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Goldstein Lab
Teaching
DAMTP Summer School on Fluid Dynamics of Sustainability and the Environment
Supplementary Reading (Biological Physics)
The following is a collection of primary references for the main topics of the Summer School lectures.
General reviews
- T.J. Pedley and J.O. Kessler, "Hydrodynamic Phenomena
in Suspensions of Swimming Microorganisms", Annu. Rev. Fluid Mech. 24, 313-358 (1992).
- E. Lauga and T.R. Powers, "The Hydrodynamics
of Swimming Microorganisms", Rep. Prog. Phys. 72, 096601 (2009).
- S. Ramaswamy, "The Mechanics and Statistics
of Active Matter", Annu. Rev. Cond. Matt. Phys. 1, 323-345 (2010).
- T.R. Powers, "Dynamics of Filaments and Membranes
in a Viscous Fluid", Rev. Mod. Phys. 82, 1607-1631 (2010).
- R. Golestanian, J.M. Yeomans, and N. Uchida,
"Hydrodynamic Synchronization at Low Reynolds Number," Soft Matter 7, 3074-3082 (2011).
- D.L. Koch and G. Subramanian, "Collective
Hydrodynamics of Swimming Microorganisms: Living Fluids," Annu. Rev. Fluid Mech. 43,
637-659 (2011).
- E. Lauga and R.E. Goldstein, "Dance of the
Microswimmers", Physics Today 65, 30-35 (2012).
Swimming of Individual Organisms
- G. Taylor, "Analysis of the Swimming of
Microscopic Organisms", Proc. R. Soc. Lond. A 209, 447-461 (1951).
- M.J. Lighthill, "On the Squirming Motion of
Nearly Spherical Deformable Bodies through Liquids at Very Small Reynolds Numbers",
Comm. Pure Appl. Math. 5, 109-118 (1951).
- K.E. Machin,
"Wave Propagation Along Flagella", J. Exp. Biol.
35, 796-806 (1958).
- H.A. Stone and A.D.T. Samuel, "Propulsion of
Microorganisms by Surface Distortions", Phys. Rev. Lett. 77, 4102-4104 (1996).
- C.H. Wiggins and R.E. Goldstein,
"Flexive and Propulsive Dynamics of
Elastica at Low Reynolds Number", Phys. Rev. Lett. 80, 3879-3882 (1998).
- S. Camalet, F. Jülicher, and J. Prost,
"Self-Organized Beating and Swimming of
Internally Driven Filaments", Phys. Rev. Lett. 82, 1590-1593 (1999).
- T.S. Yu, E. Lauga, and A.I. Hosoi,
"Experimental Investigations of Elastic Tail
Propulsion at low Reynolds Number", Phys. Fluids 18, 091701 (2006).
- K. Drescher, R.E. Goldstein, N. Michel, M. Polin,
and I. Tuval, "Direct Measurement of the Flow Field Around
Swimming Microorganisms", Phys. Rev. Lett. 105, 168101 (2010).
- J.S. Guasto, K.A. Johnson, and
J.P. Gollub, "Oscillatory Flow Induced by Microorganisms
Swimming in Two Dimensions", Phys. Rev. Lett. 105, 168102 (2010).
- K. Drescher, R.E. Goldstein, and I. Tuval,
"Fidelity of Adaptive Phototaxis", Proc. Natl. Acad. Sci. USA 107, 11171-11176 (2010).
- K. Drescher, J. Dünkel, L.H. Cisneros, S. Ganguly,
and R.E. Goldstein, "Fluid Dynamics and Noise in Bacterial Cell-Cell and Cell-Surface Scattering",
Proc. Natl. Acad. Sci. USA 108, 10940-10945 (2011).
Flagellar Synchronization
- M. Kim, J.C. Bird, A.J. Van Parys, K.S. Breuer, and
T.R. Powers, "A Macroscopic Scale Model of Bacterial Flagellar Bundling",
Proc. Natl. Acad. Sci. USA 100, 15481-15485 (2003).
- M. Kim and T.R. Powers, "Hydrodynamic Interactions
Between Rotating Helices," Phys. Rev. E 69, 061910 (2004).
