This page lists the assigned readings for each lecture session, plus the paper for the podcast associated with some sessions.
There is no single required textbook for this course. Israelachvili's 1992 book (as cited in the table) provides a good treatment of some fundamentals, but many reading assignments are from more recent published papers.
| LEC # | TOPICS | READINGS | PODCAST PAPERS |
|---|---|---|---|
| 1 | Introduction to nanomechanics |
Scanning electron microscopy images of bacteria on the head of a pin. Feynman, R. P. "There's Plenty of Room at the Bottom." December 29th 1959 Annual meeting of the American Physical Society at the California Institute of Technology (Caltech). Drexler, K. E. "Engines of Construction." Chapter 1 in Engines of Creation: The Coming Era of Nanotechnology. New York, NY: Doubleday, New York, 1987. ISBN: 9780385199735. "Nanotechnology: Shaping the World Atom by Atom." Report by the National Science and Technology Council (NSTC) Committee on Technology The Interagency Working Group on Nanoscience, Engineering and Technology (IWGN) (1999). Shao, J. "Measuring Piconewton Forces and Its Application in Cellular and Molecular Biomechanics." Advances in Biomechanics (2001): 47-51. | |
| 2 | High resolution force spectroscopy (HRFS): The force transducer |
Van Vliet, K. J., G. Bao, and S. Suresh. "The Biomechanics Toolbox: Experimental Approaches for Living Cells and Biomolecules." Acta Materialia 51 (2003): 5881-5905. Ortiz, C. Appendix to 3.052 Lecture 2: Cantilever Summary (PDF) "Basic Introduction to Nanopositioning with Piezoelectric Technology." Tutorial by Physik Instruments, Inc. ( | |
| 3 | Additional nanomechanics instrumentation components | Heinz, W. F., and J. H. Hoh. "Spatially Resolved Force Spectroscopy of Biological Surfaces using the Atomic Force Microscope." Tibtech 17 (1999): 143-150. |
Podcast: Lipid bilayer formation Associated paper: Pera, I., and J. Fritz. "Sensing Lipid Bilayer Formation and Expansion with a Microfabricated Cantilever Array." Langmuir 23, no. 3 (January 30, 2007): 1543-7. |
| 4 | Force versus distance curves |
"Probing Nano-Scale Forces with the Atomic Force Microscope." Veeco Metrology Group. ( Binning, G., C. F. Quate, and C. Gerber. "Atomic Force Microscope." Physical Review Letters 56 (1986): 930-933. | |
| 5 | Atomic force microscope (AFM) imaging |
Baselt, D. "Atomic Force Microscopy: Measuring Intermolecular Interaction Forces." California Institute of Technology, 1993 PhD Thesis, NRL code 6177. Scanning probe/Atomic force microscopy: Technology overview and update. Veeco Metrology Group. ( AFM review articles bibliography (C. Ortiz supplementary course material) Karp, G. "Covalent Bonds" (Section 2.1), and "Noncovalent Bonds" (Section 2.2) in Cell and Molecular Biology. 2nd ed. New York, NY: John Wiley and Sons, Inc., 1999. ISBN: 9780471192794. | |
| 6 | AFM imaging II: Artifacts and applications |
Podcast: Structured water layers Associated paper: Higgins, M. J., et al. "Structured Water Layers Adjacent to Biological Membranes." Biophys J 91 (2006): 2532-2542. | |
| 7 | Single cell mechanics | Dao, M., et al. "Mechanics of the Human Red Blood Cell Deformed by Optical Tweezers." J Mech Phys Solids 53 (2003): 2259-2280. |
Podcast: Mechanics of diseased single cells: Malaria Associated paper: Suresh, et al. "Connections Between Single-cell Biomechanics and Human Disease States: Gastrointestinal Cancer and Malaria." Acta Biomaterialia 1 (2005): 15-30. |
| 8 | Qualitative introduction to intra - and intermolecular forces |
