Unit 1: Models of Action Potential Generation and Neural Circuits

D. W. Tank, Depts. of Molecular Biology and Physics
J. J. Hopfield , Dept. of Molecular Biology

David Tank's Power Point slides (converted to pdf format) - note that although David gave four lectures, the slides are all contained in these three files.
David Tank's Slides #1 (pdf)
David Tank's Slides #2 (pdf)
David Tank's Slides #3 (pdf)

Date
Topic
Readings


9/13
   Overview of nervous system organization and electrochemical signaling in neurons (Tank)  Purves et al, Neuroscience, 2nd edition, Chapters 1,2, Reserve MOL508
9/18
    The Hodgkin/Huxley model of the action potential (Tank)  
  • 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. The Croonian Lecture: Ionic Movements and Electrical Activity in Giant Nerve Fibres, Proceedings of the Royal Society of London, Series B, Biological Sciences, 148(930):1-37 (1958).
  • D. Johnston and S. M-S. Wu. Foundations of Cellular Neurophysiology, Chapter 6, Reserve APC591
    • 9/20
    		   Generalization of Hodgkin/Huxley and simplified models of spiking neurons (Tank)  
    9/25
    		   Neural circuit models of persistent neural activity and short term memory (Tank)  
  • H. S. Seung, D. D. Lee, B. Y. Reis, and D. W. Tank. Stability of the Memory of Eye Position in a Recurrent Network of Conductance-Based Model Neurons. Neuron 26:259-271 (2000).
  • H. S. Seung, D. D. Lee, B. Y. Reis, and D. W. Tank. The autapse: a simple illustration of short-term analog memory storage by tuned synaptic feedback. Journal of Computational Neuroscience 9:171-85 (2000).
  • E. Aksay, G. Gamkrelidze, H. S. Seung, R. Baker, and D. W. Tank. In vivo intracellular recording and perturbation of persistent activity in a neural integrator. Nature Neuroscience 4:184- 93 (2001).
    • 9/27
    		   Neural computation through action potential synchrony (Hopfield)  
  • J. J. Hopfield and C. Brody. What is a moment? "Cortical" sensory integration over a brief interval. Proc Natl Acad Sci USA. 97(25):13919-24 (2000).
  • J. J. Hopfield and C. Brody. What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration. Proc Natl Acad Sci USA. 98(3):1282-7 (2001).
  • W. Singer. Neuronal synchrony: a versatile code for the definition of relations? Neuron 24:49-65 (1999).
  • M. N. Shadlen and J. A. Movshon. Synchrony unbound: A critical evaluation of the temporal binding hypothesis. Neuron 24:67-77 (1999).
    • 10/2
    		  Neural computation through action potential synchrony, continued (Hopfield)  

