living matter lab


me239 - mechanics of the cell


me239 - mechanics of the cell 11

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

winter 2011
tue thu 3:15-4:30



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.


  • 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 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

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