- Invited
- Perspective
- Access by Xinjiang University
Modeling complex particle suspensions: Perspectives on the rigid multiblob method
Phys. Rev. Fluids 10, 100701 – Published 3 October, 2025
DOI: https://doi.org/10.1103/64b1-lfmc
Abstract
Many suspensions contain particles with complex shapes that are affected not only by hydrodynamics but also by thermal fluctuations, internal activity, kinematic constraints, and other long-range nonhydrodynamic interactions. Modeling these systems represents a significant numerical challenge due to the interplay between different effects and the need to accurately capture multiscale phenomena. In this article we review recent developments to model large suspensions of particles of arbitrary shapes and multiple couplings with controllable accuracy within the rigid multiblob framework. We discuss the governing equations, highlight key numerical developments, and illustrate applications ranging from microswimmers to complex colloidal suspensions. This review illustrates the effectiveness and versatility of the rigid multiblob method in tackling a wide range of physical problems in fluid mechanics, soft matter physics, biophysics, materials, and colloidal science.
Physics Subject Headings (PhySH)
Article Text
References (176)
- W. Li, H. Palis, R. Mérindol, J. Majimel, S. Ravaine, and E. Duguet, Colloidal molecules and patchy particles: Complementary concepts, synthesis and self-assembly, Chem. Soc. Rev. 49, 1955 (2020).
- P. Bourrianne, V. Niggel, G. Polly, T. Divoux, and G. H. McKinley, Tuning the shear thickening of suspensions through surface roughness and physico-chemical interactions, Phys. Rev. Res. 4, 033062 (2022).
- iNaturalist (2017), https://www.inaturalist.org/photos/11624974.
- K. A. Syed and K. E. Klose, Vibrio cholerae flagellar synthesis and virulence, Epidemiological and Molecular Aspects on Cholera (Springer, Berlin, 2010), pp. 203–212.
- S. Sacanna, W. T. Irvine, P. M. Chaikin, and D. J. Pine, Lock and key colloids, Nature (London) 464, 575 (2010).
- A. McMullen, M. Holmes-Cerfon, F. Sciortino, A. Y. Grosberg, and J. Brujic, Freely jointed polymers made of droplets, Phys. Rev. Lett. 121, 138002 (2018).
- M. S. D. Wykes, J. Palacci, T. Adachi, L. Ristroph, X. Zhong, M. D. Ward, J. Zhang, and M. J. Shelley, Dynamic self-assembly of microscale rotors and swimmers, Soft Matter 12, 4584 (2016).
- A. M. Brooks, M. Tasinkevych, S. Sabrina, D. Velegol, A. Sen, and K. J. Bishop, Shape-directed rotation of homogeneous micromotors via catalytic self-electrophoresis, Nat. Commun. 10, 495 (2019).
- W. Yan, E. Corona, D. Malhotra, S. Veerapaneni, and M. Shelley, A scalable computational platform for particulate Stokes suspensions, J. Comput. Phys. 416, 109524 (2020).
- L. Crowder, T. Li, E. Corona, and S. Veerapaneni, Boundary integral equation analysis for spheroidal suspensions, arXiv:2506.20809.
- Y. Bao, M. Rachh, E. E. Keaveny, L. Greengard, and A. Donev, A fluctuating boundary integral method for Brownian suspensions, J. Comput. Phys. 374, 1094 (2018).
- J. W. Swan and G. Wang, Rapid calculation of hydrodynamic and transport properties in concentrated solutions of colloidal particles and macromolecules, Phys. Fluids 28, 011902 (2016).
- J. F. Brady and G. Bossis, Stokesian dynamics, Annu. Rev. Fluid Mech. 20, 111 (1988).
- J. McCammon and J. Deutch, Frictional properties of nonspherical multisubunit structures: Application to tubules and cylinders, Biopolymers: Orig. Res. Biomol. 15, 1397 (1976).
- J. Rotne and S. Prager, Variational treatment of hydrodynamic interaction in polymers, J. Chem. Phys. 50, 4831 (1969).
- H. Yamakawa, Transport properties of polymer chains in dilute solution: Hydrodynamic interaction, J. Chem. Phys. 53, 436 (1970).
- H. Nakajima and Y. Wada, A general method for evaluation of diffusion constants, dilute-solution viscoelasticity, and the dielectric property of a rigid macromolecule with an arbitrary configuration. I, Biopolymers: Orig. Res. Biomol. 16, 875 (1977).