    Unit 2: Biological Pattern Formation

    E. C. Cox , Dept. of Molecular Biology
    S. Y. Shvartsman, Dept. of Chemical Engineering

    Ted Cox's Power Point slides (converted to pdf format)
    Ted Cox's Slides #1 (pdf)
    Ted Cox's Slides #2 (pdf)
    Ted Cox's Slides #3 (pdf)
    Stas Shvartsman's Lecture Notes
    Stas Shvartsman's Notes #1 (pdf)
    Stas Shvartsman's Notes #2 (pdf)
    Date
    Topic
    Readings
    10/4
    		    How bacteria find their food  
  • H. C. Berg and D. A. Brown. (1972) Chemotaxis in E. coli analyzed by three-dimensional tracking. Nature 239:500-504.
  • R. M. Macnab and D. E. Koshland Jr. (1972) The gradient-sensing mechanism in bacterial chemotaxis. Proc Natl Acad Sci USA 69:2509-2512
  • D. A. Brown and H. C. Berg.(1974) Temporal stimulation of chemotaxis in Escherichia coli. Proc Natl Acad Sci USA 71:1388-1392
  • G. L. Hazelbauer, R. E. Mesibov, and J. Adler. (1969) Escherichia coli mutants defective in chemotaxis toward specific chemicals. Proc Natl Acad Sci USA 64:1300-1307
  • S. M. Block and H. C. Berg. (1984) Successive incorporation of force-generating units in the bacterial rotary motor. Nature 1984 309:470-472
  • General reference: H. C. Berg, Random Walks in Biology, Princeton University Press, 1983, Reserve APC591
    • 10/9
    		   Order from disorder in the cellular slime modes  
  • R. H. Kessin, Dictyostelium: evolution, cell biology, and the development of multicellularity, Cambridge University Press, 2001, Chapters 1 and 2. Reserve APC591
  • E. Palsson, K. J. Lee, R. E. Goldstein, J. Franke, R. H. Kessin, and E. C. Cox. (1997) Selection for spiral waves in the social amoebae Dictyostelium. Proc. Natl. Acad. Sci. USA 94:13719-13723
  • K. L. Lee, R. E. Golstein, and E. C. Cox. (2001) Resetting wave forms in Dictyostelium territories. Phys. Rev. Letters 87:068101
  • G. Byrne and E. C. Cox. (1987) Genesis of a spatial pattern in the cellular slime mold Polysphondylium pallidum. Proc. Natl. Acad. Sci. USA 84:4140-4144
    • 10/11
    		  Random walks and diffusion of molecules and microorganisms  
  • G. H. Weiss, Aspects and applications of the random walk, Reserve APC591
  • E. F. Keller and L. A. Segel. A model for chemotaxis, J. Theor. Biol., 30(2):225, 1971
  • H. G. Othmer, S. R. Dunbar, and W. Alt. Models of dispersal in biological systems. J. Math. Biol. 26(3):263-298, 1988
    • 10/16
    		   Modeling the cAMP relay system in the slime molds  
  • J. L. Martiel and A. Goldbeter. A model based on receptor desensitization for cyclic-AMP signaling in Dictyostelium cells. Biophys. J. 52(5):807-828, 1987.
  • A. Goldbeter, Biochemical oscillations and cellular rhythms, Reserve APC591
  • M. Schmitzer. Theory of continuum random walks and application to chemotaxis., Phys. Rev. E 48:2553-2568, 1993.
  • M. A. Rivero, R. T. Tranquillo, H. M. Buettner, and D. A. Lauffenburger, Transport models for chemotactic cell populations based on individual cell behavior, Chemical Engineering Science, 44(12):2881-2897, 1989.
    • 10/18
    		   The importance of being spiral  
    10/23
    		  Random walks and feedback loops in models for slime mold aggregation  

    Unit 3: Dynamics of Disease

    S. A. Levin , Dept. of Ecology and Evolutionary Biology
    M. A. Nowak , Program in Theoretical Biology , Institute for Advanced Study
    J. G. Dushoff, Dept. of Ecology and Evolutionary Biology

    Martin Nowak's Power Point Slides (converted to pdf format)
    Martin Nowak's Slides #1 (pdf)
    Martin Nowak's Slides #2 (pdf)
    Martin Nowak's Slides #3 (pdf)
    Date
    Topic
    Readings

    10/25
    		   Introduction to the dynamics of disease (Levin)  
  • R. M. May, ``Population Biology of Microparasitic Infections'', pp.405-442 of Mathematical Ecology, ed. Hallam and Levin, Reserve APC591
  • M. A. Nowak and R. M. May, Virus Dynamics, Oxford University Press, 2000, Reserve ASPC591, EEB524
  • Perelson and Weisbuch, Immunology for Physicists , Rev. Mod. Physics, 69:1219--1267, 1997
  • Chapter 7 and first part of Chapter 8 of Mathematical Models in Population Biology and Epidemiology by F. Brauer and C. Castillo-Chavez; ( errata )
    • 10/30, 11/1
    		    FALL RECESS  
    11/6
    		  Virus dynamics I (Nowak)  
    11/8
    		   Virus dynamics II (Nowak)  
    11/13
    		   Influenza dynamics and vaccination strategies (Levin)  
    11/15
    		  Influenza dynamics (Dushoff)  
    11/20
    		   Influenza dynamics, continued (Dushoff)  
    11/23
    		    THANKSGIVING RECESS  

    Unit 4: Intracellular Networks

    W. S. Bialek, Dept. of Physics

    Bill Bialek's Notes
    Bill Bialek's Notes #1 (pdf)

