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Molecular, Cellular, and Tissue Biomechanics

3-0-9 units · Graduate

Develops and applies scaling laws and the methods of continuum mechanics to biomechanical phenomena over a range of length scales. Topics include structure of tissues and the molecular basis for macroscopic properties; chemical and electrical effects on mechanical behavior; cell mechanics, motility and adhesion; biomembranes; biomolecular mechanics and molecular motors. Experimental methods for probing structures at the tissue, cellular, and molecular levels. Students taking graduate version complete additional assignments.

Spring 2003 · Molecular, Cellular and Tissue Biomechanics (BE.410J)

Topics

  • Introduction: From Tissue Biomechanics to Molecular Nanomechanics
  • Viscoelastic (Time-Dependent) Behavior of Tissues (cont.)
  • Poroelastic (Time-Dependent) Behavior of Tissues (cont.)
  • The Cytoskeleton (cont.)

Readings

  • Fung, Y. C. Biomechanics: Mechanical Properties of Living Tissues . New York, NY: Springer-Verlag, 1993. ISBN: 9780387979472.
    Listed reading
  • Nossal, R., and L. Lecar. Molecular and Cell Biophysics . Cambridge, MA: Perseus Books, 1991. ISBN: 9780201195606.
    Listed reading
  • Lodish, H., et. al. Molecular Cell Biology . New York, NY: Scientific American Books/W.H. Freeman, 1995. ISBN: 9780716723806.
    Listed reading
  • Dill, K. A., and S. Bromberg. Molecular Driving Forces . New York, NY: Routledge, 2002. ISBN: 9780815320517.
    Listed reading
  • [GKM-Text] = Grodzinsky, A., R. Kamm, and L. Mahadevan. Molecular, Cell and Tissue Biomechanics. Draft of textbook in preparation, 2003.
    Listed reading
  • Daune, Michel. Chapter 2 in Molecular Biophysics . New York, NY: Oxford University Press, 1999. ISBN: 9780198577836.
    Listed reading
  • Dill, K. A., and S. Bromberg. Chapters 6, 8 and 10 in Molecular Driving Forces . New York, NY: Routledge, 2002. ISBN: 9780815320517.
    Listed reading
  • Boal, David H. Chapter 2 in Mechanics of the Cell_ ._ Cambridge, UK: Cambridge University Press, 2002. ISBN: 9780521792585.
    Listed reading
  • Stricka, Terence, Jean-Francois Allemanda, Vincent Croquettea, and David Bensimon. “Twisting and stretching single DNA molecules.” Progress in Biophysics & Molecular Biology 74 (2002): 115-140.
    Listed reading
  • Coccoa, Simona, John F. Markob, and Remi Monasson. “Theoretical Models for Single - Molecule DNA and RNA Experiments: from Elasticity to Unzipping.” C. R. Physique 3 (2002): 569-584.
    Listed reading
  • Liphardt, Jan, Bibiana Onoa, Steven B. Smith, Ignacio Tinoco Jr., and Carlos Bustamante. “Reversible Unfolding of Single RNA Molecules by Mechanical Force.” Science 292 (April 2001): 733-737.
    Listed reading
  • Howard, Johnathon. Chapters 5 and 10 in Mechanics of Motor Proteins and the Cytoskeleton_ ._ Sunderland, MA: Sinauer Associates, 2001. ISBN: 9780878933341.
    Listed reading
  • Vale Ronald D., and Ronald A. Milligan. “The Way Things Move: Looking Under the Hood of Molecular Motor Proteins.” Science 288 (April 2000): 88-95.
    Listed reading
  • Mahadevan, L., and P. Matsudaira. “Motility Powered by Supramolecular Springs and Ratchets.” Science 288 (April 2000): 95-99.
    Listed reading
  • Ward, J. P. Solid Mechanics . New York, NY: Springer, 1992. ISBN: 9780792319498.
    Listed reading
  • Lodish, H., et. al. Molecular Cell Biology . 3rd. ed. New York, NY: Scientific American Books/W.H. Freeman, 1995. ISBN: 9780716723806.
    Listed reading
  • Malvern, Lawrence E. Chapter 6 in Introduction to the Mechanics of a Continuous Medium . Englewood Cliffs, N.J.: Prentice-Hall, 1969, pp. 278-282. ISBN: 134876032.
    Listed reading
  • Ferry, J. D. “The Nature of Viscoelastic Behavior.” Chapter 1 in Viscoelastic Properties of Polymers . New York, NY: Wiley, 1980. ISBN: 9780471048947.
    Listed reading
