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Published online by Cambridge University Press: 09 September 2020
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- The Fluid Dynamics of Cell Motility , pp. 353 - 370Publisher: Cambridge University PressPrint publication year: 2020
References
Alberts, B., Johnson, A., Lewis, J., et al. 2007. Molecular Biology of the Cell. 5th edn. New York, NY: Garland Science.CrossRefGoogle Scholar
Alexander, D. E. 2002. Nature’s Flyers: Birds, Insects, and the Biomechanics of Flight. Baltimore, MD: The Johns Hopkins University Press.Google Scholar
Anderson, J. 1989. Colloidal transport by interfacial forces. Annu. Rev. Fluid Mech., 21, 61–99.Google Scholar
Audoly, B. and Pomeau, Y. 2010. Elasticity and Geometry: From Hair Curls to the Nonlinear Response of Shells. Oxford, UK: Oxford University Press.Google Scholar
Avron, J. E., Kenneth, O., and Oaknin, D. H. 2005. Pushmepullyou: An efficient microswimmer. New J. Phys., 7, 234.Google Scholar
Barnes, H. A. 1995. A review of the slip (wall depletion) of polymer solutions, emulsions and particle suspensions in viscometers: Its cause, character, and cure. J. Non-Newt. Fluid Mech., 56, 221–231.Google Scholar
Batchelor, G. K. 1967. An Introduction to Fluid Dynamics. Cambridge, UK: Cambridge University Press.Google Scholar
Batchelor, G. K. 1970a. The stress system in a suspension of force-free particles. J. Fluid Mech., 41, 545–570.Google Scholar
Batchelor, G. K. 1970b. Slender body theory for particles of arbitrary cross section in Stokes flow. J. Fluid Mech., 44, 419–440.Google Scholar
Batchelor, G. K. 1976. Developments in microhydrodynamics. In Koiter, W.T. (ed.), Theoretical and Applied Mechanics. North-Holland, Amsterdam. Pages 33–55.Google Scholar
Bennett, R. R. and Golestanian, R. 2013. Phase-dependent forcing and synchronization in the three-sphere model of Chlamydomonas. New J. Phys., 15, 075028.Google Scholar
Berg, H. C. 2003. The rotary motor of bacterial flagella. Annu. Rev. Biochem., 72, 19–54.Google Scholar
Berg, H. C. and Anderson, R. A. 1973. Bacteria swim by rotating their flagellar filaments. Nature, 245, 380–382.Google Scholar
Berg, H. C. and Brown, D. A. 1972. Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature, 239, 500–504.Google Scholar
Berg, H. C. and Turner, L. 1979. Movement of microorganisms in viscous environments. Nature, 278, 349–351.Google Scholar
Berg, H. C. and Turner, L. 1990. Chemotaxis of bacteria in glass capillary arrays: Escherichia coli, motility, microchannel plate, and light scattering. Biophys. J., 58, 919–930.CrossRefGoogle ScholarPubMed
Berke, A. P., Turner, L., Berg, H. C., and Lauga, E. 2008. Hydrodynamic attraction of swimming microorganisms by surfaces. Phys. Rev. Lett., 101, 038102.Google Scholar
Berman, R. S., Kenneth, O., Sznitman, J., and Leshansky, A. M. 2013. Undulatory locomotion of finite filaments: Lessons from Caenorhabditis elegans. New J. Phys., 15, 075022.Google Scholar
Bianchi, S., Saglimbeni, F., and Di Leonardo, R. 2017. Holographic imaging reveals the mechanism of wall entrapment in swimming bacteria. Phys. Rev. X, 7, 011010.Google Scholar
Bird, R. B. and Wiest, J. M. 1995. Constitutive equations for polymeric liquids. Annu. Rev. Fluid Mech., 27, 169–193.CrossRefGoogle Scholar
Bird, R. B., Armstrong, R. C., and Hassager, O. 1987a. Dynamics of Polymeric Liquids. Vol. 1: Fluid Mechanics. 2nd edn. New York, NY: Wiley-Interscience.Google Scholar
Bird, R. B., Curtiss, C. F., Armstrong, R. C., and Hassager, O. 1987b. Dynamics of Polymeric Liquids. Vol. 2: Kinetic Theory. 2nd edn. New York, NY: Wiley-Interscience.Google Scholar
Blake, J. R. 1971a. A note on the image system for a stokeslet in a no-slip boundary. Proc. Camb. Phil. Soc., 70, 303–310.Google Scholar
Blake, J. R. 1971b. A spherical envelope approach to ciliary propulsion. J. Fluid Mech., 46, 199–208.Google Scholar
Blake, J. R. 1971c. Infinite models for ciliary propulsion. J. Fluid Mech., 49, 209–222.CrossRefGoogle Scholar
Blake, J. R. 1972. A model for the micro-structure in ciliated organisms. J. Fluid Mech., 55, 1–23.Google Scholar
Blake, J. R. and Chwang, A. T. 1974. Fundamental singularities of viscous-flow. Part 1: Image systems in vicinity of a stationary no-slip boundary. J. Eng. Math., 8, 23–29.CrossRefGoogle Scholar
Blake, J. R. and Sleigh, M. A. 1974. Mechanics of ciliary locomotion. Biol. Rev. Camb. Phil. Soc., 49, 85–125.Google Scholar
Brady, J. F. and Bossis, G. 1988. Stokesian dynamics. Annu. Rev. Fluid Mech., 20, 111–157.CrossRefGoogle Scholar
Brennen, C. 1974. Oscillating boundary layer theory for ciliary propulsion. J. Fluid Mech., 65, 799–824.Google Scholar
Brennen, C. and Winet, H. 1977. Fluid mechanics of propulsion by cilia and flagella. Annu. Rev. Fluid Mech., 9, 339–398.Google Scholar
Brenner, H. 1967. Coupling between the translational and rotational Brownian motions of rigid particles of arbitrary shape: II. General theory. J. Colloid Interface Sci., 23, 407–436.CrossRefGoogle Scholar
Bretherton, F. P. 1962. The motion of rigid particles in a shear flow at low Reynolds number. J. Fluid Mech., 14, 284–304.CrossRefGoogle Scholar
Brinkman, H. C. 1947. A calculation of the viscous force exerted by a flowing fluid on a dense swarm of particles. Appl. Sci. Res. A, 1, 27–34.Google Scholar
Brokaw, C. J. 1972. Flagellar movement: A sliding filament model. Science, 178, 455–462.Google Scholar
Brokaw, C. J. 1989. Direct measurements of sliding between outer doublet microtubules in swimming sperm flagella. Science, 243, 1593–1596.Google Scholar
Brotto, T., Caussin, J.-B., Lauga, E., and Bartolo, D. 2013. Hydrodynamics of confined active fluids. Phys. Rev. Lett., 110, 038101.Google Scholar
Brumley, D. R., Polin, M., Pedley, T. J., and Goldstein, R. E. 2012. Hydrodynamic synchronization and metachronal waves on the surface of the colonial alga Volvox carteri. Phys. Rev. Lett., 109, 268102.Google Scholar
Brumley, D. R., Wan, K. Y., Polin, M., and Goldstein, R. E. 2014. Flagellar synchronization through direct hydrodynamic interactions. eLife, 3, e02750.CrossRefGoogle ScholarPubMed
Brumley, D. R., Polin, M., Pedley, T. J., and Goldstein, R. E. 2015. Metachronal waves in the flagellar beating of Volvox and their hydrodynamic origin. J. Roy. Soc. Interface, 12, 20141358.CrossRefGoogle ScholarPubMed
Butenko, A. V., Mogilko, E., Amitai, L., Pokroy, B., and Sloutskin, E. 2012. Coiled to diffuse: Brownian motion of a helical bacterium. Langmuir, 28, 12941–7.Google Scholar
Calladine, C. R. 1978. Change of waveform in bacterial flagella: The role of mechanics at the molecular level. J. Mol. Biol., 118, 457–479.Google Scholar
Camalet, S. and Jülicher, F. 2000. Generic aspects of axonemal beating. New J. Phys., 2, 1–23.Google Scholar
Cates, M. E. and Tailleur, J. 2015. Motility-induced phase separation. Annu. Rev. Condens. Matter Phys., 6, 219–244.Google Scholar
Chaikin, P. M. and Lubensky, T. C. 2000. Principles of Condensed Matter Physics. Cambridge, UK: Cambridge University Press.Google Scholar
Chamolly, A., Ishikawa, T., and Lauga, E. 2017. Active particles in periodic lattices. New J. Phys., 19, 115001.Google Scholar
Chan, B. 2009. Bio-inspired fluid locomotion. Ph.D. thesis, Massachusetts Institute of Technology, Cambridge, MA.Google Scholar
Chan, B., Balmforth, N. J., and Hosoi, A. E. 2005. Building a better snail: Lubrication and adhesive locomotion. Phys. Fluids, 17, 113101.Google Scholar