- J. G. De La Torre and V. A. Bloomfield, Hydrodynamic properties of macromolecular complexes. I. Translation, Biopolymers: Orig. Res. Biomol. 16, 1747 (1977).
- J. G. De La Torre and V. A. Bloomfield, Hydrodynamics of macromolecular complexes. II. Rotation, Biopolymers: Orig. Res. Biomol. 16, 1765 (1977).
- J. G. de la Torre and V. A. Bloomfield, Hydrodynamic properties of complex, rigid, biological macromolecules: Theory and applications, Q. Rev. Biophys. 14, 81 (1981).
- M. Zurita-Gotor, J. Bławzdziewicz, and E. Wajnryb, Motion of a rod-like particle between parallel walls with application to suspension rheology, J. Rheol. 51, 71 (2007).
- T. T. Bringley and C. S. Peskin, Validation of a simple method for representing spheres and slender bodies in an immersed boundary method for Stokes flow on an unbounded domain, J. Comput. Phys. 227, 5397 (2008).
- A. Pandey, P. S. Kumar, and R. Adhikari, Flow-induced nonequilibrium self-assembly in suspensions of stiff, apolar, active filaments, Soft Matter 12, 9068 (2016).
- B. Cichocki and K. Hinsen, Stokes drag on conglomerates of spheres, Phys. Fluids 7, 285 (1995).
- M. X. Fernandes and J. G. de la Torre, Brownian dynamics simulation of rigid particles of arbitrary shape in external fields, Biophys. J. 83, 3039 (2002).
- J. G. de la Torre, M. L. Huertas, and B. Carrasco, Calculation of hydrodynamic properties of globular proteins from their atomic-level structure, Biophys. J. 78, 719 (2000).
- V. Lobaskin and B. Dünweg, A new model for simulating colloidal dynamics, New J. Phys. 6, 54 (2004).
- R. Kutteh, Rigid body dynamics approach to Stokesian dynamics simulations of nonspherical particles, J. Chem. Phys. 132, 174107 (2010).
- M. Długosz and J. M. Antosiewicz, Hydrodynamic effects on the relative rotational velocity of associating proteins, J. Phys. Chem. B 117, 6165 (2013).
- S. Poblete, A. Wysocki, G. Gompper, and R. G. Winkler, Hydrodynamics of discrete-particle models of spherical colloids: A multiparticle collision dynamics simulation study, Phys. Rev. E 90, 033314 (2014).
- A. Ortega, D. Amorós, and J. G. De La Torre, Prediction of hydrodynamic and other solution properties of rigid proteins from atomic-and residue-level models, Biophys. J. 101, 892 (2011).
- A. Gastaldi and M. Vanni, The distribution of stresses in rigid fractal-like aggregates in a uniform flow field, J. Colloid Interface Sci. 357, 18 (2011).
- J. J. Molina and R. Yamamoto, Direct numerical simulations of rigid body dispersions. I. Mobility/friction tensors of assemblies of spheres, J. Chem. Phys. 139, 234105 (2013).
- M. Reichert and H. Stark, Synchronization of rotating helices by hydrodynamic interactions, Eur. Phys. J. E 17, 493 (2005).
- R. Cortez, L. Fauci, and A. Medovikov, The method of regularized Stokeslets in three dimensions: Analysis, validation, and application to helical swimming, Phys. Fluids 17, 031504 (2005).
- A. Codutti, F. Bachmann, D. Faivre, and S. Klumpp, Bead-based hydrodynamic simulations of rigid magnetic micropropellers, Front. Robot. AI 5, 109 (2018).
- S. Bianchi, V. C. Sosa, G. Vizsnyiczai, and R. Di Leonardo, Brownian fluctuations and hydrodynamics of a microhelix near a solid wall, Sci. Rep. 10, 4609 (2020).
- K. Hinsen, Hydrolib: A library for the evaluation of hydrodynamic interactions in colloidal suspensions, Comput. Phys. Commun. 88, 327 (1995).
- J. W. Swan, J. F. Brady, R. S. Moore et al., Modeling hydrodynamic self-propulsion with Stokesian dynamics. Or teaching Stokesian dynamics to swim, Phys. Fluids 23, 071901 (2011).
- S. Delong, F. B. Usabiaga, and A. Donev, Brownian dynamics of confined rigid bodies, J. Chem. Phys. 143, 144107 (2015).
