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ECE498-ECENeuroScience-S21

ECE-498NS Weekly Schedule Spring 2021

Part I: Lectures, Reading assignments + videos: Calendar Weeks 4-6: Video Index I
WeekMWF
4L1: Read: \(\ \S \) 1.1 (Preface: pp vii-x; Ch 1: History pp 1-8)
360 Lec 1 (Starts @6:00 mins)
L2: Read: \( \S \) 1.2 (p. 8-11)
360 Lec 2 (Starts @14:00 mins)
L3: Read: \( \S \) 1.3 (p. 11-19)
360 Lec 3
5L4: Read:Scott Ch. 12, \( \S \) 12.1 (p. 293-298); 360 Lec 4
Assignment: NS1: Due by Lec 11; (NS1.pdf, Gscope, Solution: (NS1-sol.pdf); Network Postulates.pdf)
L5: Read: 2.1, .2 (p. 25-31, 189, 208) Generic neurons (Fig. 2.1) Neuron, Body
360 Lec 5 (Starts @2:15m)
L6: Read: 2.2.2-.3 (p. 31-35) Nonlinear Diffusion lines
360 Lec 6
6L7: Read: \(\S\) 2.3 (p. 35-40) Synapses & Gap junction
360 Lec 7 (@1:00m)
L8: Read: \(\S\) 10-.1.2 AI models: (pp. 233-241), Neural Boolean Hilbert-space analysis;
360 Lec 8 (Starts (@4:00 m); 360 (??open to public??)
L9: Read: \(\S\) 10.2 (p. 241-248),
360-open Lec 9 (@0:37m)
L/WDDateDaily lectures
    Part I: Introduction and History
1/4M1/25L1: Introduction to Neuroscience for engineers; von Helmholtz; History; Dynamics of a Nerve Impulse, Spikes and their propagation:
Thermodynamic models are critical in neuroscience, models
2W1/27L2: The structure of a nerve cell Neuron, Body
DNA and Genetics, Quanta Magazine articles
3F1/29L3: Organization of the brain; Numbers and density of neurons in the human brain;
McCullochPitts.43.pdf; AI and brain waves;
4/5M2/1L4: The Hierarchical Nature of Brain Dynamics; Integration of the 5 main sensory inputs;
Brain fumction and integration Orexin & the Theory of weight gain/loss
Assignment: NS1: Matlab homework on the diffusion and wave equations. Due by Lec 11; (pdf), Postulates
For a discussion of the solution method look at Book; \(\S\) 4.8.3 (pp. 143-147). A detailed example is discussed on pages 149-151;
5W2/3L5: The generic neuron; Σ-∆ codec, png
6F2/5L6: Nonlinear diffusion model General solution (Green's function method): Green's function method;
Transmission line (ABCD) method: Examples; Solving simple differential equations
7/6M2/8L7: Chemical synapse, gap junction, Neuron, Body, types of Neurotransmitters
8W2/10L8: McCulloch-Pitts (MP) AI neuron (model), \(\S\) 10.1.1-.2: (pp. 235-241) Boolean Hilbert space;
(M-P model; pdf); How do AI models work?)
9F2/12L9: Deep-learning concepts: STFT and fast convolution; ConvNetJS discussion, Sejnowski.20.pdf
Assignment: NS2 (pdf, sol), Gscope, Due by Lec 14
Part II: Lectures, Reading assignments + videos: Calendar Weeks 6-11
WeekMWF
7L10: Read: \( \S \) 3, 3.1 (p. 49-53) 360 Lec10
Holiday --No Class--
L11: Read: \( \S \) 3.2 (p. 53-55) Solution: (NS1-sol.pdf) 360 Lec 11
8L12: Read: \( \S \) 3.3 (p. 56-57) 360 Lec 12 (@1:25 min)
L13: Read: \( \S \) 3.3.3 (p. 58-60) 360 Lec 13 (Starts @ 2:30 12:19--13:19)
L14: ''Read: \( \S \) 3.4 (p. 60-63) Membrane models 360 Lec 14 (@1:30); NS2 due
9L15: Exam I
L16: Read: \( \S \) 3.5 (p. 63-65) Na & K pumps and Nernst potentials 360 Lec16 (@3:00)
L17: Read: \( \S \) 4.1, (p. 67-69) 360 Lec 17
10L18: Read: \( \S \) 4.1-4.2 (p. 70-74) 360 Lec 18
L19: Read: \( \S \) 4.3 (p. 74-77)
L20: Read: \( \S \) 4.4, 4.5 (p. 77-80) Lec 20 (@2:20)
11L21: Read: \( \S \) 3.4, 4.5.2, 4.6, (p. 80-87) Figs 4.5-4.8 360 L21
L22: Read: \(\S\) 4.7 Matlab similink 2-Diode model, 360 (Topic\(_1\) @0:50, Topic\(_2\) @36:40, T\(3\) @39:00); NS3 due
L23: Exam II
L/WDDateDaily lectures
    Part II: Structure of a Neuron