Chandrasekhar, S. 1943. Stochastic problems in physics and astronomy. Rev. Mod. Phys., 15, 1–89.Google Scholar
Chen, D. T. N., Heymann, M., Fraden, S., Nicastro, D., and Dogic, Z. 2015. ATP consumption of eukaryotic flagella measured at a single-cell level. Biophys. J., 109, 2562–2573.Google Scholar
Childress, S. 1981. Mechanics of Swimming and Flying. Cambridge, UK: Cambridge Universtity Press.Google Scholar
Childress, S. 2012. A thermodynamic efficiency for Stokesian swimming. J. Fluid Mech., 705, 77–97.Google Scholar
Childress, S., Levandowsky, M., and Spiegel, E. A. 1975. Pattern formation in a suspension of swimming microorganisms: Equations and stability theory. J. Fluid Mech., 69, 591–613.Google Scholar
Chwang, A. T. and Wu, T. Y. 1971. Helical movement of microorganisms. Proc. Roy. Soc. Lond. B, 178, 327–346.Google Scholar
Chwang, A. T. and Wu, T. Y. 1975. Hydromechanics of low-Reynolds-number flow. Part 2: Singularity method for Stokes flows. J. Fluid Mech., 99, 411–431.Google Scholar
Cisneros, L., Dombrowski, C., Goldstein, R. E., and Kessler, J. O. 2006. Reversal of bacterial locomotion at an obstacle. Phys. Rev. E, 73, 030901.Google Scholar
Cisneros, L. H., Cortez, R., Dombrowski, C., Goldstein, R. E., and Kessler, J. O. 2007. Fluid dynamics of self-propelled microorganisms, from individuals to concentrated populations. Exp. Fluids, 43, 737–753.CrossRefGoogle Scholar
Copeland, M. F. and Weibel, D. B. 2009. Bacterial swarming: A model system for studying dynamic self-assembly. Soft Matter, 5, 1174–1187.Google Scholar
Cox, R. G. 1970. The motion of long slender bodies in a viscous fluid. Part 1: General Theory. J. Fluid Mech., 44, 791–810.Google Scholar
Darnton, N. C. and Berg, H. C. 2007. Force-extension measurements on bacterial flagella: Triggering polymorphic transformations. Biophys. J., 92, 2230–2236.Google Scholar
Darnton, N. C., Turner, L., Rojevsky, S., and Berg, H. C. 2007. On torque and tumbling in swimming Escherichia coli. J. Bacteriol., 189, 1756–1764.Google Scholar
Darnton, N. C., Turner, L., Rojevsky, S., and Berg, H. C. 2010. Dynamics of bacterial swarming. Biophys. J., 98, 2082–2090.Google Scholar
Dauparas, J. and Lauga, E. 2016. Flagellar flows around bacterial swarms. Phys. Rev. Fluids, 1, 043202.Google Scholar
De Langre, E. 2008. Effects of wind on plants. Annu. Rev. Fluid Mech., 40, 141–168.CrossRefGoogle Scholar
De Lillo, F., Cencini, M., Durham, et al. 2014. Turbulent fluid acceleration generates clusters of gyrotactic microorganisms. Phys. Rev. Lett., 112, 044502.CrossRefGoogle ScholarPubMed
Denissenko, P., Kantsler, V., Smith, D. J., and Kirkman-Brown, J. 2012. Human spermatozoa migration in microchannels reveals boundary-following navigation. Proc. Natl. Acad. Sci. U.S.A., 109, 8007–8010.Google Scholar
Di Leonardo, R., Angelani, L., Dell’Arciprete, D., et al. 2010. Bacterial ratchet motors. Proc. Natl. Acad. Sci. U.S.A., 107, 9541–9545.Google Scholar
Di Leonardo, R., Dell’Arciprete, D., Angelani, L., and Iebba, V. 2011. Swimming with an image. Phys. Rev. Lett., 106, 038101.Google Scholar
Di Leonardo, R., Búzás, A., Kelemen, L., et al. 2012. Hydrodynamic synchronization of light driven microrotors. Phys. Rev. Lett., 109, 034104.Google Scholar
DiLuzio, W. R., Turner, L., Mayer, M., et al. 2005. Escherichia coli swim on the right-hand side. Nature, 435, 1271–1274.Google Scholar
Doi, M. and Edwards, S. F. 1988. The Theory of Polymer Dynamics. Oxford, UK: Oxford University Press.Google Scholar
Dombrowski, C., Cisneros, L., Chatkaew, S., Goldstein, R. E., and Kessler, J. O. 2004. Self-concentration and large-scale coherence in bacterial dynamics. Phys. Rev. Lett., 93, 098103.Google Scholar
Doostmohammadi, A., Ignés-Mullol, J., Yeomans, J. M., and Sagués, F. 2018. Active ne-matics. Nature Comm., 9, 3246.Google Scholar
Drescher, K., Goldstein, R. E., Michel, N., Polin, M., and Tuval, I. 2010a. Direct measurement of the flow field around swimming microorganisms. Phys. Rev. Lett., 105, 168101.Google Scholar
Drescher, K., Goldstein, R. E., and Tuval, I. 2010b. Fidelity of adaptive phototaxis. Proc. Natl. Acad. Sci. U.S.A., 107, 11171–11176.Google Scholar
Drescher, K., Dunkel, J., Cisneros, L. H., Ganguly, S., and Goldstein, R. E. 2011. Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering. Proc. Natl. Acad. Sci. U.S.A., 108, 10940–10945.Google Scholar
Dudley, R. 2002. The Biomechanics of Insect Flight: Form, Function, Evolution. Princeton, NJ: Princeton University Press.Google Scholar
Durham, W. M., Kessler, J. O., and Stocker, R. 2009. Disruption of vertical motility by shear triggers formation of thin phytoplankton layers. Science, 323, 1067–1070.Google Scholar
Durham, W. M., Climent, E., and Stocker, R. 2011. Gyrotaxis in a steady vortical flow. Phys. Rev. Lett., 106, 238102.Google Scholar
Durham, W. M., Climent, E., Barry, M., et al. 2013. Turbulence drives microscale patches of motile phytoplankton. Nature Comm., 4, 2148.Google Scholar
Ebbens, S. J. and Howse, J. R. 2011. Direct observation of the direction of motion for spherical catalytic swimmers. Langmuir, 27, 12293–12296.Google Scholar
Elfring, G. J. and Lauga, E. 2009. Hydrodynamic phase locking of swimming microorganisms. Phys. Rev. Lett., 103, 088101.CrossRefGoogle ScholarPubMed
Elfring, G. J. and Lauga, E. 2011a. Passive hydrodynamic synchronization of two-dimensional swimming cells. Phys. Fluids, 23, 011902.Google Scholar
Elfring, G. J. and Lauga, E. 2011b. Synchronization of flexible sheets. J. Fluid Mech., 674, 163–173.Google Scholar
Elgeti, J. and Gompper, G. 2013. Emergence of metachronal waves in cilia arrays. Proc. Natl. Acad. Sci. U.S.A., 110, 4470–4475.Google Scholar
Ellington, C. P. 1984. The Aerodynamics of Hovering Insect Flight. London, UK: The Royal Society.Google Scholar
Eloy, C. and Lauga, E. 2012. Kinematics of the most efficient cilium. Phys. Rev. Lett., 109, 038101.Google Scholar
Ermak, D. L. and McCammon, J. A. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys., 69, 1352–1360.Google Scholar
Espinosa-Garcia, J., Lauga, E., and Zenit, R. 2013. Elasticity increases locomotion of flexible swimmers. Phys. Fluids, 25, 031701.Google Scholar
Eytan, O. and Elad, D. 1999. Analysis of intra-uterine fluid motion induced by uterine contractions. Bull. Math. Biol., 61, 221–238.Google Scholar
Fauci, L. J. 1990. Interaction of oscillating filaments: A computational study. J. Comput. Phys., 86, 294–313.Google Scholar
Fauci, L. J. and Dillon, R. 2006. Biofluidmechanics of reproduction. Annu. Rev. Fluid Mech., 38, 371–394.Google Scholar
Fauci, L. J. and McDonald, A. 1995. Sperm motility in the presence of boundaries. Bull. Math. Biol., 57, 679–699.Google Scholar
Fish, F. E. and Lauder, G. V. 2006. Passive and active flow control by swimming fishes and mammals. Annu. Rev. Fluid Mech., 38, 193–224.Google Scholar
Flores, H., Lobaton, E., Mendez-Diez, S., Tlupova, S., and Cortez, R. 2005. A study of bacterial flagellar bundling. Bull. Math. Biol., 67, 137–168.Google Scholar
Friedrich, B. M., Riedel-Kruse, I. H., Howard, J., and Jülicher, F. 2010. High-precision tracking of sperm swimming fine structure provides strong test of resistive force theory. J. Exp. Biol., 213, 1226–1234.Google Scholar
