Goldstein Lab

Teaching

Biological Physics and Complex Fluids (Part III, Michaelmas 2016)

Lecture Schedule (all lectures in MR14 at 11:00-12:00)

• 7-19 October: REG - intro, molecular forces, fluctuations, elasticity
• 21 October - 2 November: EL - viscoelasticity
• 4-16 November: REG - chemical kinetics, patterns
• 18-30 November: EL - phoretic motion, sensing

Lecture notes

Examples Classes

• 1: Wednesday, 26 October, 2016: MR11, CMS: 14:15-16:15
• 2: Monday, 7 November, 2016: MR12, CMS: 14:00-16:00
• 3: Monday, 21 November, 2016: MR12, CMS: 16:15-18:15
• 4: Thursday, 23 January, 2017: MR12, CMS: 14:00-16:00

Examples Sheets

• 2016 Examples Sheet 1
• 2016 Examples Sheet 2
• 2016 Examples Sheet 3 (Answers)
• 2016 Examples Sheet 4

Handouts/Lectures from prior years

• 1415Lecture 1
• 1415Lecture 2
• 1415Lecture 3
• 1415Lecture 4
• 1415Lecture 5
• 1415Lecture 6
• 1415Lecture 7 [Michaelis_Menten.m]
• 1415Lecture 8
• 1415Lecture 9
• 1415Lecture 10 [nonlindiffusion.m] [fisher.m]
• 1415Lecture 11 [Lotka_Volterra.m] [Lotka_Volterra2.m]
• 1415Lecture 12 [FHN.m]

Supplementary Reading

Introductory Reading

• P. Nelson. Biological Physics. W.H. Freeman (2007).
• J.D. Murray. Mathematical Biology I. & II. Springer (2007, 2008).
• K. Dill & S. Bromberg. Molecular Driving Forces. Garland (2009).
• National Committee for Fluid Mechanics Films on "Rheological Behavior of Fluids" and "Low Reynolds Number Flow" [link]
• D.V. Boger & K. Walters, Rheological Phenomena in Focus (1993 Elsevier).

Reading to complement course material

• B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter. Molecular Biology of the Cell. 5th edition. Garland Science (2007).
• J.N. Israelachvili. Intermolecular and Surface Forces. 2nd edition. Academic Press (1992).
• E.J.W. Verwey and J.Th.G. Overbeek. Theory of the Stability of Lyophobic Colloids. Elsevier (1948).
• M. Doi and S.F. Edwards. The Theory of Polymer Dynamics. OUP (1986).
• A. Parsegian. Van der Waals Forces. CUP (2005).
• D. Andelman & W. Poon. Condensed Matter Physics in Molecular and Cell Biology. Taylor & Francis (2006).
• H.C. Berg. Random Walks in Biology. Princeton University Press (1993).
• E. Schrödinger. What is Life? CUP (1992).
• M. Haw. Middle World. Macmillan (2006).
• J.B.S. Haldane: On Being the Right Size

van der Waals forces

• B.R. Holstein, "The van der Waals interaction," Am. J. Phys. 69, 441-449 (2000).
• H.C. Hamaker, "The London-van der Waals attraction between spherical particles," Physica 4, 1058-1072 (1937).
• B.M. Axilrod and E. Teller, "Interaction of the van der Waals type between three atoms," J. Chem. Phys. 11, 299-300 (1943).
• K.K. Mon, N.W. Ashcroft, and G.V. Chester, "Core polarization and the structure of simple metals," Phys. Rev. B 19, 5103-5122 (1979).

DLVO Theory and Charged Membranes

• M. Winterhalter and W. Helfrich, "Effect of surface charge on the curvature elasticity of membranes," J. Phys. Chem. 92, 6865-6867 (1988).
• H.N.W. Lekkerkerker, "Contribution of the electric double layer to the curvature elasticity of charged amphiphilic monolayers," Physica A 159, 319-328 (1989).
• D.J. Mitchell and B.W. Ninham, "Curvature elasticity of charged membranes," Langmuir 5, 1121-1123 (1989).
• R.E. Goldstein, A.I. Pesci, and V. Romero-Rochin, "Electric double layers near modulated surfaces," Phys. Rev. A 41, 5504-5515 (1990).
• B. Duplantier, R.E. Goldstein, V. Romero-Rochin, and A.I. Pesci, "Geometrical and topological aspects of electric double layers near curved surfaces," Phys. Rev. Lett. 65, 508-511 (1990).
• C. Gutsche, U.F. Keyser, K. Kegler, F. Kremer, and P. Linse, "Forces between single pairs of charged colloids in aqueous solutions," Phys. Rev. E 76, 031403 (2007).
  

