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| tue || may || 18 || midterm || || | | tue || may || 18 || midterm || || | ||
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| − | | thu || may || 20 || mechanotransduction II - electrophysiology in nerve cells || [http://biomechanics.stanford.edu/me239_10/me239_n16.pdf n16] || [http://biomechanics.stanford.edu/me239_10/me239_s16.pdf s16 | + | | thu || may || 20 || mechanotransduction II - electrophysiology in nerve cells || [http://biomechanics.stanford.edu/me239_10/me239_n16.pdf n16] || [http://biomechanics.stanford.edu/me239_10/me239_s16.pdf s16] |
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| tue || may || 25 || mechanotransduction III - excitation contraction in skeletal muscle and heart cells || [http://biomechanics.stanford.edu/me239_10/me239_n17.pdf n17] || [http://biomechanics.stanford.edu/me239_10/me239_s17.pdf s17] | | tue || may || 25 || mechanotransduction III - excitation contraction in skeletal muscle and heart cells || [http://biomechanics.stanford.edu/me239_10/me239_n17.pdf n17] || [http://biomechanics.stanford.edu/me239_10/me239_s17.pdf s17] | ||
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| − | | tue || may || 25 || mechanics of the cell - the inner life || [http://biomechanics.stanford.edu/me239_10/me239_n18.pdf n18] || | + | | tue || may || 25 || mechanics of the cell - the inner life || [http://biomechanics.stanford.edu/me239_10/me239_n18.pdf n18] || ] [https://www.ebiomedia.com/index.php?page=shop.product_details&flypage=shop.flypage&product_id=60&category_id=7&manufacturer_id=0&option=com_virtuemart&Itemid=38 l01] [http://multimedia.mcb.harvard.edu/anim_innerlife.html l02] |
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| thu || may || 27 || final projects - oral presentations I || [http://biomechanics.stanford.edu/me239_10/me239_p02.pdf p02] || | | thu || may || 27 || final projects - oral presentations I || [http://biomechanics.stanford.edu/me239_10/me239_p02.pdf p02] || | ||
Revision as of 16:25, 30 December 2010
Contents |
me239 - mechanics of the cell
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me239 - mechanics of the cell 11 ellen kuhl, manuel rausch winter 2011 |
goals
cells are the fundamental building blocks of life. the understanding of their characteristic biological features, their motility, their biochemistry and their interaction with the environment is crucial when cells are to be applied, modified or engineered in health care and modern medical therapies. this class focuses on the mechanical aspects of the cell which can be two fold: on the one hand, cell biology and biochemistry influence the mechanical properties of the cell. on the onther hand the mechanical environment, load, pressure, stress or strain can influence the cell's shape and integrity, and eventually its biology and biochemistry. in the first part of this class, we will discuss how cell properties can be measured experimentally and how they can be characterized in the form of equations. concepts of energy and entropy will be elaborated for different structural units of the cell: biopolymers, i.e., microtubules, actin, and intermediate filaments and biomembranes, i.e., the lipid bi-layer that forms the cell membrane. computational simulation tools will be introduced to explain and understand cell behavior in silico. on the second part, we address aspects of mechanotransduction which are part of active research in cell mechanics. we discuss different aspects of how cells sense loads and how signals are transmitted within the cell and through the extracellular matrix.
grading
- 30 % homework - 3 homework assignments, 10% each
- 30 % midterm - closed book, closed notes, one single page cheat sheet
- 20 % final project oral presentations - graded by the class
- 20 % final project essay - graded by instructor
syllabus
| day | date | topic | notes | material | |
|---|---|---|---|---|---|
| tue | jan | 04 | introduction I - cell biology | s01 q01 | |
| thu | jan | 06 | introduction II - cytoskeletal biology, stem cells | n02 | s02 l02 |
| tue | jan | 11 | introduction III - structural mechanics | n03 | s03 |
| thu | jan | 13 | biopolymers I - energy, tension, bending | n04 | s04 |
| tue | jan | 18 | homework I - biopolymers, directed stem cell differentiation | h01 | m04 |
| thu | jan | 20 | biopolymers II - entropy, FJC and WLC model | n05 | s05 |
| tue | jan | 25 | biopolymers III - polymerization kinetics in amoeba | n06 | s06 m06 |
| thu | jan | 27 | cytoskeletal mechanics I - fiber bundle model for filopodia | n07 | s07 m07 |
| tue | jan | 29 | cytoskeletal mechanics II - network model for red blood cells | n08 | s08 |
| tue | apr | 27 | cytoskeletal mechanics III - tensegrity model for generic eukaryotic cells | n09 | s09 m09 |
| tue | apr | 27 | homework II - cytoskeleton, cell mechanics challenges | h02 | m10 |
| thu | apr | 29 | biomembranes I - micropipette aspiration in white blood cells and cartilage cells | n10 | s10 |
| tue | may | 04 | biomembranes II - lipid bilayer, soap bubble, cell membrane | n11 | s11 |
| thu | may | 06 | biomembranes III - energy, tension, shear, bending | n12 | s12 |
| tue | may | 11 | homework III - micropipette aspiration, final project | h03 | m12 |
| tue | may | 11 | mechanotransduction I - inter- and intracellular signaling, bone cells | n13 | s13 |
| thu | may | 13 | summary and midterm preparation | n14 | s14 |
| tue | may | 18 | midterm | ||
| thu | may | 20 | mechanotransduction II - electrophysiology in nerve cells | n16 | s16 |
| tue | may | 25 | mechanotransduction III - excitation contraction in skeletal muscle and heart cells | n17 | s17 |
| tue | may | 25 | mechanics of the cell - the inner life | n18 | ] l01 l02 |
| thu | may | 27 | final projects - oral presentations I | p02 | |
| tue | jun | 01 | final projects - oral presentations II | ||
| tue | jun | 01 | final projects - written projects due | p01 |
copyright ron kwon, ellen kuhl, chris jacobs, stanford, fall 2007, ellen kuhl, spring 2010
course summary
course summary developed in last year's class
42 answers to life, the universe, and everything
example of final project
predicting microtubules structure using molecular dynamics, mechanotransduction in hair cells: translating sound waves into neural signals, modeling cell membrane dynamics, fast and slow adaptation in inner ear hair cells, dielectrophoresis properties and their microfluidic application, cell concentrator, theoretical and experimental study of the mechanics of penetration of the cell membrane, integrin and its role in mechanotransduction, finite element analysis of cell deformation, the tensegrity paradigm, the primary cilium: a well-designed fluid flow sensor (download example)
zheng c, doll jc, gu e, hager-barnard e, huang z, kia aa, ortiz m, petzold b, shi y, suk sd, usui t, kwon r, jacobs c, kuhl e. exploring cellular tensegrity: physical modeling and computational simulation. proceedings of the ASME 2008 summer bioengineering conference 2008, marco island, florida. SBC2008-192407 (download).
additional reading
|
(1) phillips r, kondev j, theriot j (2) boal d (3) howard j (4) alberts b et al |