Frymier, P. D., Ford, R. M., Berg, H. C., and Cummings, P. T. 1995. Three-dimensional tracking of motile bacteria near a solid planar surface. Proc. Natl. Acad. Sci. U.S.A., 92, 6195–6199.CrossRefGoogle Scholar
Fu, H. C., Wolgemuth, C. W., and Powers, T. R. 2008. Beating patterns of filaments in viscoelastic fluids. Phys. Rev. E, 78, 041913–1–12.Google Scholar
Fu, H. C., Wolgemuth, C. W., and Powers, T. R. 2009. Swimming speeds of filaments in nonlinearly viscoelastic fluids. Phys. Fluids, 21, 033102.Google Scholar
Fu, H. C., Shenoy, V. B., and Powers, T. R. 2010. Low-Reynolds-number swimming in gels. Europhys. Lett., 91, 24002.CrossRefGoogle Scholar
Fujii, M., Shibata, S., and Aizawa, S.-I. 2008. Polar, peritrichous, and lateral flagella belong to three distinguishable flagellar families. J. Mol. Biol., 379, 273–283.Google Scholar
Fulford, G. R., Katz, D. F., and Powell, R. L. 1998. Swimming of spermatozoa in a linear viscoelastic fluid. Biorheol., 35, 295–309.Google Scholar
Gaffney, E. A., Gadelha, H., Smith, D. J., Blake, J. R., and Kirkman-Brown, J. C. 2011. Mammalian sperm motility: Observation and theory. Annu. Rev. Fluid Mech., 43, 501–528.CrossRefGoogle Scholar
Gagnon, D. A., Shen, X. N., and Arratia, P. E. 2013. Undulatory swimming in fluids with polymer networks. Europhys. Lett., 104, 14004.Google Scholar
Galajda, P., Keymer, J. E., Chaikin, P., and Austin, R. H. 2007. A wall of funnels concentrates swimming bacteria. J. Bacteriol., 189, 8704–8707.Google Scholar
Garcia, X., Rafai, S., and Peyla, P. 2013. Light control of the flow of phototactic microswimmer suspensions. Phys. Rev. Lett., 110, 138106.CrossRefGoogle ScholarPubMed
Gardiner, B., Berry, P., and Moulia, B. 2016. Wind impacts on plant growth, mechanics and damage. Plant Sci., 245, 94–118.Google Scholar
Gest, H. 2004. The discovery of microorganisms by Robert Hooke and Antoni Van Leeuwenhoek, fellows of the Royal Society. Notes Rec. Roy. Soc. London, 58 187–201.Google Scholar
Geyer, V. F., Jülicher, F., Howard, J., and Friedrich, B. M. 2013. Cell-body rocking is a dominant mechanism for flagellar synchronization in a swimming alga. Proc. Natl. Acad. Sci. U.S.A., 110, 18058–18063.Google Scholar
Ghosh, A. and Fischer, P. 2009. Controlled propulsion of artificial magnetic nanostructured propellers. Nano Lett., 9, 2243–2245.Google Scholar
Giacché, D., Ishikawa, T., and Yamaguchi, T. 2010. Hydrodynamic entrapment of bacteria swimming near a solid surface. Phys. Rev. E, 82, 056309.Google Scholar
Gibbons, B. H. and Gibbons, I. R. 1972. Flagellar movement and adenosine triphosphatase activity in sea urchin sperm extracted with Triton X-100. J. Cell Bio., 54, 75–97.Google Scholar
Gilboa, A. and Silberberg, A. 1976. In-situ rheological characterization of epithelial mucus. Biorheol., 13, 59–65.Google Scholar
Godinez, F. A., Koens, L., Montenegro-Johnson, T. D., Zenit, R., and Lauga, E. 2015. Complex fluids affect low-Reynolds number locomotion in a kinematic-dependent manner. Exp. Fluids, 56, 97.CrossRefGoogle Scholar
Goldman, A. J., Cox, R. G., and Brenner, H. 1967. Slow viscous motion of a sphere parallel to a plane wall: II Couette flow. Chem. Eng. Sci., 22, 653–660.Google Scholar
Goldstein, R. E. 2015. Green algae as model organisms for biological fluid dynamics. Annu. Rev. Fluid Mech., 47, 343–75.Google Scholar
Goldstein, R. E., Polin, M., and Tuval, I. 2009. Noise and synchronization in pairs of beating eukaryotic flagella. Phys. Rev. Lett., 103, 168103.Google Scholar
Golestanian, R., Liverpool, T. B., and Ajdari, A. 2007. Designing phoretic micro- and nano-swimmers. New J. Phys., 9, 126.CrossRefGoogle Scholar
Götz, T. 2000. Interactions of fibers and flow: Asymptotics, theory and numerics. Ph.D. thesis, Universität Kaiserslautern, Germany.Google Scholar
Graham, M. D. 2018. Microhydrodynamics, Brownian Motion, and Complex Fluids. Cambridge, UK: Cambridge University Press.CrossRefGoogle Scholar
Gray, J. and Hancock, G. J. 1955. The propulsion of sea-urchin spermatozoa. J. Exp. Biol., 32, 802–814.Google Scholar
Grotberg, J. B. 1994. Pulmonary flow and transport phenomena. Annu. Rev. Fluid Mech., 26, 529–571.Google Scholar
Guasto, J. S., Johnson, K. A., and Gollub, J. P. 2010. Oscillatory flows induced by microorganisms swimming in two dimensions. Phys. Rev. Lett., 105, 168102.Google Scholar
Guasto, J. S., Rusconi, R., and Stocker, R. 2012. Fluid mechanics of planktonic microorganisms. Annu. Rev. Fluid Mech., 44, 373–400.Google Scholar
Gueron, S. and Levit-Gurevich, K. 1999. Energetic considerations of ciliary beating and the advantage of metachronal coordination. Proc. Natl. Acad. Sci. U.S.A., 96, 12240–12245.Google Scholar
Gueron, S. and Liron, N. 1993. Simulations of three-dimensional ciliary beats and cilia interactions. Biophys. J., 65, 499–507.Google Scholar
Gueron, S., Levit-Gurevich, K., Liron, N., and Blum, J. J. 1997. Cilia internal mechanism and metachronal coordination as the result of hydrodynamical coupling. Proc. Natl. Acad. Sci. U.S.A., 94, 6001–6006.Google Scholar
Guirao, B. and Joanny, J. F. 2007. Spontaneous creation of macroscopic flow and metachronal waves in an array of cilia. Biophys. J., 92, 1900–1917.Google Scholar
Guyon, E., Hulin, J., Petit, L., and Mitescu, C. 2001. Physical Hydrodynamics. Oxford, UK: Oxford University Press.Google Scholar
Hall, W. F. and Busenberg, S. N. 1969. Viscosity of magnetic suspensions. J. Chem. Phys., 51, 137–144.Google Scholar
Hamel, A., Fish, C., Combettes, L., Dupuis-Williams, P., and Baroud, C. N. 2011. Transitions between three swimming gaits in Paramecium escape. Proc. Natl. Acad. Sci. U.S.A., 108, 7290–7295.CrossRefGoogle ScholarPubMed
Hancock, G. J. 1953. The self-propulsion of microscopic organisms through liquids. Proc. Roy. Soc. Lond. A, 217, 96–121.Google Scholar
Happel, J. and Brenner, H. 1965. Low Reynolds Number Hydrodynamics. Englewood Cliffs, NJ: Prentice Hall.Google Scholar
Hasegawa, K., Yamashita, I., and Namba, K. 1998. Quasi- and nonequivalence in the structure of bacterial flagellar filament. Biophys. J., 74, 569–575.Google Scholar
Hatwalne, Y., Ramaswamy, S., Rao, M., and Simha, R. A. 2004. Rheology of active-particle suspensions. Phys. Rev. Lett., 92, 118101.Google Scholar
Heil, M. and Hazel, A. L. 2011. Fluid-structure interaction in internal physiological flows. Annu. Rev. Fluid Mech., 43, 141–162.Google Scholar
Hewitt, D. R. and Balmforth, N. J. 2017. Taylor’s swimming sheet in a yield-stress fluid. J. Fluid Mech., 828, 33–56.Google Scholar
Hewitt, D. R. and Balmforth, N. J. 2018. Viscoplastic slender-body theory. J. Fluid Mech., 856, 870–897.Google Scholar
Higdon, J. J. L. 1979a. Hydrodynamic analysis of flagellar propulsion. J. Fluid Mech., 90, 685–711.Google Scholar
Higdon, J. J. L. 1979b. Hydrodynamics of flagellar propulsion: Helical waves. J. Fluid Mech., 94, 331–351.Google Scholar
Hill, J., Kalkanci, O., McMurry, J. L., and Koser, H. 2007. Hydrodynamic surface interactions enable Escherichia coli to seek efficient routes to swim upstream. Phys. Rev. Lett., 98, 068101.Google Scholar
Hohenegger, C. and Shelley, M. J. 2010. Stability of active suspensions. Phys. Rev. E, 81, 046311.Google Scholar
Hohenegger, C. and Shelley, M. J. 2011. Dynamics of complex biofluids. New Trends in the Physics and Mechanics of Biological Systems: Lecture Notes of the Les Houches Summer School. Volume 92, July 2009, 92, 65.Google Scholar
