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)
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