Ahlrichs, P., Everaers, R. & Dünweg, B.
2001
Screening of hydrodynamic interactions in semidilute polymer solutions: a computer simulation study. Phys. Rev. E
64 (4 Pt 1), 040501.

Ando, T. & Skolnick, J.
2010
Crowding and hydrodynamic interactions likely dominate *in vivo* macromolecular motion. Proc. Natl Acad. Sci. USA
107 (43), 18457–18462.

Aponte-Rivera, C. & Zia, R. N.
2016
Simulation of hydrodynamically interacting particles confined by a spherical cavity. Phys. Rev. Fluids
1 (2), 023301.

Banchio, A. J. & Brady, J. F.
2003
Accelerated Stokesian dynamics: Brownian motion. J. Chem. Phys.
118 (22), 10323–10332.

Batchelor, G. K.
1976
Brownian diffusion of particles with hydrodynamic interaction. J. Fluid Mech.
74, 1–29.

Batchelor, G. K.
1982
Sedimentation in a dilute polydisperse system of interacting spheres. Part 1. General theory. J. Fluid Mech.
119, 379–407.

Bhattacharya, S.
2008
Cooperative motion of spheres arranged in periodic grids between two parallel walls. J. Chem. Phys.
128 (7), 074709.

Bhattacharya, S., Mishra, C. & Bhattacharya, S.
2010
Analysis of general creeping motion of a sphere inside a cylinder. J. Fluid Mech.
642, 295–328.

Bickel, T.
2007
A note on confined diffusion. Physica A
377 (1), 24–32.

Brady, J. F.
1994
The long-time self-diffusivity in concentrated colloidal dispersions. J. Fluid Mech.
272, 109–133.

Brady, J. F. & Bossis, G.
1988
Stokesian dynamics. Annu. Rev. Fluid Mech.
20, 111–157.

Brangwynne, C. P., Koenderink, G. H., MacKintosh, F. C. & Weitz, D. A.
2008
Cytoplasmic diffusion: molecular motors mix it up. J. Cell Biol.
183 (4), 583–587.

Brangwynne, C. P., Koenderink, G. H., MacKintosh, F. C. & Weitz, D. A.
2009
Intracellular transport by active diffusion. Trends in Cell Biology
19 (9), 423–427.

Brenner, H.
1961
The slow motion of a sphere through a viscous fluid towards a plane surface. Chem. Engng Sci.
16 (3–4), 242–251.

Chow, E. & Skolnick, J.
2015
Effects of confinement on models of intracellular macromolecular dynamics. Proc. Natl Acad. Sci. USA
112 (48), 14846–14851.

Colby, R. H.
2010
Structure and linear viscoelasticity of flexible polymer solutions: comparison of polyelectrolyte and neutral polymer solutions. Rheol. Acta
49 (5), 425–442.

Crocker, J. C. & Hoffman, B. D.
2007
Multiple-particle tracking and two-point microrheology in cells. Meth. Cell Biol.
83 (7), 141–178.

Cunningham, E.
1910
On the velocity of steady fall of spherical particles through fluid medium. Proc. R. Soc. Lond. A
83 (563), 357–365.

Daniels, B. R., Masi, B. C. & Wirtz, D.
2006
Probing single-cell micromechanics *in vivo*: the microrheology of *C. elegans* developing embryos. Biophys. J.
90 (12), 4712–4719.

Durlofsky, L. & Brady, J. F.
1987
Analysis of the Brinkman equation as a model for flow in porous media. Phys. Fluids
30 (11), 3329–3341.

Durlofsky, L., Brady, J. F. & Bossis, G.
1987
Dynamic simulation of hydrodynamically interacting particles. J. Fluid Mech.
180, 21–49.

Foss, D. R. & Brady, J. F.
2000
Structure, diffusion and rheology of Brownian suspensions by Stokesian dynamics simulation. J. Fluid Mech.
407, 167–200.

de Gennes, P. G.
1976
Dynamics of entangled polymer solutions. Part II. Inclusion of hydrodynamic interactions. Macromolecules
9 (4), 594–598.

Golden, A.
2000
Cytoplasmic flow and the establishment of polarity in *C. elegans* 1-cell embryos. Curr. Opin. Genetics Develop.
10 (4), 414–420.

Golding, I. & Cox, E.
2006
Physical nature of bacterial cytoplasm. Phys. Rev. Lett.
96 (9), 098102.

Gönczy, P. & Rose, L. S.2005 Asymmetric cell division and axis formation in the embryo. In WormBook, The *C. elegans* Research Community.

