Last Modified : Wed, 24 Aug 22
ECE410-ECENeuroScience-S22
- Neural circuits and systems (NE-410/ECE-410: Neuroscience for Engineers: Science of Brain function)
- Syllabus: Syllabus;
- Schedule: 410NS, ECE 410NS: CRN 70830 Spring 2022, Official Calendar
- Time: 3:00-3:50 PM; 2017 ECEB (Attendence required) Neural Circuits and Systems;
- PUBLIC ACCESS to Allen recorded Lectures (videos): S22 Lec-15-end
- Office hrs: Friday 4-5 PM or by apt.
- Homework to be submitted to Gradescope: Use Entry Code: 2RNBYX
- Class Text: Neuroscience: A mathematical primer Scott (2002) pdf; abridged-pdf-@Apr5.21?;
Allen math text: An Invitation to Mathematical Physics; pdf;
Membrane Models of red blood cells Evans & Skalak (1978) pdf,?;
Matlab Symbolic Math Toolbox--User's Guide - Supplement material: Abbott & Dayan (pdf);Basic Brain Facts?: Duke Challenge; Layman-level articles of interest
- Independent research (senior thesis), ISUR
- Instructor: Prof. Jont Allen (netID jontalle; Office 3062ECEB); Tuesday 2PM Location: Zoom
- 'Today's schedule'; Final Exam information: See below;
ECE-410/NE-410 Weekly Schedule Spring 2022
| Part I: Lectures, Reading assignments + videos: Calendar Weeks 4-6: Video Index I? | |||
|---|---|---|---|
| Week | M | W | F |
| 3 | Martin Luther King Day | L1: Read: \(\ \S \) 1.1 (Preface: pp vii-x; Ch 1: History pp 1-8); 2021 360 Lec 1 (Starts @6:00 mins) | L2: Read: \( \S \) 1.2 (p. 8-11); 2021 360 Lec 2 (Starts @14:00 mins) |
| 4 | L3: Read: \( \S \) 1.3 (p. 11-19); \(\S\) 9.1 p. 187-104; 2021 360 Lec 3 | L4: Read:Scott Ch. 12, \( \S \) 12.1 (p. 293-298); Network Postulates? Assignment: NS1: Due by Lec 11; (NS1.pdf?, pp. 150-151 Allen (2020); Solution: (NS1-sol.pdf?); 2021 360: Lec 4 | L5: Read: 2.1, .2 (p. 25-31, 189, 208); Generic neurons (Scott: Fig. 2.1); 2021 360: Lec 5 (@2:15m) |
| 5 | L6: Read: 2.2.2-.3 (p. 31-35) Nonlinear Diffusion lines 360 Lec 6 | L7: Read: \(\S\) 2.3 (p. 35-40) Synapses & Gap junction; 2021 360 Lec 7 (@1:00m) | L8: Read: \(\S\) 10-.1.2 AI models: (pp. 233-241), Neural Boolean Hilbert-space; Discuss how solve NS1 problems; 2021 360 Lec 8 (@4:00 m) |
| 6 | L9: Read: \(\S\) 10.2 (p. 241-248), 2021 360Lec 9 (@0:37m) | ||
| L/W | D | Date | Daily lectures |
|---|---|---|---|
| Part I: Introduction and History | |||
| 1/3 | W | 1/19 | L1: Introduction to Neuroscience for engineers; The role of H. von Helmholtz; Younger years, Dynamics of a Nerve Impulse,; von Helmholtz; history, Virtual Rat:, computational models; Thermodynamics of the Lungs (hypertension): SpO2, CO2 and O2 lung transport models + Basics; A piece of thermodynamic history; Source of Hypertension; Theory of Hypertension; Arterial Pressure model |
| 2 | F | 1/21 | L2: The structure of a nerve cell Brain anatomy; Body, Neuron? Glia, DNA and Genetics, Quanta Magazine articles, #1 |
| 3/4 | M | 1/24 | L3: Dendritic trees \(\S\) 9.0, p. 187; 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 | W | 1/26 | 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 | F | 1/28 | L5: The generic neuron; Action potentials; Voltage-gated membrane channels; Neuron?, Body Σ-∆ codec, |