Ortiz, C. "Qualitative Summary of Intra and Intermolecular Forces." MIT Department of Materials Science and Engineering 3.052 Nanomechanics of Materials and Biomaterials; Lecture Notes. Ashby, M. F., and D. R. H. Jones. Chapter 3 "The Elastic Moduli," and Chapter 4 "Bonding Between Atoms." In Engineering Materials 1 - An Introduction to Properties, Applications, and Design. 3rd ed. Burlington MA: Elsevier Butterworth-Heinemann, 2005. ISBN: 9780750663809. Van Vlack, L. H. "Introduction to Materials: Review of Chemical Bonding." Chapter 2 in Elements of Materials Science and Engineering. 5th ed. Boston, MA: Addison-Wesley, 1985. ISBN: 9780201080865. Israelachvili, J. "Classification of Forces." Section 2.6 in Intermolecular and Surface Forces. New York, NY: Academic Press, 1992. ISBN: 9780123751812. | |
| 9 | Quantitative description of intra - and intermolecular forces |
Van Vlack, L. H. "Introduction to Materials: Review of Chemical Bonding." Chapter 2 in Elements of Materials Science and Engineering. 5th ed. Boston, MA: Addison-Wesley, 1985. ISBN: 9780201080865. Israelachvili, J. "Classification of Forces." Section 2.6 in Intermolecular and Surface Forces. New York, NY: Academic Press, 1992. ISBN: 9780123751812. ———. "Contrasts between Intermolecular, Interparticle, and Intersurface Forces." Chapter 10 in Intermolecular and Surface Forces. Malescio, G. "Intermolecular Potentials - Past, Present, and Future." Nature Materials 2 (2003): 501. |
Podcast: Heparin biosensors Associated Paper: Milovic, N. M., et al. "Monitoring of Heparin and its Low-molecular-weight Analogs by Silicon Field Effect." PNAS 103, no. 36 (2006): 13374-13379. |
| 10 | Molecule - surface interactions |
Israelachvili, J. "Contrasts Between Intermolecular, Interparticle, and Intersurface Forces." Chapter 10 in Intermolecular and Surface Forces. ———. "Van der Waals Forces Between Surfaces: The Force Laws for Bodies of Different Geometries - The Hamaker Constant." Chapter 11.1 in Intermolecular and Surface Forces. pp. 176-179. "Table 9.1: Hamaker Constant for various materials." From Freitas, Robert J. Nanomedicine, Volume I: Basic Capabilities. Georgetown, TX: Landes Bioscience, 1999. (JPG) | |
| 11 | Colloids and interparticle potentials | Lewis, J. A. "Colloidal Processing of Ceramics." J Am Ceram Soc 83, no. 10 (2000): 2341-59. |
Podcast: Boundary lubrication Associated Paper: Briscoe, W. H., et al. "Boundary Lubrication Under Water." Nature 444 (2006): 191-194. |
| 12 | Van der Waals forces at work: Gecko feet adhesion |
Autumn, K. "How Gecko Toes Stick." American Scientist 94 (2006): 124-133. Tian, Yu., et al. "Adhesion and Friction in Gecko Toe Attachment and Detachment." PNAS 103, no. 51 (2006): 19320-5. | |
| Midterm exam - during class time 1 hour | |||
| 13 | Midterm exam solutions review | Dupres, V. et al. "Nanoscale Mapping and Functional Analysis of Individual Adhesins on Living Bacteria." Nature Methods 2, no. 7 (2005): 515-520. | |
| 14 | The electrical double layer (EDL) - part 1 |
Israelachvili, J. "Electrostatic Forces Between Surfaces in Liquids." Chapter 12 in Intermolecular and Surface Forces. Buckwalter, J. A., H. J. Mankin, and A. J. Grodinzinsky. "Articular Cartilage and Osteoarthritis." AAOS Instructional Course Lectures 54 (2005): 465-480. |
Podcast: Boundary lubrication Associated Paper: Briscoe, W. H., et al. "Boundary Lubrication Under Water." Nature 444 (2006): 191-194. |
| 15 | The electrical double layer (EDL) - part 2 |
Israelachvili, J. "Electrostatic Forces Between Surfaces in Liquids." Chapter 12 in Intermolecular and Surface Forces. Buckwalter, J. A., H. J. Mankin, and A. J. Grodinzinsky "Articular Cartilage and Osteoarthritis." AAOS Instructional Course Lectures 54 (2005): 465-480. |
Podcast: Cartilage aggrecan Associated Paper: Dean, D., et al. "Compressive Nanomechanics of Opposing Aggrecan Macromolecules." J Biomech 39 (2006): 2555-2565. |
| 16 | Nanomechanics of cartilage |
Ortiz, C. "A Review of Elasticity Models for the Extension of Single Polymer Chains." MIT Department of Materials Science and Engineering 3.052 Nanomechanics of Materials and Biomaterials; supplementary course material. Treloar, L. R. G. "The Elasticity of Long Chain Molecules," and "Non-Gaussian Chain Statistics and Network Theory." Chapters 3 and 6 in The Physics of Rubber Elasticity. Oxford, UK: Clarendon Press, 1975. |