    Date
    Topic
    Readings
    11/27
    		   What are we trying to explain?  
  • Single photon detection by rod cells of the retina. F Rieke & DA Baylor, Revs. Mod. Phys. 70:1027-1036 (1998).
  • Gain and kinetics of activation in the G-protein cascade of phototransduction. TD Lamb, Proc. Nat'l. Acad. Sci. (USA) 93:566-570 (1996).
  • Molecular origin of continuous dark noise in rod photoreceptors. F Rieke & DA Baylor, Biophys J., 71:2553-2572 (1996).
  • Origin of reproducibility in the responses of retinal rods to single photons, F Rieke & DA Baylor, Biophys J. 75:1836-1857 (1998).
  • The gain of rod phototransduction: reconciliation of biochemical and electrophysiological measurements. IB Leskov, VA Klenchin, JW Handy, GG Whitlock, VI Govardovskii, MD Bownds, TD Lamb TD, EN Pugh Jr & VY Arshavsky, Neuron 27:525-537 (2000).
  • Engineering aspects of enzymatic signal transduction: photoreceptors in the retina. PB Detwiler, S Ramanathan, A Sengupta & BI Shraiman, Biophys J. 79:2801-2817 (2000).
    • 11/29
    		   Building blocks  
    12/4
    		  Bacterial chemotactic behavior  
  • Physics of chemoreception. HC Berg & EM Purcell, Biophys. J. 20:193--219 (1977)
  • Impulse responses in bacterial chemotaxis. SM Block, JE Segall & HC Berg, Cell 31:215-226 (1982).
  • Adaptation kinetics in bacterial chemotaxis. SM Block, JE Segall & HC Berg, J. Bacteriol. 154:312-323 (1983).
  • Temporal comparisons in bacterial chemotaxis. JE Segall, SM Block & HC Berg, Proc. Nat'l. Acad. Sci. (USA) 83:8987-8981 (1986).
  • Robustness in simple biochemical networks. N Barkai & S Leibler, Nature 387:913-917 (1997).
  • Robustness in bacterial chemotaxis. U Alon, MG Surette, N Barkai & S Leibler, Nature 397:168-171 (1999).
  • Activity-Dependent Regulation of Conductances in Model Neurons. G LeMasson, E Marder & LF Abbott, Science 259:1915-1917 (1993).
  • Chemotactic responses of Escherichia coli to small jumps of photoreleased L-aspartate. R Jasuja, J Keyoung, GP Reid, DR Trentham & S Khan, Biophys. J. 76:1706-1719 (1999).
  • Response tuning in bacterial chemotaxis. R Jasuja, Y Lin, DR Trentham & S Khan, Proc. Nat'l. Acad. Sci. (USA) 96:11346-11351 (1999).
  • Heightened sensitivity of a lattice of membrane receptors. TA Duke & D Bray, Proc. Nat. Acad. Sci. (USA) 96:10104-10108 (1999).
  • An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells. P Cluzel, M Surette & S Leibler, Science 287:1652-1655 (2000).
    • 12/6
    		   Networks for chemotactic computation  
    12/11
    		   Counting photons and molecules  
    12/13
    		   Switches, oscillators and (maybe) state machines  
  • Regulation of brain type II Ca^{2+}/calmodulin--dependent protein kinase by autophosphorylation: A Ca^{2+}-triggered molecular switch. SG Miller and MB Kennedy, Cell 44:861--870 (1986).
  • A mechanism for memory storage insensitive to molecular turnover: A bistable autophosphorylating kinase. JE Lisman, Proc. Nat. Acad. Sci. (USA) 82:3055-3057 (1985).
  • Feasibility of long-term storage of graded information by the Ca^{2+}/calmodulin-dependent protein kinase molecules of the postsynaptic density. JE Lisman and MA Goldring, Proc. Nat. Acad. Sci. (USA) 85:5320--5324 (1988).
  • A Genetic Switch: Phage lambda and Higher Organisms, 2nd Edition. M. Ptashne (Blackwell, Cambridge MA, 1992). Reserve APC591
  • Stochastic mechanisms in gene expression. HH McAdams & A Arkin. Proc. Nat'l. Acad. Sci. (USA) 94:814-819 (1997).
  • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. A Arkin, J Ross & HH McAdams Genetics 149:1633--1648 (1998).
  • Stability and noise in biochemical switches. W Bialek, in Advances in Neural Information Processing 13, TK Leen, TG Dietterich & V Tresp, eds., pp. 103--109 (MIT Press, Cambridge, 2001). cond-mat/0005235.
  • Stability Puzzles in Phage Lambda. E Aurell, S Brown, J Johanson, & K Sneppen, cond-mat/0010286.
  • Epigenetics as a first exit problem. E Aurell & K Sneppen, cond-mat/0103080.