- A. M. Fiore and J. W. Swan, Fast Stokesian dynamics, J. Fluid Mech. 878, 544 (2019).
- F. B. Usabiaga, B. Kallemov, B. Delmotte, A. P. S. Bhalla, B. E. Griffith, and A. Donev, Hydrodynamics of suspensions of passive and active rigid particles: A rigid multiblob approach, Comm. App. Math. and Comp. Sci. 11, 217 (2016).
- B. Sprinkle, F. B. Usabiaga, N. A. Patankar, and A. Donev, Large scale Brownian dynamics of confined suspensions of rigid particles, J. Chem. Phys. 147, 244103 (2017).
- F. B. Usabiaga and B. Delmotte, A numerical method for suspensions of articulated bodies in viscous flows, J. Comput. Phys. 464, 111365 (2022).
- T. A. Westwood, B. Delmotte, and E. E. Keaveny, A generalised drift-correcting time integration scheme for Brownian suspensions of rigid particles with arbitrary shape, J. Comput. Phys. 467, 111437 (2022).
- B. Delmotte and F. B. Usabiaga, A scalable method to model large suspensions of colloidal phoretic particles with arbitrary shapes, J. Comput. Phys. 518, 113321 (2024).
- H. Gidituri, G. Kabacaoğlu, M. Ellero, and F. B. Usabiaga, Mapping flagellated swimmers to surface-slip driven swimmers, J. Comput. Phys. 510, 113081 (2024).
- E. Krucker-Velasquez, J. W. Swan, and Z. Sherman, Immersed boundary method for dynamic simulation of polarizable colloids of arbitrary shape in explicit ion electrolytes, arXiv:2401.04865.
- R. Cortez, The method of regularized Stokeslets, SIAM J. Sci. Comput. 23, 1204 (2001).
- C. S. Peskin, The immersed boundary method, Acta numerica 11, 479 (2002).
- M. Maxey and B. Patel, Localized force representations for particles sedimenting in Stokes flow, Int. J. Multiphase Flow 27, 1603 (2001).
- GitHub repository, https://github.com/stochasticHydroTools/RigidMultiblobsWall.
- T. Dombrowski, S. K. Jones, G. Katsikis, A. P. S. Bhalla, B. E. Griffith, and D. Klotsa, Transition in swimming direction in a model self-propelled inertial swimmer, Phys. Rev. Fluids 4, 021101 (2019).
- H. Gidituri, M. Ellero, and F. Balboa Usabiaga, Swimming efficiently by wrapping, J. Fluid Mech. 993, A7 (2024).
- M. Driscoll, B. Delmotte, M. Youssef, S. Sacanna, A. Donev, and P. Chaikin, Unstable fronts and motile structures formed by microrollers, Nat. Phys. 13, 375 (2017).
- B. Sprinkle, E. B. Van Der Wee, Y. Luo, M. M. Driscoll, and A. Donev, Driven dynamics in dense suspensions of microrollers, Soft Matter 16, 7982 (2020).
- B. Sprinkle, S. Wilken, S. Karapetyan, M. Tanaka, Z. Chen, J. R. Cruise, B. Delmotte, M. M. Driscoll, P. Chaikin, and A. Donev, Sedimentation of a colloidal monolayer down an inclined plane, Phys. Rev. Fluids 6, 034202 (2021).
- Q. Brosseau, F. B. Usabiaga, E. Lushi, Y. Wu, L. Ristroph, J. Zhang, M. Ward, and M. J. Shelley, Relating rheotaxis and hydrodynamic actuation using asymmetric gold-platinum phoretic rods, Phys. Rev. Lett. 123, 178004 (2019).
- Q. Brosseau, F. B. Usabiaga, E. Lushi, Y. Wu, L. Ristroph, M. D. Ward, M. J. Shelley, and J. Zhang, Metallic microswimmers driven up the wall by gravity, Soft Matter 17, 6597 (2021).
- E. B. van der Wee, B. C. Blackwell, F. B. Usabiaga, A. Sokolov, I. T. Katz, B. Delmotte, and M. M. Driscoll, A simple catch: Fluctuations enable hydrodynamic trapping of microrollers by obstacles, Sci. Adv. 9, eade0320 (2023).
