issue. These are being addressed for the resubmission.
  5. K. Torre and J. de Graaf, Hydrodynamic Interactions in Particle Suspensions: A Perspective on Stokesian Dynamics, under revision (2025)
    The first submission contained a low-level analysis of the potential for neural-networks in SD simulations for three particles. We have since improved upon this by considering sedimenting clusters.
  6. B. Verhoef, R. Hermsen, and J. de Graaf, Fluid-derived lattices for unbiased modeling of bacterial colony growth, PloS one 20, e0330491 (2025)
  7. K. Torre, R. Schram, and J. de Graaf, Python-JAX-based fast Stokesian dynamics, SciPost Physics Codebases 056, 2 (2025)
  8. J. Melio, S. Riedel, A. Azadbakht, S. Caipa Cure, T. Evers, M. Babaei, A. Mashaghi, J. de Graaf, and D. Kraft, The motion of catalytically active colloids approaching a surface, Soft Matter 21, 2541 (2025)
    It would have been nice to have referenced work by Popescu and Uspal, as well as work by the Maldarelli and Velegol groups.
  9. K. Torre and J. de Graaf, Delayed gravitational collapse of attractive colloidal suspensions, J. Fluid Mech. 1000, A73 (2024)
  10. H. Nemati and J. de Graaf, The cellular Potts model on disordered lattices, Soft Matter 20, 8337 (2024)
  11. 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)
  12. K. Torre and J. de Graaf, Hydrodynamic Lubrication in Colloidal Gels, Soft Matter 19, 7388 (2023)
    There may be an issue with the way in which we implemented the two-step time integration. Whether this has affected the reported physics is currently under investigation.
  13. J. de Graaf, K. Torre, W. Poon, and M. Hermes, Hydrodynamic stability criterion for colloidal gelation under gravity, Phys. Rev. E 107, 034608 (2023)
  14. K. Torre and J. de Graaf, Structuring Colloidal Gels via Micro-Bubble Oscillations, Soft Matter 19, 2771 (2023)
  15. 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)
  16. 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)
  17. 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)
  18. 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)
    The modeling of the elastohydrodynamic effect is internally consistent and carried out correctly, although in hindsight I wonder how accurately it captures the physics of the experiment. Note, however, that this is a Corona-period publication and things were difficult at that time. Any issues with the descriptiveness of the modeling are not to be attributed to the student R. Hardeman, who carried out the work.
  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. 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)
  24. C. Abaurrea-Velasco, C. Lozano, C. Bechinger, and J. de Graaf, Autonomously Probing Viscoelasticity in Disordered Suspensions, 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, see above. 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)].
  25. S. Ketzetzi, J. de Graaf, and D. Kraft, Diffusion-based height analysis reveals robust microswimmer-wall separation, Phys. Rev. Lett. 125, 238001 (2020)
  26. 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)
  27. Z. Zhang, J. de Graaf, and S. Faez, Regulating the aggregation of colloidal particles in an electro-osmotic micropump, Soft Matter 16, 10707 (2020)
    The modeling in the manuscript is internally consistent, though I question how well it captures the physics of the experiment.
  28. J. de Graaf and S. Samin, Self-Thermoelectrophoresis at Low Salinity, Soft Matter 15, 7219 (2019)
  29. 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)
  30. M. Kuron, P. Stärk, C. Burkard, J. de Graaf, and C. Holm, A Lattice Boltzmann Model for Squirmers, J. Chem. Phys. 150, 144110 (2019)
    In this work, 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 boundary-localized momentum leak. The presumed small bug in WaLBerLa is likely 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. In conclusion, squirmer particles in LB likely do not require the diameters that we report in [M. Kuron et al., J. Chem. Phys. 150, 144110 (2019)]. I did not dig down into the code to repair the bug, as I was compelled to sever my ties to the Institute for Computational Physics, when it became clear that fixing such issues was not appreciated.
  31. 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)
  32. 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)
  33. M. Palusa, J. de Graaf, A. Brown, and A. Morozov, Sedimentation of a rigid helix in viscous media, Phys. Rev. Fluids 3, 124301 (2018)
    Some care needs to be taken in assigning the dynamics to the center of mass, which need not correspond to the hydrodynamic center. We are working on a follow-up publication that illustrates how having these two points coincide (or not) can impact the dynamics of a shape-anisotropic sedimenting object.
