living matter lab


spring 12 - me239 - mechanics of the cell

Tensegrity model.jpg

me239 - mechanics of the cell 12

ellen kuhl, manuel rausch
durand 217
course syllabus

spring 2012
tue thu 12:50-2:05
edu 128



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 course 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 course, we will discuss how cell properties can be measured experimentally and how they can be characterized in the form of equations. we will elaborate concepts of energy and entropy 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. to explore the cell's behavior in silico, we will introduce computational simulation tools. in the second part, we address aspects of mechanotransduction. we discuss different aspects of how cells sense loads and how signals are transmitted within the cell and through the extracellular matrix.


  • 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


day date topic notes material
tue apr 03 introduction I - cell biology s01
thu apr 05 introduction II - cytoskeletal biology, stem cells n02 s02 l02
tue apr 10 introduction III - structural mechanics n03 s03
thu apr 12 biopolymers I - energy, tension, bending n04 s04
thu apr 12 homework I - biopolymers, directed stem cell differentiation h01 m04
tue apr 17 biopolymers II - entropy, FJC and WLC model n05 s05
thu apr 19 biopolymers III - polymerization kinetics in amoeba n06 s06 m06
tue apr 24 cytoskeletal mechanics I - fiber bundle model for filopodia n07 s07 m07
thu apr 26 cytoskeletal mechanics II - network model for red blood cells n08 s08
thu apr 26 homework II - cytoskeleton, cell mechanics challenges h02 m10
tue may 01 cytoskeletal mechanics III - tensegrity model for generic eukaryotic cells n09 s09 m09
thu may 03 biomembranes I - micropipette aspiration in white blood cells and cartilage cells n10 s10
tue may 08 biomembranes II - lipid bilayer, soap bubble, cell membrane n11 s11
thu may 10 biomembranes III - energy, tension, shear, bending n12 s12
tue may 15 mechanotransduction I - inter- and intracellular signaling, bone cells n13 s13
tue may 15 homework III - micropipette aspiration, final project h03 m12
thu may 17 summary and midterm preparation n14 s14
tue may 22 midterm
thu may 24 mechanotransduction II - electrophysiology in nerve cells n16 s16
tue may 29 mechanotransduction III - excitation contraction in skeletal muscle and heart cells n17 s17
thu may 31 final projects I - oral presentations n18 l01 l02
tue jun 05 final projects II - oral presentations p01
thu jun 07 no class
fri jun 08 final projects - written projects due p02

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