Hotani, H. 1982. Micro-video study of moving bacterial flagellar filaments III: Cyclic transformation induced by mechanical force. J. Mol. Biol., 156, 791.Google Scholar
Howard, J. 2001. Mechanics of Motor Proteins and the Cytoskeleton. Sunderland, MA: Sinauer Associates.Google Scholar
Howse, J. R., Jones, R. A. L., Ryan, A. J., et al. 2007. Self-motile colloidal particles: From directed propulsion to random walk. Phys. Rev. Lett., 99, 048102.Google Scholar
Hu, D. L., Nirody, J., Scott, T., and Shelley, M. J. 2009. The mechanics of slithering locomotion. Proc. Natl. Acad. Sci. U.S.A., 106, 10081–10085.Google Scholar
Hu, J., Yang, M., Gompper, G., and Winkler, R. G. 2015. Modelling the mechanics and hydrodynamics of swimming E. coli. Soft Matter, 11, 7867–7876.Google Scholar
Hyon, Y., Marcos, Powers, Stocker, T. R., R., and Fu, H. C. 2012. The wiggling trajectories of bacteria. J. Fluid Mech., 705, 58–76.Google Scholar
Ishijima, S., Oshio, S., and Mohri, H. 1986. Flagellar movement of human spermatozoa. Gamete Res., 13, 185–197.Google Scholar
Ishikawa, T., Simmonds, M. P., and Pedley, T. J. 2006. Hydrodynamic interaction of two swimming model micro-organisms. J. Fluid Mech., 568, 119–160.Google Scholar
Ishikawa, T., Sekiya, G., Imai, Y., and Yamaguchi, T. 2007. Hydrodynamic interaction between two swimming bacteria. Biophys. J., 93, 2217–2225.Google Scholar
Ishimoto, K. and Gaffney, E. A. 2015. Fluid flow and sperm guidance: A simulation study of hydrodynamic sperm rheotaxis. J. Roy. Soc. Interface, 12, 20150172.Google Scholar
Ishimoto, K. and Yamada, M. 2012. A coordinate-based proof of the scallop theorem. SIAM J. Applied Math., 72, 1686–1694.Google Scholar
Izri, Z., van der Linden, M. N., Michelin, S., and Dauchot, O. 2014. Self-propulsion of pure water droplets by spontaneous Marangoni stress driven motion. Phys. Rev. Lett., 113, 248302.Google Scholar
Jacobs, K. 2010. Stochastic Processes for Physicists: Understanding Noisy Systems. Cambridge, UK: Cambridge University Press.Google Scholar
Jahn, T. L. and Votta, J. J. 1972. Locomotion of protozoa. Annu. Rev. Fluid Mech., 4, 93–116.Google Scholar
Jarrell, K. F. and McBride, M. J. 2008. The surprisingly diverse ways that prokaryotes move. Nature Rev. Microbiol., 6, 466–476.Google Scholar
Jeffery, G. B. 1922. The motion of ellipsoidal particles immersed in a viscous fluid. Proc. Roy. Soc. A, 102, 161–179.Google Scholar
Jibuti, L., Qi, L., Misbah, C., et al. 2014. Self-focusing and jet instability of a microswimmer suspension. Phys. Rev. E, 90, 063019.Google Scholar
Johnson, R. E. 1980. An improved slender body theory for Stokes flow. J. Fluid Mech., 99, 411–431.Google Scholar
Johnson, R. E. and Brokaw, C. J. 1979. Flagellar hydrodynamics: A comparison between resistive-force theory and slender-body theory. Biophys. J., 25, 113.Google Scholar
Jülicher, F., Ajdari, A., and Prost, J. 1997. Modeling molecular motors. Rev. Mod. Phys., 69, 1269.Google Scholar
Jülicher, F., Grill, S. W., and Salbreux, G. 2018. Hydrodynamic theory of active matter. Rep. Prog. Phys., 81, 7.Google Scholar
Kamiya, R., Asakura, S., and Yamaguchi, S. 1980. Formation of helical filaments by copolymerization of two types of straight flagellins. Nature, 286, 628–630.Google Scholar
Kantsler, V., Dunkel, J., Polin, M., and Goldstein, R. E. 2013. Ciliary contact interactions dominate surface scattering of swimming eukaryotes. Proc. Natl. Acad. Sci. U.S.A., 110, 1187–1192.Google Scholar
Kantsler, V., Dunkel, J., Blayney, M., and Goldstein, R. E. 2014. Rheotaxis facilitates upstream navigation of mammalian sperm cells. eLife, 3, e02403.Google Scholar
Kasyap, T. V., Koch, D. L., and Wu, M. 2014. Hydrodynamic tracer diffusion in suspensions of swimming bacteria. Phys. Fluids, 26, 081901.Google Scholar
Katz, D. F. 1974. On the propulsion of micro-organisms near solid boundaries. J. Fluid Mech., 64, 33–49.Google Scholar
Katz, D. F. and Berger, S. A. 1980. Flagellar propulsion of human sperm in cervical mucus. Biorheol., 17, 169–175.Google Scholar
Katz, D. F., Blake, J. R., and Paveri-Fontana, S. L. 1975. On the movement of slender bodies near plane boundaries at low Reynolds number. J. Fluid Mech., 72, 529–540.Google Scholar
Kaya, T. and Koser, H. 2009. Characterization of hydrodynamic surface interactions of Escherichia coli cell bodies in shear flow. Phys. Rev. Lett., 103, 138103.Google Scholar
Kaya, T. and Koser, H. 2012. Direct upstream motility in Escherichia coli. Biophys. J., 102, 1514–1523.Google Scholar
Kearns, D. B. 2010. A field guide to bacterial swarming motility. Nature Rev. Microbiol., 8, 634–644.Google Scholar
Keim, N. C., Garcia, M., and Arratia, P. E. 2012. Fluid elasticity can enable propulsion at low Reynolds number. Phys. Fluids, 24, 081703.Google Scholar
Keller, J. B. and Rubinow, S. I. 1976. Slender body theory for slow viscous flow. J. Fluid Mech., 75, 705–714.Google Scholar
Kessler, J. O. 1985. Hydrodynamic focusing of motile algal cells. Nature, 313, 218–220.Google Scholar
Khurana, N., Blawzdziewicz, J., and Ouellette, N. T. 2011. Reduced transport of swimming particles in chaotic flow due to hydrodynamic trapping. Phys. Rev. Lett., 106, 198104.Google Scholar
Kim, M. and Powers, T. R. 2004. Hydrodynamic interactions between rotating helices. Phys. Rev. E, 69, 061910.Google Scholar
Kim, M., Bird, J. C., Van Parys, A. J., Breuer, K. S., and Powers, T. R. 2003. A macroscopic scale model of bacterial flagellar bundling. Proc. Natl. Acad. Sci. U.S.A., 100, 15481–15485.Google Scholar
Kim, M. J. and Breuer, K. S. 2004. Enhanced diffusion due to motile bacteria. Phys. Fluids, 16, L78–L81.Google Scholar
Kim, M. J., Kim, M. M. J., Bird, J. C., et al. 2004. Particle image velocimetry experiments on a macro-scale model for bacterial flagellar bundling. Exp. Fluids, 37, 782–788.Google Scholar
Kim, S. and Karrila, J. S. 1991. Microhydrodynamics: Principles and Selected Applications. Boston, MA: Butterworth-Heinemann.Google Scholar
Koch, D. L. and Shaqfeh, E. S. G. 1989. The instability of a dispersion of sedimenting spheroids. J. Fluid Mech., 209, 521–542.Google Scholar
Koch, D. L. and Subramanian, G. 2011. Collective hydrodynamics of swimming microorganisms: Living fluids. Annu. Rev. Fluid Mech., 43, 637–659.Google Scholar
Koens, L. and Lauga, E. 2014. The passive diffusion of Leptospira interrogans. Phys. Biol., 11, 066008.Google Scholar
Koens, L. and Lauga, E. 2017. Analytical solutions to slender-ribbon theory. Phys. Rev. Fluids, 2, 084101.Google Scholar
Koens, L. and Lauga, E. 2018. The boundary integral formulation of Stokes flows includes slender-body theory. J. Fluid Mech., 850, R1.Google Scholar
Kotar, J., Leoni, M., Bassetti, B., Lagomarsino, M. C., and Cicuta, P. 2010. Hydrodynamic synchronization of colloidal oscillators. Proc. Natl. Acad. Sci. U.S.A., 107, 7669–7673.Google Scholar
Kotar, J., Debono, L., Bruot, N., et al. 2013. Optimal hydrodynamic synchronization of colloidal rotors. Phys. Rev. Lett., 111, 228103.Google Scholar
Koumakis, N., Lepore, A., Maggi, C., and Di Leonardo, R. 2013. Targeted delivery of colloids by swimming bacteria. Nature Comm., 4, 2588.Google Scholar
Kruse, K., Joanny, J.-F., Jülicher, F., Prost, J., and Sekimoto, K. 2004. Asters, vortices, and rotating spirals in active gels of polar filaments. Phys. Rev. Lett., 92, 078101.Google Scholar