| 6/5 | M | 1/31 | L6: Nonlinear diffusion model General solution ;NL-RC Neural Spike model (.cir)?; , using spice [.asc?]; The nonlinear diffusion line and why it acts as a delay line, Diode circuit model of spike propagation?, Results from circuit model? Results of LT spice model from William Walters (HW6 4/6/21)? Leading edge models: Chap. 5, p. 95; NGspice users manual (pdf)? |
| 7/5 | W | 2/2 | L7: Chemical synapse, gap junction, Neuron?, Body, types of Neurotransmitters; Neuropeptides; oral Ketamine uses |
| 8/- | F | 2/4 | L8: McCulloch-Pitts (MP) AI neuron (model), \(\S\) 10.1.1-.2: (pp. 235-241) Boolean Hilbert space; Dendritic Boolean logic;Generalized scalar products (Allen book \( \S \) 3.5.1, Fig 3.4); Just how smart is AI?; , Basic brain anatomy, (pdf)? (M-P model; pdf?); ); Water on Mars (@7:02); The beginning of live on earth |
| 9/6 | M | 2/7 | L9: Deep-learning concepts: STFT and fast convolution;? ConvNetJS discussion, Assignment: NS2 (pdf?, (sol)?, Gscope, Due by Lec 14 |
| Part II: Lectures, Reading assignments + videos: Calendar Weeks 6-11 | |||
|---|---|---|---|
| Week | M | W | F |
| 6 | L10: Read: \( \S \) 3, 3.1 (p. 49-53) 360 Lec10 | L11: Read: \( \S \) 3.2 (p. 53-55) Solution: (NS1-sol.pdf?) 360 Lec 11 | |
| 7 | 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; (sol)?, |
| 8 | L15: 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 |
| 9 | 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) |
| 10 | 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: Moved Exam II to Lec 28 |
| L/W | D | Date | Daily lectures |
|---|---|---|---|
| Part II: Structure of a Neuron | |||
| 10/6 | W | 2/9 | L10: Lipid bilayers and their electro/mechanical properties Allen Lec 11, 2021; Allen Lec 10, 2022; Lipid bilayers, Transport mechanisms, Fun with bubbles, AI and protein folding |
| 11 | F | 2/11 | L11: Electrochemical properties of membranes; hemoglobum and oxyen transport; See Hill Equation in biochemistry; Blue whale's heart rate Assignment: NS1 due, Solution: (NS1-sol.pdf?) |
| 12/7 | M | 2/14 | L12: Transmembrane currents; Channels & types; Calculating partial pressures (It is an impedance calculation.) |
| 13 | W | 2/16 | L13: Einstein's relation (1905-III) and the derivation Four 1905 papers (@ Princeton.edu), Basic Solutions, Numerical solutions; System Postulates.pdf? |
| 14 | F | 2/18 | L14: Review for Exam I NS2 Due; NS2 Solution? |
| 15/8 | M | 2/21 | L15: --NO CLASS-- Exam I: 3--5 PM Rm. 2017 ECEB Next year:Move Exam I to Lec 23; Compress/combine/reduce Lec 16-22; More on brain Assemblies (Ch 11); eye & ear & touch transduction |
| 16 | W | 2/23 | L16: Ionic currents (conduction, diffusion currents), electrochemistry Assignment: NS3 pdf?, Due by Lec 22 NS3 Solution? |
| 17 | F | 2/25 | L17: Redox Resting potentials and pumps HH matlab model; Helmholtz measures velocity of spikes |
| 18/9 | M | 2/28 | L18: Ch. 4,Hodgkin Huxley model: U Mich.s; Fine-tuning the HH model to work off the spike rising onset; HH model (matlab code); Ion distribution during a spike; Neural oscillators |
| 19 | W | 3/2 | L19: Squid Voltage patch clamp for single cell recording; Adrian and nerve pulses first neural recording from toad eye (1928) |