10/7M2/15L10: Lipid bilayers and their electro/mechanical properties Lipid bilayers, Transport mechanisms, Fun with bubbles, AI and protein folding
--W2/17 University Holiday; No Class
11F2/19L11: Electrochemical properties of membranes;Hill functions in Biology hemoglobum and oxyen transport
Assignment: NS1 due, Solution: (NS1-sol.pdf)
12/8M2/22L12: Transmembrane currents; channel types; Calculating partial pressures
13W2/24L13: Einstein's relation (1905-III) and the derivation Four 1905 papers (@ Princeton.edu), Basic Solutions, Numerical solutions
14F2/26L14: Membrane two-diode (min/max) models; NS2 Due;
15/9M3/1L15: --NO CLASS-- Exam I: 8--11 AM Rm. 2017 ECEB
16W3/3L16: Ionic currents (conduction, diffusion currents), electrochemistry
Assignment: NS3 pdf, Due by Lec 22 NS3 Solution
17F3/5L17: Nernst, Plank and Einstein relations; Membrane models Resting potentials and pumps
18/10M3/8L18: Ch. 4, Hodgkin-Huxley model; Current analysis Ion distribution during a spike HH matlab model; Helmholtz measures velocity of spikes, Neural oscillators, Adrian and nerve pulses
19W3/10L19: Squid Voltage patch clamp; first neural recording from toade eye (1928)
20F3/12L20: The nonlinear diffusion line and why it acts as a delay line, Diode circuit model, output from circuit model
21/11M3/15L21: Critical point in nonlinear diffusion (cable) equation Muscle dynamics, Neurological disorders, Guillain-Barre syndrom, Demylination disorders; Talk on neural regeneration Jan 25, NSP
22W3/17L22: Topic 1: Diode model of spike propagation: Code for Matlab Simlink simulaton of diode model:To run: type '>>open hhmodel_V1.slx; LT spice model from William Walters (HW6 4/6/21)
Leading edge models: Chap. 5, p. 95;
Krebs cycle as the energy source;Alternative topic Bernoulli trials: 1) Examples, 2) bias and odds ratio, 3) What is the bias? 4) How to measure it?
NS3 due, NS3 Solution
23F3/19L23: Exam II
Part III: Lectures, Reading assignments + videos: Calendar Weeks 12-18
WeekMWF
12L24: Read: \(\S\) Chaps 5&6; \(\S\) 9.1 (187-199, Fig. 9.1)--9.2 (201-204);
Chaps. 5 & 6: @3:00m; 9--9.2: @33:40m
Holiday --No Class--L25: Read: Spike Velocity on myelinated nerves; \(\S\) 9.3 (206-213), 9.4 (217-220);
360 Lec 25 @2:25; topic II: @38:25
13L26: 360 Lec 26 (@1);
Read: \( \S \) 11-.3 (258-274)
L27: (360 L27 @3:00);
Read: \( \S \) 9.2, 9.3 (199-207), 11.5-11.8 (277-282)
L28: (360 L28 A(@0:48); B(@11:30); \(\bf noise\) @35:00)
Read: \( \S \) 10-10.1.1 (233-237), 11-11.2 (256-265)
14L29: 360 L29 (@0)
Read: \( \S \) 9.3.2, 10.1.2, 11.3: Dendritic Boolean logic
L30: 360 L30 (A @0): Tesla Valve: linear diode,
(B @15:15): Brain Anatomy (pdf); cortex anatomyRead: \( \S \) 10.2.2 (241-248)
L31: L31 360 (@4:25),
Continued: Brain Anatomy (pdf);Read: \( \S \) 9.3, 10.3 (248-252)
15L32: Lec32 360 (@0:25)
L33: Lec 33-360: role of the thalamus
L34: The manufacturing of protein manufacturing via DNA and RNA
16L35: L35-360 S21: The eyes and ears (@3:15m)
L36: L36-360 S21: Hearing (@1:00),
L37: L37-360: Cochlear Transduction
17L38: Cochlear nonlinear processing (@2min), NL Cochlear processing (pdf), Ashmore Lecture
L39: Read: \( \S \) 8.0-8.3 (165-169)); Sensory systems; Vrius, Crisper (360 S21: Audio starts @ 22m)
L40: 360 S21 (@1m) AI's furure, AI darkside; Conscious;
Short term memory
18L41: Guest Lecture: Prof Mark HJ on training AI (@55 sec);; 360 with bad audio
L42: Guest Lecture 360 S21Assignment: NS7 Due
First day of Exams
L/WDDateDaily Lectures
    Part III: Neuronal Assemblies
24/12M3/22L24: Dendritic trees; Information processing; search the brain, Neural comutation-I, Neural computation-II