Kruse, K., Joanny, J.-F., Jülicher, F., Prost, J., and Sekimoto, K. 2005. Generic theory of active polar gels: A paradigm for cytoskeletal dynamics. Eur. Phys. J. E, 16, 5–16.Google Scholar
Kühn, M. J., Schmidt, F. K., Eckhardt, B., and Thormann, K. M. 2017. Bacteria exploit a polymorphic instability of the flagellar filament to escape from traps. Proc. Natl. Acad. Sci. U.S.A., 114, 6340–6345.Google Scholar
Lagomarsino, M. C., Bassetti, B., and Jona, P. 2002. Rowers coupled hydrodynamically: Modeling possible mechanisms for the cooperation of cilia. Europ. Phys. J. B, 26, 81–88.Google Scholar
Lagomarsino, M. C., Jona, P., and Bassetti, B. 2003. Metachronal waves for deterministic switching two-state oscillators with hydrodynamic interaction. Phys. Rev. E, 68, 021908.Google Scholar
Landau, L. D. and Lifshitz, E. M. 1980. Statistical Physics. 3rd edn. Oxford, UK: Butterworth-Heinemann.Google Scholar
Landau, L. D. and Lifshitz, E. M. 1986. Theory of Elasticity. 3rd edn. Oxford, UK: Butterworth-Heinemann.Google Scholar
Larson, R. G. 1988. Constitutive Equations for Polymer Melts and Solutions. Boston, MA: Butterworth-Heinemann.Google Scholar
Larson, R. G. 1999. The Structure and Rheology of Complex Fluids. Oxford, UK: Oxford Universtity Press.Google Scholar
Lauga, E. 2011a. Enhanced diffusion by reciprocal swimming. Phys. Rev. Lett., 106, 178101.Google Scholar
Lauga, E. 2014. Locomotion in complex fluids: Integral theorems. Phys. Fluids, 26, 081902.Google Scholar
Lauga, E. and Bartolo, D. 2008. No many-scallop theorem: Collective locomotion of reciprocal swimmers. Phys. Rev. E, 78, 030901.Google Scholar
Lauga, E. and Eloy, C. 2013. Shape of optimal active flagella. J. Fluid Mech., 730, R1.Google Scholar
Lauga, E. and Nadal, F. 2017. Clustering instability of focused swimmers. Europhys. Lett., 116, 64004.Google Scholar
Lauga, E. and Powers, T. R. 2009. The hydrodynamics of swimming microorganisms. Rep. Prog. Phys., 72, 096601.Google Scholar
Lauga, E., DiLuzio, W. R., Whitesides, G. M., and Stone, H. A. 2006. Swimming in circles: Motion of bacteria near solid boundaries. Biophys. J., 90, 400–412.Google Scholar
Lauga, E., Brenner, M. P., and Stone, H. A. 2007. Microfluidics: The no-slip boundary condition. In Foss, J., Tropea, C., and Yarin, A. (eds), Handbook of Experimental Fluid Dynamics. New York, NY: Springer. Pages 1219–1240.Google Scholar
Lazier, J. R. N. and Mann, K. H. 1989. Turbulence and the diffusive layers around small organisms. Deep Sea Res. A, 36, 1721–1733.Google Scholar
Leal, L. G. 2007. Advanced Transport Phenomena: Fluid Mechanics and Convective Transport Processes. Cambridge, UK: Cambridge University Press.Google Scholar
Leifson, E. 1960. Atlas of Bacterial Flagellation. New York and London: Academic Press.Google Scholar
Lemelle, L., Palierne, J. F., Chatre, E., and Place, C. 2010. Counterclockwise circular motion of bacteria swimming at the air-liquid interface. J. Bacteriol, 192, 6307–6308.Google Scholar
Lemelle, L., Palierne, J.-F., Chatre, E., Vaillant, C., and Place, C. 2013. Curvature reversal of the circular motion of swimming bacteria probes for slip at solid/liquid interfaces. Soft Matter, 9, 9759–9762.Google Scholar
Leoni, M., Kotar, J., Bassetti, B., Cicuta, P., and Lagomarsino, M. C. 2009. A basic swimmer at low Reynolds number. Soft Matter, 5, 472–476.Google Scholar
Leptos, K. C., Guasto, J. S., Gollub, J. P., Pesci, A. I., and Goldstein, R. E. 2009. Dynamics of enhanced tracer diffusion in suspensions of swimming eukaryotic microorganisms. Phys. Rev. Lett., 103, 198103.Google Scholar
Leshansky, A. M. 2009. Enhanced low-Reynolds-number propulsion in heterogeneous viscous environments. Phys. Rev. E, 80, 051911.Google Scholar
Leshansky, A. M. and Kenneth, O. 2008. Surface tank treading: Propulsion of Purcell’s toroidal swimmer. Phys. Fluids, 20, 063104.Google Scholar
Li, G., Tam, L.-K., and Tang, J. X. 2008. Amplified effect of Brownian motion in bacterial near-surface swimming. Proc. Natl. Acad. Sci. U.S.A., 105, 18355–18359.Google Scholar
Liao, Q., Subramanian, G., DeLisa, M. P., Koch, D. L., and Wu, M. M. 2007. Pair velocity correlations among swimming Escherichia coli bacteria are determined by force-quadrupole hydrodynamic interactions. Phys. Fluids, 19, 061701.Google Scholar
Lighthill, M. J. 1952. On the squirming motion of nearly spherical deformable bodies through liquids at very small Reynolds numbers. Commun. Pure Appl. Math., 5, 109–118.Google Scholar
Lighthill, M. J. 1976. Flagellar hydrodynamics: The John von Neumann Lecture, 1975. SIAM Rev., 18, 161–230.Google Scholar
Lighthill, M. J. 1996a. Helical distributions of stokeslets. J. Eng. Math., 30, 35–78.Google Scholar
Lighthill, M. J. 1996b. Reinterpreting the basic theorem of flagellar hydrodynamics. J. Eng. Math., 30, 25–34.Google Scholar
Lin, Z., Thiffeault, J.-L., and Childress, S. 2011. Stirring by squirmers. J. Fluid Mech., 669, 167–177.Google Scholar
Lisicki, M., Reigh, S. Y., and Lauga, E. 2018. Autophoretic motion in three dimensions. Soft Matter, 14, 3304–3314.Google Scholar
Liu, B., Powers, T. R., and Breuer, K. S. 2011. Force-free swimming of a model helical flagellum in viscoelastic fluids. Proc. Natl. Acad. Sci. U.S.A., 108, 19516–19520.Google Scholar
Lopez, D. and Lauga, E. 2014. Dynamics of swimming bacteria at complex interfaces. Phys. Fluids, 26, 071902.Google Scholar
Lovely, P. S. and Dahlquist, F. W. 1975. Statistical measures of bacterial motility and chemotaxis. J. Theor. Biol., 50, 477–496.Google Scholar
Lowe, C. P. 2003. Dynamics of filaments: Modelling the dynamics of driven microfila-ments. Phil. Trans. Roy. Soc. B, 358, 1543–1550.Google Scholar
Lushi, E., Kantsler, V., and Goldstein, R. E. 2017. Scattering of biflagellate microswimmers from surfaces. Phys. Rev. E, 96, 023102.Google Scholar
Machin, K. E. 1963. The control and synchronization of flagellar movement. Proc. Roy. Soc. B, 158, 88–104.Google Scholar
Macnab, R. M. 1977. Bacterial flagella rotating in bundles: A study in helical geometry. Proc. Natl. Acad. Sci. U.S.A., 74, 221–225.Google Scholar
Macnab, R. M. and Ornston, M. K. 1977. Normal to curly flagellar transitions and their role in bacterial tumbling: Stabilization of an alternative quaternary structure by mechanical force. J. Mol. Biol., 112, 1–30.Google Scholar
Magariyama, Y. and Kudo, S. 2002. A mathematical explanation of an increase in bacterial swimming speed with viscosity in linear-polymer solutions. Biophys. J., 83, 733–739.Google Scholar
Magariyama, Y., Ichiba, M., Nakata, K., et al. 2005. Difference in bacterial motion between forward and backward swimming caused by the wall effect. Biophys. J., 88, 3648–3658.Google Scholar
Makino, M. and Doi, M. 2005. Migration of twisted ribbon-like particles in simple shear flow. Phys. Fluids, 17, 103605.Google Scholar
Man, Y. and Lauga, E. 2015. Phase-separation models for swimming enhancement in complex fluids. Phys. Rev. E, 92, 023004.Google Scholar
Man, Y., Page, W., Poole, R. J., and Lauga, E. 2017. Bundling of elastic filaments induced by hydrodynamic interactions. Phys. Rev. Fluids, 2, 123101.Google Scholar
Marchetti, M. C., Joanny, J.-F., Ramaswamy, S., et al. 2013. Hydrodynamics of soft active matter. Rev. Mod. Phys., 85, 1143.CrossRefGoogle Scholar
Marcos, Fu, Powers, H. C. T. R., and Stocker, R. 2012. Bacterial rheotaxis. Proc. Natl. Acad. Sci. U.S.A., 109, 4780–4785.Google Scholar