- M. Reichert and H. Stark, "Synchronization of
Rotating Helices by Hydrodynamic Interactions," Eur. Phys. J. 17, 493-500 (2005).
- T. Niedermayer, B. Eckhardt, and P. Lenz,
"Synchronization, phase locking, and metachronal wave formation in ciliary chains," Chaos
18, 037128 (2008).
- B. Qian, H. Jiang, D.A. Gagnon, K.S. Breuer, and
T.R. Powers, "Minimal model for synchronization induced by hydrodynamic interactions,"
Phys. Rev. E 80, 061919 (2009).
- M. Polin, I. Tuval, K. Drescher, J.P. Gollub, and
R.E. Goldstein, "Chlamydomonas Swims with Two `Gears' in a Eukaryotic Version of
Run-and-Tumble Locomotion", Science 325, 487-490 (2009).
- R.E. Goldstein, I. Tuval, and M. Polin, "Noise
and Synchronization in Pairs of Beating Eukaryotic Flagella", Phys. Rev. Lett. 103,
168103 (2009).
- N. Uchida and R. Golestanian,
"Synchronization and Collective Dynamics in a Carpet of Microfluidic Rotors," Phys. Rev. Lett.
104, 178103 ().
- R.E. Goldstein, I. Tuval, and M. Polin,
"Emergence of Synchronized Beating During the Regrowth of Eukaryotic Flagella",
Phys. Rev. Lett. 107, 148103 (2011).
- N. Uchida and R. Golestanian, "Generic
Conditions for Hydrodynamic Synchronization," Phys. Rev. Lett. 106, 058104 (2011).
Swimmers and Transport
- A. Acrivos and T.D. Taylor, "Heat and Mass Transfer From
Single Spheres in Stokes Flow," Phys. Fluids 5, 387-394 (1962).
- H.C. Berg and E.M. Purcell, "Physics of chemoreception,"
Biophys. J. 20, 193-219 (1977).
- V. Magar, T. Goto, and T.J. Pedley, "Nutrient Uptake
by a Self-Propelled Steady Squirmer," Q. J. Mech. Appl. Math. 56, 65-91 (2003).
- M.B. Short, C.A. Solari, S. Ganguly, T.R. Powers,
J.O. Kessler, and R.E. Goldstein, "Flows Driven by Flagella of Multicellular Organisms Enhance
Long-Range Molecular Transport," Proc. Natl. Acad. Sci. USA 103, 8315-8319 (2006).
Collective Behaviour
- S. Childress, M. Levandowsky, and
E.A. Spiegel, "Pattern Formation in a Suspension of Swimming Micro-organisms: Equations and
Stability Theory," J. Fluid Mech. 63, 591-613 (1975).
- A.J. Hillesdon, T.J. Pedley, and
J.O. Kessler, "The Development of Concentration Gradients in a Suspension of Chemotactic Bacteria,"
Bull. Math. Bio. 57, 299-344 (1995).
- X.-L. Wu and A. Libchaber, "Particle Diffusion in a
Quasi-Two-Dimensional Bacterial Bath," Phys. Rev. Lett. 84, 3017-3020 (2000).
- R.A. Simha and S. Ramaswamy, "Hydrodynamic
Fluctuations and Instabilities in Ordered Suspensions," Phys. Rev. Lett. 89,
058101 (2002).
- Y. Hatwalne, S. Ramaswamy, M. Rao, and R.A. Simha,
"Rheology of Active-Particle Suspensions," Phys. Rev. Lett. 92, 118101.
- C. Dombrowski, L. Cisneros, S. Chatkaew,
R.E. Goldstein, and J.O. Kessler, "Self-Concentration and Large-Scale Coherence in Bacterial Dynamics,"
Phys. Rev. Lett. 93, 098103 (2004).
- J.P. Hernandez-Ortiz, C.G. Stoltz, and
M.D. Graham, "Transport and Collective Dynamics in Suspensions of Confined Swimming Particles ,"
Phys. Rev. Lett. 95, 204501 (2005).
