Goldstein Lab

Teaching

Soft Matter & Biological Physics (Part III, Michaelmas 2014)

PRELIMINARY Lecture notes

• Lecture Notes

Examples Classes

• 1: Thursday, 23 October, 2014: MR14, Centre for Mathematical Sciences (CMS): 16:30-18:00
• 2: Thursday, 6 November, 2014: MR14, Centre for Mathematical Sciences (CMS): 16:30-18:00
• 3: Thursday, 27 November, 2014: MR14, Centre for Mathematical Sciences (CMS): 16:30-18:00
• 4 (physics): Tuesday, 2 December, 2014: Small Lecture Theatre, Cavendish Laboratory: 16:30-18:00
• 4 (math): Thursday, 15 January, 2015: MR14, Centre for Mathematical Sciences (CMS): 16:30-18:00

Examples Sheets

• 2014/15 Examples Sheet 1: (Answers)
• 2014/15 Examples Sheet 2: (Answers)
• 2014/15 Examples Sheet 3: (Answers)
• 2014/15 Examples Sheet 4: (Answers)

Handouts/Lectures

• 1415Lecture 1 (10/10/14)
• 1415Lecture 2 (13/10/14)
• 1415Lecture 3 (15/10/14)
• 1415Lecture 4 (17/10/14)
• 1415Lecture 5 (20/10/14)
• 1415Lecture 6 (22/10/14)
• 1415Lecture 7 (24/10/14) [Michaelis_Menten.m]
• 1415Lecture 8 (27/10/14)
• 1415Lecture 9 (29/10/14)
• 1415Lecture 10 (31/10/14) [nonlindiffusion.m] [fisher.m]
• 1415Lecture 11 (03/11/14) [Lotka_Volterra.m] [Lotka_Volterra2.m]
• 1415Lecture 12 (05/11/14) [FHN.m]
• Keyser Lectures I (ufk)
• Keyser Lectures II (ufk)

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).

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. Riveling, 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).

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).

Optical Tweezers

Books

Reviews

• K.C. Neuman and S.M. Block, "Optical Trapping", Rev. Sci. Instr. 75, 2787-2809 (2004)
• F. Gittes and C.F. Schmidt, "Signals and Noise in Micromechanical Measurements", Methods in Cell Biology 55, 129-156 (1998)
• C. Bustamante, Z. Bryant, and S.B. Smith, "Ten Years of Tension: Single Molecule DNA mechanics", Nature 421, 423-427 (2003)
• A. Ashkin, "Optical trapping and manipulation of neutral particles using lasers", Proc. Natl. Acad. Sci. USA 94, 4853-4860 (1997)

Research Papers

• C. Bustamante, Y.R. Chemla, N.R. Forde, and D. Izhaky, "Mechanical Processes in Biochemistry", Annu. Rev. Biochem. 73, 705-748 (2004)
• U.F. Keyser, J. van der Does, C. Dekker, and N.H. Dekker, "Optical tweezers for force measurements on DNA in nanopores", Rev. Sci. Instr. 77, 105105 (2006)
• O. Otto, F. Dzerwinski, J.L. Gornall, G. Stober, L.B. Oddershede, R. Seidel, and U.F. Keyser, "Real-time Particle Tracking at 10,000 fps using Optical Fiber Illumination", Optics Express 18, 22722-22733 (2010)
• E.J.G. Peterman, F. Gittes, and C.F. Schmidt, "Laser-induced Heating in Optical Traps", Biophys. J. 84, 1308-1316 (2003)

Links

• The Padgett group in Glasgow has many movies about optical tweezers: link
• More on microscopy can be found at the Olympus website: link
• Even more from Nikon, with nice Java applets: link
• Optical tweezers TETRIS: link