Mathijssen, A. J. T. M., Shendruk, T. N., Yeomans, J. M., and Doostmohammadi, A. 2016. Upstream swimming in microbiological flows. Phys. Rev. Lett., 116, 028104.Google Scholar
Mazo, R. M. 2002. Brownian Motion: Fluctuations, Dynamics, and Applications. Oxford, UK: Oxford University Press.Google Scholar
Mendelson, N. H., Bourque, A., Wilkening, K., Anderson, K. R., and Watkins, J. C. 1999. Organized cell swimming motions in Bacillus subtilis colonies: Patterns of short-lived whirls and jets. J. Bacteriol., 181, 600–609.Google Scholar
Mettot, C. and Lauga, E. 2011. Energetics of synchronized states in three-dimensional beating flagella. Phys. Rev. E, 84, 061905.Google Scholar
Mhetar, V. and Archer, L. A. 1998. Slip in entangled polymer solutions. Macromolecules, 31, 6639–6649.Google Scholar
Michelin, S. and Lauga, E. 2010a. Efficiency optimization and symmetry-breaking in a model of ciliary locomotion. Phys. Fluids, 22, 111901.Google Scholar
Michelin, S. and Lauga, E. 2010b. The long-time dynamics of two hydrodynamically-coupled swimming cells. Bull. Math. Biol., 72, 973–1005.Google Scholar
Michelin, S., Lauga, E., and Bartolo, D. 2013. Spontaneous autophoretic motion of isotropic particles. Phys. Fluids, 25, 061701.Google Scholar
Miño, G. L., Dunstan, J., Rousselet, A., Clément, E., and Soto, R. 2013. Induced diffusion of tracers in a bacterial suspension: Theory and experiments. J. Fluid Mech., 729, 423–444.Google Scholar
Montenegro-Johnson, T. D., and Lauga, E. 2014. Optimal swimming of a sheet. Phys. Rev. E, 89, 060701.CrossRefGoogle ScholarPubMed
Morse, M., Huang, A., Li, G., Maxey, M. R., and Tang, J. X. 2013. Molecular adsorption steers bacterial swimming at the air/water interface. Biophys. J., 105, 21–28.Google Scholar
Mussler, M., Rafai, S., Peyla, P., and Wagner, C. 2013. Effective viscosity of non-gravitactic Chlamydomonas reinhardtii microswimmer suspensions. Europhys. Lett., 101, 54004.Google Scholar
Myers, K. M. and Elad, D. 2017. Biomechanics of the human uterus. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 5, e1388.Google Scholar
Navier, C.-L. 1823. Mémoire sur les lois du mouvement des fluides. Mémoires de l’Académie Royale des Sciences de l’Institut de France, VI, 389–440.Google Scholar
Niedermayer, T., Eckhardt, B., and Lenz, P. 2008. Synchronization, phase locking, and metachronal wave formation in ciliary chains. Chaos, 18, 037128.Google Scholar
Nonaka, S., Tanaka, Y., Okada, Y., et al. 1998. Randomization of left–right asymmetry due to loss of nodal cilia generating leftward flow of extraembryonic fluid in mice lacking KIF3B motor protein. Cell, 95, 829–837.Google Scholar
Nonaka, S., Yoshiba, S., Watanabe, D., et al. 2005. De novo formation of left–right asymmetry by posterior tilt of nodal cilia. PLoS Biol., 3, e268.Google Scholar
Normand, T. and Lauga, E. 2008. Flapping motion and force generation in a viscoelastic fluid. Phys. Rev. E, 78, 061907.Google Scholar
Okada, Y., Takeda, S., Tanaka, Y., Belmonte, J.-C. I., and Hirokawa, N. 2005. Mechanism of nodal flow: A conserved symmetry breaking event in left-right axis determination. Cell, 121, 633–644.Google Scholar
Osterman, N. and Vilfan, A. 2011. Finding the ciliary beating pattern with optimal efficiency. Proc. Natl. Acad. Sci. U.S.A., 108, 15727–15732.Google Scholar
Pak, O. S. and Lauga, E. 2010. The transient swimming of a waving sheet. Proc. Roy. Soc. A, 466, 107–126.Google Scholar
Pak, O. S. and Lauga, E. 2014. Generalized squirming motion of a sphere. J. Eng. Math., 88, 1–28.Google Scholar
Pak, O. S., Normand, T., and Lauga, E. 2010. Pumping by flapping in a viscoelastic fluid. Phys. Rev. E, 81, 036312.Google Scholar
Pak, O. S., Zhu, L., Brandt, L., and Lauga, E. 2012. Micropropulsion and microrheology in complex fluids via symmetry breaking. Phys. Fluids, 24, 103102.Google Scholar
Palacci, J., Sacanna, S., Steinberg, A. P., Pine, D. J., and Chaikin, P. M. 2013. Living crystals of light-activated colloidal surfers. Science, 339, 936–940.Google Scholar
Papavassiliou, D. and Alexander, G. P. 2017. Exact solutions for hydrodynamic interactions of two squirming spheres. J. Fluid Mech., 813, 618–646.Google Scholar
Pedley, T. J. 2000. Blood flow in arteries and veins. In Batchelor, G.K., Moffatt, H.K., and Worster, M.G. (eds), Perspectives in Fluid Mechanics. Cambridge, UK: Cambridge University Press. Pages 105–158.Google Scholar
Pedley, T. J. and Kessler, J. O. 1987. The orientation of spheroidal microorganisms swimming in a flow field. Proc. Roy. Soc. B, 231, 47–70.Google Scholar
Pedley, T. J. and Kessler, J. O. 1992. Hydrodynamic phenomena in suspensions of swimming microorganisms. Annu. Rev. Fluid Mech., 24, 313–358.Google Scholar
Pedley, T. J., Brumley, D. R., and Goldstein, R. E. 2016. Squirmers with swirl: A model for Volvox swimming. J. Fluid Mech., 798, 165–186.Google Scholar
Pironneau, O. and Katz, D. F. 1974. Optimal swimming of flagellated microorganisms. J. Fluid Mech., 66, 391–415.Google Scholar
Popel, A. S. and Johnson, P. C. 2005. Microcirculation and hemorheology. Annu. Rev. Fluid Mech., 37, 43–69.Google Scholar
Powers, T. R. 2002. Role of body rotation in bacterial flagellar bundling. Phys. Rev. E, 65, 040903.Google Scholar
Powers, T. R. 2010. Dynamics of filaments and membranes in a viscous fluid. Rev. Mod. Phys., 82, 1607.Google Scholar
Pozrikidis, C. 1992. Boundary Integral and Singularity Methods for Linearized Viscous Flow. Cambridge, UK: Cambridge University Press.Google Scholar
Purcell, E. M. 1997. The efficiency of propulsion by a rotating flagellum. Proc. Natl. Acad. Soc. U.S.A., 94, 11307–11311.Google Scholar
Pushkin, D. O., Shum, H., and Yeomans, J. M. 2013. Fluid transport by individual microswimmers. J. Fluid Mech., 726, 5–25.Google Scholar
Qian, B., Jiang, H., Gagnon, D. A., Breuer, K. S., and Powers, T. R. 2009. Minimal model for synchronization induced by hydrodynamic interactions. Phys. Rev. E, 80, 061919.Google Scholar
Qin, B., Gopinath, A., Yang, J., Gollub, J. P., and Arratia, P. E. 2015. Flagellar kinematics and swimming of algal cells in viscoelastic fluids. Sci. Rep., 5, 9190.Google Scholar
Qiu, T., Lee, T.-C., Mark, A. G., et al. 2014. Swimming by reciprocal motion at low Reynolds number. Nature Comm., 5, 5119.Google Scholar
Quaranta, G., Aubin-Tam, M.-E., and Tam, D. 2015. Hydrodynamics versus intracellular coupling in the synchronization of eukaryotic flagella. Phys. Rev. Lett,, 115, 238101.Google Scholar
Rafai, S., Jibuti, L., and Peyla, P. 2010. Effective viscosity of microswimmer suspensions. Phys. Rev. Lett., 104, 098102.Google Scholar
Ramia, M., Tullock, D. L., and Phan-Thien, N. 1993. The role of hydrodynamic interaction in the locomotion of microorganisms. Biophys. J., 65, 755–778.Google Scholar
Reichert, M. and Stark, H. 2005. Synchronization of rotating helices by hydrodynamic interactions. Eur. Phys. J. E, 17, 493–500.Google Scholar
Reigh, S. Y., Winkler, R. G., and Gompper, G. 2012. Synchronization and bundling of anchored bacterial flagella. Soft Matter, 8, 4363–4372.Google Scholar
Reigh, S. Y., Winkler, R. G., and Gompper, G. 2013. Synchronization, slippage, and un-bundling of driven helical flagella. PloS One, 8, e70868.Google Scholar
Riedel, I. H., Kruse, K., and Howard, J. 2005. A self-organized vortex array of hydrodynamically entrained sperm cells. Science, 309, 300–303.Google Scholar
