Molecular, Cellular and Tissue Biomechanics (BE.410J) >> Content Detail

Study Materials


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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.

Amazon logo Daune, Michel. Chapter 2 in Molecular Biophysics. New York, NY: Oxford University Press, 1999. ISBN: 9780198577836.

Amazon logo Dill, K. A., and S. Bromberg. Chapters 6, 8 and 10 in Molecular Driving Forces. New York, NY: Routledge, 2002. ISBN: 9780815320517.

Amazon logo 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.

Amazon logo 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.

Amazon logo Ward, J. P. Solid Mechanics. New York, NY: Springer, 1992. ISBN: 9780792319498.

Amazon logo 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.

Amazon logo Fung, Y. C. Biomechanics: Mechanical Properties of Living Tissues. New York, NY: Springer-Verlag, 1993. ISBN: 9780387979472.

Amazon logo 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.

L1Introduction: From Tissue Biomechanics to Molecular Nanomechanics
Molecular Mechanics
L2Length, 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].


Dill, Chapter 6.
L3Thermodynamics and Elementary Statistical Mechanics

Review of Classical Thermodynamics: Entropy, Equilibrium, Open Systems, Ensembles, Boltzmann Distribution, Entropic Forces
Dill, Chapter 8.
L4Ideal 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

Mahadevan, chapters on Molecular Mechanics from [GKM-Text].

Journal articles.
L5Persistent 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.

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.
L7Motility 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.
L8Linear Elasticity

Continuum Mechanics - Basis of Linear Elasticity: Stress, Strain vs. Strain-rate, Hooke's Law, Experiments to Measure the Moduli
Tissue Mechanics
L9Composition and Structure of the Extracellular Matrix (ECM)

Collagens, Proteoglycans, Elastin - Cellular Synthesis and Secretion of ECM Macromolecules - Cell-mediated Assembly of ECM

Journal articles.

Comper, W. D., ed. Extracellular Matrix. Collagen Superfamily, Proteoglycan Superfamily, and Elastin.
L10Pushing and Pulling on Molecules

Guest Lecturer: Prof. Matt Lang
L11Elastic (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

Isotropic Cross-linked Gels Compared to Fibrous Tissues such as Arterial Wall, Cornea (Relevant to Corneal Dystrophy), Tendon, Ligament, Cartilage, Bone, Lung


Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text].

Journal articles.
L13Viscoelastic (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)

Journal articles.



Grodzinsky, "Time Dependent Mechanical Behavior of Hydrated Biological Tissues," from [GKM-Text].
L14Viscoelastic (Time-Dependent) Behavior of Tissues (cont.)
L15Poroelastic (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].
E1Midterm Quiz
L16Poroelastic (Time-Dependent) Behavior of Tissues (cont.)
L17Electromechanical 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].
L18Muscle 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
L19Structure 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

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.
L21The 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

Kamm, chapters on Cell Mechanics from [GKM-text].
L22Cell Peeking and Poking

Guest Lecturer: Prof. Peter So
L23The Cytoskeleton (cont.)
L24Cell 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/E2Cell 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].



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