| 20 | F | 3/4 | L20:Critical point in nonlinear diffusion (cable) equation Muscle dynamics, Neurological disorders, Guillain-Barre syndrom, Demylination disorders; Talk on neural regeneration Jan 25, NSP |
| 21/10 | M | 3/7 | L21: Nodes of Ranvier; Krebs cycle as the energy source; |
| 22 | W | 3/9 | L22: Read:\(\S\)9.1 (187-199, Fig. 9.1) Spike models @3m; Myelin-Sheath @11m; Information processing: \(\S\)9--9.2: @33:40m; @49 bifurcations; |
| 23 | F | 3/11 | L23: Review sol to NS3; Moved Exam II to Lec 28Read: \(\S\)10 (p. 233-241); 360 Lec 25 @2:25; topic II: @38:25 NS3 due, NS3 Solution? |
| -/11 | MWF | 3/14 | Spring Break |
| Part III: Lectures, Reading assignments + videos: Calendar Weeks 12-17 | |||
|---|---|---|---|
| Week | M | W | F |
| 12 | L24: 360 Lec 26 (@1); Read: Donald Hebb \(\S\)11 (pp. 17-19); | L25: (360 L27 @3:00);Read: Cell-Assembly, \( \S \) 11-.3 (pp. 257-265) of word frequencies; | L26: Cell-Assembly and language hypothesis; |
| 13 | L27: Zipf's log-linear Law; Brief review for Exam II | L28: Exam II | L29: (360 L28 A(@0:48); B(@11:30); Read: \( \S \) 10-10.1.1 (233-237), 11-11.2 (256-265) |
| 14 | L30: Hypertension and its source: 360 L29 (@0) Read: \( \S \) 9.3.2, 10.1.2, 11.3: Dendritic Boolean logic | L31: L30-360 (2021); cortex anatomy Read: \( \S \) 10.2.2 (241-248) | L32: Molecular Transport; Protein creation; L34-360: (2021): Discovery of DNA and RNA; L33-360: (2022) Thalamus, L32-360: (2021) (@0:25), Hippocampus, L31-360: (2021) (@4:25) Topic: Brain anatomy; Read: \( \S \) 9.3, 10.3 (248-252) |
| 15 | L33: L35-360 S21: The eyes and ears (@3:15m) ; | L34: Overview of Sensory systems (Hearing) L36-360 S21: Hearing (@1:00), | L35: L37-360: Cochlear Transduction |
| 16 | L36: The inner ear and its function; Cochlear nonlinear processing (@2min), NL Cochlear processing (pdf), Ashmore Lecture | L37: Organ of Corti | L38: Cochlear nonlinearities and its function |
| 17 | L39: Sensory systems; Vrius; Crisper (360 S21: Audio starts @ 22m) Read: \( \S \) 8.0-8.3 (165-169)); | L40:Last lecture 360 S21 (@1m) AI's furure, AI darkside; Conscious; Short term memory Assignment: NS7 Due | Thur: Reading Day; Friday: First day of Exams |
| L/W | D | Date | Daily Lectures |
|---|---|---|---|
| Part III: Neuronal & Cell Assemblies | |||
| 24/12 | M | 3/21 | L24: Information processing; Dendritic information processing; Dendritic logic processing (Ch 9; State machines & Branching rules in dendrites); Cell assemblies: Recent Evidence; , proteins; EM micrographs Synaptic processing videos: Neural computation power, How brains learn, How networks learn: (Audio podcast 163): (no video) @1:00; Synaptic Information processing (Audio podcast 148): @0:16 (no video), Backpropagation Methods for machine learning:; Hinton's BackProb Training ; Assignment: Due by Lec 28; (NS4.pdf?; NS4-sol.pdf?) |
| 25 | W | 3/23 | L25: (-->L27) Energy sources; mitrohcondrial membrane; Rebooting how cells remember structure: Levin lecture @4:39m; Levin: New Yorker article on his regeneration research: |
| 26 | F | 3/25 | L26: (-->L25) Early Evidence for Cell Assemblies (Hebb) ; Brain facts |
| 27/13 | M | 3/28 | L27: (-->L26) Zipf-Model?, ; Zipf's log-linear and the Brown Corpus; Zipf's word Brevity-law |