Riedel-Kruse, I. H., Hilfinger, A., Howard, J., and Jülicher, F. 2007. How molecular motors shape the flagellar beat. HFSP J., 1, 192–208.Google Scholar
Riley, E. E. and Lauga, E. 2014. Enhanced active swimming in viscoelastic fluids. Europhys. Lett., 108, 34003.Google Scholar
Riley, E. E. and Lauga, E. 2015. Small-amplitude swimmers can self-propel faster in viscoelastic fluids. J. Theor. Biol., 382, 345–55.Google Scholar
Riley, E. E., Das, D., and Lauga, E. 2018. Swimming of peritrichous bacteria is enabled by an elastohydrodynamic instability. Sci. Rep., 8, 10728.Google Scholar
Riley, K. F., Hobson, M. P., and Bence, S. J. 1999. Mathematical Methods for Physics and Engineering. Oxford, UK: Oxford University Press.Google Scholar
Rodenborn, B., Chen, C.-H., Swinney, H. L., Liu, B., and Zhang, H. P. 2013. Propulsion of microorganisms by a helical flagellum. Proc. Natl. Acad. Sci. U.S.A., 110, E338–E347.Google Scholar
Romanczuk, P., Bär, M., Ebeling, W., Lindner, B., and Schimansky-Geier, L. 2012. Active Brownian particles. Eur. Phys. J. Spec. Top., 202, 1–162.Google Scholar
Rothschild, L. 1963. Non-random distribution of bull spermatozoa in a drop of sperm suspension. Nature, 198, 1221.Google Scholar
Rusconi, R., Guasto, J. S., and Stocker, R. 2014. Bacterial transport suppressed by fluid shear. Nature Phys., 10, 212–217.Google Scholar
Ryan, S. D., Haines, B. M., Berlyand, L., Ziebert, F., and Aranson, I. S. 2011. Viscosity of bacterial suspensions: Hydrodynamic interactions and self-induced noise. Phys. Rev. E, 83, 050904.Google Scholar
Saintillan, D. and Shelley, M. J. 2007. Orientational order and instabilities in suspensions of self-locomoting rods. Phys. Rev. Lett., 99, 058102.Google Scholar
Saintillan, D. and Shelley, M. J. 2008a. Instabilities and pattern formation in active particle suspensions: Kinetic theory and continuum simulations. Phys. Rev. Lett., 100, 178103.Google Scholar
Saintillan, D. and Shelley, M. J. 2008b. Instabilities, pattern formation, and mixing in active suspensions. Phys. Fluids, 20, 123304.Google Scholar
Saintillan, D. and Shelley, M. J. 2013. Active suspensions and their nonlinear models. C. R. Physique, 14, 497–517.Google Scholar
Sanchez, T., Welch, D., Nicastro, D., and Dogic, Z. 2011. Cilia-like beating of active microtubule bundles. Science, 333, 456–459.Google Scholar
Sandoval, M., Marath, N. K., Subramanian, G., and Lauga, E. 2014. Stochastic dynamics of active swimmers in linear flows. J. Fluid Mech., 742, 50–70.Google Scholar
Saragosti, J., Silberzan, P., and Buguin, A. 2012. Modeling E. coli tumbles by rotational diffusion: Implications for chemotaxis. PloS One, 7, e35412.Google Scholar
Sartori, P., Geyer, V. F., Scholich, A., Jülicher, F., and Howard, J. 2016. Dynamic curvature regulation accounts for the symmetric and asymmetric beats of Chlamydomonas flagella. eLife, 5, e13258.Google Scholar
Sauzade, M., Elfring, G. J., and Lauga, E. 2011. Taylor’s swimming sheet: Analysis and improvement of the perturbation series. Physica D, 240, 1567–1573.Google Scholar
Schamel, D., Mark, A. G., Gibbs, J. G., et al. 2014. Nanopropellers and their actuation in complex viscoelastic media. ACS Nano., 8, 8794–8801.Google Scholar
Schnitzer, O. and Yariv, E. 2015. Osmotic self-propulsion of slender particles. Phys. Fluids, 27, 031701.Google Scholar
Shen, X. N. and Arratia, P. E. 2011. Undulatory swimming in viscoelastic fluids. Phys. Rev. Lett., 106, 208101.Google Scholar
Shiratori, H. and Hamada, H. 2006. The left-right axis in the mouse: From origin to morphology. Development, 133, 2095–2104.Google Scholar
Silverman, M. and Simon, M. 1974. Flagellar rotation and the mechanism of bacterial motility. Nature, 249, 73–74.Google Scholar
Simha, R. A. and Ramaswamy, S. 2002. Hydrodynamic fluctuations and instabilities in ordered suspensions of self-propelled particles. Phys. Rev. Lett., 89, 058101.Google Scholar
Smith, D. J., Blake, J. R., and Gaffney, E. A. 2008. Fluid mechanics of nodal flow due to embryonic primary cilia. J. Roy. Soc. Int., 5, 567–573.Google Scholar
Smith, D. J., Smith, A. A., and Blake, J. R. 2011. Mathematical embryology: The fluid mechanics of nodal cilia. J. Eng. Math., 70, 255–279.Google Scholar
Sokolov, A. and Aranson, I. S. 2009. Reduction of viscosity in suspension of swimming bacteria. Phys. Rev. Lett., 103, 148101.Google Scholar
Sokolov, A. and Aranson, I. S. 2012. Physical properties of collective motion in suspensions of bacteria. Phys. Rev. Lett., 109, 248109.Google Scholar
Sokolov, A., Aranson, I. S., Kessler, J. O., and Goldstein, R. E. 2007. Concentration dependence of the collective dynamics of swimming bacteria. Phys. Rev. Lett., 98, 158102.Google Scholar
Sokolov, A., Apodaca, M. M., Grzybowski, B. A., and Aranson, I. S. 2010. Swimming bacteria power microscopic gears. Proc. Natl. Acad. Sci. U.S.A., 107, 969–974.Google Scholar
Solomentsev, Y. and Anderson, J. L. 1994. Electrophoresis of slender particles. J. Fluid Mech., 279, 197–215.Google Scholar
Son, K., Guasto, J. S., and Stocker, R. 2013. Bacteria can exploit a flagellar buckling instability to change direction. Nature Phys., 9, 494–498.Google Scholar
Soni, G. V., Jaffar Ali, B. M., Hatwalne, Y., and Shivashankar, G. V. 2003. Single particle tracking of correlated bacterial dynamics. Biophys. J., 84, 2634–2637.Google Scholar
Sowa, Y. and Berry, R. M. 2008. Bacterial flagellar motor. Q. Rev. Biophys., 41, 103–132.Google Scholar
Spagnolie, S. E. and Lauga, E. 2010. The optimal elastic flagellum. Phys. Fluids, 22, 031901.Google Scholar
Spagnolie, S. E. and Lauga, E. 2011. Comparative hydrodynamics of bacterial polymorphism. Phys. Rev. Lett., 106, 058103.Google Scholar
Spagnolie, S. E. and Lauga, E. 2012. Hydrodynamics of self-propulsion near a boundary: Predictions and accuracy of far-field approximations. J. Fluid Mech., 700, 105–147.Google Scholar
Spagnolie, S. E., Liu, B., and Powers, T. R. 2013. Locomotion of helical bodies in viscoelastic fluids: Enhanced swimming at large helical amplitudes. Phys. Rev. Lett., 111, 068101.Google Scholar
Spagnolie, S. E., Moreno-Flores, G. R., Bartolo, D., and Lauga, E. 2015. Geometric capture and escape of a microswimmer colliding with an obstacle. Soft Matter, 11, 3396– 3411.Google Scholar
Srigiriraju, S. V. and Powers, T. R. 2005. Continuum model for polymorphism of bacterial flagella. Phys. Rev. Lett., 94, 248101.Google Scholar
Srigiriraju, S. V. and Powers, T. R. 2006. Model for polymorphic transitions in bacterial flagella. Phys. Rev. E, 73, 011902.Google Scholar
Stone, H. A. and Samuel, A. D. T. 1996. Propulsion of microorganisms by surface distortions. Phys. Rev. Lett., 77, 4102–4104.Google Scholar
Subramanian, G. and Koch, D. L. 2009. Critical bacterial concentration for the onset of collective swimming. J. Fluid Mech., 632, 359–400.Google Scholar
Takagi, D., Palacci, J., Braunschweig, A. B., Shelley, M. J., and Zhang, J. 2014. Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft Matter, 10, 1784–1789.Google Scholar
Tam, D. and Hosoi, A. E. 2011. Optimal kinematics and morphologies for spermatozoa. Phys. Rev. E, 83, 045303.Google Scholar
Tamm, S. L. 1972. Ciliary motion in Paramecium: A scanning electron microscope study. J. Cell Biol., 55, 250–255.Google Scholar
Tavaddod, S., Charsooghi, M. A., Abdi, F., Khalesifard, H. R., and Golestanian, R. 2011. Probing passive diffusion of flagellated and deflagellated Escherichia coli. Eur. Phys. J. E, 34, 1–7.Google Scholar
