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These readings are presented in chronological order. The table below maps the readings to specific lecture sessions. Suggested Readings
[GKM-Text] = Grodzinsky, A., R. Kamm, and L. Mahadevan. Molecular, Cell and Tissue Biomechanics. Draft of textbook in preparation, 2003.
Daune, Michel. Chapter 2 in Molecular Biophysics. New York, NY: Oxford University Press, 1999. ISBN: 9780198577836.
Dill, K. A., and S. Bromberg. Chapters 6, 8 and 10 in Molecular Driving Forces. New York, NY: Routledge, 2002. ISBN: 9780815320517.
Boal, David H. Chapter 2 in Mechanics of the Cell. Cambridge, UK: Cambridge University Press, 2002. ISBN: 9780521792585.
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.
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.
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.
Howard, Johnathon. Chapters 5 and 10 in Mechanics of Motor Proteins and the Cytoskeleton. Sunderland, MA: Sinauer Associates, 2001. ISBN: 9780878933341.
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.
Mahadevan, L., and P. Matsudaira. "Motility Powered by Supramolecular Springs and Ratchets." Science 288 (April 2000): 95-99.
Ward, J. P. Solid Mechanics. New York, NY: Springer, 1992. ISBN: 9780792319498.
Lodish, H., et. al. Molecular Cell Biology. 3rd. ed. New York, NY: Scientific American Books/W.H. Freeman, 1995. ISBN: 9780716723806.
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.
Fung, Y. C. Biomechanics: Mechanical Properties of Living Tissues. New York, NY: Springer-Verlag, 1993. ISBN: 9780387979472.
Ferry, J. D. "The Nature of Viscoelastic Behavior." Chapter 1 in Viscoelastic Properties of Polymers. New York, NY: Wiley, 1980. ISBN: 9780471048947.
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.
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.
Notes on Fiber Matrix Permeability. (PDF)
Kamm, R. "Derivation of the Viscous Flow Equations." 1999. (PDF)
Sonin, A. A. The Physical Basis of Dimensional Analysis. 2nd ed. (Self-published work.) MIT, 2001.
Stamenovic, D., and D. E. Ingber. "Models of Cytoskeletal Mechanics of Adherent Cells." Biomechan Model Mechanobiol. 1 (2002): 95-108.
Problem from Spring 2002: Oscillatory Compression of Poroelastic Tissue. (PDF)
Pollard Thomas D., and Gary G. Borisy. "Cellular Motility Driven by Assembly and Disassembly of Actin Filaments." Cell 112 (February 2003): 453-465.
Mogilner, Alex, and George Ostery. "Force Generation by Actin Polymerization II: The Elastic Ratchet and Tethered Filaments." Biophysical Journal 84 (March 2003): 1591-1605.
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.
| L1 | Introduction: From Tissue Biomechanics to Molecular Nanomechanics | | | Molecular Mechanics | | L2 | Length, Time and Forces in Biology
Molecules of Interest: DNA, Proteins, Actin, Peptides, Lipids
Molecular Forces: Charges, Dipole, Van der Waals, Hydrogen Bonding
kT as Ruler of Molecular Forces
Thermal Forces and Brownian Motion
Life at Low Reynolds Number | Mahadevan, chapters on Molecular Mechanics from [GKM-Text].
Daune.
Dill, Chapter 6. | | L3 | Thermodynamics and Elementary Statistical Mechanics
Review of Classical Thermodynamics: Entropy, Equilibrium, Open Systems, Ensembles, Boltzmann Distribution, Entropic Forces | Dill, Chapter 8. | | L4 | Ideal Polymer Chains and Entropic Elasticity
Statistics of Random Walks - Freely Jointed Chain - Origins of Elastic Forces
Extreme Extension of a FJC and Modeling Force as an Effective Potential Field | Boal.
Mahadevan, chapters on Molecular Mechanics from [GKM-Text].
Journal articles. | | L5 | Persistent Chain Model and Cooperativity
The Worm-like Chain Model - Persistence Length as a Measure of Rigidity - Cooperativity Modeled using Ising Models
Examples: Actin Length Fluctuations, Pulling on DNA and Synthetic Polymers | Dill, Chapter 10.
Journal articles. | | L6 | Mechano-Chemistry
Reactions and Chemical Equilibrium - Kramers/Eyring Rate Theories - Effect of Forces on Chemical Equilibrium
Examples: Pulling on Titin, Bond Rupture Experiments | Howard, Chapter 5.
Journal articles. | | L7 | Motility at the Macromolecular Level
Forces by Polymerization - Concept of Equilibrium Force - Motor Proteins - Molecular Springs
Examples: Listeria, Acto-myosin Motors, Kinesin, Vorticellid | Howard, Chapter 10.
Journal articles. | | L8 | Linear Elasticity
Continuum Mechanics - Basis of Linear Elasticity: Stress, Strain vs. Strain-rate, Hooke's Law, Experiments to Measure the Moduli | Ward. | | Tissue Mechanics | | L9 | Composition and Structure of the Extracellular Matrix (ECM)
Collagens, Proteoglycans, Elastin - Cellular Synthesis and Secretion of ECM Macromolecules - Cell-mediated Assembly of ECM | Lodish.