- S.-Y. Chen, H. M. L. Rios, M. O. de la Cruz, and M. Driscoll, Restructuring a passive colloidal suspension using a rotationally driven particle, Soft Matter 20, 2151 (2024).
- M. Długosz, B. Cichocki, and P. Szymczak, Estimating near-wall diffusion coefficients of arbitrarily shaped rigid macromolecules, Phys. Rev. E 106, 014407 (2022).
- M. Długosz, B. Cichocki, and P. Szymczak, First coarse grain then scale: How to estimate diffusion coefficients of confined molecules, J. Chem. Phys. 159, 214101 (2023).
- D. Kundu, F. B. Usabiaga, and M. Ellero, Settling dynamics of a non-Brownian suspension of spherical and cubic particles in Stokes flow, J. Fluid Mech. 1010, A63 (2025).
- N. Moreno, D. Moreno-Chaparro, F. B. Usabiaga, and M. Ellero, Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses, Sci. Rep. 12, 11080 (2022).
- D. Moreno-Chaparro, N. Moreno, F. B. Usabiaga, and M. Ellero, Computational modeling of passive transport of functionalized nanoparticles, J. Chem. Phys. 158, 104108 (2023).
- N. Moreno, D. Vazquez-Cortes, and E. Fried, Sedimentation dynamics of triply-twisted Möbius bands: Geometry versus topology, arXiv:2402.13017.
- F. B. Usabiaga and M. Ellero, Rheology of moderated dilute suspensions of star colloids: The shape factor, Phys. Fluids 36, 053321 (2024).
- U. Makanga, M. Sepahi, C. Duprat, and B. Delmotte, Obstacle-induced lateral dispersion and nontrivial trapping of flexible fibers settling in a viscous fluid, Phys. Rev. Fluids 8, 044303 (2023).
- U. Makanga, C. Duprat, and B. Delmotte, Sedimentation of flexible fibers through ordered arrays of pillars (unpublished).
- Y. Gao, B. Sprinkle, E. Springer, D. W. Marr, and N. Wu, Rolling of soft microbots with tunable traction, Sci. Adv. 9, eadg0919 (2023).
- E. S. Bililign, F. B. Usabiaga, Y. A. Ganan, A. Poncet, V. Soni, S. Magkiriadou, M. J. Shelley, D. Bartolo, and W. T. Irvine, Motile dislocations knead odd crystals into whorls, Nat. Phys. 18, 212 (2022).
- T. Yang, B. Sprinkle, Y. Guo, J. Qian, D. Hua, A. Donev, D. W. Marr, and N. Wu, Reconfigurable microbots folded from simple colloidal chains, Proc. Natl. Acad. Sci. USA 117, 18186 (2020).
- X. Wang, B. Sprinkle, H. K. Bisoyi, T. Yang, L. Chen, S. Huang, and Q. Li, Colloidal tubular microrobots for cargo transport and compression, Proc. Natl. Acad. Sci. USA 120, e2304685120 (2023).
- S. Kim and S. J. Karrila, Microhydrodynamics: Principles and Selected Applications, Butterworth-Heinemann Series in Chemical Engineering (Butterworth-Heinemann, Boston, MA, 1991).
- J. L. Anderson, Colloid transport by interfacial forces, Annu. Rev. Fluid Mech. 21, 61 (1989).
- R. Golestanian, T. Liverpool, and A. Ajdari, Designing phoretic micro-and nano-swimmers, New J. Phys. 9, 126 (2007).
- J. Blake, A spherical envelope approach to ciliary propulsion, J. Fluid Mech. 46, 199 (1971).
- C. Pozrikidis, Boundary Integral and Singularity Methods for Linearized Viscous Flow, Cambridge Texts in Applied Mathematics (Cambridge University Press, Cambridge, UK, 1992).
- D. J. Smith, M. T. Gallagher, R. Schuech, and T. D. Montenegro-Johnson, The role of the double-layer potential in regularised Stokeslet models of self-propulsion, Fluids 6, 411 (2021).
- The adjoint property ensures that the power dissipated by the motion of the particle surface integrated over the whole surface matches the power dissipated by the motion of a rigid particle. For a particle without surface velocity (), (47)
- is the space of vector-valued functions in , i.e., , defined on the manifold (the particle surface) whose Euclidean norm is square integrable on , i.e., . We think this function space is a safe choice for , but it might not be the most appropriate.
- H. A. Stone and A. D. T. Samuel, Propulsion of microorganisms by surface distortions, Phys. Rev. Lett. 77, 4102 (1996).