| 28 | W | 3/30 | L28: Exam II: NS3, NS4, Historical events |
| 29 | F | 4/1 | L29: L29: Hyppocampus and memory; ; , Measures of inntelligence (IQ): Mental images; Induced love between mice Limbic System? Assignment: NS5, Due on L32 (pdf?, NS5-sol?) |
| 30/14 | M | 4/4 | L30 Role of vital signs: How the heart rate is regulated by the body (video), , , , , ; |
| 31 | W | 4/6 | L31: A:Brain Anatomy; B:Field Theories for the Neocortex \(\S 9.3\); Models of Brain Anatomy (Dynamics I-II) Friston Predictive model, claustrum Limits of brain and muscle; Senses of Orientation (NIH); Allen Inst: 12 easy pieces: sentory systems; Allen Inst Brain Atlas; Allen Inst Home Page; Start @ 6 min; Lung alternatives;, Where does thirst come from? The Chinese room argument |
| 32 | F | 4/8 | L32: Molecular transport: DNA information processing video, comments, RNA information processing video Momecular motors: Now they work, Switching attention in the brain: Central manimpulation of DNA to enhance memory Michael Halassa: Thalamic Switching, Michael Halassa: Talk @ Allen Inst; Rubisco: The enzime for life;The makeup of a virus: vurlient DNA, What is a virus; |
| 33/15 | M | 4/11 | L33: Elements of sensory systems:Psychophysics of sound; Associative Network; Information processing; Assignment: NS6 due on Lec 37 (pdf?); NS5 Due |
| 34 | W | 4/13 | L34: Overview on hearing: Speech and hearing science: Loudness and its JND; Sense of Touch and Heat; electronic odor (smell) sensors; Jeremy Nathans: A complex speech task explained'; Fungi that explodes ants; Metathesis molecular metathesis synthesis |
| 35 | F | 4/15 | L35: Topics on hearing: Speech and hearing science: The middle ear: Window to hearing ; Effects of Negative Middle Ear Pressure on Wideband Acoustic Immittance in Normal-Hearing Adults, pdf Otitis Media & hearing loss |
| 36/16 | M | 4/18 | L36: Topics on hearing: Speech and hearing science: The inner ear (cochlea); Cochlear modeling, |
| 37 | W | 4/20 | L37: Auditory systems: the organ of Corti, hair cell transduction, Allen (1980) "Cochlear micromechanics: A physical model of transduction"; Fahey & Allen 1985 (pdf); , How we can see with our ears., ; An example of auditiory (neural) signal processing |
| 38 | F | 4/22 | L38: Topics on hearing: Cochlear nonlinear in the auditory nerve: Transduction & the Organ of Corti, brain map & meaning; circuit1?, circuit2?, SigmaDelta, |
| 39/17 | M | 4/25 | L39: Virus, bactaeria, antibodies, bacteriophages, organoids and CRISPER (phage, Parasites, Organoids, CRISPER, New studies re weight loss Assignment: NS6 Due (Octave code that implements spike propagation) |
| 40 | W | 4/27 | L40: Bing-Ze Lin: bzlin2@ |
| 41 | F | 4/29 | L41: NO Class (Allen in San Jose for family funeral) |
| 42/18 | M | 4/2 | L42: Allen speech feature research: Techniques and implications (e.g., cell assemblies) for speech recognition and Machine Learning |
| 43 | W | 5/4 | L43: Final Lecture: Koch on consciousness (@1:13), Giulio Tononi on Consciousness |
| L/W | D | Date | |
|---|---|---|---|
| -/18 | W | 5/4 | Instruction Ends |
| -/18 | R | 5/5 | Reading Day |
| -/19 | T | 5/10 | Final Exam TBD (Official Schedule) |
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