Miscellaneous handouts
Below are a handouts that are useful for the course. I'll post them as the course goes on.
- Course syllabus
- Images of a Drosophila embryo for homework 1
- A table of physical quantities and their dimensions
- A tutorial on how to use SciPy's odeint to solve systems of ODEs
- A short primer on linear stability analysis
- G. I. Taylor's discussion and demos on low Reynolds number fluid mechanics (There are some sound synching issues.)
- A calculation of the storage and loss moduli of a Maxwell material
Slides shown in lecture
Almost all of the lecture material is done on the chalk board, but I occasionally show slides with useful images. For your reference, you can download all of the slides shown during lectures.
- L1: browser-based presentation, slides pdf
- L2: slides
- L3: slides
- L4: slides
- L5: slides
- L6: slides
- L7: slides
- L8: slides
- L9: entirely chalk talk
- L10: entirely chalk talk
- L11: had slides, but were repeats of L1 slides (pdf)
- L12: slides
- L13: browser-based presentation, slides pdf
- L14: entirely chalk talk
- L15: browser-based presentation, slides pdf
- L16: browser-based presentation, slides pdf
- L17: browser-based presentation, slides pdf
- L18: browser-based presentation, slides pdf
- L19: slides
- L20: browser-based presentation, slides pdf
Papers mentioned in lecture
I often mention papers during lectures. Some I mention in passing, while others we dwell on for quite some time. Below are PDFs of most of the papers I have mentioned in lecture (excluding the ones that are part of the required reading). Ones with a (*) are of greatest interest.
- L1 (*): J. Sedzinski, et al., Polar actomyosin contractility destabilizes the position of the cytokinetic furrow, Nature, 476, 462-466, 2011
- L1 (*): K. J. Polach and J. Widom, Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation, J. Mol. Biol., 254, 130-149, 1995
- L1: K. J. Polach and J. Widom, A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites, J. Mol. Biol., 258, 800-812, 1996
- L1: H Schiessel, The physics of chromatin, J. Phys.: Condens. Matter, 15, R699-R774, 2003
- L1: O. Campàs, et al., Scaling and shear transformations capture beak shape variation in Darwin’s finches, PNAS, 107, 3356-3360, 2010
- L1: T. D. Pollard, et al., Actin dynamics, J. Cell. Sci., 113, 3, 2001
- L3 (*): K. Visscher, et al., Single kinesin molecules studied with a molecular force clamp, Nature, 400, 184-189, 1999
- L3 (*): J. Howard, et al., Turing’s next steps: the mechanochemical basis of morphogenesis, Nature Rev. Mol. Cell. Biol., 12, 392-398, 2011
- L4 (*): R. Phillips and S. R. Quake, The biological frontier of physics, Phys. Today, 59, 38-43, 2006
- L4: E. T. Jaynes, Information theory and statistical mechanics, Phys. Rev., 106, 620-630, 1957
- L4: C. E. Shannon, A mathematical theory of communication, Bell Sys. Tech. J., 17, 379-423, 1948
- L8 (*): T. S. Gardner, C. R. Cantor, and J. J. Collins, Construction of a genetic toggle switch in Escherichia coli, Nature, 403, 339-342, 2000
- L8: J. M. G. Vilar, C. C. Guet, and S. Leibler, Modeling network dynamics: the lac operon, a case study, J. Cell Biol., 161, 471-476, 2003
- L11 (*): S. B. Smith, L. Finzi, and C. Bustamante, Direct mechanical measurements of the elasticity of single DNA molecules using magnetic beads Science, 258, 1122-1126, 1992
- L11 (*): Entropic elasticity of λ-phage DNA, Science, 265, 1599-1600, 1994. Note: this short note in a way corrects the previous paper in that it uses the WLC to model the force-extension.
- L13: D. Saintillan and M. J. Shelley, Instabilities, pattern formation, and mixing in active suspensions, Phys. Fluids, 20, 123304, 2008
- L13: V. Schaller, et al., Polar patterns of driven filaments, Nature, 467, 73-77, 2010
- L13: T. Sanchez, et al., Spontaneous motion in hierarchically assembled active matter, Nature, 491, 431-434, 2012
- L14: T. D. Pollard, Rate Constants for the Reactions of ATP- and ADP-Actin with the Ends of Actin Filaments, J. Cell. Biol., 103, 2747-2754, 1986
- L14: B. M. Friedrich, et al., Sarcomeric Pattern Formation by Actin Cluster Coalescence PLoS Comput. Biol., 8, e1002544, 2012
- L16 (*): V. Varga, et al., Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner, Nature Cell Biol., 8, 957-962, 2006
- L16 (*): V. Varga, et al., Kinesin-8 motors act cooperatively to mediate length-dependent microtubule depolymerization, Cell, 138, 1174-1183, 2009
- L16 (*): R. E. Goldstein, et al., Microfluidics of cytoplasmic streaming and its implications for intracellular transport, PNAS, 105, 3663-3667, 2008
- L16 (*): S. Ganguly, et al., Cytoplasmic streaming in Drosophila oocytes varies with kinesin activity and correlates with the microtubule cytoskeleton architecture PNAS, 109, 15109-15114, 2012
- L16: T. M. Svitkina and G. G. Borisy, Arp2/3 complex and actin depolymerizing factor/cofilin in dendritic organization and treadmilling of actin filament array in lamellipodia, J. Cell Biol., 145, 1009-1026, 1999
- L16: R. M. Parton, et al., A PAR-1-dependent orientation gradient of dynamic microtubules directs posterior cargo transport in the Drosophila oocyte J. Cell Biol., 194, 121-135, 2011
- L16: S. Mische, et al., Direct observation of regulated ribonucleoprotein transport across the nurse cell/oocyte boundary Molec. Biol. Cell, 18, 2254-2263, 2007
- L17 (*): M. Mayer, et al., Anisotropies in cortical tension reveal the physical basis of polarizing cortical flows Nature, 467, 617-621, 2010
- L17: N. W. Goehring, et al., Polarization of PAR proteins by advective triggering of a pattern-forming system Science, 334, 1137-1141, 2011
- L17: M. Behrndt, et al., Forces driving epithelial spreading in zebrafish gastrulation, Science, 338, 256-260, 2012
- L17: P. J. Keller, et al., Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy Science, 322, 1065-1029, 2008
- L18 (*): S. Grill, et al., The distribution of active force generators controls mitotic spindle position, Science, 201, 518-521, 2003
- L18: J. Pecreaux, et al., Spindle oscillations during asymmetric cell division require a threshold number of active cortical force generators Curr. Biol., 16, 2111-2122, 2006