living matter lab
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==goals==
 
==goals==
  
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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.
+
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. in 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==
 
==grading==
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! day !! date !! !! topic !! notes !! material
 
! day !! date !! !! topic !! notes !! material
 
|-
 
|-
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| tue || mar || 30 || introduction I - cell biology ||  || [http://biomechanics.stanford.edu/me239_10/me239_s01.pdf s01] [http://biomechanics.stanford.edu/me239_10/me239_q01r.pdf q01]  
+
| tue || jan || 04 || introduction I - cell biology ||  || [http://biomechanics.stanford.edu/me239_11/me239_s01.pdf s01] [http://biomechanics.stanford.edu/me239_11/me239_q01r.pdf q01]  
 
|-
 
|-
−
| thu || apr || 01 || introduction II - cytoskeletal biology, stem cells || [http://biomechanics.stanford.edu/me239_10/me239_n02.pdf n02] || [http://biomechanics.stanford.edu/me239_10/me239_s02.pdf s02] [http://multimedia.mcb.harvard.edu/anim_innerlife.html l02]
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| thu || jan || 06 || introduction II - cytoskeletal biology, stem cells || [http://biomechanics.stanford.edu/me239_11/me239_n02.pdf n02] || [http://biomechanics.stanford.edu/me239_11/me239_s02.pdf s02] [http://multimedia.mcb.harvard.edu/anim_innerlife.html l02]
 
|-
 
|-
−
| tue || apr || 06 || introduction III - structural mechanics || [http://biomechanics.stanford.edu/me239_10/me239_n03.pdf n03] || [http://biomechanics.stanford.edu/me239_10/me239_s03.pdf s03]
+
| tue || jan || 11 || introduction III - structural mechanics || [http://biomechanics.stanford.edu/me239_11/me239_n03.pdf n03] || [http://biomechanics.stanford.edu/me239_11/me239_s03.pdf s03]
 
|-
 
|-
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| thu || apr || 08 || biopolymers I - energy, tension, bending || [http://biomechanics.stanford.edu/me239_10/me239_n04.pdf n04] || [http://biomechanics.stanford.edu/me239_10/me239_s04.pdf s04]
+
| thu || jan || 13 || biopolymers I - energy, tension, bending || [http://biomechanics.stanford.edu/me239_11/me239_n04.pdf n04] || [http://biomechanics.stanford.edu/me239_11/me239_s04.pdf s04]
 
|-
 
|-
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| thu || apr || 08 || homework I - biopolymers, directed stem cell differentiation || [http://biomechanics.stanford.edu/me239_10/me239_h01_all.pdf h01] || [http://biomechanics.stanford.edu/me239_10/engler06.pdf m04]  
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| thu || jan || 13 || homework I - biopolymers, directed stem cell differentiation || [http://biomechanics.stanford.edu/me239_11/me239_h01.pdf h01] || [http://biomechanics.stanford.edu/me239_11/engler06.pdf m04]  
 
|-
 
|-
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| tue || apr || 13 || biopolymers II - entropy, FJC and WLC model|| [http://biomechanics.stanford.edu/me239_10/me239_n05.pdf n05] || [http://biomechanics.stanford.edu/me239_10/me239_s05.pdf s05]  
+
| tue || jan || 18 || biopolymers II - entropy, FJC and WLC model|| [http://biomechanics.stanford.edu/me239_11/me239_n05.pdf n05] || [http://biomechanics.stanford.edu/me239_11/me239_s05.pdf s05]  
 
|-
 
|-
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| thu || apr || 15 || biopolymers III - polymerization kinetics in amoeba ||  [http://biomechanics.stanford.edu/me239_10/me239_n06.pdf n06] || [http://biomechanics.stanford.edu/me239_10/me239_s06.pdf s06] [http://biomechanics.stanford.edu/me239_10/me239_m06.pdf m06]  
+
| thu || jan || 20 || biopolymers III - polymerization kinetics in amoeba ||  [http://biomechanics.stanford.edu/me239_11/me239_n06.pdf n06] || [http://biomechanics.stanford.edu/me239_11/me239_s06.pdf s06] [http://biomechanics.stanford.edu/me239_11/me239_m06.pdf m06]  
 
|-
 
|-
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| tue || apr || 20 || cytoskeletal mechanics I - fiber bundle model for filopodia || [http://biomechanics.stanford.edu/me239_10/me239_n07.pdf n07] || [http://biomechanics.stanford.edu/me239_10/me239_s07.pdf s07] [http://biomechanics.stanford.edu/me239_10/vignjevic06.pdf m07]     
+
| tue || jan || 25 || cytoskeletal mechanics I - fiber bundle model for filopodia || [http://biomechanics.stanford.edu/me239_11/me239_n07.pdf n07] || [http://biomechanics.stanford.edu/me239_11/me239_s07.pdf s07] [http://biomechanics.stanford.edu/me239_11/vignjevic06.pdf m07]     
 
