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.

- 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) - K. Torre and
__J. de Graaf__,*Hydrodynamic Lubrication in Colloidal Gels*, Soft Matter**19**, 7388 (2023) __J. de Graaf__, K. Torre, W. Poon, and M. Hermes,*Hydrodynamic stability criterion for colloidal gelation under gravity*, Phys. Rev. E**107**, 034608 (2023)- K. Torre and
__J. de Graaf__,*Structuring Colloidal Gels via Micro-Bubble Oscillations*, Soft Matter**19**, 2771 (2023) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - C. Abaurrea-Velasco, C. Lozano, C. Bechinger, and
__J. de Graaf__,*Autonomously Probing Viscoelasticity in Disordered Suspensions*, Phys. Rev. Lett.**125**, 258002 (2020) - S. Ketzetzi,
__J. de Graaf__, and D. Kraft,*Diffusion-based height analysis reveals robust microswimmer-wall separation*, Phys. Rev. Lett.**125**, 238001 (2020) - 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) - Z. Zhang,
__J. de Graaf__, and S. Faez,*Regulating the aggregation of colloidal particles in an electro-osmotic micropump*, Soft Matter**16**, 10707 (2020) __J. de Graaf__and S. Samin,*Self-Thermoelectrophoresis at Low Salinity*, Soft Matter**15**, 7219 (2019)- 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) - M. Kuron, P. Stärk, C. Burkard,
__J. de Graaf__, and C. Holm,*A Lattice Boltzmann Model for Squirmers*, J. Chem. Phys.**150**, 144110 (2019) __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)- 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) - M. Palusa,
__J. de Graaf__, A. Brown, and A. Morozov,*Sedimentation of a rigid helix in viscous media*, Phys. Rev. Fluids**3**, 124301 (2018) - 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) - 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) - 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) - 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) __J. de Graaf__and J. Stenhammar,*Lattice-Boltzmann Simulations of Microswimmer-Tracer Interactions*, Phys. Rev. E**95**, 023302 (2017)- 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) __J. de Graaf__and J. Stenhammar,*Stirring by Periodic Arrays of Microswimmers*, J. Fluid Mech.**811**, 487 (2016)- S. Ilse, C. Holm, and
__J. de Graaf__,*Surface Roughness Stabilizes the Clustering of Self-Propelled Triangles*, J. Chem. Phys.**145**, 134904 (2016) - 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) - G. Rempfer, G. Davies, C. Holm, and
__J. de Graaf__,*Reducing Spurious Flow in Simulations of Electrokinetic Phenomena*, J. Chem. Phys.**145**, 044901 (2016) - 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) __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)__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)- 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) - 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) __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)- 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) __J. de Graaf__, G. Rempfer, and C. Holm,*Diffusiophoretic Self-Propulsion for Partially Catalytic Spherical Colloids*, IEEE Trans. Nanobiosci.**14**, 272 (2015)- 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) - 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) - 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) - 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) - 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) __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)- 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) __J. de Graaf__, N. Boon, M. Dijkstra, and R. van Roij,*Electrostatic Interactions between Janus Particles*, J. Chem. Phys.**137**, 104910 (2012)- 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) - 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) __J. de Graaf__, R. van Roij, and M. Dijkstra,*Dense Regular Packings of Irregular Nonconvex Particles*, Phys. Rev. Lett.**107**, 155501 (2011)- 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) __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)__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)- 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) __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)- 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)

- In [W.H. Evers

- Both papers on the raspberry-particle method for fluid coupling [J. de Graaf

- In [M. Kuron

- Finally, for [C. Abaurrea-Velasco

- 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)* __J. de Graaf__and L. Manna,*A Roadmap for the Assembly of Polyhedral Particles*, Science**337**, 417 (2012)**__J. de Graaf__,*Anisotropic Nanocolloids: self-assembly, interfacial adsorption, and electrostatic screening*, PhD Thesis, Utrecht University (2012)- 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) __J. de Graaf__,*Ions Near Curved Oil-Water Interfaces: Towards a Microscopic Theory for Pickering Emulsions*, Master's Thesis, Utrecht University (2008)__J. de Graaf__,*Bidisperse Mixtures Of Colloidal Rods In A Dipolar External Field*, Bachelor's Thesis, Utrecht University (2006)

** 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.