- R. Kubo, The fluctuation-dissipation theorem, Rep. Prog. Phys. 29, 255 (1966).
- W. B. Russel, Brownian motion of small particles suspended in liquids, Annu. Rev. Fluid Mech. 13, 425 (1981).
- S. R. de Groot and P. Mazur, Non-Equilibrium Thermodynamics (Dover Publications, Oxford, UK, 1984).
- E. Guazzelli and J. F. Morris, A Physical Introduction to Suspension Dynamics (Cambridge University Press, Cambridge, UK, 2011), Vol. 45.
- L. Landau and E. Lifshitz, Fluid Mechanics (Pergamon Press, Oxford, UK, 1959).
- G. De Fabritiis, M. Serrano, R. Delgado-Buscalioni, and P. V. Coveney, Fluctuating hydrodynamic modeling of fluids at the nanoscale, Phys. Rev. E 75, 026307 (2007).
- E. J. Hinch, Application of the Langevin equation to fluid suspensions, J. Fluid Mech. 72, 499 (1975).
- B. Noetinger, Fluctuating hydrodynamics and Brownian motion, Physica A 163, 545 (1990).
- J.-N. Roux, Brownian particles at different times scales: A new derivation of the Smoluchowski equation, Physica A 188, 526 (1992).
- S. Delong, F. B. Usabiaga, R. Delgado-Buscalioni, B. E. Griffith, and A. Donev, Brownian dynamics without Green's functions, J. Chem. Phys. 140, 134110 (2014).
- D. L. Ermak and J. A. McCammon, Brownian dynamics with hydrodynamic interactions, J. Chem. Phys. 69, 1352 (1978).
- T. Ando, E. Chow, Y. Saad, and J. Skolnick, Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations, J. Chem. Phys. 137, 064106 (2012).
- B. Delmotte and E. E. Keaveny, Simulating Brownian suspensions with fluctuating hydrodynamics, J. Chem. Phys. 143, 244109 (2015).
- B. Sprinkle, A. Donev, A. P. S. Bhalla, and N. Patankar, Brownian dynamics of fully confined suspensions of rigid particles without Green's functions, J. Chem. Phys. 150, 164116 (2019).
- P. Leishangthem and X. Xu, Thermodynamic effects are essential for surface entrapment of bacteria, Phys. Rev. Lett. 132, 238302 (2024).
- M. Fixman, Construction of Langevin forces in the simulation of hydrodynamic interaction, Macromolecules 19, 1204 (1986).
- T. Ando, E. Chow, and J. Skolnick, Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations, J. Chem. Phys. 139, 121922 (2013).
- E. Chow and Y. Saad, Preconditioned Krylov subspace methods for sampling multivariate Gaussian distributions, SIAM J. Sci. Comput. 36, A588 (2014).
- E. E. Keaveny, Fluctuating force-coupling method for simulations of colloidal suspensions, J. Comput. Phys. 269, 61 (2014).
- R. Dreyfus, J. Baudry, M. L. Roper, M. Fermigier, H. A. Stone, and J. Bibette, Microscopic artificial swimmers, Nature (London) 437, 862 (2005).
- B. Jang, E. Gutman, N. Stucki, B. F. Seitz, P. D. Wendel-García, T. Newton, J. Pokki, O. Ergeneman, S. Pané, Y. Or et al., Undulatory locomotion of magnetic multilink nanoswimmers, Nano Lett. 15, 4829 (2015).
- P. Liao, L. Xing, S. Zhang, and D. Sun, Magnetically driven undulatory microswimmers integrating multiple rigid segments, Small 15, 1901197 (2019).
- H. C. Berg and R. A. Anderson, Bacteria swim by rotating their flagellar filaments, Nature (London) 245, 380 (1973).
- S. Trachtenberg and I. Hammel, The rigidity of bacterial flagellar filaments and its relation to filament polymorphism, J. Struct. Biol. 109, 18 (1992).
- O. F. Müller, Kleine Schriften aus der Naturhistorie (Buchhandlung der Gelehrten, Dessau, Germany, 1782), Vol. 1.
- M. R. M. Kapinga and R. Gordon, Cell attachment in the motile colonial diatom bacillaria paxillifer, Diatom Res. 7, 215 (1992).