Taylor, G. I. 1951. Analysis of the swimming of microscopic organisms. Proc. Roy. Soc. A, 209, 447–461.Google Scholar
Taylor, G. I. 1952. The action of waving cylindrical tails in propelling microscopic organisms. Proc. Roy. Soc. A, 211, 225–239.Google Scholar
Taylor, G. I. 1967. Low-Reynolds-Number Flows. Cambridge, MA: National Committee for Fluid Mechanics Films.Google Scholar
Taylor, J. R. and Stocker, R. 2012. Trade-offs of chemotactic foraging in turbulent water. Science, 338, 675–679.Google Scholar
Ten Hagen, B., Wittkowski, R., and Löwen, H. 2011. Brownian dynamics of a self-propelled particle in shear flow. Phys. Rev. E, 84, 031105.Google Scholar
Tennekes, H. and Lumley, J. L. 1972. A First Course in Turbulence. Cambridge, MA: The MIT Press.Google Scholar
Teran, J., Fauci, L., and Shelley, M. 2010. Viscoelastic fluid response can increase the speed and efficiency of a free swimmer. Phys. Rev. Lett., 104, 038101.Google Scholar
Thiffeault, J.-L. 2015. Distribution of particle displacements due to swimming microorganisms. Phys, Rev. E, 92, 023023.Google Scholar
Thomas, D., Morgan, D. G., and DeRosier, D. J. 2001. Structures of bacterial flagellar motors from two FliF-FliG gene fusion mutants. J. Bacteriol., 183, 6404–6412.Google Scholar
Thomases, B. and Guy, R. D. 2014. Mechanisms of elastic enhancement and hindrance for finite-length undulatory swimmers in viscoelastic fluids. Phys. Rev. Lett., 113, 098102.Google Scholar
Thutupalli, S., Seemann, R., and Herminghaus, S. 2011. Swarming behavior of simple model squirmers. New J. Phys., 13, 073021.Google Scholar
Toner, J. and Tu, Y. 1998. Flocks, herds, and schools: A quantitative theory of flocking. Phys. Rev. E, 58, 4828.Google Scholar
Tornberg, A. K. and Shelley, M. J. 2004. Simulating the dynamics and interactions of flexible fibers in Stokes flow. J. Comput. Phys., 196, 8–40.Google Scholar
Trevelyan, B. J. and Mason, S. G. 1951. Particle motions in sheared suspensions. I: Rotations. J. Colloid Sci., 6, 354–367.Google Scholar
Triantafyllou, M. S., Triantafyllou, G. S., and Yue, D. K. P. 2000. Hydrodynamics of fish-like swimming. Annu. Rev. Fluid Mech., 32, 33–53.Google Scholar
Trouilloud, R., Yu, T. S., Hosoi, A. E., and Lauga, E. 2008. Soft swimming: Exploiting deformable interfaces for low Reynolds number locomotion. Phys. Rev. Lett., 101, 048102.Google Scholar
Tung, C.-K., Ardon, F., Roy, A., et al. 2015. Emergence of upstream swimming via a hydrodynamic transition. Phys. Rev. Lett., 114, 108102.Google Scholar
Turner, L., Ryu, W. S., and Berg, H. C. 2000. Real-time imaging of fluorescent flagellar filaments. J. Bacteriol., 182, 2793–2801.Google Scholar
Uchida, N. and Golestanian, R. 2011. Generic conditions for hydrodynamic synchronization. Phys. Rev. Lett., 106, 058104.Google Scholar
Vélez-Cordero, J. R. and Lauga, E. 2013. Waving transport and propulsion in a generalized Newtonian fluid. J. Non-Newt. Fluid Mech., 199, 37–50.Google Scholar
Vicsek, T., Czirok, A., Benjacob, E., Cohen, I., and Shochet, O. 1995. Novel type of phase-transition in a system of self-driven particles. Phys. Rev. Lett., 75, 1226–1229.Google Scholar
Vig, D. K. and Wolgemuth, C. W. 2012. Swimming dynamics of the lyme disease spiro-chete. Phys. Rev. Lett., 109, 218104.Google Scholar
Vogel, S. 1988. Life’s Devices: The Physical World of Animals and Plants. Princeton, NJ: Princeton University Press.Google Scholar
Vogel, S. and Calvert, R. A. 1993. Vital Circuits: On Pumps, Pipes, and the Workings of Circulatory Systems. New York, NY: Oxford University Press.Google Scholar
Wan, K. Y. and Goldstein, R. E. 2016. Coordinated beating of algal flagella is mediated by basal coupling. Proc. Natl. Acad. Sci. U.S.A., 113, E2784–E2793.Google Scholar
Was, L. and Lauga, E. 2013. Optimal propulsive flapping in Stokes flows. Bioinsp. Biomim., 9, 016001.Google Scholar
Watari, N. and Larson, R. G. 2010. The hydrodynamics of a run-and-tumble bacterium propelled by polymorphic helical flagella. Biophys. J., 98, 12–17.Google Scholar
Wiggins, C. H. and Goldstein, R. E. 1998. Flexive and propulsive dynamics of elastica at low Reynolds number. Phys. Rev. Lett., 80, 3879–3882.Google Scholar
Williams, C. R., and Bees, M. A. 2011. Photo-gyrotactic bioconvection. J. Fluid Mech., 678, 41–86.Google Scholar
Wollin, C. and Stark, H. 2011. Metachronal waves in a chain of rowers with hydrodynamic interactions. Eur. Phys. J. E, 34, 42.Google Scholar
Woolley, D. M. 2010. Flagellar oscillation: A commentary on proposed mechanisms. Biol. Rev., 85, 453–470.Google Scholar
Woolley, D. M., and Vernon, G. G. 2001. A study of helical and planar waves on sea urchin sperm flagella, with a theory of how they are generated. J. Exp. Biol., 204, 1333–1345.Google Scholar
Woolley, D. M., Crockett, R. F., Groom, W. D. I., and Revell, S. G. 2009. A study of synchronisation between the flagella of bull spermatozoa, with related observations. J. Exp. Biol., 212, 2215–2223.Google Scholar
Wu, X. L. and Libchaber, A. 2000. Particle diffusion in a quasi-two-dimensional bacterial bath. Phys. Rev. Lett., 84, 3017–3020.Google Scholar
Wu, Y., Hosu, B. G., and Berg, H. C. 2011. Microbubbles reveal chiral fluid flows in bacterial swarms. Proc. Natl. Acad. Sci. U.S.A., 108, 4147–4151.Google Scholar
Xie, L., Altindal, T., Chattopadhyay, S., and Wu, X. L. 2011. Bacterial flagellum as a propeller and as a rudder for efficient chemotaxis. Proc. Natl. Acad. Sci. U.S.A., 108, 2246–2251.Google Scholar
Xu, G., Wilson, K. S., Okamoto, R. J., et al. 2016. Flexural rigidity and shear stiffness of flagella estimated from induced bends and counterbends. Biophys. J., 110, 2759– 2768.Google Scholar
Xu, Y.-L. 1996. Fast evaluation of the Gaunt coefficients. Math. Comp., 65, 1601–1612.Google Scholar
Yang, Y., Elgeti, J., and Gompper, G. 2008. Cooperation of sperm in two dimensions: Synchronization, attraction, and aggregation through hydrodynamic interactions. Phys. Rev. E, 78, 061903.Google Scholar
Yosida, K. 1949. Brownian motion on the surface of the 3-sphere. Ann. Math. Stat., 20, 292–296.Google Scholar
Zhang, L., Peyer, K. E., and Nelson, B. J. 2010. Artificial bacterial flagella for microma-nipulation. Lab on a Chip, 10, 2203–2215.Google Scholar
Zhu, L., Do-Quang, M., Lauga, E., and Brandt, L. 2011. Locomotion by tangential deformation in a polymeric fluid. Phys. Rev. E, 83, 011901.Google Scholar
Zhu, L., Lauga, E., and Brandt, L. 2012. Self-propulsion in viscoelastic fluids: Pushers vs. pullers. Phys. Fluids, 24, 051902.Google Scholar
Zhu, L., Lauga, E., and Brandt, L. 2013. Low-Reynolds-number swimming in a capillary tube. J. Fluid Mech., 726, 285–311.Google Scholar
Zhuang, J. and Sitti, M. 2016. Chemotaxis of bio-hybrid multiple bacteria-driven microswimmers. Sci. Rep., 6, 32135.Google Scholar
Zhuang, J., Park, B.-W., and Sitti, M. 2017. Propulsion and chemotaxis in bacteria-driven microswimmers. Adv. Sci., 4, 1700109.Google Scholar
Zöttl, A. and Stark, H. 2012. Nonlinear dynamics of a microswimmer in Poiseuille flow. Phys. Rev. Lett., 108, 218104.Google Scholar
Zöttl, A. and Stark, H. 2013. Periodic and quasiperiodic motion of an elongated microswimmer in Poiseuille flow. Eur. Phys. J. E, 36, 4.Google Scholar
Zöttl, A. and Yeomans, J. M. 2017. Enhanced bacterial swimming speeds in macromolecular polymer solutions. Nature Phys., 15, 554–558.Google Scholar