Fundamentals of Neuromechanics: course syllabus

Fundamentals of Neuromechanics
Instructor: Bradly Alicea, e-mail:
Class Time, Location: TBA

The course content will be divided into two modules (introduction and case studies), covering 1/3 and 2/3 of the term, respectively.

Module I: Introduction (weeks 1-5)

Week 1: What is Neuromechanics?

Weeks 1, 2, and 3: fundamentals of movement: kinematics in animals and machines.

Weeks 3 and 4: fundamentals of movement: kinetics and energetics in animals.

Weeks 4 and 5: movement and the nervous system.

Module II: Academic Case Studies (weeks 6-15)

Week 6: Insect brains and body-brain-environment.

Week 7: Passive Dynamic Walking.

Week 8: Prey capture in fishes and amphibians.

Week 9: Swallowing and specialized behaviors.

Week 10: Motor Learning and Memory.

Week 11: Balance and virtual environments.

Week 12: Legged locomotion.

Week 13: Functional scaling/biomechatronics.

Week 14: Embodiment and neuroanthropology.

Week 15: Applications.

What is Neuromechanics?

Neuromechanics is an integrative science at the nexus of sensation and perception, neurobiology, animal behavior, biomechanics, and robotics. The empirical component is grounded in experimentation. Therefore, we will cover a number of experimental case studies over the course of the term. The theoretical component can be best understood by covering the basics, understanding the case studies, and reviewing major applications related to the field.


There are two exams (one at the conclusion of Module I, and the other at the scheduled final exam time). There will also be two homework assignments (online), and one set of written reviews for Module II (online). One homework assignment will be given on topics covered during the measurement techniques section, while the other will involve a topic covered during the application section of the course. During Module II, each person in the class will choose ONE of the model systems and produce a short (2-4 pgs., double spaced) review. All second-hand information must be accompanied by a reasonable citation and cited in a bibliography, and there is to be no collaboration or plagiarism.

Assignment Percent of grade
Homework #1 16
Midterm 26
Model system report 16
Homework #2 16
Homework #3 * 10
Final 26
Total 110

NOTE: there is an optional Homework #3. It adds 10% to your grade, so that you can earn a maximum of 110%. Please take advantage of this opportunity. Homework #3 will most likely involve a quick research project proposing the application of neuromechanical principles to a particular problem. This could turn into a much more beneficial and large-scale research project down the road.

Module I: Introduction.

1. Fundamentals of Movement: kinematics in animals and machines

Central pattern generation (CPGs): This will focus on central pattern generators (CPGs). The basic unit of movement production in the nervous system, CPGs can be defined as oscillatory primitives that serve as the basis for movement production in a wide variety of animal taxa, from insects to tetrapods. We will discuss how simple structures like CPGs have evolved into specialized types of movement such as flying, walking, and swimming.

Case study: NaturalMotion. Demos (Virtual and Physical): YouTube VideoApplication Downloads.

Physical: indoor lab (TBA). CPGs and mechanisms such as emergent phenomena have also been incorporated into human motion generation simulations for video games and other interactive virtual environments. We will explore the work of Torsten Reil and his NaturalMotion method, with an exercise based on this simulation environment.

Movement disorders: This will focus on balance disorders and their neuromechanical substrates. Featured disorders will include: ALS, muscular dystrophy, and balance disorders. We will also include a discussion of therapeutic techniques such as brain-machine interfaces, gene therapy, and sensory augmentation.

Measurement techniques: This will focus on ways to measure movement, from motion capture (MoCap) and accelerometer systems to high-speed cameras, differential GPS, and stroboscopic methods. To segue into the kinetics section, EMG, imaging, and molecular methods will also be covered. There may be a homework assignment focusing on the computation of kinematic data.

2. Fundamentals of Movement: kinetics and energetics in animals

Basics of muscle, neural tissue, and plasticity: This will focus on the basic functional units of movement and force production. A broad survey of muscle, connective tissues, sensory receptors, and brain tissues such as neurons, glia, and astrocytes will be featured. In addition, there will be a brief lecture section on the mechanical properties of biological tissues (e.g. Young’s modulus). There may be a homework assignment on the mechanical properties of tissue.

Energetics and movement: This will focus on the energetic demands of motility. The focus will be on a series of papers by James Marden and colleagues, who have done work on linkages between force production, type of movement (e.g. swimming, flying, walking), the underlying mechanisms, and scaling between force production and movement. There may be a homework assignment involving this class module.

3. Movement and the Nervous System

Molecular aspects of brain and muscle function: This part of the lecture schedule will focus on the molecular bases of motor learning and memory and muscle plasticity. Recent findings have clarified the major pathways, genes, transcripts, and proteins involved in neuromuscular adaptation. This will be a very basic introduction.

* Surface Reaction Forces, Gravity, and Adaptation:

Case study: Basilisk running.

