David Kleinfeld Laboratory at UC San Diego: Physics 171/271

Physics 171/271

Physics 173/
BGGN 266


	Physics 171/271
		Course overview The objective of this course is to provide the biophysical basis for neuronal function. We provide an analytical path from basic physical processes, such as electrodiffusion, to equations for the dynamics of single cells, and then on to two forms of network activity, each of which involves models wher the description of a neuron is reduced to a single state-variable. The first involves networks of weakly coupled neuronal oscillators in which each neuron is described by the phase in its limit cycle. These networks provide a natural means to discuss collective dynamics, such as oscillations and waves in networks of inhibitory neurons. The second form of network activity involves recurrent circuits of asynchronous neurons in which each neuron is descibed by its Poisson firing rate. These provide a natural means to discuss associative memories and attractor-based computational circuits for sensory processing and motor control. Aspects of applied mathematics and experimental procedures are discussed as needed.
		Tentative lecture plan for Fall 2009 7130 Urey Hall; 8:00 to 9:20 AM on Tues and Thurs 24 Sept - Action potentials: How the brain codes sensation and drives motion Guest lecture by Dr. Tatyana Sharpee (Salk) 29 Sept - Nernst, Johnson/Nyquist and Boltzmann: Scales of batteries, noise, and thresholds Notes (4.8Mb PDF) 1 Oct - Diffusion and compartmentalization Notes (3.4Mb PDF) Homework Set #1 (due 13 Oct) Handout (0.1Mb PDF) 6 Oct - Cables: Attenuation, filtering and dendritic integration Notes (2.3Mb PDF) London and Häusser reprint (0.8Mb PDF) Magee reprint (0.9Mb PDF) 6 Oct - Matlab tutorial Solve a simple first order differential equation numerically and compare against the analytic solution Code (0.1Mb m). Solve the diffusion equation numerically and compare against the analytic solution Code (0.1Mb m). Guest lecture by Mr. Jeffrey Moore 8 Oct - Subthreshold voltage gain Notes (2.0Mb PDF) 13 Oct - Conductance equations: Action potentials Notes (2.6Mb PDF) 15 Oct - Channels as the basis of membrane currents Guest lecture by Prof. Herbert Levine 20 Oct - Synaptic channels and cell-to-cell communication Guest lecture by Prof. Herbert Levine 22 Oct - Conductance equations: Subthreshold oscillations in thalamic relay cells Steriade, McCormick and Sejnowski reprint (1.7Mb PDF) 27 Oct - Reduction to two-dimensions: Hopf bifurcations and front propagation Notes (1.1Mb PDF) 29 Oct - Reduction to one-dimension: Phase coupled oscillators Notes (1.6Mb PDF) 3 Nov - Networks of phase coupled neuronal oscillators Ermentrout and Kleinfeld reprint (1.0Mb PDF) 5 Nov - Organization of the mammalian nervous system Barbas notes (1.7Mb PDF) 10 Nov - Rate-based descriptions of networks: Reverse correlation, principle components, etc. Notes (0.2Mb PDF) Golomb, Kleinfeld, Reid, Shapley and Shraiman reprint (4.9Mb PDF) 12 Nov - Sensory transduction approximated by a linear filter Notes (5.5Mb PDF) 17 Nov - Feedforward networks: Perceptrons and more Serre, Oliva and Poggio reprint (0.9Mb PDF) 19 Nov - Rate-based recurrent networks: Basis for associative memory Notes abstracted from Hertz, Krogh and Palmer (1.2Mb PDF) Notes on absence of multistability in linear recurrent networks (0.1 Mb PDF) Notes on storage capacity in associative networks for perfect recall (0.1 Mb PDF) 24 Nov - Derivation of rate equations from single-cell conductance equations Notes (0.1 Mb PDF) 1 Dec - Line attractors: Precision feedback in recurrent networks for motor control Seung reprint (0.5Mb PDF) Figures from Tank laboratory (1.6Mb PDF) 3 Dec - The ring model: Sharpening of weak inputs by recurrent networks Ben-Yishai, Hansel and Sompolinsky reprint (0.3Mb PDF) Shapley and Sompolinsky reprint (1.1Mb PDF) Lecture notes - 2006 3050B York Hall; 2:00 to 3:20 PM; Tues/Thurs 21 Sept - Nernst potentials and Johnson noise: Voltage scales for single cells; Notes (0.3Mb PDF) Figures (6.1Mb PDF) 26 Sept - Phenomenology of action potentials and synaptic transmission (Flavio Frohlich) Notes (1.6Mb PDF) 28 Sept - Boltzman factors, voltage gating, and Nernst-Plank; Notes (264kb PDF) 3 Oct - Subthreshold gain voltage gating; Notes (2.4Mb PDF) 5 Oct - The ionic basis of action potentials; Notes (2.6Mb PDF) 10 Oct - Two-time scale models and Hopf bifurcations to spiking; Notes (1.2Mb PDF) 12 Oct - Three-time scale models of neurons and subthreshold oscillations (Maxim Bazhenov); Notes (0.48Mb PDF) 17 Oct - Kuromoto’s phase reduction for interacting neuronal oscillators; Notes (1.6Mb PDF) 19 Oct - Ca2+ currents and bursts of action potentials (Maxim Bazhenov); Notes (0.43Mb PDF) 24 Oct - Ermentrout’s analysis of networks of phase oscillators; Publication (966kB PDF) 26 Oct - When rate not time matters: Linear analysis of stimulus/response; Notes (1.6Mb PDF) Figures (5.6Mb PDF) 31 Oct - Phenomenology and circuit equations for recurrent networks; Notes (1.3Mb PDF) 2 Nov - Averaging and Sompolinsky’s reduction of conductance to rate equations; Notes (0.1Mb PDF) 7 Nov - Recurrent networks with fixed attractors and the associative memory model of Hopfield Notes (0.1Mb PDF) 9 Nov - Precision feedback in recurrent networks and the line-attractor model for motor control; Publication (0.5Mb PDF) Figures (1.6Mb PDF) 14 Nov - Amplification of weak inputs in recurrent networks and the ring model for sensory processing; Publication (0.3Mb PDF) Publication (1.1Mb PDF) 16 Nov - Excess variability and balanced inputs to attractor networks 21 Nov - Diffusion, cables, and chemical and electrical front propagation 28 Nov - Ca2+ concentration dynamics in spatially extended cells (Flavio Frohlich); Notes (0.4Mb PDF) 30 Nov - Intracellular [Ca2+] gradients for cell-based memory Lecture Notes - 2005 Topic #1: Ions, Membranes, Noise Levels, and Scales of Voltage Lecture Handout (4.8Mb PDF) Topic #2: Diffusion and Chemical Compartmentalization Lecture Handout (3.3Mb PDF) Topic #3: Electrodiffusion: Gauss Meets Boltzman Lecture handout (264kb PDF) Note #3A: Cables: Electrotonic Length, Attenuation and Filtering Lecture Handout (2.0Mb PDF) Topic #4: Subthreshold Gain Lecture Handout (2.4Mb PDF) Topic #5: Action Potentials: Conductance Equations Lecture Handout (2.6Mb PDF) Topic #6: Action Potentials: Reduction to Phase Space Lecture Handout (1.2Mb PDF) Note #6A: Spiking Behavior with Hopf versus Saddle-node Bifurcations in preparation Topic #7: Networks of Phase Coupled Neuronal Oscillators Lecture Handout (1.6Mb PDF) Ermentrout and Kleinfeld reprint (966kB PDF) Topic #8: Rate-based Recurrent Networks: Basis for Associative Memory Lecture Handout - Abstracted from Hertz, Krogh and Palmer (1.2Mb PDF) Note #8A: Absence of Multistability in Linear Recurrent Networks Lecture Handout (40kb PDF) Note #8B: Storage Capacity in Associative Networks for (Near) Perfect Recall Lecture Handout (44kb PDF) Topic #9: Derivation of Rate Equations from Single-cell Conductance Equations Lecture Handout (100Kb PDF) Topic #10: Applications of Recurrent Networks Kleinfeld and Sompolinsky reprint (1.3MB PDF) Ben-Yishai, Lev Bar-Or and Sompolinsky reprint (1.1MB PDF) Lecture Notes - 2000, 2002 and 2004 Topic #1: Ions and Voltages Lecture Notes (310kb PDF) Figures (6,233kb PDF) Topic #2: Spikes and Reliability Lecture Notes (270kb PDF) Figures (5,604kb PDF) Topic #3: Diffusive Dynamics Lecture Notes (334kb PDF) Figures (3,553kb PDF) Topic #4: Electrodiffusion: Gauss Meets Boltzman Lecture Notes (288kb PDF) Figures (509kb PDF) Topic #5: Cables Lecture Notes (302kb PDF) Figures (4,040kb PDF) Topic #6: Compartments and Subthreshold Gain Lecture Notes (262kb PDF) Figures (3,568kb PDF) Topic #7: Action Potentials: Cole's Impedance Measurements Lecture Notes (173kb PDF) Figures (2,887kb PDF) Topic #8: Action Potentials: Hodgkin, Huxley, Kirchoff and Boltzman Lecture Notes (318kb PDF) Figures (1,205kb PDF) Reprint (5,3416kb PDF) Topic #9: Extracellular Signals and Spike Sorting Lecture Notes (162kb PDF) Figures (13,766kb PDF) Topic #10: Action Potentials: Brutal Approximations and the Phase Plane Lecture Notes (319kb PDF) Figures (2,404kb PDF) IDL Code (61kb PDF) Topic #11: Synaptic Dynamics Figures (1,430kb PDF) Topic #12: Phase Coupled Neuronal Oscillators Lecture Notes (288kb PDF) Figures (19,347kb PDF) Reprint (966kB PDF)




	Date Modified: 10/2009	David Kleinfeld, PhD Physics Department UC San Diego dk@physics.ucsd.edu