|-
 
|-
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| thu || apr || 22 || cytoskeletal mechanics II - network model for red blood cells || [http://biomechanics.stanford.edu/me239_10/me239_n08.pdf n08] || [http://biomechanics.stanford.edu/me239_10/me239_s08.pdf s08]   
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| thu || jan || 27 || cytoskeletal mechanics II - network model for red blood cells || [http://biomechanics.stanford.edu/me239_11/me239_n08.pdf n08] || [http://biomechanics.stanford.edu/me239_11/me239_s08.pdf s08]   
 
|-
 
|-
−
| tue || apr || 27 || cytoskeletal mechanics III - tensegrity model for generic eukaryotic cells || [http://biomechanics.stanford.edu/me239_10/me239_n09.pdf n09] || [http://biomechanics.stanford.edu/me239_10/me239_s09.pdf s09] [http://biomechanics.stanford.edu/me239_10/ingber98.pdf m09] 
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| thu || jan || 27 || homework II - cytoskeleton, cell mechanics challenges || [http://biomechanics.stanford.edu/me239_11/me239_h02.pdf h02] || [http://biomechanics.stanford.edu/me239_11/me239_m10.pdf m10]
 
|-
 
|-
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| tue || apr || 27 || homework II - cytoskeleton, cell mechanics challenges || [http://biomechanics.stanford.edu/me239_10/me239_h02.pdf h02] || [http://biomechanics.stanford.edu/me239_10/me239_m10.pdf m10]
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| tue || feb || 01 || cytoskeletal mechanics III - tensegrity model for generic eukaryotic cells || [http://biomechanics.stanford.edu/me239_11/me239_n09.pdf n09] || [http://biomechanics.stanford.edu/me239_11/me239_s09.pdf s09] [http://biomechanics.stanford.edu/me239_11/ingber98.pdf m09] 
 
|-
 
|-
−
| thu || apr || 29 || biomembranes I - micropipette aspiration in white blood cells and cartilage cells || [http://biomechanics.stanford.edu/me239_10/me239_n10.pdf n10]  || [http://biomechanics.stanford.edu/me239_10/me239_s10.pdf s10]
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| thu || feb || 03 || biomembranes I - micropipette aspiration in white blood cells and cartilage cells || [http://biomechanics.stanford.edu/me239_11/me239_n10.pdf n10]  || [http://biomechanics.stanford.edu/me239_11/me239_s10.pdf s10]
 
|-
 
|-
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| tue || may || 04 || biomembranes II - lipid bilayer, soap bubble, cell membrane || [http://biomechanics.stanford.edu/me239_10/me239_n11.pdf n11] ||    [http://biomechanics.stanford.edu/me239_10/me239_s11.pdf s11]
+
| tue || feb|| 08 || biomembranes II - lipid bilayer, soap bubble, cell membrane || [http://biomechanics.stanford.edu/me239_11/me239_n11.pdf n11] ||    [http://biomechanics.stanford.edu/me239_11/me239_s11.pdf s11]
 
|-
 
|-
−
| thu || may || 06 || biomembranes III - energy, tension, shear, bending || [http://biomechanics.stanford.edu/me239_10/me239_n12.pdf n12] || [http://biomechanics.stanford.edu/me239_10/me239_s12.pdf s12]  
+
| thu || feb || 10 || biomembranes III - energy, tension, shear, bending || [http://biomechanics.stanford.edu/me239_11/me239_n12.pdf n12] || [http://biomechanics.stanford.edu/me239_11/me239_s12.pdf s12]  
 
|-
 
|-
−
| tue || may || 11 || homework III - micropipette aspiration, final project || [http://biomechanics.stanford.edu/me239_10/me239_h03.pdf h03] || [http://biomechanics.stanford.edu/me239_10/me239_m12.pdf m12]
+
| tue || feb || 15 || mechanotransduction I - inter- and intracellular signaling, bone cells || [http://biomechanics.stanford.edu/me239_11/me239_n13.pdf n13] || [http://biomechanics.stanford.edu/me239_11/me239_s13.pdf s13]
 
