Readings

[Phillips] = Phillips, R., J. Kondev, and J. Theriot. Physical Biology of the Cell. Garland Science, 2008. ISBN: 9780815341635.

[Dill & Bromberg] = Dill, K., and S. Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry & Biology. Garland Publishing, 2003. [Preview with Google Books]

[Howard] = Howard, J. Mechanics of Motor Proteins and the Cytoskeleton. Sinauer Associates, 2001. ISBN: 9780878933334.

[Jackson] = Jackson, M. B. Molecular and Cellular Biophysics. Cambridge University Press, 2006. ISBN: 9780521624701. [Preview with Google Books]

[Grodzinsky] = Grodzinsky, A. Fields, Forces and Flows in Biological Systems. Garland Science, 2011. ISBN: 9780815342120. [Preview with Google Books]

[Lodish] = Lodish, H., D. Baltimore, et al. Molecular Cell Biology. W. H. Freeman and Company, 2012. ISBN: 9781464109812.

LEC # TOPICS READINGS
Molecular Mechanics
1

Length, Time, & Molecular-scale Forces in Biology

Mahadevan. Macromolecular Mechanics. Chapter 3.

[Phillips] Sections 1.2, 2.1–2.3, 3.1, and 3.4.

2

Single Molecule Mechanics

[Dill & Bromberg] Chapter 17.

[Howard] Chapters 4 and 6.

3

Energy Landscapes and Transition States

[Jackson] Sections 7.1–7.4.
4

Mechanochemistry at the Molecular Scale

[Grodzinsky] Chapter 1, pp. 15–21.
5

Kramer’s and Bell’s Models of Reversible Binding

[Howard] Chapter 5.

Yu, Hao, et al. “Energy Landscape Analysis of Native Folding of the Prion Protein Yields the Diffusion Constant, Transition Path Time, and Rates.” Proceedings of the National Academy of Sciences of the United States of America 109, no. 36 (2012): 14452–7.

6

Experimental Methods in Single Molecule Mechanics

[Phillips] Section 8.3.

Vliet, Van, et al. “The Biomechanics Toolbox: Experimental Approaches for Living Cells and Biomolecules.” Acta Materialia 51, no. 19 (2003): 5881–905.

Tissue Mechanics: Time-Independent Tissue Behavior (Elasticity)
7

Composition of Extracellular Matrix Constituents of Tissues; Relevance to Elastic (Time-independent) Behavior of Tissues

[Grodzinsky] Chapters 7, Section 7.3.

Hynes, Richard O., and Alexandra Naba. “Overview of the Matrisome—an Inventory of Extracellular Matrix Constituents and Functions.” Cold Spring Harbor Perspectives in Biology 4, no. 1 (2012): a004903.

8

Elastic (Time-independent) Behavior of Tissues (cont.)

Kadler, Karl E., Clair Baldock, et al. “Collagens at a Glance.” Journal of Cell Science 120, no. 12 (2007): 1955–8.
9

Elastic (Time-independent) Behavior of Tissues (cont.)

Gordon, Marion K., and Rita A. Hahn. “Collagens.” Cell and Tissue Research 339, no. 1 (2010): 247–57.
Time–dependent Tissue Behavior (Viscoelasticity and Poroelasticity)
10

Finish Topics on Tissue Elasticity; Begin Viscoelasticity

Schwartz, Nancy B. “Proteoglycans.” eLS (2009).
11

Time-dependent Viscoelasticity of Tissues

[Grodzinsky] Chapter 7, Section 7.4.

Gautieri, Alfonso, et al. “Viscoelastic Properties of Model Segments of Collagen Molecules.” Matrix Biology 31, no. 2 (2012): 141–9.

12

Dynamic (Frequency–dependent) Viscoelasticity

Darling, E. M., et al. “Viscoelastic Properties of Zonal Articular Chondrocytes Measured by Atomic Force Microscopy.” Osteoarthritis and Cartilage 14, no. 6 (2006): 571–9.
13

Poroelastic (Time–dependent) Behavior of Tissues

[Grodzinsky] Chapter 7, Section 7.5.

Rosenbluth, Michael J., et al. “Slow Stress Propagation in Adherent Cells.” Biophysical Journal 95, no. 12 (2008): 6052–9.

14

Poroelastic (Frequency–dependent) Behavior of Tissues

[Grodzinsky] Chapter 7, Section 7.5.

Nia, Hadi Tavakoli, et al. “Poroelasticity of Cartilage at the Nanoscale.” Biophysical Journal 101, no. 9 (2011): 2304–13.

Nia, Hadi Tavakoli, et al. “High-bandwidth AFM-based Rheology Reveals that Cartilage is most Sensitive to High Loading Rates at Early Stages of Impairment.” Biophysical Journal 104, no. 7 (2013): 1529–37.

15

Dynamic Nanomechanical Behavior of Extracellular Matrix Macromolecules

[Grodzinsky] Chapter 7, Section 7.6.

Nia, Hadi Tavakoli, et al. “Aggrecan Nanoscale Solid–Fluid Interactions Are a Primary Determinant of Cartilage Dynamic Mechanical Properties.” ACS Nano 9, no. 3 (2015): 2614–25.

16

Time-and Frequency-dependent Behavior of Intracellular Networks

Moeendarbary, Emad, et al. “The Cytoplasm of Living Cells Behaves as a Poroelastic Material.” Nature Materials 12, no. 3 (2013): 253–61.
Cell Mechanics
17

Cell Mechanics: Structure of the Cell

[Lodish] Sections 18.1–3, 19.1–3, and 19.6.

Kamm. Chapter 2.2 (PDF) “Mechanics of the Cytoskeleton.” pp. 1–15.

18

Visco / Poroelasticity, Large Amplitude Deformations

[Lodish] Sections 18.4–18.5.

Kamm. Chapter 2.2: “Mechanics of the Cytoskeleton.” pp. 15–32.

19

Microstructural Models of the Cytoskeleton

Kamm. Chapter 2.2: “Mechanics of the Cytoskeleton.” pp. 32–42.

20

The Cell Membrane

Kamm. Chapter 2.1 (PDF – 1.3MB) “Cell Membrane Mechanics and Adhesion.” pp. 1–13 and 25–30.

21

Cell Motility and Mechanotransduction

[Lodish] Section 18.6.

Kamm. Chapter 2.3 (PDF – 1.4MB) “Active Cell Processes.” pp. 7–17 and 32–48.

Even–Ram, Sharona, and Kenneth M. Yamada. “Cell Migration in 3D Matrix.” Current Opinion in Cell Biology 17, no. 5 (2005): 524–32.

Capstone Problems
22

The Physics of Cancer

Wirtz, Denis, et al. “The Physics of Cancer: The Role of Physical Interactions and Mechanical Forces in Metastasis.” Nature Reviews Cancer 11, no. 7 (2011): 512–22.

23

Molecular Electromechanics: Electromechanical and Physicochemical Properties of Tissues

[Grodzinsky] Chapter 7, Section 7.6.

Wieland, Heike A., et al. “Osteoarthritis—an Untreatable Disease?Nature Reviews Drug Discovery 4, no. 4 (2005): 331–44.

Frank, Eliot H., et al. “Streaming Potentials: A Sensitive Index of Enzymatic Degradation in Articular Cartilage.” Journal of Orthopaedic Research 5, no. 4 (1987): 497–508.

24 Muscle from the Molecular, Cellular and Tissue Perspectives Kamm. Chapter 2.3 (PDF - 1.4MB) “Active Cell Processes.” pp. 18–32.