Magnetic Tweezers and Supercoiled DNA

Research papers

• C. Gosse and V. Croquette, "Magnetic Tweezers: Micromanipulation and Force Measurements at the Molecular Level", Biophys. J. 82, 3314-3329 (2002)
• A. Crut, D.A. Koster, R. Seidel, C.H. Wiggins, and N.H. Dekker, "Fast dynamics of supercoiled DNA revealed by single-molecule experiments", Proc. Natl. Acad. Sci. USA 104, 11957-11962 PNAS (2007)
• D.A. Koster, V. Croquette, C. Dekker, S. Shuman, and N.H. Dekker, "Friction and torque govern the relaxation of DNA supercoils by e ukaryotic topoisomerase IB", Nature 434, 671-674 (2005)
• D.A. Koster, K. Palle, E.S.M. Bot, M.-A. Bjornsti, and N.H. Dekker, "Antitumour drugs impede DNA uncoiling by topoisomerase I", Nature 448, 213-217 (2007)
• J.F. Allemand, D. Bensimon, R. Lavery, and V. Croquette, "Stretched and overwound DNA forms a Pauling-like structure with exposed bases", Proc. Natl. Acad. Sci. USA 95, 14152-14157 (1998)

DNA, Force-extension, FJC, ...

Books

Research papers

• M.D. Wang, H. Yin, R. Landick, J. Gelles, and S.M. Block, "Stretching DNA with Optical Tweezers", Biophys. J. 72, 1335-1346 (1997)
• C. Bouchiat, M.D. Wang, J.-F. Allemand, T. Strick, S.M. Block, and V. Croquette, "Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements", Biophys. J. 76, 409-413 (1999)
• C.G. Baumann, S.B. Smith, V.A. Bloomfield, and C. Bustamante, "Ionic effects on the elasticity of single DNA molecules", Proc. Natl. Acad. Sci. USA 94, 6185-6190 (1997)

Atomic Force Microscopy

Review

• C. Bustamante and C. Rivetti, "Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope", >i>Ann. Rev. Biophys. Biomol. Struct. 25, 395-429 (1996)

Research Papers

• A. Engel and D.J. Müller, "Observing single biomolecules at work with the atomic force microscope", Nature Struct. Biol. 7, 715-718 (2000)
• H.G. Hansma, J. Vesenka, C. Siegerist, G. Kelderman, H. Morrett, R.E. Sinsheimer, V. Elings, C. Bustamante, and P.K. Hansma, "Reproducible Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic ForceMicroscope", Science 256, 1180-1184 (1992)
• D.J. Müller and A.Engel, "Atomic force microscopy and spectroscopy of native membrane proteins", Nature Protocols 2, 2191-2197 (2007)
• F. Moreno-Herrero, M. de Jager, N.H. Dekker, R. Kanaar, C. Wyman, and C. Dekker, "Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon binding DNA", Nature 437, 440-443 (2005)

Proteins, Folding and Unfolding

Books

Research Papers

• P.E. Leopold, M. Montal, and J.N. Onuchic, "Protein folding funnels, A kinetic approach to the sequence-structure relationship", Proc. Natl. Acad. Sci. USA 89, 8721-8725 (1992)
• M. Rief, M. Gautel, F. Oesterhelt, J.M. Fernandez, and H.E. Gaub, "Reversible Unfolding of Individual Titin Domains by AFM", Science 276, 1109-1112 (1997)
• R. Zwanzig, A. Szabo, and B. Bagchi "Levinthal's paradox", Proc. Natl. Acad. Sci. USA 89, 20-22 (1992)

(Colloid) Electrophoresis/Electrokinetic phenomena

Reviews

• A.V. Delgado, F. González-Caballero, R.J. Hunter, L.K. Koopal, and J. Lyklema, "Measurement and interpretation of electrokinetic phenomena", J. Coll. Interface Sci. 309, 194-224 (2007)

Research papers

• O. Otto, C. Gutsche, F. Kremer, and U.F. Keyser, "Optical tweezers with 2.5 kHz bandwidth video detection for single-colloid electrophoresis", Rev. Sci. Instr. 79, 023710 (2008)
• I. Semenov, O. Otto, G. Stober, P. Papadopoulos, U.F. Keyser, and F. Kremer, "Single colloid electrophoresis", J. Coll. Interface Sci. 337, 260-264 (2009)