Hsieh, S.T. and Lauder, G.V. (2004). Running on water: three-dimensional force generation by basilisk lizards. PNAS USA, 101, 48, 16784–16788.

(1996). A walk on the wild side - hydrodynamic model explains how Basiliscus lizard skips across water.

Demos (Virtual and Physical):

Physical: outdoor lab (TBA)

Neural correlates of force production and movement: This part of the lecture schedule will focus on the neural correlates of force production and movement. The approach will be to review neuroimaging and animal model studies to understand what parts of the brain are involved in imagined movement, changes in the recruitment of motor units during the course of training, and basic sensation and perception.

Aging and disorders of the CNS and movement: This part of the lecture schedule will focus on aging processes in human and other animal species. Of particular interest will be the effects of aging on bone, muscle, and neural systems. Case studies will be included that focus upon myelination, Alzheimer’s disease,
and neurorehabilitation strategies.

Selected Readings/Reference Books and Articles: 

Basic Resources (all will be on hold at library or otherwise made available):
Enoka, R. (2001). Neuromechanics of Human Movement. Human Kinetics, Champaign, IL.

Shadmehr, R. and Wise, S.P. (2005). Computational Neurobiology of Reaching and Pointing. MIT Press, Cambridge, MA.

Wolfe, J.M., Kluender, K.R., Levi, D.M., Bartoshuk, L.M., Herz, R.S., Klatzky, R.L., and Lederman, S.J. (2006). Sensation and Perception. Sinauer Associates, Sunderland, MA.

Useful Reviews Articles:
Barry, B.K. and Enoka, R.M. (2007). The Neurobiology of muscle fatigue: 15 years later. Integrative and Comparative Biology, 47(4), 465-473.

Bejan, A. and Marden, J.H. (2006). Unifying constructal theory for scale effects in running, swimming, and flying. Journal of Experimental Biology, 209, 238-248.

Chong, L., Culotta, E., Sugden, A. (2000). On the move: molecular to robotic. Science, 288, 79-106.

Delcomyn, F. (1980). Neural basis of rhythmic behavior in animals. Science, 210, 492-498.

Enoka, R.M. and Duchateau, J. (2008). Muscle Fatigue: what, why, and how it influences muscle function. Journal of Physiology, 586.1, 11-23.

Enoka, R.M. and Fuglevand, A.J. (2001). Motor unit physiology: some unresolved issues. Muscle and Nerve, 24, 4-17.

Enoka, R.M. and Stuart, D.G. (1992). The neurobiology of muscle fatigue. Journal of Applied Physiology, 72(5), 1631-1648.

Marden, J.H. and Allen, L.R. (2002). Molecules, muscles, and machines: universal performance characteristics of motors. PNAS USA, 99(7), 4161-4166.

Montooth, K.L., Marden, J.H., and Clark, A.G. (2003). Mapping determinants of variation in energy metabolism, respiration, and flight in Drosophila. Genetics 165(2): 623-635.

Morasso, P., Bottaro, A., Casadio, M., and Sanguinetti, V. (2005). Preflexes and internal models in biomimetic robot systems. Cognitive Processing, 6(1), 25-36.

Terrier, P. (2000). High-precision satellite positioning system as a new tool to study the biomechanics of human locomotion. Journal of Biomechanics, 33(12), 1717-1722.

Part II: Academic Case Studies Synopses.

Randall Beer: insect neuroethology and brain-body-environment interaction.

Selected Readings: 

Beer, R.D. (2006). Beyond Control: The Dynamics of Brain-Body-Environment Interaction in Motor Systems. In D. Sternad ed. Progress in Motor Control V: a multidisciplinary perspective. Springer, Berlin. 

Phattanasri, P., Chiel, H.J. and Beer, R.D. (2007). The dynamics of associative learning in evolved model circuits. Adaptive Behavior 15(4), 377-396. 

Tad McGeer and Andy Ruina: dynamic walking

Selected Readings: 

McGeer, T. (1990) Passive dynamic walking, International Journal of Robotics Research, Vol. 9, No., 2, pp. 62-82.

Collins, S.H., Ruina, A.L., Tedrake, R., Wisse, M. (2005) Efficient bipedal robots based on passive-dynamic walkers, Science, 307: 1082-1085. 

Kiisa Nishikawa and Malcolm MacIver: prey capture in lizards and fish

Selected Readings: 

Corbacho, F.J., Nishikawa, K.C., Weerasuriya, A., Liaw, J-S., and Arbib, M.A. (2005). Schema-based learning of adaptable and flexible prey-catching in anurans I. The basic architecture. Biological Cybernetics, 93(6), 391-409. 

Herrel, A., Meyers, J.J. Aerts, P. and Nishikawa, K.C. (2001). Functional implications of supercontracting muscle in the chameleon tongue retractors. Journal of Experimental Biology, 204, 3621-3627.