  • Huang, Chun-Yuh, Michael A. Soltz, Monika Kopacz, Van C. Mow, and Gerard A. Ateshian. “Experimental Verification of the Roles of Intrinsic Matrix Viscoelasticity and Tension - Compression Nonlinearity in the Biphasic Response of Cartilage.” Transactions of the ASME 125 (February 2003): 84-93.
    Listed reading
  • Smita, Theo H., Jacques M. Huygheb, and Stephen C. Cowin. “Estimation of the Poroelastic Parameters of Cortical Bone.” Journal of Biomechanics 35 (2002): 829-835.
    Listed reading
  • Kamm, R. “Derivation of the Viscous Flow Equations.” 1999. ( PDF ) ↗
    Listed reading
  • Sonin, A. A. The Physical Basis of Dimensional Analysis. 2nd ed. (Self-published work.) MIT, 2001.
    Listed reading
  • Stamenovic, D., and D. E. Ingber. “Models of Cytoskeletal Mechanics of Adherent Cells.” Biomechan Model Mechanobiol. 1 (2002): 95-108.
    Listed reading
  • Problem from Spring 2002: Oscillatory Compression of Poroelastic Tissue. ( PDF ) ↗
    Listed reading
  • Pollard Thomas D., and Gary G. Borisy. “Cellular Motility Driven by Assembly and Disassembly of Actin Filaments.” Cell 112 (February 2003): 453-465.
    Listed reading
  • Mogilner, Alex, and George Ostery. “Force Generation by Actin Polymerization II: The Elastic Ratchet and Tethered Filaments.” Biophysical Journal 84 (March 2003): 1591-1605.
    Listed reading
  • Orsello, Chase E., Douglas A. Lauffenburger, and Daniel A. Hammer. “Molecular Properties in Cell Adhesion: A Physical and Engineering Perspective.” TRENDS in Biotechnology 19, no. 8 (August 2001): 310-316.
    Listed reading
  • Length, Time and Forces in Biology
    Listed reading
  • kT as Ruler of Molecular Forces
    Listed reading
  • Mahadevan, chapters on Molecular Mechanics from [GKM-Text].
    Listed reading
  • Dill, Chapter 6.
    Listed reading
  • Thermodynamics and Elementary Statistical Mechanics
    Listed reading
  • Ideal Polymer Chains and Entropic Elasticity
    Listed reading
  • Persistent Chain Model and Cooperativity
    Listed reading
  • Examples : Actin Length Fluctuations, Pulling on DNA and Synthetic Polymers
    Listed reading
  • Dill, Chapter 10.
    Listed reading
  • Mechano-Chemistry
    Listed reading
  • Examples : Pulling on Titin, Bond Rupture Experiments
    Listed reading
  • Howard, Chapter 5.
    Listed reading
  • Motility at the Macromolecular Level
    Listed reading
  • Examples : Listeria, Acto-myosin Motors, Kinesin, Vorticellid
    Listed reading
  • Howard, Chapter 10.
    Listed reading
  • Linear Elasticity
    Listed reading
  • Composition and Structure of the Extracellular Matrix (ECM)
    Listed reading
  • Pushing and Pulling on Molecules
    Listed reading
  • Elastic (Time-Independent) Behavior of Tissues
    Listed reading
  • Viscoelastic (Time-Dependent) Behavior of Tissues
    Listed reading
  • Poroelastic (Time-Dependent) Behavior of Tissues
    Listed reading
  • Examples : Muscle and Soft Tissues in Health and Disease - e.g., Arthritis and Joint Degeneration
    Listed reading
  • Electromechanical and Physicochemical Properties of Tissues
    Listed reading
  • Examples : Bone, Muscle, Soft Connective Tissues – Streaming Potentials and Electro-osmosis – Tissue Swelling and Molecular Electromechanical Forces
    Listed reading
  • Muscle Constriction From the Molecular to Macro Scale
    Listed reading
  • Structure of the Cell
    Listed reading
  • Biomembranes
    Listed reading
  • Kamm, chapters on Cell Mechanics from [GKM-text].
    Listed reading
  • The Cytoskeleton
    Listed reading
  • Cell Peeking and Poking
    Listed reading
  • Cell Adhesion and Aggregation
    Listed reading
  • Cell Migration and Mechanotransduction
    Listed reading

Prerequisites & course information

Same subject as 3.971[J] , 6.4842J, 10.537[J] , 20.410[J] Subject meets with 2.797[J] , 3.053[J] , 6.4840J, 20.310[J] Prereq: Biology (GIR) and 18.03 Acad Year 2027-2028: Not offered Acad Year 2028-2029: G (Spring) 3-0-9 units

Sources