Last Modified : Thu, 08 Sep 22
ECE498-ECENeuroScience-S21
- Neural circuits and systems (NE-410/ECE-410: Neuroscience for Engineers: Science of Brain function)
- Syllabus: Syllabus; Schedule: 498-NS, ECE 498NS: CRN 70830: Scroll down to 498-NS; UIUC Spring 2021,
Official Calendar
- Time: 10:00-10:50 AM; 3017 ECEB, Neural Circuits and Systems;**Join Zoom Meeting zoom link
- Office hrs: Friday 11-12 via zoom; or on request.
- ICES forms; \(\S\)Class Text: Neuroscience: A mathematical primer (Scott, 2002) abridged-pdf-@Apr5.21; unabridged-pdf;
\(\S\)Allen math text: An Invitation to Mathematical Physics; pdf;
\(\S\) Membrane Models of red blood cells Evans & Skalak, Supplement material: Abbott & Dayan (pdf); Layman-level articles of interest
**Basic Brain Facts
**Independent research (senior thesis), ISUR
- Instructor: Prof. Jont Allen (netID jontalle; Office 3062ECEB); Tuesday 2PM Location: Zoom
- For public access to all lectures, click here
- Today's schedule here; Final Exam information: Apr 14, 8-11 AM; Gradescope
- Videos: Video Index S21
ECE-498NS Weekly Schedule Spring 2021
| Part I: Lectures, Reading assignments + videos: Calendar Weeks 4-6: Video Index I | |||
|---|---|---|---|
| Week | M | W | F |
| 4 | L1: 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 |
| 5 | L4: 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 |
| 6 | L7: 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/W | D | Date | Daily lectures |
|---|---|---|---|
| Part I: Introduction and History | |||
| 1/4 | M | 1/25 | L1: Introduction to Neuroscience for engineers; The role of H. von Helmholtz; Younger years, Dynamics of a Nerve Impulse,; von Helmholtz; history, Thermodynamic models, computational models; Thermodynamics of the Lungs (hypertension): SpO2, CO2 and O2 lung transport models + Basics; Heart Rate vs Mortality |
| 2 | W | 1/27 | L2: The structure of a nerve cell Brain anatomy Body, Neuron Glia, DNA and Genetics, Quanta Magazine articles, #1 |
| 3 | F | 1/29 | L3: Organization of the brain; Numbers and density of neurons in the human brain (p. 274); McCullochPitts.43.pdf; AI and brain waves; The making a brain map |
| 4/5 | M | 2/1 | L4: 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; |
| 5 | W | 2/3 | L5: The generic neuron; Σ-∆ codec, png |
| 6 | F | 2/5 | L6: Nonlinear diffusion model General solution (Green's function method): Green's function method; Transmission line (ABCD) method: Examples; Solving simple differential equations |
| 7/6 | M | 2/8 | L7: Chemical synapse, gap junction, Neuron, Body, types of Neurotransmitters; Ketamine uses |
| 8 | W | 2/10 | L8: 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?) |
| 9 | F | 2/12 | L9: 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 | |||
|---|---|---|---|
| Week | M | W | F |
| 7 | L10: 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 |
| 8 | L12: 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 | L14: ''Read: \( \S \) 3.4 (p. 60-63) Membrane models 360 Lec 14 (@1:30); NS2 due |
| 9 | L15: Exam I | L16: Read: \( \S \) 3.5 (p. 63-65) Na & K pumps and Nernst potentials L 16 @3:00 | L17: Read: \( \S \) 4.1, (p. 67-69) 360 Lec 17 |
| 10 | L18: 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) |
| 11 | L21: 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/W | D | Date | Daily lectures |
|---|---|---|---|
| Part II: Structure of a Neuron | |||
| 10/7 | M | 2/15 | L10: Lipid bilayers and their electro/mechanical properties Lipid bilayers, Transport mechanisms, Fun with bubbles, AI and protein folding |
| -- | W | 2/17 | University Holiday; No Class |
| 11 | F | 2/19 | L11: Electrochemical properties of membranes;Hill functions in Biology Lec 11, 2021; hemoglobum and oxyen transport Assignment: NS1 due, Solution: (NS1-sol.pdf) |
| 12/8 | M | 2/22 | L12: Transmembrane currents; channel types; Calculating partial pressures |
| 13 | W | 2/24 | L13: Einstein's relation (1905-III) and the derivation Four 1905 papers (@ Princeton.edu), Basic Solutions, Numerical solutions |
| 14 | F | 2/26 | L14: Membrane two-diode (min/max) models; NS2 Due; |
| 15/9 | M | 3/1 | L15: --NO CLASS-- Exam I: 8--11 AM Rm. 2017 ECEB |
| 16 | W | 3/3 | L16: Ionic currents (conduction, diffusion currents), electrochemistry Assignment: NS3 pdf, Due by Lec 22 NS3 Solution |
| 17 | F | 3/5 | L17: Nernst, Plank and Einstein relations; Membrane models Resting potentials and pumps |
| 18/10 | M | 3/8 | L18: 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 |
| 19 | W | 3/10 | L19: Squid Voltage patch clamp; first neural recording from toade eye (1928) |