González, A., White, J. A., Román, F. L. & Evans, R.
1998
How the structure of a confined fluid depends on the ensemble: hard spheres in a spherical cavity. J. Chem. Phys.
109 (9), 3637–3650.

Henderson, G. P., Gan, L. & Jensen, G. J.
2007
3-D ultrastructure of *O. tauri*: electron cryotomography of an entire eukaryotic cell. PLoS ONE
2 (8).

Hoh, N. J. & Zia, R. N.
2016a
Force-induced diffusion in suspensions of hydrodynamically interacting colloids. J. Fluid Mech.
795, 739–783.

Hoh, N. J. & Zia, R. N.
2016b
The impact of probe size on measurements of diffusion in active microrheology. Lab on a Chip
16, 3114–3129.

Hoogerbrugge, P. J. & Koelman, J. M. V. A.
1992
Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Eur. Phys. Lett.
19 (3), 155–160.

Hunter, G. L., Edmond, K. V. & Weeks, E. R.
2014
Boundary mobility controls glassiness in confined colloidal liquids. Phys. Rev. Lett.
112 (21), 218302.

Jaensch, S., Decker, M., Hyman, A. A. & Myers, E. W.
2010
Automated tracking and analysis of centrosomes in early *Caenorhabditis elegans* embryos. Bioinformatics
26 (12), 13–20.

Jeffrey, D. J. & Onishi, Y.
1984
Calculation of the resistance and mobility functions for two unequal rigid spheres in low-Reynolds-number flow. J. Fluid Mech.
139, 261–290.

Jones, R. B.
2009
Dynamics of a colloid in a spherical cavity. In Theoretical Methods for Micro Scale Viscous Flows (ed. Feuillebois, F. & Sellier, A.), chap. 4, pp. 61–104. Transworld Research Network.

Keys, A. S., Iacovella, C. R. & Glotzer, S. C.
2011
Characterizing complex particle morphologies through shape matching: descriptors, applications, and algorithms. J. Comput. Phys.
230 (17), 6438–6463.

Kim, S. H., Park, J. G., Choi, T. M., Manoharan, V. N. & Weitz, D. A.
2014
Osmotic-pressure-controlled concentration of colloidal particles in thin-shelled capsules. Nat. Commun.
5, 3068.

Ladd, A. J. C.
1994
Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 1. Theoretical foundation. J. Fluid Mech.
271, 285–309.

Ladyzhenskaya, O. A.
1969
The Mathematical Theory of Viscous Incompressible Flow, 2nd edn. Gordon and Breach Science Publishers.

Lau, A. W. C., Hoffman, B. D., Davies, A., Crocker, J. C. & Lubensky, T. C.
2003
Microrheology, stress fluctuations, and active behavior of living cells. Phys. Rev. Lett.
91 (19), 198101.

Leighton, D. & Acrivos, A.
1987
The shear-induced migration of particles in concentrated suspensions. J. Fluid Mech.
181, 415–439.

Marshall, W. F., Straight, A., Marko, J. F., Swedlow, J., Dernburg, A., Belmont, A., Murray, A. W., Agard, D. A. & Sedat, J. W.
1997
Interphase chromosomes undergo constrained diffusional motion in living cells. Current Biology: CB
7 (12), 930–939.

McGuffee, S. R. & Elcock, A. H.
2010
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput. Biol.
6 (3), e1999694.

Navardi, S. & Bhattacharya, S.
2010
A new lubrication theory to derive far-field axial pressure difference due to force singularities in cylindrical or annular vessels. J. Math. Phys.
51 (4), 043102.

Navardi, S., Bhattacharya, S. & Wu, H.
2015
Stokesian simulation of two unequal spheres in a pressure-driven creeping flow through a cylinder. Comput. Fluids
121, 145–163.

Németh, Z. T. & Löwen, H.
1999
Freezing and glass transition of hard spheres in cavities. Phys. Rev. E
59 (6), 6824–6829.

O’Neill, M. E. & Majumdar, S. R.
1970
Asymmetrical slow viscous fluid motions caused by the translation or rotation of two spheres. Part II. Asymptotic forms of the solutions when the minimum clearance. Z. Angew. Math. Phys.
21, 180–187.

Oseen, C. W.
1927
Neuere Methoden und Ergebnisse in der Hydrodynamik. Akademische Verlagsgesellschaft M.B.H.

Peng, Y., Chen, W., Fischer, T. M., Weitz, D. A. & Tong, P.
2009
Short-time self-diffusion of nearly hard spheres at an oil–water interface. J. Fluid Mech.
618, 243–261.