Links

• Santiago Lab at Stanford for imaging of flows in channels: link

Entropic Trapping

Research papers

• S.W.P. Turner, M. Cabodi, and H.G. Craighead, "Confinement-Induced Entropic Recoil of Single DNA Molecules in a Nanofluidic Structure", Phys. Rev. Lett. 88, 128103 (2002)
• L. Liu, P. Li, and S.A. Asher, "Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel", Nature 397, 141-144 (1999)
• J.T. Del Bonis-O'Donnell, W. Reisner, and D. Stein, "Pressure-driven DNA transport across an artificial nantopography", New Journal of Physics 11, 075032 (2009)

(Gel) Electrophoresis

Books

Reviews

• J.-L. Viovy, "Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms", Rev. Mod. Phys. 72, 813-872 (2000)
• B.H. Zimm and S.D. Levene, "Problems and prospects in the theory of gel electrophoresis of DNA", Quart. Rev. Biophys. 25, 171-204 (1992)

Nanopores

Books

Reviews

• U.F. Keyser, S. van Dorp, and S.G. Lemay, "Tether forces in DNA electrophoresis", Chem. Soc. Rev. 39, 939-947 (2010)
• C. Dekker, "Solid-state Nanopores", Nature Nanotech. 2, 209-215 (2007)

Research papers

• J.J. Kasianowicz, E. Brandin, D. Branton, and D.W. Deamer, "Characterization of individual polynucleotide molecules using a membrane channel", Proc. Natl. Acad. Sci. USA 93, 13770-13773 (1996)
• J. Li, D. Stein, C. McMullan, D. Branton, M.J. Aziz, and J.A. Golovchenko, "Ion-beam sculpting at nanometre length scales", Nature 412, 166-169 (2001)
• J. Li, M. Gershow, D. Stein, E. Brandin, and J.A. Golovchenko, "DNA molecules and configurations in a solidstate nanopore microscope", Nature Mat. 2, 611-615 (2003)
• A.J. Storm, C. Storm, J. Chen, H. Zandbergen, J.-F. Joanny, and C. Dekker, "Fast DNA Translocation through a Solid-State Nanopore", Nano Letters 5, 1193-1197 (2005) pdf
• R.M.M. Smeets, U.F. Keyser, D. Krapf, M.-Y. Wu, N.H. Dekker, and C. Dekker, "Salt dependence of ion transport and DNA translocation through solid-state nanopores", Nano Letters 6, 89-95 (2006)
• U.F. Keyser, B.N. Koeleman, S. van Dorp, D. Krapf, R.M.M. Smeets, S.G. lemay, N.H. Dekker, and C. Dekker, "Direct force measurements on DNA in a solid-state nanopore", Nature Phys. 2, 473-477 (2006)
• S. van Dorp, U.F. Keyser, N.H. Dekker, C. Dekker, and S.G. Lemay, "Origin of the electrophoretic force on DNA in solid-state nanopores", Nature Phys. 5, 347-351 (2009)
• S. Garaj, W. Hubbard, A. Reina, J. Kong, D. Branton, and J.A. Golovchenko, "Graphene as a subnanometre trans-electrode membrane", Nature 467, 190-193 (2010)
• J.E. Hall, "Resistance of a small circular pore", J. Gen. Physiol. 66, 531-532 (1975)

Membranes and Membrane Proteins

Books

Reviews

• H.C. Berg, "The Rotary Motor of Bacterial Flagella", Annu. Rev. Biochem. 72, 19-54 (2003)

Research Papers

• C.V. Gabel and H.C. Berg, "The speed of the flagellar rotary motor of Escherichia coli varies linearly with protonmotive force", Proc. Natl. Acad. Sci. USA 100, 8748-8751 (2003)
• H.C. Berg and L. Turner, "Torque Generated by the Flagellar Motor of Escherichia coli", Biophys. J. 65, 2201-2216 (1993)