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MAE 188/298: MECHANICS OF THE CELL

Spring 2014

Time and Place: MW 12:00 PM 1:50 PM FRANZ 2258A

Instructor: William Klug, 48-121B Engr. IV, (310) 794-7347, klug@ucla.edu

Office Hours: TBD

Course Description: This is an exciting time to be studying Biology. Fantastic advances in molecularand structural biology, and physical experimental techniques such as atomic force microscopy and opticaltweezers are leading increasing abundance of quantitative experimental data describing the mechanics ofmolecules and cells. Imaging techniques and single molecule experiments allow us toalmost literallysee and feel the molecules that work together to produce life. In many cases, these techniques enabledetermination of mechancal properties for molecular structures in much the same way as for macroscopicmaterials: 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 ofthe course will be the idea that the type of quantitative data which is becoming routine in biology calls for acorresponding quantitative modeling framework. The primary tools that we will use for this framework arethose 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 nothave much of a background in building quantitative physical models, this course will be reading-intensiveas you work to make up in part for what you lack. The most important reference for the course will bePhysical Biology of The Cell, 2nd editionby Rob Phillips, Jane Kondev, Julie Theriot, and Hernan Garcia.PBoC is a one of a kind book that shares our main goal of learning biology by constructing quantitativephysical/mathematical models of processes and structures. Most of our models and topics of discussionwill be straight out of PBoC. The book is rich with detail and very readable, and should be an must-haveaddition to your personal library.

Our second text isIntroduction to Cell Mechanics and Mechanobiologyby Jacobs, Huang, and Kwon. Itis not as deep or as broad as PBoC, but has some very good material. In particular it has some very nicesections on muscle mechanics, and also some good primers on solid mechanics and fluid mechanics thatyou might find 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 thephysics and biology of the cell, as well as articles from the current literature. Following is a list of the bookswhich, 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 CellBiology, Garland Publishing, 2003. An introductory undergraduate Biology text. Usually the firstplace 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 isstill quite comprehensible for engineers.

J. Howard, Mechanics of Motor Proteins and the Cytoskeleton, Sinauer Associates, 2001. An-other physics-ish text which contains some very interesting topics.

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H. C. Berg, Random Walks in Biology, Princeton University Press, 1993. Short enough to readin 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 throughon topics you find interesting by checking out these additional references.

Course Website: Handouts, homework, announcements, textbook chapters, and other info will be com-municated 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 twoweeks, and you should expect fairly extensive reading assignments. Your grades will be based upon yourhomework 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 atleast 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 becarefully explained and the significance 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 discussthe 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 anotherpersons computer files, are considered acts of academic dishonesty by the University Academic IntegrityPolicy and the UCLA Student Code of Conduct (www.deanofstudents.ucla.edu), to which I will holdyou accountable.

Under no circumstances should you share (by electronic, printed, visual, or any other means) any of yourwork with another student. I am very serious about this point If you ever find yourself tempted to cheat,please talk to me instead, or look to the Dean of Students Office (www.deanofstudents.ucla.edu) forother 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 mindand your character. Honesty inyour 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 configurations

The Boltzman distribution

Entropy and free energy

Applications: entropic springs, ligand-receptor binding, the law of mass action, mechanosensitiveion channels

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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)

Rectified 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

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