Percus, J. K. & Yevick, G. J.
1958
Analysis of classical statistical mechanics by means of collective coordinates. Phys. Rev.
110 (1), 1–13.

Rallison, J. M. & Hinch, E. J.
1986
The effect of particle interactions on dynamic light scattering from a dilute suspension. J. Fluid Mech.
167, 131–168.

Shinar, T., Mana, M., Piano, F. & Shelley, M. J.
2011
A model of cytoplasmically driven microtubule-based motion in the single-celled *Caenorhabditis elegans* embryo. Proc. Natl Acad. Sci. USA
108 (26), 10508–10513.

Sierou, A. & Brady, J. F.
2001
Accelerated Stokesian dynamics simulations. J. Fluid Mech.
448, 115–146.

Snook, I. K. & Henderson, D.
1978
Monte Carlo study of a hard-sphere fluid near a hard wall. J. Chem. Phys.
68 (5), 2134–2139.

Steinhardt, P. J., Nelson, D. R. & Ronchetti, M.
1983
Bond-orientational order in liquids and glasses. Phys. Rev. B
28 (2), 784–805.

Su, Y., Swan, J. W. & Zia, R. N.
2017
Pair mobility functions for rigid spheres in concentrated colloidal dispersions: stresslet and straining motion couplings. J. Chem. Phys.
146, 124903.

Suh, J., Wirtz, D. & Hanes, J.
2003
Efficient active transport of gene nanocarriers to the cell nucleus. Proc. Natl Acad. Sci. USA
100 (7), 3738–3882.

Sun, J. & Weinstein, H.
2007
Toward realistic modeling of dynamic processes in cell signaling: quantification of macromolecular crowding effects. J. Chem. Phys.
127 (15), 155105.

Swan, J. W. & Brady, J. F.
2010
Particle motion between parallel walls: hydrodynamics and simulation. Phys. Fluids
22 (10), 103301.

Swan, J. W. & Brady, J. F.
2011a
Anisotropic diffusion in confined colloidal dispersions: the evanescent diffusivity. J. Chem. Phys.
135, 014701.

Swan, J. W. & Brady, J. F.
2011b
The hydrodynamics of confined dispersions. J. Fluid Mech.
687, 254–299.

Tabei, S. M. A., Burov, S., Kim, H. Y., Kuznetsov, A., Huynh, T., Jureller, J., Philipson, L. H., Dinner, A. R. & Scherer, N. F.
2013
Intracellular transport of insulin granules is a subordinated random walk. Proc. Natl Acad. Sci. USA
110 (13), 4911–4916.

Teich, E. G., van Anders, G., Klotsa, D., Dshemuchadse, J. & Glotzer, S. C.
2016
Clusters of polyhedra in spherical confinement. Proc. Natl Acad. Sci. USA
113 (6), E669–E678.

Tough, R. J. A. & van den Broeck, C.
1989
Diffusion within a sphere: a non-Gaussian statistical model for particle displacements in a dense colloidal suspension. Physica A
157, 769–796.

Verkman, A. S.
2002
Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem. Sci.
27 (1), 27–33.

Vogel, N., Utech, S., England, G. T., Shirman, T., Phillips, K. R., Koay, N., Burgess, I. B., Kolle, M., Weitz, D. A. & Aizenberg, J.
2015
Color from hierarchy: diverse optical properties of micron-sized spherical colloidal assemblies. Proc. Natl Acad. Sci. USA
112 (35), 10845–10850.

Wachsmuth, M., Waldeck, W. & Langowski, J.
2000
Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. J. Molecular Biol.
298 (4), 677–689.

Weber, S. C. & Brangwynne, C. P.
2015
Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Current Biology
25, 1–6.

Weber, S. C., Theriot, J. A. & Spakowitz, A. J.
2010
Subdiffusive motion of a polymer composed of subdiffusive monomers. Phys. Rev. E
82 (1), 1–11.

Weeks, E. R., Crocker, J. C., Levitt, A. C., Schofield, A. & Weitz, D. A.
2000
Three-dimensional direct imaging of structural relaxation near the colloidal glass transition. Science
287 (5453), 627–631.

Weiss, M., Elsner, M., Kartberg, F. & Nilsson, T.
2004
Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells. Biophys. J.
87 (5), 3518–3524.

Wodarz, A.
2002
Establishing cell polarity in development. Nature Cell Biol.
4, 39–44.

Zia, R. N., Swan, J. W. & Su, Y.
2015
Pair mobility functions for rigid spheres in concentrated colloidal dispersions: force, torque, translation, and rotation. J. Chem. Phys.
143, 224901.