- R. Gordon, Partial synchronization of the colonial diatom Bacillaria “paradoxa,” Res. Ideas Outcomes 2, e7869 (2016).
- R. Featherstone, Robot Dynamics Algorithms, Robotics: Vision, Manipulation and Sensors (Springer U.S., New York, NY, 1987), Vol. 22.
- S. F. Schoeller, A. K. Townsend, T. A. Westwood, and E. E. Keaveny, Methods for suspensions of passive and active filaments, J. Comput. Phys. 424, 109846 (2021).
- H. Shum, E. A. Gaffney, and D. J. Smith, Modelling bacterial behaviour close to a no-slip plane boundary: The influence of bacterial geometry, Proc. Roy. Soc. A: Math. Phys. Eng. Sci. 466, 1725 (2010).
- H. Shum and J. M. Yeomans, Entrainment and scattering in microswimmer-colloid interactions, Phys. Rev. Fluids 2, 113101 (2017).
- B. J. Walker, R. J. Wheeler, K. Ishimoto, and E. A. Gaffney, Boundary behaviours of Leishmania Mexicana: A hydrodynamic simulation study, J. Theor. Biol. 462, 311 (2019).
- J. L. Moran and J. D. Posner, Phoretic self-propulsion, Annu. Rev. Fluid Mech. 49, 511 (2017).
- H. Stark, Artificial chemotaxis of self-phoretic active colloids: Collective behavior, Acc. Chem. Res. 51, 2681 (2018).
- P. Illien, R. Golestanian, and A. Sen, “Fuelled” motion: Phoretic motility and collective behaviour of active colloids, Chem. Soc. Rev. 46, 5508 (2017).
- A. Domínguez and M. N. Popescu, A fresh view on phoresis and self-phoresis, Curr. Opin. Colloid Interface Sci. 61, 101610 (2022).
- A. Zöttl and H. Stark, Modeling active colloids: From active brownian particles to hydrodynamic and chemical fields, Annu. Rev. Condens. Matter Phys. 14, 109 (2023).
- S.-Y. Lu, Diffusion and reaction in regular arrays of spheres, J. Chem. Phys. 109, 4985 (1998).
- S. Michelin and E. Lauga, Phoretic self-propulsion at finite Péclet numbers, J. Fluid Mech. 747, 572 (2014).
- A. P. S. Bhalla, B. E. Griffith, N. A. Patankar, and A. Donev, A minimally-resolved immersed boundary model for reaction-diffusion problems, J. Chem. Phys. 139, 214112 (2013).
- S. Marbach and L. Bocquet, Osmosis, from molecular insights to large-scale applications, Chem. Soc. Rev. 48, 3102 (2019).
- G. Wang and J. W. Swan, Surface heterogeneity affects percolation and gelation of colloids: Dynamic simulations with random patchy spheres, Soft Matter 15, 5094 (2019).
- G. Vizsnyiczai, G. Frangipane, S. Bianchi, F. Saglimbeni, D. Dell'Arciprete, and R. Di Leonardo, A transition to stable one-dimensional swimming enhances E. coli motility through narrow channels, Nat. Commun. 11, 2340 (2020).
- E. Wajnryb, K. A. Mizerski, P. J. Zuk, and P. Szymczak, Generalization of the Rotne–Prager–Yamakawa mobility and shear disturbance tensors, J. Fluid Mech. 731, R3 (2013).
- A. Broms, M. Sandberg, and A.-K. Tornberg, A locally corrected multiblob method with hydrodynamically matched grids for the Stokes mobility problem, J. Comput. Phys. 487, 112172 (2023).
- P. J. Zuk, E. Wajnryb, K. A. Mizerski, and P. Szymczak, Rotne–Prager–Yamakawa approximation for different-sized particles in application to macromolecular bead models, J. Fluid Mech. 741, R5 (2014).
- B. Delmotte, Viscosity ratio across interfaces controls the stability and self-assembly of microrollers, Phys. Rev. Fluids 8, L062302 (2023).
- J. W. Swan and J. F. Brady, Simulation of hydrodynamically interacting particles near a no-slip boundary, Phys. Fluids 19, 113306 (2007).
- W. Yan and M. Shelley, Universal image system for non-periodic and periodic Stokes flows above a no-slip wall, J. Comput. Phys. 375, 263 (2018).
- W. Yan and R. Blackwell, Kernel aggregated fast multipole method: Efficient summation of Laplace and Stokes kernel functions, Adv. Comput. Math. 47, 69 (2021).
