Syllabus

Course Meeting Times

Lectures: 2 sessions / week, 1.5 hours / session.

Recitation: 2 sessions / week, 1 hour / session.

Prerequisites

2.370 Fundamentals of Nanoengineering or 20.110J Thermodynamics of Biomolecular Systems

18.03SC Differential Equations or 3.016 Mathematics for Materials Scientists and Engineers

Biology (GIR)

One of the following courses:

• 7.01SC Fundamentals of Biology
• 7.012 Introductory Biology
• 7.013 Introductory Biology
• 7.014 Introductory Biology
• 7.016 Introductory Biology

Course Description

This course develops and applies scaling laws and the methods of continuum and statistical mechanics to biomechanical phenomena over a range of length scales, from molecular to cellular to tissue or organ level. It is intended for undergraduate students who have taken a course in differential equations and an introductory course in molecular cell biology. In addition, some background in either statistical or classical thermodynamics is useful. Topics include:

• Molecular mechanics: Mechanics at the nanoscale: Intermolecular forces and their origins; Single molecules; Thermodynamics and statistical mechanics; Formation and dissolution of bonds: Mechanochemistry; Polymer mechanics, Motion at the molecular and macromolecular level; Muscle mechanics; Experimental methods at the single molecule level—optical and magnetic traps, force spectroscopy, single molecule biophysics.

• Tissue mechanics: Elastic (time independent), viscoelastic and poroelastic (yime-dependent) behavior of tissues; Continuum and microstructural models, constitutive laws, electromechanical and physicochemical properties of tissues; Physical regulation of cellular metabolism; Experimental methods—macroscopic rheology.

• Cellular mechanics: Static and dynamic cell processes; Cell migration; Mechanics of biomembranes; The cytoskeleton and cortex; The nucleus; Microrheological properties and their implications; Mechanobiology; Experimental methods—passive and active microrheology, microindentation; Models of cell mechanics.

Textbooks

There are no required textbooks. Most of the reading material will come from journal articles and notes provided by the instructors. Reading material presented in class came from these textbooks:

• Grodzinsky, A. Fields, Forces and Flows in Biological Systems. Garland Science, 2011. ISBN: 9780815342120. [Preview with Google Books]
• Boal, D. Mechanics of the Cell. Cambridge University Press, 2001. ISBN: 9780815342120.
• Lodish, H., D. Baltimore, et al. Molecular Cell Biology. W. H. Freeman & Company, 2012. ISBN: 9781464109812.
• Dill, K., S. Bromberg. Molecular Driving Forces: Statistical Thermodynamics in Chemistry & Biology. Garland Science, 2003. [Preview with Google Books]
• Howard, J. Mechanics of Motor Proteins and the Cytoskeleton. Sinauer Associates, 2001. ISBN: 9780878933334.
• Phillips, R., J. Kondev, et al. Physical Biology of the Cell. Garland Science, 2008. ISBN: 9780815341635.
• Jackson, M. B. Molecular and Cellular Biophysics. Cambridge University Press, 2006. ISBN: 9780521624701. [Preview with Google Books]

These textbooks provide background material that may be useful:

• Nelson, P. Biophysics Chemistry. Wiley-blackwell, 2008. ISBN: 9781405124362.
• Mofrad, M., and R. Kamm. Cytoskeletal Mechanics: Models and Measurements in Cell Mechanics. Cambridge University Press, 2011. ISBN: 9781107648289.
• Mofrad, M., and R. Kamm. Cellular Mechanotransduction: Diverse Perspectives from Molecules to Tissues. Cambridge University Press, 2009. ISBN: 9780521895231.
• Haynie, D. Biological Thermodynamics. Cambridge University Press, 2008. ISBN: 9780521711340. [Preview with Google Books]
• Wales, D. J. Energy Landscapes. With Applications to Clusters, Biomolecules, and Glasses. Cambridge University Press, 2004. ISBN: 9780521814157.
• Downarowicz, T. Entropy in Dynamical Systems. Cambridge University Press, 2011. ISBN: 9780521888851. [Preview with Google Books]
• Ben-naim, A. Entropy Demystified: The Second Law Reduced to Plain Common Sense. World Scientific, 2008. ISBN: 9789812832252. [Preview with Google Books]

Grading