Nelson, M. E., M. A. MacIver, and S. S. Coombs (2002). Modeling electrosensory and mechanosensory images during the predatory behavior of weakly electric fish. Brain, Behavior, and Evolution 59(4):199-210. 

Hillel Chiel and Lawrence Rome: swallowing and other specialized neuromuscular behaviors. 

Selected Readings: 

Neustadter, D.M., Drushel, R.F., Crago, P.E., Adams, B.W., and Chiel, H.J. (2002). A kinematic model of swallowing in Aplysia californica based on radula/odontophore kinematics and in vivo MRI. Journal of Experimental Biology, 205, 3177-3206.

Sutton, G.P., Mangan, E.V., Neustadter, D.M., Beer, R.D., Crago, P.E., and Chiel, H.J. (2004). Neural control exploits changing mechanical advantage and context dependence to generate different feeding responses in Aplysia. Biological Cybernetics, 91, 333-345.

Young, I.S. and Rome, L.C. (2001). Mutually exclusive muscle designs: the power output of the locomotory and sonic muscles of the oyster toadfish (Opsanus tau). Proceedings of the Royal Society of London B, 268, 1965-1970. 

Sandro Mussa-Ivaldi and Reza Shadmehr: motor learning and memory

Selected Readings: 

Mussa-Ivaldi, F.A. (1995). Geometrical Principles in Motor Control. In: M.A. Arbib (Ed.) Handbook of Brain Theory. MIT Press, Cambridge, MA.

Mussa-Ivaldi, F.A., Giszter, F.A. and Bizzi, E. (1994). Linear combination of primitives in vertebrate motor control. PNAS USA, 91, 7534-7538. 

John Jeka and Fay Horak: balance and virtual environments

Selected Readings: 

Jeka, J.J. (2006). Light touch contact: not just for surfers. The Neuromorphic Engineer, 3(1), 5-6.

Jeka, J.J., Kiemel, T., Creath, R., Horak, F.B., and Peterka, R. (2004). Controlling human upright stance: Velocity information is more accurate than position or acceleration. Journal of Neurophysiology, 92, 2368-237. 

Robert Full: legged locomotion (anchors and templates)

Selected Readings: 

Full, R.J. and Koditschek, D.E. (1999). Templates and Anchors: neuromechanical hypotheses of legged locomotion on land. Journal of Experimental Biology, 202, 3325–3332.

Holmes, P., Full, R.J., Koditschek, D., and Guckenheimer, J. (2006). Dynamics of legged locomotion: Models, analysis, and challenges. SIAM Review, 48(2), 207-304.

James Marden and Hugh Herr: functional scaling and biomechatronics

Selected Readings:

Herr, H. and Dennis, R.G. (2004). A swimming robot actuated by living muscle tissue. Journal of Neuroengineering Rehabilitation, 1, 6.

Herr, H.M., Huang, G.T. and McMahon, T.A. (2002). A model of scale effects in mammalian quadrupedal running. Journal of Experimental Biology, 205, 959-967. 

Bejan, A. and Marden, J.H. (2006). Unifying constructal theory for scale effects in running, swimming and flying. Journal of Experimental Biology, 209, 238-24  

Andy Clark and Greg Downey: Embodiment and Neuroanthropology

Selected Readings:

Downey, G.   Listening to Capoeira: Phenomenology, Embodiment, and the Materiality of Music. Ethnomusicology, 46(3), 487-509 (2002).

Clark, A. and Grush, R.   Towards a Cognitive Robotics. Adaptive Behavior 7(1), 5-16 (1999).


1. Augmented Cognition and Performance Augmentation: This will introduce the concepts of augmented cognition and performance augmentation at an introductory level. There will also be an introduction to the basic tools of the field, such as the application of mitigation strategies and creating performance state gauges.

2. Neurorehabilitation: This will provide a recap of prior studies and technologies covered in class along with additional examples. The additional examples will focus on recovery of function after stroke using robotic systems and the use of virtual environments and other digital media to retrain postural stability in the elderly. 

3. Mechano-interfaces (exoskeletons, piezoelectric devices, and harnessing power): This will provide a glimpse into the future of neuromechanical applications, bringing together all of the topics in this class module. We will explore the world of wearable devices that produce electricity, the making of artificial muscles, and wearable devices that increase your strength and endurance!

Human-powered devices.

With all the recent hype over renewable energies and the proliferation of mobile devices, one emerging area of research is in harnessing the output of human neuromuscular systems for purposes of small-scale electrical generation. 

4. Haptics, Haptic Interfaces, and Proprioception: This will provide a quick introduction to the senses of touch and somatosensation. We will explore some of the neural pathways and coding strategies involved. There will also be discussion of applying scientific findings about this sensory modality to interface and prosthetic technology design.

No comments:

Post a Comment