Podcast: Nanomechanics of chondrocytes Associated Paper: Ng, Laurel, et al. "Nanomechanical Properties of Individual Chondrocytes and Their Developing Growth Factor-stimulated Pericellular Matrix." J Biomech 40, no. 5 (2007): 1011-1023. |
| 17 | Protein - surface interactions |
Marko, J. F., and E. D. Siggia. "Stretching DNA." Macromolecules 28 (1995): 8759-8770. Kratky, O. and G. Porod. "X-ray Investigation of Dissolved Chain Molecules." Recueil des Travaux Chimiques des Pays-Bas et de la Belgique (Recl Trav Chim Pas-Bas) 68 (1949): 1106-1122. | |
| 18 | Nanomechanics and biocompatibility: Protein - biomaterial interactions, part 2 | Same as prior session. | |
| 19 | Elasticity of single polymer chains: Theoretical formulations |
Fixman, M. and J. Kovac. "Polymer Conformational Statistics. III. Modified Gaussian Models of Stiff Chains." J Chem Phys 58 (1973): 1574-1568. Bouchiat, C., M. D. Wang, J. F. Allemand, T. Strick, S. M. Block, and V. Croquette. "Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements." Biophysical Journal 76 (1999): 409-413. Odijk, T. "Stiff Chains and Filaments under Tension." Macromolecules 28 (1995): 7016-7018. Rief, M., and H. Helmut Grubmuller. "Force Spectroscopy of Single Biomolecules." ChemPhysChem 3 (2002): 255-261. Fisher, T. E., A. F. Oberhauser, M. Carrion-Vazquez, P. E. Marszalek, and J. M. Fernandez. "The Study of Protein Mechanics With the Atomic Force Microscope." TIBS 24 (1999): 379-384. Austin, R. H., J. P. Brody, E. C. Cox, T. Duke, and W. Volkmuth. "Stretch Genes." Physics Today 50 (1997): 32-38. Clausen-Schaumann, H., M. Rief, C. Tolksdorf, and H. E. Gaub. "Mechanical Stability of Single DNA Molecules." Biophysical Journal 78 (2000): 1997-2007. Smith, B. L., T. E. Schaffer, M. Viani, J. B. Thompson, N. A. Frederick, J. Kindt, A. Belcher, G. D. Stucky, D. E. Morse, and P. K. Hansma. "Molecular Mechanistic Origin of the Toughness of Natural Adhesives, Fibres and Composites." Nature 399 (1999): 761-763. Van Landingham, M., J. S. Villarubia, W. F. Guthrie, and G. F. Meyers. "Nanoindentation of Polymers: An Overview." Macromolecular Symposia 167 (2001): 15-43. |
Podcast: Elasticity of fibronectin Associated Paper: Abu-Lail, N. I., et al. "Understanding the Elasticity of Fibronectin Fibrils: Unfolding Strengths of FN-III and GFP Domains Measured by Single Molecule Force Spectroscopy." Matrix Biology 25 (2006): 175-184. |
| 20 | Theoretical aspects of single molecule force spectroscopy: Extensibility and the worm-like chain (WLC) | Same as prior session. |
Podcast: Sacrificial bonding Associated Paper: Fantner, G. E., et al. "Sacrificial Bonds and Hidden Length: Unraveling Molecular Mesostructures in Tough Materials." Biophys J 90 (2006): 1411-1418. |
| 21 | Single chain elasticity of biomacromolecules: The giant protein titin and DNA | ||
| 22 | Theoretical aspects of nanoindentation |
Oliver, W. C., and G. M. Pharr. "An Improved Technique for Determining Hardness and Elastic-modulus Using Load and Displacement Sensing Indentation Expermiments." J Mater Res 7, no. 6 (June 1992): 1564-1583. Sneddon, Ian. "The Relation Between Load and Penetration in the Axisymmetric Boussinesq Problem for a Punch of Arbitrary Profile." Journal of Engineering Science 3 (1965): 47-57. | |
| 23 | Nanoindentation 2: Oliver-Pharr method and one literature example: Nacre | Bruet, B. J. F., et al. "Nanoscale Morphology and Indentation of Individual Nacre Tablets From the Gastropod Mollusc Trochus Niloticus." J Mater Res 20, no. 9 (September 2005): 2400-2419. | |
| 24 | Intermolecular interactions in motility of a biological spring (Guest lecture by Danielle France, course TA) | Mahadevan, L, and P. Matsudaira. "Motility Powered by Supramolecular Springs and Ratchets." Science 288 (April 7, 2000): 95-99. | |
| Final exam during finals week |