|-
 
|-
−
| tue || may || 11 || mechanotransduction I - inter- and intracellular signaling, bone cells || [http://biomechanics.stanford.edu/me239_10/me239_n13.pdf n13] || [http://biomechanics.stanford.edu/me239_10/me239_s13.pdf s13]  
+
| tue || feb || 15 || homework III - micropipette aspiration, final project || [http://biomechanics.stanford.edu/me239_11/me239_h03.pdf h03] || [http://biomechanics.stanford.edu/me239_11/me239_m12.pdf m12]  
 
|-
 
|-
−
| thu || may || 13 || summary and midterm preparation || [http://biomechanics.stanford.edu/me239_10/me239_n18.pdf n14]  || [http://biomechanics.stanford.edu/me239_10/me239_s14.pdf s14]   
+
| thu || feb || 17 || summary and midterm preparation || [http://biomechanics.stanford.edu/me239_11/me239_n18.pdf n14]  || [http://biomechanics.stanford.edu/me239_11/me239_s14.pdf s14]   
 
|-
 
|-
−
| tue || may || 18 || midterm ||  ||   
+
| tue || feb || 22 || midterm ||  ||   
 
|-
 
|-
−
| 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] [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]
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| thu || feb || 24 || mechanotransduction II - electrophysiology in nerve cells  || [http://biomechanics.stanford.edu/me239_11/me239_n16.pdf n16]  || [http://biomechanics.stanford.edu/me239_11/me239_s16.pdf s16]
 
|-
 
|-
−
| 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]  [http://multimedia.mcb.harvard.edu/anim_innerlife.html l02]
+
| tue || mar || 01 || mechanotransduction III - excitation contraction in skeletal muscle and heart cells  || [http://biomechanics.stanford.edu/me239_11/me239_n17.pdf n17] ||  [http://biomechanics.stanford.edu/me239_11/me239_s17.pdf s17]   
 
|-
 
|-
−
| thu || may || 27 || final projects - oral presentations I || [http://biomechanics.stanford.edu/me239_10/me239_p02.pdf p02] ||  
+
| thu || mar || 03 || mechanics of the cell - the inner life  || [http://biomechanics.stanford.edu/me239_11/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]
 
|-
 
|-
−
| tue || jun || 01 || final projects - oral presentations II || ||
+
| tue || mar || 08 || final projects - oral presentations I || [http://biomechanics.stanford.edu/me239_11/me239_p02.pdf p02] ||  
 
|-
 
|-
−
| tue || jun || 01 || final projects - written projects due || [http://biomechanics.stanford.edu/me239_10/me239_p01.doc p01]  ||  
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| thu || mar || 10 || final projects - oral presentations II ||  ||
 +
|-
 +
| fri || mar || 11 || final projects - written projects due || [http://biomechanics.stanford.edu/me239_11/me239_p01.doc p01]  ||  
 
|-
 
|-
 
|}
 
|}
 
copyright ron kwon, ellen kuhl, chris jacobs, stanford, fall 2007,
 
copyright ron kwon, ellen kuhl, chris jacobs, stanford, fall 2007,
 +
ellen kuhl, fall 2008,
 
ellen kuhl, spring 2010
 
ellen kuhl, spring 2010
  
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[[42 answers to life, the universe, and everything]]
 
[[42 answers to life, the universe, and everything]]
  
−
==last year's final projects==
+
==example of final project==
  
 
predicting microtubules structure using molecular dynamics,
 
predicting microtubules structure using molecular dynamics,
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proceedings of the ASME 2008 summer bioengineering conference 2008,
 
proceedings of the ASME 2008 summer bioengineering conference 2008,
 
marco island, florida. SBC2008-192407 [http://biomechanics.stanford.edu/confr/zheng08.pdf (download)].
 
marco island, florida. SBC2008-192407 [http://biomechanics.stanford.edu/confr/zheng08.pdf (download)].
−
 
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==last year's cell design contest==
 
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−
design the stiffest and yet lightest cell! we will carry out simple tension and shear tests on your cell and determine its homogenized tension and shear stiffness. the stiffest and lightest cell will win. most creative designs will be awarded as well! [http://biomechanics.stanford.edu/me339/me339_d01.pdf and the winner is...]
 