- C. Aponte-Rivera and R. N. Zia, Simulation of hydrodynamically interacting particles confined by a spherical cavity, Phys. Rev. Fluids 1, 023301 (2016).
- M. Fixman, Simulation of polymer dynamics. I. General theory, J. Chem. Phys. 69, 1527 (1978).
- F. B. Usabiaga, R. Delgado-Buscalioni, B. E. Griffith, and A. Donev, Inertial coupling method for particles in an incompressible fluctuating fluid, Comput. Methods Appl. Mech. Eng. 269, 139 (2014).
- X. Liu and E. Chow, Large-scale hydrodynamic Brownian simulations on multicore and manycore architectures, in Proceedings of the 2014 IEEE 28th International Parallel and Distributed Processing Symposium (IEEE, Piscataway, NJ, 2014), pp. 563–572.
- R. Singh and R. Adhikari, PyStokes: Phoresis and Stokesian hydrodynamics in python, J. Open Source Softw. 5, 2318 (2020).
- A. K. Townsend, Stokesian dynamics in python, J. Open Source Softw. 9, 6011 (2024).
- R. P. Peláez, P. Ibáñez-Freire, P. Palacios-Alonso, A. Donev, and R. Delgado-Buscalioni, Universally adaptable multiscale molecular dynamics (UAMMD): A native-GPU software ecosystem for complex fluids, soft matter, and beyond, Comput. Phys. Commun. 306, 109363 (2025).
- K. W. Torre, R. D. Schram, and J. de Graaf, Python-JAX-based fast Stokesian dynamics, SciPost Phys. Codeb. 056 (2025).
- Z. Liang, Z. Gimbutas, L. Greengard, J. Huang, and S. Jiang, A fast multipole method for the Rotne–Prager–Yamakawa tensor and its applications, J. Comput. Phys. 234, 133 (2013).
- A. M. Fiore, F. Balboa Usabiaga, A. Donev, and J. W. Swan, Rapid sampling of stochastic displacements in Brownian dynamics simulations, J. Chem. Phys. 146, 124116 (2017).
- A. M. Fiore and J. W. Swan, Rapid sampling of stochastic displacements in Brownian dynamics simulations with stresslet constraints, J. Chem. Phys. 148, 044114 (2018).
- H. Su and E. E. Keaveny, Accelerating the force-coupling method for hydrodynamic interactions in periodic domains, J. Comput. Phys. 510, 113060 (2024).
- P. J. Atzberger, P. R. Kramer, and C. S. Peskin, A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales, J. Comput. Phys. 224, 1255 (2007).
- P. J. Atzberger, Stochastic eulerian lagrangian methods for fluid-structure interactions with thermal fluctuations, J. Comput. Phys. 230, 2821 (2011).
- P. Plunkett, J. Hu, C. Siefert, and P. J. Atzberger, Spatially adaptive stochastic methods for fluid–structure interactions subject to thermal fluctuations in domains with complex geometries, J. Comput. Phys. 277, 121 (2014).
- A. Hashemi, R. P. Peláez, S. Natesh, B. Sprinkle, O. Maxian, Z. Gan, and A. Donev, Computing hydrodynamic interactions in confined doubly periodic geometries in linear time, J. Chem. Phys. 158, 154101 (2023).
- B. Kallemov, A. Bhalla, B. Griffith, and A. Donev, An immersed boundary method for rigid bodies, Comm. App. Math. and Comp. Sci. 11, 79 (2016).
- It is also necessary that the discretization of the Stokes equations preserves some of the original symmetries, specifically , which is true in the continuum setting but it is not respected by all discretizations [93].
- B. Delmotte, E. E. Keaveny, F. Plouraboue, and E. Climent, Large-scale simulation of steady and time-dependent active suspensions with the force-coupling method, J. Comput. Phys. 302, 524 (2015).
- J. Higdon, The hydrodynamics of flagellar propulsion: Helical waves, J. Fluid Mech. 94, 331 (1979).
- H. Goldstein, C. Poole, and J. Safko, Classical Mechanics, 3rd ed. (Addison-Wesley, Boston, MA, 2001).
- B. Delmotte, E. Climent, and F. Plouraboué, A general formulation of bead models applied to flexible fibers and active filaments at low Reynolds number, J. Comput. Phys. 286, 14 (2015).