- I. Tuval, L. Cisneros, C. Dombrowski, C.W. Wolgemuth,
J.O. Kessler, and R.E. Goldstein, "Bacterial Swimming and Oxygen Transport Near Contact Lines,"
Proc. Natl. Acad. Sci. USA 102, 2272-2282 (2005).
- D. Saintillan and M.J. Shelley,
"Orientational Orer and Instabilities in Suspensions of Self-Locomoting Rods,"
Phys. Rev. Lett. 99, 058102 (2007).
- D. Saintillan and M.J. Shelley,
"Instabilities and Pattern Formation in Active Particle Suspensions: Kinetic Theory and
Continuum Simulations",
Phys. Rev. Lett. 100, 178103 (2008).
- K.C. Leptos, J.S. Guasto, J.P. Gollub, A.I. Pesci,
and R.E. Goldstein, "Dynamics of Enhanced Tracer Diffusion in Suspensions of Swimming
Eukaryotic Microorganisms", Phys. Rev. Lett. 103, 198103 (2009).
- I. Rushkin, V. Kantsler, and Raymond E.
Goldstein, "Fluid Velocity Fluctuations in a Suspension of Swimming Protists",
Phys. Rev. Lett. 105, 188101 (2010).
- H. Kurtuldu, J.S. Guasto, K.A. Johnson,
and J.P. Gollub, "Enhancement of Biomixing by Swimming Algal Cells in Two-Dimensional Films",
Proc. Natl. Acad. Sci. USA 108 10391-10395 (2011).
Cytoplasmic Streaming and Related Phenomena
- T. Shimmen, "The Sliding Theory of Cytoplasmic
Streaming: Fifty Years of Progress", J. Plant Res. 120, 31-43 (2007).
- E.A. Nothnagel and W.W. WEbb,
"Hydrodynamic Models of Viscous Coupling Between Motile Myosin and Endoplasm in
Characean Algae", J. Cell Biol. 94, 444-454 (1982).
- P.W. Hochachka, "The metabolic implications of
intracellular circulation", Proc. Natl. Acad. Sci. USA 96, 12233-12239 (1999).
- W.F. Pickard, "The Role of Cytoplasmic Streaming
in Symplastic Transport", Plant Cell Env. 26, 1-15 (2003).
- W.F. Pickard, "Absorption by a Moving Spherical
Organelle in a Heterogeneous Cytoplasm: Implications for the Role of Trafficking in a
Symplast", J. Theor. Biol. 240, 288-301 (2006).
- R.E. Goldstein, I. Tuval, and
J.-W. van de Meent, "Microfluidics of Cytoplasmic Streaming and its Implications for
Intracellular Transport", Proc. Natl. Acad. Sci. USA 105, 3663-3667 (2008).
- J.-W. van de Meent, I. Tuval,
and R.E. Goldstein, "Nature's Microfluidic Transporter: Rotational Cytoplasmic Streaming at
High Péclet Numbers", Phys. Rev. Lett. 101, 178102 (2008).
- J.-W. van de Meent, A.J. Sederman, L.F. Gladden,
and R.E. Goldstein, "Measurement of Cytoplasmic Streaming in Single Plant Cells by
Magnetic Resonance Velocimetry", J. Fluid Mech. 642, 5-14 (2010).
- Y.-N. Young and M.J. Shelley,
"Stretch-Coil Transition and Transport of Fibers in Cellular Flows",
Phys. Rev. Lett. 99, 058303 (2007).
- V. Kantsler and R.E. Goldstein,
"Fluctuations, Dynamics, and the Stretch-Coil Transition of Single Actin Filaments in
Extensional Flows", Phys. Rev. Lett. 108, 038103 (2012).
- C. Vèzy, G. Massiera, and A. Viallat,
"Adhesion Induced Non-Planar and Asynchronous Flow of a Giant Vesicle Membrane in an External Shear Flow",
Soft Matter 3, 844-851 (2007).
- F.G. Woodhouse and R.E. Goldstein,
"Shear-Driven Circulation Patterns in Lipid Membrane Vesicles", J. Fluid Mech. 705, 165-175 (2012).
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