  34. 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)
  35. 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)
  36. 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)
  37. 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)
  38. J. de Graaf and J. Stenhammar, Lattice-Boltzmann Simulations of Microswimmer-Tracer Interactions, Phys. Rev. E 95, 023302 (2017)
  39. 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)
  40. J. de Graaf and J. Stenhammar, Stirring by Periodic Arrays of Microswimmers, J. Fluid Mech. 811, 487 (2016)
  41. S. Ilse, C. Holm, and J. de Graaf, Surface Roughness Stabilizes the Clustering of Self-Propelled Triangles, J. Chem. Phys. 145, 134904 (2016)
  42. 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)
  43. G. Rempfer, G. Davies, C. Holm, and J. de Graaf, Reducing Spurious Flow in Simulations of Electrokinetic Phenomena, J. Chem. Phys. 145, 044901 (2016)
  44. 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)
  45. 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)
  46. 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)
  47. 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)
  48. 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)
  49. 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)
    This paper contains minor mistakes that I have corrected and identified in the latest arXiv version of the manuscript in bold face. Rectifications were not issued, as these were not permitted by the institute lead.
  50. 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)
    This paper contains minor mistakes that I have corrected and identified in the latest arXiv version of the manuscript in bold face. Rectifications were not issued, as these were not permitted by the institute lead.
  51. J. de Graaf, G. Rempfer, and C. Holm, Diffusiophoretic Self-Propulsion for Partially Catalytic Spherical Colloids, IEEE Trans. Nanobiosci. 14, 272 (2015)
  52. 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)
  53. 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)
  54. 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)
  55. 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)
  56. 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)
  57. 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)
  58. 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)
    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)].
  59. J. de Graaf, N. Boon, M. Dijkstra, and R. van Roij, Electrostatic Interactions between Janus Particles, J. Chem. Phys. 137, 104910 (2012)
  60. 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)
  61. 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)
  62. J. de Graaf, R. van Roij, and M. Dijkstra, Dense Regular Packings of Irregular Nonconvex Particles, Phys. Rev. Lett. 107, 155501 (2011)
  63. 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)
  64. 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)
  65. 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)
  66. 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)
  67. 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)
  68. 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)

Other Publications

  1. J. de Graaf Chapter: Advanced Molecular Dynamics in the Book: Active Matter edited by G. Volpe, in press (2026)
    This chapter was written in a time that I struggled with difficulties in my personal life as a consequence of a lengthy period of isolation during the Corona crisis. Unfortunately, this means that the chapter is not up to the standard that I would set for myself. I have communicated as much to the editors of the book, repairing the chapter as much as my (then) abilities permitted. I would recommend anyone interested in accelerating simulations to consult another source. If I find time in the next few months, I might prepare a nice lecture on the topic that addresses some of the issues I have with the chapter. Please do not transplant any lack of quality in this chapter to the book series as a whole.
  2. 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)
    For this paper, I wrote most of the SPP1726 grant, I co-supervised the research, wrote the conspectus, and reviewed part of the writing before submission; hence my inclusion of this work here. 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.
    Note that I would have preferred to not put this information in the public domain. However, when major grant proposals are rejected because I do not make it sufficiently clear that I am not going to use ESPResSo for my project (something which I never claimed I would do), then I am left no choice as to make it abundantly clear as to why I am never using ESPResSo again or, in fact, working with the Institute for Computational Physics. Unfortunately, this is only one of the reasons for that. The journal is aware of the issues surrounding this publication and chose to push away responsibility for taking action.
  3. J. de Graaf and L. Manna, A Roadmap for the Assembly of Polyhedral Particles, Science 337, 417 (2012)
    This publication is an editorial perspective on the simulation work carried out in the group of S. Glotzer. The vast majority of the writing was carried out by L. Manna, who took charge. I am very grateful for being offered the opportunity to co-author.
  4. J. de Graaf, Anisotropic Nanocolloids: self-assembly, interfacial adsorption, and electrostatic screening, PhD Thesis, Utrecht University (2012)
  5. 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)
  6. J. de Graaf, Ions Near Curved Oil-Water Interfaces: Towards a Microscopic Theory for Pickering Emulsions, Master's Thesis, Utrecht University (2008)
  7. J. de Graaf, Bidisperse Mixtures Of Colloidal Rods In A Dipolar External Field, Bachelor's Thesis, Utrecht University (2006)