Journal articles.
Comper, W. D., ed. Extracellular Matrix. Collagen Superfamily, Proteoglycan Superfamily, and Elastin. | | L10 | Pushing and Pulling on Molecules
Guest Lecturer: Prof. Matt Lang | | | L11 | Elastic (Time-Independent) Behavior of Tissues
Stress and Strain in Tissues Modeled via Hookian Constitutive Law - Homogeneous/NonHomogeneous - Isotropic/Anisotropic - Linear/Nonlinear Behavior of Tissues and Relation to the ECM - Relation between Molecular Constituents and Macroscopic Tensile, Compressive, and Shear Properties of Connective Tissues | | | L12 | Examples
Isotropic Cross-linked Gels Compared to Fibrous Tissues such as Arterial Wall, Cornea (Relevant to Corneal Dystrophy), Tendon, Ligament, Cartilage, Bone, Lung | Fung.
Flory.
Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text].
Journal articles. | | L13 | Viscoelastic (Time-Dependent) Behavior of Tissues
Time-dependent Viscoelastic Behavior of Tissues as Single-phase Materials - Transient Behavior (Creep and Stress Relaxation) - Dynamic Behavior (Storage and Loss Moduli) - Lumped Parameter Models (Advantages and Limitations)
Examples | Journal articles.
Ferry.
Fung.
Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text]. | | L14 | Viscoelastic (Time-Dependent) Behavior of Tissues (cont.) | | | L15 | Poroelastic (Time-Dependent) Behavior of Tissues
The Role of Fluid/Matrix Interactions in Tissue Biomechanics - Darcy's Law and Hydraulic Permeability, Continuity, Conservation of Momentum - Creep, Stress Relaxation, Dynamic Moduli Revisited - Poro-viscoelastic Behavior
Examples: Muscle and Soft Tissues in Health and Disease - e.g., Arthritis and Joint Degeneration | Journal articles.
Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text]. | | E1 | Midterm Quiz | | | L16 | Poroelastic (Time-Dependent) Behavior of Tissues (cont.) | | | L17 | Electromechanical and Physicochemical Properties of Tissues
Role of Electrical and Chemical Phenomena in Determining Tissue Biomechanical Behavior - Fluid Convection of Ions During Tissue Deformation and the Resulting "Electrokinetic" Phenomena - Electrostatic Interactions between Charged ECM
Molecules: Tissue Swelling and Donnan Osmotic Swelling Pressure
Examples: Bone, Muscle, Soft Connective Tissues -- Streaming Potentials and Electro-osmosis -- Tissue Swelling and Molecular Electromechanical Forces | Journal articles.
Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text]. | | L18 | Muscle Constriction From the Molecular to Macro Scale
Characteristics of Contracting Muscle - Hill's Equation - Force-velocity Curves - Muscle Energetics, Activation - Cross-bridge Dynamics - Models for Muscle Behavior | Kamm, chapters on Cell Mechanics from [GKM-text]. | | Cell Mechanics | | L19 | Structure of the Cell
Cellular Anatomy, Cytoskeleton, Membrane, Types of Attachment to Neighboring Cells or the ECM, Receptors, Different Cell Types, Experimental Measurements of Mechanical Behavior | Lodish. | | L20 | Biomembranes
Stiffness and Role of Transmembrane Proteins - Equations for a 2-D Elastic Plate - Patch-clamp Experiments - Membrane Cortex - Vesicles: Model Systems | Kamm, chapters on Cell Mechanics from [GKM-text].
Journal articles. | | L21 | The Cytoskeleton
Fiber Microstructure - Actin and Microtubule Dynamics, Methods of Visualizing Actin Diffusion and Polymerization - Rheology of the Cytoskeleton - Active and Passive Measures of Deformation - Storage and Loss Moduli and their Measurements - Models of the Cytoskeleton: Continuum, Microstructural - Tensegrity, Cellular Solids, Polymer Solution | Lodish.
Kamm, chapters on Cell Mechanics from [GKM-text]. | | L22 | Cell Peeking and Poking
Guest Lecturer: Prof. Peter So | | | L23 | The Cytoskeleton (cont.) | | | L24 | Cell Adhesion and Aggregation
Cell Adhesion Assays, Cell-free Adhesion Assays - Receptor-ligand Interactions Mediated by the Cytoskeleton and the Cell Membrane - Focal Adhesions | Kamm, chapters on Cell Mechanics from [GKM-text].
Journal articles. | | L25/E2 | Cell Migration and Mechanotransduction
Measurement of Cell Motility (Speed, Persistence, "Diffusivity") - Simple Models for Cell Migration - Actin Filament Assembly/Crosslinking and Disassembly - Intracellular Signaling Relating to Physical Force - Molecular Mechanisms of Force Transduction - Force Estimates and Distribution within the Cell | Kamm, chapters on Cell Mechanics from [GKM-text].
Orsello. |
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