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<html>
 
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    <center>
 
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    <table>
 
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        <tr>
 
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        <td><img src="me339/DESIGN/cell_brian02.jpg">
 
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        <td><img src="me339/DESIGN/cell_lizzie02.jpg">
 
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        <td><img src="me339/DESIGN/cell_joey01.jpg">
 
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        <td><img src="me339/DESIGN/cell_zubin01.jpg">
 
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        </tr>
 
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    </table>
 
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    </center>
 
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</html>
 
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<html>
 
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    <center>
 
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    <table>
 
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        <tr>
 
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        <td><img src="me339/DESIGN/cell_chunhua04.jpg">
 
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        <td><img src="me339/DESIGN/cell_joey02.jpg">
 
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        <td><img src="me339/DESIGN/cell_ellen01.jpg">
 
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        <td><img src="me339/DESIGN/cell_takane01.jpg">
 
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        </tr>
 
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    </table>
 
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    </center>
 
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</html>
 
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<html>
 
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    <center>
 
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    <table>
 
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        <tr>
 
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        <td><img src="me339/DESIGN/cell_lizzie03.jpg">
 
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        <td><img src="me339/DESIGN/cell_brian01.jpg">
 
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        <td><img src="me339/DESIGN/cell_lizzie01.jpg">
 
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        <td><img src="me339/DESIGN/cell_chunhua03.jpg">
 
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        </tr>
 
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    </table>
 
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    </center>
 
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</html>
 
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==matlab files for cell design==
 
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tensegrity structures have been known as architectual elements in structural design for a long time. due to the sophisticated structural interplay between compressive trusses tied together by tensile ropes they are super light weight structures with an incredible degree of stiffness and stability. a biological cell can be modeled as a tensegrity structure with microtubules as compressive elements and actin and intermediate filaments as prestressed tensile elements.  <br>
 
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<html>
 
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    <center>
 
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    <table>
 
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        <tr>
 
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        <td><img src="tensegrity01/cell01d.jpg">
 
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        <td><img src="tensegrity01/cell02d.jpg">
 
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        <td><img src="tensegrity01/cell03d.jpg">
 
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        <td><img src="tensegrity01/cell04d.jpg">
 
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        </tr>
 
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    </table>
 
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    </center>
 
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</html>
 
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the above tensegrity structures have been plotted with the matlab codes below. you might want to look at them as examples.
 
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[http://biomechanics.stanford.edu/me339/design_cell01.m design_cell01.m] ... the one we did in class<br>
 
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[http://biomechanics.stanford.edu/me339/design_cell02.m design_cell02.m] ... the one without nucleus <br>
 
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[http://biomechanics.stanford.edu/me339/design_cell03.m design_cell03.m] ... the one with nucleus <br>
 
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[http://biomechanics.stanford.edu/me339/design_cell04.m design_cell04.m] ... the one with discretized nucleus <br>
 
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now design your own cell! use the above files as examples. define the nodel coordinates q0 and the element connectivity el. plot and describe your cell design!
 
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==matlab files for fe analysis of cells==
 
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now, if you wanted to see how your cell behaves when subjected to loading, you would have to download the finite element files below.
 
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<html>
 
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    <center>
 
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    <table>
 
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        <tr>
 
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        <td><img src="tensegrity01/cell01.jpg">
 
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        <td><img src="tensegrity01/cell02.jpg">
 
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        <td><img src="tensegrity01/cell03.jpg">
 
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        <td><img src="tensegrity01/cell04.jpg">
 
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        <td><img src="tensegrity01/cell05.jpg">
 
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        </tr>
 
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    </table>
 
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    </center>
 
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</html>
 
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download the matlab nonlinear finite element code for the tensegrity cell 
 
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[http://biomechanics.stanford.edu/me339/matlab_cell.tar.gz *now*]
 
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and you'll get a second one for your grandmother for free: [http://biomechanics.stanford.edu/me339/matlab_cell.tar.gz matlab_cell.tar.gz] !<br>
 
−
 
−
* start the finite element program by typing 'nlin_fem' into the matlab editor! you should see the undeformed cell structure on the left, the red trusses represent microtubules as compressive elements and the blue ropes represent the intermediate filaments as tensile elements. <br>
 
−
* load the structure by typing 'step,,5' which applies a load to the three top nodes while the bottom nodes are fixed! you should see the sequence of configurations depicted above. in the matlab editor, you see the quadratic convergence of the newton method which is applied to solve the non linear finite element tensegrity equations.<br>
 
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* add an additional load by typing 'step,,10' and then unload by typing 'step,,-14'! check the characteristic features of tensegrity structures whose members rotate with respect to the vertical loading axis to stiffen the structure. the color code reflects the stress state of the elements, blue is tension, red is compression, compressive ropes are not depicted. <br>
 
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* try to do the same with the second input file by editing the 'nlin_fem.m' file and putting the % symbol in front of the 8th line rather than the 7th! <br>
 
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* modify the material parameters, the boundary conditions, the loading or the prestress by editing the input file! you will experience that the tensegrity cell structure is extremely sensitive to the prestress vs loading relation because its ropes will collapse in compression. the calculation fails because the structure loses integrity, the stiffness matrix is no longer invertible.
 
