580.423/623 Systems Bioengineering: The nervous system

Objective: The course introduces the central nervous system from an engineering perspective.  This is a core course in the curriculum of undergraduate and Masters students at Hopkins Biomedical Engineering.


Course Director: Reza Shadmehr


Teaching Assistants: Julia Choi (jchoi AT bme.jhu.edu), Sarah Hemminger (shemming AT bme.jhu.edu), Christina Randall (rchris10 AT bme.jhu.edu), Debora Castillo (dcastil1 AT jhu.edu)


Course Coordinator: Jennifer Lewis (jenniferlewis AT jhu.edu)


Meeting Times: MWF 4:00-5:00 PM, Hodson 210




1.       Tuesday, February 06, 2007

2.       Tuesday, February 20, 2007

3.       Tuesday, March 06, 2007

4.       Tuesday, March 27, 2007

5.       Tuesday, April 10, 2007

6.       Tuesday, April 24, 2007


Exams from previous years:

           1. Midterm 2002 Final 2002

           2. Midterm 2003 Final 2003

           3. Midterm 2004 Final 2004

           4. Midterm 2005 Final 2005

           5. Midterm 2006 Final 2006



Lecture 1. Reza Shadmehr

Introduction to the central nervous system: anatomy. text slides


Lecture 2. Reza Shadmehr

Functional specialization of the cerebral cortex. text slides

Principle of contralateral control; study of language; perception of color, motion, and faces; memory and amnesia; left and right cerebral hemispheres.


Lecture 3. Reza Shadmehr

Neurons. text slides

Neurons and glia, properties of action potentials, neurotransmitters, second messengers, memory via synaptic plasticity and long-term potentiation, neuronal turnover in the brain, brain imaging.


Lecture 4. Jay Baraban

Genes and behavior.  text slides


Lecture 5. Eric Young

Examples of neural circuits and what they do.  

Recording from the nervous system; examples from the olfactory system; examples of plasticity from the electric fish.


Lecture 6. Eric Young

Neural excitability. 

Synaptic membrane dynamics; construction of action potentials via the HH model; Calcium dependent potassium channels; bursting; T calcium channels.


Lecture 7. Eric Young

Models of synaptic mechanisms. 

Synaptic transmission; synaptic vesicle hypothesis; post-synaptic receptors; model of ionotropic effects; strength of a synapse; threshold and refractoriness; temporal summation of EPSPs.


Lecture 8. Eric Young


Short and long pathways of metabotropic mechanisms; G-proteins.


Lecture 9.  Eric Young

Cable properties of neurons. 

Location of synaptic terminals on a neuron; cable model of neuron morphology; derivation of the cable equation; cable equation parameters; solutions for a semi-infinite cable.


Lecture 10. Alfredo Kirkwood

Cellular mechanisms of learning (1). slides


Lecture 11. Alfredo Kirkwood

Cellular mechanisms of learning (2). slides


Lecture 12. Xiaoqin Wang

Sensory systems: sensation, perception, psychophysics. slides

Modality, location, timing of a stimulus; sensory modality and labeled line; spatial distribution of stimulus; intensity of stimulus; psychophysical laws governing perception


Lecture 13. Xiaoqin Wang

Audition, vision, proprioception. slides

Auditory receptors: inner ear, basilar membrane, hair cells; Visual receptors: retina, rods and cones, color vision; Somatic receptors: mechanoreceptors, spatial discrimination receptive fields


Lecture 14. Xiaoqin Wang

Properties of spike trains. slides

Spike trains and measurement of neuronal response; average discharge rate; temporal coding; neural firing as Poisson processes


Lecture 15. Xiaoqin Wang

Concept of receptive field. slides

RF for visual and auditory inputs; size varies with sensory area; RF may have both inhibitory and excitatory components


Lecture 16. Xiaoqin Wang

Transformation of neural codes from PNS to CNS. slides

Pathways for sensory system in vision, audition, and proprioception; sensory regions of the cerebral cortex; topographic maps in the sensory system of the cortex; increase in complexity of neuronal properties; cortical columns; vision for localization vs. identification


Lecture 17. Xiaoqin Wang

Neural plasticity in the cortex. slides

Broadmann’s designation of cortical areas in humans; sensory inputs and development; modification of cortical maps due to experience; illusions; perception and neural activity; damage to the cortex and effect on behavior


Lecture 18.  Nitish Thakor

Neuroengineering: decoding the brain.  slides


Lecture 19.  Larry Schramm

Neuro-regeneration. slides


Lecture 20. Kechen Zhang

Realistic and simplified neural models. 

Integrate and fire models; perceptrons and feedforward networks; exclusive or problem; multi-layer perceptrons;


Lecture 21. Kechen Zhang

Synaptic plasticity. 

Supervised learning; Hebb’s learning rule; LTP in the hippocampus.


Lecture 22. Kechen Zhang

Recurrent networks.

Hopfield network and associative memory; energy functions; short-term memory networks;


Lecture 23. Kechen Zhang

Dynamics of neuronal networks.

Attractors, waves, oscillations, and synchrony


Lecture 24. Kechen Zhang

Population coding and distributed representations


Lecture 25. Kechen Zhang

Self-organizing networks and map formation


Lecture 26. Kechen Zhang

Cortical processing of tactile information.


Lecture 27. Eric Young

Auditory prosthetics


Lecture 28. Ed Conner

Central visual pathways


Lecture 29. Reza Shadmehr

Introduction to the computational problem of motor control.  slides notes


Lecture 30.  Reza Shadmehr

Force generation and control of a limb. slides notes

Motor neurons; muscle length-tension properties; motor units; muscle’s sensory system; control of posture


Lecture 31. Reza Shadmehr

Proprioception and reflex pathways. slides notes

Fatigue, spike triggered averaging, spindles and golgi tendon organs; delay in feedback control; loss of proprioception; functional electrical stimulation.


Lecture 32. Reza Shadmehr

Going from vision to action. slides notes

Visual pathways to the cortex; descending tracts from the brain; split brain patients; role of brainstem centers in control of posture; encoding of visual scene by neurons in the visual cortex; gain fields.


Lecture 33. Reza Shadmehr

Adaptation of visuomotor maps.  slides notes

Computations involved in reaching; prism adaptation; disorders of parietal cortex; neglect.


Lecture 34.  Reza Shadmehr

Motor areas of the frontal lobe.  slides notes

Motor cortex and somatotopic maps, change in the motor maps due to injury and plasticity; control of movements by the motor cortex; translation of movement plans into action.


Lecture 35.  Amy Bastian

Motor disorders.


Lecture 36.  Tissue engineering of neurons and axonal regeneration.


Lecture 37.  Tissue engineering of neurons.