Hydration Repulsion

• S. Marcelja and N. Radic, "Repulsion of Interfaces due to Boundary Water," Chem. Phys. Lett. 42, 129-130 (1976).
• V.A. Parsegian, N. Fuller, and R.P. Rand "Measured Work of Deformation and Repulsion of Lecithin Bilayers," Proc. Natl. Acad. Sci. USA 76, 2750-2754 (1979).

Manning Condensation

• G.S. Manning, "Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties," J. Chem. Phys. 51, 924-933 (1969).

Brownian Motion

• R. Brown, "A brief account of microscopical observations made in the months of June, July and August, 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies," Phil. Mag. 4, 161-173 (1828).
• A. Einstein, "Investigations on the theory of the Brownian movement," Ann. d. Phys. 17, 549-560 (1905).

Entropic Forces

• M.E. Fisher, "Walls, walks, wetting, and melting," J. Stat. Phys. 34, 667-729 (1984).

Elastohydrodynamics

• K.E. Machin, "Wave propagation along flagella," J. Exp. Biol. 35, 796-806 (1958).
• C.H. Wiggins, D. Riveline, A. Ott, and R.E. Goldstein, "Trapping and wiggling: elastohydrodynamics of driven microfilaments," Biophys. J. 74, 1043-1060 (1998).
• C. Levinthal and H.R. Crane, "On the Unwinding of DNA," Proc. Natl. Acad. Sci. (USA) 42, 436-438 (1956).
• C.W. Wolgemuth, T.R. Powers, and R.E. Goldstein, "Twirling and Whirling: Viscous Dynamics of Rotating Elastic Filaments," Phys. Rev. Lett. 84, 1623-1626 (2000).
• R.E. Goldstein, T.R. Powers, and C.H. Wiggins, "Viscous Nonlinear Dynamics of Twist and Writhe," Phys. Rev. Lett. 80, 5232-5235 (1998).

Buckling Filaments

• M. Elbaum, D.K. Fygenson, and A. Libchaber, "Buckling Microtubules in Vesicles," Phys. Rev. Lett. 76, 4078-4081 (1996).
• D.K. Fygenson, J.F. Marko, and A. Libchaber, "Mechanics of Microtubule-Based Membrane Extension," Phys. Rev. Lett. 79, 4497-4500 (1997).

Chemoreception

• H.C. Berg and E.M. Purcell, "Physics of chemoreception," Biophys. J. 20, 193-219 (1977).

Pattern Formation

Reviews

• M.C. Cross and P.C. Hohenberg, "Pattern formation outside of equilibrium," Rev. Mod. Phys. 65, 851-1112 (1993).
• W. van Saarloos, "Front propagation into unstable states," Phys. Rep. 386, 29-222 (2003).

Research Papers

• A.M. Turing, "The chemical basis of morphogenesis," Phil. Trans. Roy. Soc. 237, 37-72 (1952).
• Q. Ouyang and H.L. Swinney, "Transition from a uniform state to hexagonal and striped turing patterns," Nature 352, 610-612 (1991).
• K.J. Lee, W.D. McCormick, Q. Ouyang, and H.L. Swinney, "Pattern formation by interacting chemical fronts," Science 261, 192-194 (1993).
• R.E.Goldstein, D.M. Petrich, and D.J. Muraki, "Interface proliferation and the growth of labyrinths in a reaction-diffusion system," Phys. Rev. E 53, 3933-3957 (1996).

Action Potentials

• A.L. Hodgkin and A.F. Huxley, "A Quantitative Description of Membrane Current and its Application to Conduction and Excitation in Nerve," J. Physiol. 117, 500-544 (1952).
• A.L. Hodgkin and A.F. Huxley, "Propagation of Electrical Signals Along Giant Nerve Fibres," Proc. Roy. Soc. Lond. B 140, 177-183 (1952).

Non-Newtonian Flows

• R. B. Bird, C. F. Curtiss, R. C. Armstrong, and O. Hassager, Dynamics of Polymeric Liquids, Vol.~1: Fluid Mechanics, 2nd ed, Wiley (1987).
• R. B. Bird and J. M. Wiest. Constitutive Equations for Polymeric Liquids. Annu. Rev. Fluid Mech. vol. 27 (1995).
• R. G. Larson. The Structure and Rheology of Complex Fluids, OUP (1999).
• F. A. Morrison. Understanding Rheology, OUP (2001).

Phoretic Motion

• J. L. Anderson. Colloid transport by interfacial forces. Annu. Rev. Fluid Mech., vol 21, 1989.

Swimming of Individual Organisms

• G. Taylor, "Analysis of the Swimming of Microscopic Organisms", Proc. R. Soc. Lond. A 209, 447-461 (1951).