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take a look @all the individual files you downloaded<br>
 
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i've tried to put comments to most of the variables, send me an email if you want moooore ;-)
 
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[http://biomechanics.stanford.edu/me339/nlin_fem.m nlin_fem.m] ... the one and only <br>
 
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[http://biomechanics.stanford.edu/me339/truss_03.m truss_03.m] ... the one with the 3d truss and rope elements <br>
 
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[http://biomechanics.stanford.edu/me339/inp_cell.m inp_cell.m] ... the cell input file with nucleus <br>
 
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[http://biomechanics.stanford.edu/me339/inp_tens.m inp_tens.m] ... the cell input file without nucleus <br>
 
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[http://biomechanics.stanford.edu/me339/extr_dof.m extr_dof.m] ... the one which extracts element information from the global
 
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field <br>
 
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[http://biomechanics.stanford.edu/me339/assm_sys.m assm_sys.m] ... the one with the strange big A operator <br>
 
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[http://biomechanics.stanford.edu/me339/res_norm.m res_norm.m] ... the one which tells you how far you are away from your ultimate goal <br>
 
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[http://biomechanics.stanford.edu/me339/solve_nr.m solve_nr.m] ... the one with the solution to all problems <br>
 
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[http://biomechanics.stanford.edu/me339/col_maps.m col_maps.m] ... the one with all the colors <br>
 
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[http://biomechanics.stanford.edu/me339/plot_mat.m plot_mat.m] ... the one to plot the undeformed configuration <br>
 
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[http://biomechanics.stanford.edu/me339/plot_spa.m plot_spa.m] ... the one to plot the deformed configuration with stresses <br>
 
  
 
==additional reading==
 
==additional reading==

Latest revision as of 15:48, 14 February 2011

Contents

[edit] me239 - mechanics of the cell

Sarcomere01.jpg
Sarcomere02.jpg

me239 - mechanics of the cell 11

ellen kuhl, manuel rausch
office hours tue 2pm, durand 217

winter 2011
tue thu 3:15-4:30
200-034

 

[edit] 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. in 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.

[edit] 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

[edit] 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
thu jan 13 homework I - biopolymers, directed stem cell differentiation h01 m04
tue jan 18 biopolymers II - entropy, FJC and WLC model n05 s05
thu jan 20 biopolymers III - polymerization kinetics in amoeba n06 s06 m06
tue jan 25 cytoskeletal mechanics I - fiber bundle model for filopodia n07 s07 m07
thu jan 27 cytoskeletal mechanics II - network model for red blood cells n08 s08
thu jan 27 homework II - cytoskeleton, cell mechanics challenges h02 m10
tue feb 01 cytoskeletal mechanics III - tensegrity model for generic eukaryotic cells n09 s09 m09
thu feb 03 biomembranes I - micropipette aspiration in white blood cells and cartilage cells n10 s10
tue feb 08 biomembranes II - lipid bilayer, soap bubble, cell membrane n11 s11
thu feb 10 biomembranes III - energy, tension, shear, bending n12 s12
tue feb 15 mechanotransduction I - inter- and intracellular signaling, bone cells n13 s13
tue feb 15 homework III - micropipette aspiration, final project h03 m12
thu feb 17 summary and midterm preparation n14 s14
tue feb 22 midterm
thu feb 24 mechanotransduction II - electrophysiology in nerve cells n16 s16
tue mar 01 mechanotransduction III - excitation contraction in skeletal muscle and heart cells n17 s17
thu mar 03 mechanics of the cell - the inner life n18 l01 l02
tue mar 08 final projects - oral presentations I p02
thu mar 10 final projects - oral presentations II
fri mar 11 final projects - written projects due p01

copyright ron kwon, ellen kuhl, chris jacobs, stanford, fall 2007, ellen kuhl, fall 2008, ellen kuhl, spring 2010

[edit] course summary

course summary developed in last year's class
42 answers to life, the universe, and everything

[edit] 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)

ME339posterASME2008.jpg

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).

[edit] additional reading

Phillips.jpg

(1) phillips r, kondev j, theriot j
physical biology of the cell, garland science, 2008

(2) boal d
mechanics of the cell, cambridge university press, cambridge, 2002

(3) howard j
mechanics of motor proteins and the cytoskeleton, sinauer associates, sunderland, 2001

(4) alberts b et al
molecular biology of the cell, garland science, taylor & francis, new york, 2002

 
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