Assignment: Due by Lec 28; (NS4.pdf; NS4-sol.pdf)
--W3/24 University Holiday --NO Class--
25F3/26L25: Branching; Tapered Fibers; Dendritic information processing and logic (Ch 9; State machines); mitrohcondrial membrane; BackProbTraining
26/13M3/29L26: Early Evidence for Cell Assemblies (Hebb)
27W3/31L27: Branching rules in dendrites (Ch 9); Cell assemblies: Recent Evidence; gap junction disorders,
proteins; EM micrographs
28F4/2L28:Psychophysics of sound; Associative Network;
Information processing; circuit1, circuit2, SigmaDelta, Role of vital signs
Assignment: NS5, Due on L32 (pdf, NS5-sol); NS4 Due
29/14M4/5L29: Dendritic Boolean logic;Generalized scalar products (Allen book \( \S \) 3.5.1, Fig 3.4);
Basic brain anatomy (pdf)
30W4/7L30: Models of Brain Anatomy (Dynamics I-II) Senses of Orientation; HH-Model; Allen Inst Brain Atlas; Allen Inst Home Page; Start @ 6 min;
Lung alternatives;, Where does thirst come from? The Chinese room argument
31F4/9L31: A:Brain Anatomy; B:Field Theories for the Neocortex \(\S 9.3\); Diode model V0, Similink model V1, Similink output V1
32/15M4/12L32:Hyppocampus and memory; Fine-tuning the HH model to work off the onset of the pulse Neurosurgry of the brain; Mental images; Induced love between mice Limbic System
Assignment: NS6 due on Lec 37 (pdf); NS5 Due
33W4/14L33: The makeup of a virus: vurlient DNA, What is a virus;
Switching attention in the brain: Central manimpulation of DNA to enhance memory Michael Halassa: Thalamic Switching, Michael Halassa: Talk @ Allen Inst;
Jeremy Nathans: A complex speech task explained'; Fungi that explodes ants
34F4/16L34: Ch 5: Attention DNA information processing video, comments, RNA information processing video
35/16M4/19L35: Topics on hearing: Introduction to speech and hearing science
electronic odor (smell) sensors
36W4/21L36: Topics on hearing: the cochlea;
Allen, J. B. (1977) "Two-dimensional cochlear fluid model: New results"; J. Acoust. Soc. Am., 61 (1) pp 110-119 How does the cochlea work?; How does the Organ of Corti work? (Organ of corti Transduction);
37F4/23L37: Auditory systems: the organ of Corti, hair cell function, Allen (1980) "Cochlear micromechanics: A physical model of transduction"; (pdf)
Mouse auditory brain map, How we can see with our ears., An example of neural auditiory signal processing
38/17M4/26L38: Topics on hearing:Fahey and Allen (1985) "Nonlinear phenomena as observed in the ear canal and the auditory nerve"; JASA
39W4/28L39: Virus, bactaeria, antibodies, bacteriophages, organoids and CRISPER (phage, Parasites, Organoids, CRISPER, Significance (Start at 29:30)), Calcium and short term memory
40F4/30L40: Lecture: Modern AI and its future; youtube Elon Musk views on AI (long); Chris Koch on conscious (@11:30);
41/18M5/3L41: Mark Hasagawa-Johnson Guest lecture: AI methods
Assignment: NS6 Due (matlab code that implements equations due)
42W5/5L42: Guest Lecture: Vikor Gruev. Title: Wearable Bio-Inspired Imaging System for Image Guided Surgery

L/WDDate 
-/18W5/5 Instruction Ends
-/18R5/6 Reading Day
-/18F5/14 Final Exam 8-11 AM; (Official Schedule)

 ||- || F || 5/?? ||  Backup: Exam III 7:00-10:00+ PM on HW1-HW11atest>><<

L= Lecture #
T= Topic #
W=week of the year, starting from Jan 1
D=day: T is Tue, W Wed, R Thur, S Sat, etc.
Each exam (I, II and Final paper) will count as 30% of your final grade, while the Assignments (NS1-DE3) plus class participation (Prof's Discussion), count for 10%. Please return the final paper by the end of the exam period.


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