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: William Klug, 48-121B Engr. IV, (310) 794-7347, klug@ucla.edu Ofce Hours: TBD Course Description: This is an exciting time to be studying Biology. Fantastic advances in molecular and structural biology, and physical experimental techniques such as atomic force microscopy and optical tweezers are leading increasing abundance of quantitative experimental data describing the mechanics of molecules and cells. Imaging techniques and single molecule experiments allow us toalmost literally see and feel the molecules that work together to produce life. In many cases, these techniques enable determination of mechancal properties for molecular structures in much the same way as for macroscopic materials: by pushing and pulling on them. This course endeavors to study the cell and its components by making quantitative models to describe what is seen from experiments. The main intellectual theme of the course will be the idea that the type of quantitative data which is becoming routine in biology calls for a corresponding quantitative modeling framework. The primary tools that we will use for this framework are those of continuum elasticity and statistical mechanics. Reading: Since some of you may not have much of a background in Biology, and some of you might not have much of a background in building quantitative physical models, this course will be reading-intensive as you work to make up in part for what you lack. The most important reference for the course will be Kondev, Julie Theriot, and Hernan Garcia. Physical Biology of The Cell, 2nd edition by Rob Phillips, Jane PBoC is a one of a kind book that shares our main goal of learning biology by constructing quantitative physical/mathematical models of processes and structures. Most of our models and topics of discussion will be straight out of PBoC. The book is rich with detail and very readable, and should be an must-have addition to your personal library. Our second text is Introduction to Cell Mechanics and Mechanobiology by Jacobs, Huang, and Kwon. It is not as deep or as broad as PBoC, but has some very good material. In particular it has some very nice sections on muscle mechanics, and also some good primers on solid mechanics and uid mechanics that you might nd helpful if youve not studied those topics before. In addition to thiese texts, I will be recommending reading from a few other outstanding books on the physics and biology of the cell, as well as articles from the current literature. Following is a list of the books which, if you are serious about this topic, youll want to read. B. Alberts, D. Bray, A. Johnson, J. Lewis, M. Raff, K. Roberts and P. Walter, Essential Cell Biology, Garland Publishing, 2003. An introductory undergraduate Biology text. Usually the rst place I turn to learn about a topic in cell Biology. D. Boal, Mechanics of the Cell, 2nd ed., Cambridge University Press, 2011. This discusses most of the topics we will cover in this course. It is written more for a physics audience, but is still quite comprehensible for engineers. J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates, 2001. Another physics-ish text which contains some very interesting topics. 1
H. C. Berg, Random Walks in Biology, Princeton University Press, 1993. Short enough to read in a couple days, but contains a bunch of great insights. We will be discussing random walks, so if you want to go a little deeper this book is great. Ill also note that PBoC is full of great suggestions for further reading. I encourage you to follow through on topics you nd interesting by checking out these additional references. Course Website: Handouts, homework, announcements, textbook chapters, and other info will be communicated through the CourseWeb website, located at http://courseweb.seas.ucla.edu. Coursework and Grading: There will be no exams. Homework will be assigned roughly every one to two weeks, and you should expect fairly extensive reading assignments. Your grades will be based upon your homework grades (100%). I will NOT accept late homeworks (late means anytime after class is over the day the homework is due) unless you have a very good excuse. If you know you will need an extension on an assignment, ask me at least 24 hours before the due date. Regarding collaboration and academic integrity: While I encourage you to discuss the course material and homework with others, your explanations and derivations must be your own. Your logic should be carefully explained and the signicance of your results should also be explained. If you hand me a sloppy (either in thinking or writing) homework, you will likely loose points. While I encourage you to discuss the course material and homework with others, your submitted work must be your own. Unauthorized collaboration, and copying or viewing another persons work, including the transfer and/or use of another persons computer les, are considered acts of academic dishonesty by the University Academic Integrity Policy and the UCLA Student Code of Conduct (www.deanofstudents.ucla.edu), to which I will hold you accountable. Under no circumstances should you share (by electronic, printed, visual, or any other means) any of your work with another student. I am very serious about this point If you ever nd yourself tempted to cheat, please talk to me instead, or look to the Dean of Students Ofce (www.deanofstudents.ucla.edu) for other ways to get help. The bottom line here: A university education is about so much more than gaining knowledge and a good GPA. Most importantly it is about challenging and developing your mind and your character. Honesty in your academic work will develop into professional integrity. Course Outline (tentative): 1. Biological structure by the numbers (12 weeks) Overview of structure in molecular cell biology Spatial scales. Rates and time. Mass, energy, and force: mechanics at the scale of the cell 2. Statistical mechanics (2 weeks) The energies of congurations The Boltzman distribution Entropy and free energy Applications: entropic springs, ligand-receptor binding, the law of mass action, mechanosensitive ion channels
3. Random walks and macromolecules (1 week) Polymers as random walks Single-molecule force-extension curvesfreely-jointed and worm-like chains Protein folding 4. Structural Mechanics in cell biology (12 weeks) Mechanics of beams: bend, twist, and writhe Applications: Transcriptional regulation, DNA packing, the cytoskeleton Biotechnology: atomic force microscopy and biosensing cantilevers Mechanics of shells and membranes: bending and stretching Applications: lipid membranes, viral capsids 5. Molecular motors (1 week) Rectied Brownian motion The polymerization ratchet The translocation ratchet 6. Electromechanics of muscle cell contraction (1 week) Biological electricity: Hodgkin-Huxley and the action potential Sarcomere mechanics 7. Pattern formation (1-2 weeks) Reaction-diffusion and spatial patterns Application: embryonic development