- W. T. Funkenbusch, K. S. Silmore, and J. W. Swan, Approaches for fast Brownian dynamics simulation with constraints, J. Comput. Phys. 509, 113043 (2024).
- F. Rojas-Pérez, B. Delmotte, and S. Michelin, Hydrochemical interactions of phoretic particles: A regularized multipole framework, J. Fluid Mech. 919, A22 (2021).
- T. D. Montenegro-Johnson, S. Michelin, and E. Lauga, A regularised singularity approach to phoretic problems, Eur. Phys. J. E 38, 139 (2015).
- B. Delmotte, A. Donev, M. Driscoll, and P. Chaikin, Minimal model for a hydrodynamic fingering instability in microroller suspensions, Phys. Rev. Fluids 2, 114301 (2017).
- F. Balboa Usabiaga, B. Delmotte, and A. Donev, Brownian dynamics of confined suspensions of active microrollers, J. Chem. Phys. 146, 134104 (2017).
- Y. Zhang, D. A. Gregory, Y. Zhang, P. J. Smith, S. J. Ebbens, and X. Zhao, Reactive inkjet printing of functional silk stirrers for enhanced mixing and sensing, Small 15, 1804213 (2019).
- R. Jahn and A.-M. M. Schmid, Revision of the brackish-freshwater diatom genus Bacillaria Gmelin (Bacillariophyta) with the description of a new variety and two new species, Eur. J. Phycol. 42, 295 (2007).
- A. P. Berke, L. Turner, H. C. Berg, and E. Lauga, Hydrodynamic attraction of swimming microorganisms by surfaces, Phys. Rev. Lett. 101, 038102 (2008).
- W. F. Paxton, K. C. Kistler, C. C. Olmeda, A. Sen, S. K. St. Angelo, Y. Cao, T. E. Mallouk, P. E. Lammert, and V. H. Crespi, Catalytic nanomotors: Autonomous movement of striped nanorods, J. Am. Chem. Soc. 126, 13424 (2004).
- J. L. Moran and J. D. Posner, Electrokinetic locomotion due to reaction-induced charge auto-electrophoresis, J. Fluid Mech. 680, 31 (2011).
- P. Kumar, Y. Zhang, S. J. Ebbens, and X. Zhao, 3D inkjet printed self-propelled motors for micro-stirring, J. Colloid Interface Sci. 623, 96 (2022).
- R. Mari, R. Seto, J. F. Morris, and M. M. Denn, Shear thickening, frictionless and frictional rheologies in non-Brownian suspensions, J. Rheol. 58, 1693 (2014).
- L. Durlofsky, J. F. Brady, and G. Bossis, Dynamic simulation of hydrodynamically interacting particles, J. Fluid Mech. 180, 21 (1987).
- C. Neto, D. R. Evans, E. Bonaccurso, H.-J. Butt, and V. S. Craig, Boundary slip in newtonian liquids: A review of experimental studies, Rep. Prog. Phys. 68, 2859 (2005).
- C. Kamal, S. Gravelle, and L. Botto, Alignment of a flexible platelike particle in shear flow: Effect of surface slip and edges, Phys. Rev. Fluids 6, 084102 (2021).
- J. W. Swan and A. S. Khair, On the hydrodynamics of “slip–stick” spheres, J. Fluid Mech. 606, 115 (2008).
- D. Moreno-Chaparro, F. B. Usabiaga, N. Moreno, and M. Ellero, Simulating non-Brownian suspensions with non-homogeneous navier slip boundary conditions, arXiv:2505.13505.
- O. Maxian, B. Sprinkle, and A. Donev, Bending fluctuations in semiflexible, inextensible, slender filaments in Stokes flow: Toward a spectral discretization, J. Chem. Phys. 158, 154114 (2023).
- T. A. Westwood and E. E. Keaveny, Coordinated motion of active filaments on spherical surfaces, Phys. Rev. Fluids 6, L121101 (2021).
- R. Fish, B. Sprinkle, R. Pérez Peláez, and A. Donev, libMobility: A fast Stokesian dynamics library, APS Division of Fluid Dynamics Meeting Abstracts (APS, New York, NY, 2024), pp. A19–006.
- A. Broms, A. H. Barnett, and A.-K. Tornberg, Accurate close interactions of Stokes spheres using lubrication-adapted image systems, J. Comput. Phys. 523, 113636 (2025).