| 20 | F | 3/12 | L20: The nonlinear diffusion line and why it acts as a delay line, Diode circuit model, output from circuit model |
| 21/11 | M | 3/15 | L21: Critical point in nonlinear diffusion (cable) equation Muscle dynamics, Neurological disorders, Guillain-Barre syndrom, Demylination disorders; Talk on neural regeneration Jan 25, NSP |
| 22 | W | 3/17 | L22: 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 |
| 23 | F | 3/19 | L23: Exam II |
| Part III: Lectures, Reading assignments + videos: Calendar Weeks 12-18 | |||
|---|---|---|---|
| Week | M | W | F |
| 12 | L24: 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 |
| 13 | L26: 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) |
| 14 | L29: 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) |
| 15 | L32: Lec32 360 (@0:25) | L33: Lec 33-360: role of the thalamus | L34: The manufacturing of protein manufacturing via DNA and RNA |
| 16 | L35: L35-360 S21: The eyes and ears (@3:15m) | L36: L36-360 S21: Hearing (@1:00), | L37: L37-360: Cochlear Transduction |
| 17 | L38: 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 |
| 18 | L41: 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/W | D | Date | Daily Lectures |
|---|---|---|---|
| Part III: Neuronal Assemblies | |||
| 24/12 | M | 3/22 | L24: Dendritic trees; Information processing; search the brain, Neural comutation-I, Neural computation-II Levin regeneration research: Rebooting how cells remember structure; Assignment: Due by Lec 28; (NS4.pdf; NS4-sol.pdf) |
| -- | W | 3/24 | University Holiday --NO Class-- |
| 25 | F | 3/26 | L25: Branching; Tapered Fibers; Dendritic information processing and logic (Ch 9; State machines); mitrohcondrial membrane; BackProbTraining |
| 26/13 | M | 3/29 | L26: Early Evidence for Cell Assemblies (Hebb) Alternate role of Cell Assemblies |
| 27 | W | 3/31 | L27: Branching rules in dendrites (Ch 9); Cell assemblies: Recent Evidence; gap junction disorders, proteins; EM micrographs |
| 28 | F | 4/2 | L28:Psychophysics of sound; Associative Network; Information processing; circuit1, circuit2, SigmaDelta, Role of vital signs Assignment: NS5, Due on L32 (pdf, NS5-sol); NS4 Due |
| 29/14 | M | 4/5 | L29: Dendritic Boolean logic;Generalized scalar products (Allen book \( \S \) 3.5.1, Fig 3.4); Just how smart is AI?; Basic brain anatomy (pdf) |
| 30 | W | 4/7 | L30: 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 |
| 31 | F | 4/9 | L31: A:Brain Anatomy; B:Field Theories for the Neocortex \(\S 9.3\); Diode model V0, Similink model V1, Similink output V1 |
| 32/15 | M | 4/12 | L32:Hyppocampus and memory; Fine-tuning the HH model to work off the onset of the pulse Neurosurgry of the brain; Spacial orientation, Mental images; Induced love between mice Limbic System Assignment: NS6 due on Lec 37 (pdf); NS5 Due |
| 33 | W | 4/14 | L33: 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; Metathesis molecular metathesis synthesis |
| 34 | F | 4/16 | L34: Ch 5: Attention DNA information processing video, comments, RNA information processing video |
| 35/16 | M | 4/19 | L35: Topics on hearing: Introduction to speech and hearing science, Sense of Touch and Heat; electronic odor (smell) sensors |
| 36 | W | 4/21 | L36: Topics on hearing: the middle ear and cochlea; OM study 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: Allen J. B. How to measure cochlear distorion products and their significance (Live demo?; Allen Fahey (1979)); (Organ of corti Transduction); Public; Private; |
| 37 | F | 4/23 | L37: 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 |
| 38/17 | M | 4/26 | L38: Topics on hearing:Fahey and Allen (1985) "Nonlinear phenomena as observed in the ear canal and the auditory nerve"; JASA |
| 39 | W | 4/28 | L39: Virus, bactaeria, antibodies, bacteriophages, organoids and CRISPER (phage, Parasites, Organoids, CRISPER, Significance Calcium and short term memory (Start at 29:30)); New studies re weight loss |
| 40 | F | 4/30 | L40: Lecture: Modern AI and its future; youtube Elon Musk views on AI (long); Chris Koch on conscious (@11:30); |
| 41/18 | M | 5/3 | L41: Mark Hasagawa-Johnson Guest lecture: AI methods Assignment: NS6 Due (matlab code that implements equations due) |
| 42 | W | 5/5 | L42: Guest Lecture: Vikor Gruev. Title: Wearable Bio-Inspired Imaging System for Image Guided Surgery |
| L/W | D | Date | |
|---|---|---|---|
| -/18 | W | 5/5 | Instruction Ends |
| -/18 | R | 5/6 | Reading Day |
| -/18 | F | 5/14 | Final Exam 8-11 AM; (Official Schedule) |
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