physical biology of the cell - iiser punecathale/lects/2012spring/slides/...physical biology of the...
TRANSCRIPT
![Page 1: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/1.jpg)
Bio435-2012
• www.iiserpune.ac.in/~cathale/blog/• Water and crowding• Macromolecular dyamics: Molecular motors,
polymerization motors, DNA packing, protein folding• Thermodynamics: out of equilibrium systems• Cellular biophysics: nerves, muscles and stem cells• Tissue dynamics and development• Experiments: FRAP, particle tracking and crowding,
bacterial patterns in colonies with substrate rigidity• Student presentations: term paper
![Page 2: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/2.jpg)
Water and Movement
Bio435
![Page 3: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/3.jpg)
(A) Left–right asymmetric arrangements of internal organs in the human body.
Hirokawa N et al. Cold Spring Harb Perspect Biol 2009;1:a000802
©2009 by Cold Spring Harbor Laboratory Press
Situs solitus Situs invertus
Norm
a l orga n orie ntatio n 99%K
artag ener’s synd rome 50%
Mou
se
embr
yo
![Page 4: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/4.jpg)
Kartagener’s Syndrome
• 50% left, 50% right heart• Bronchiectasis (breathing diffi culty)• Male sterility
• Gene expression asymmetry driven by fl ow• Flow driven by Kif3B (kinesin superfamily)
Kartagener (1933), Nonaka (1998), Hirokawa (2009)
![Page 5: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/5.jpg)
Body Axis• Nodal Flows determine
left-right asymmetry Nonaka (1998), Nonaka (2005),
Guirao (2010)
Mammals• DV-axis by
implatantion• AP-axis perpendicular• Left-Right last axis to
be determined
![Page 6: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/6.jpg)
Blood Flow
Two day Adulthttp://www.cas.vanderbilt.edu/bioimages/animals/danrer/zfi sh-devel.htm
![Page 7: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/7.jpg)
Blood Flow
Beth Roman, U. Pitt
![Page 8: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/8.jpg)
Cytoplasmic Streaming
Slow cytoplasmic streaming in a Drosophila oocyte. Endosome seen in a 8 second time-lapse movie represents 30 minutes of real time. Scale bar: 25 mm.
Serb
us e
t al (
2005
)
![Page 9: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/9.jpg)
Mechanism
Serb
us e
t al (
2005
)
![Page 10: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/10.jpg)
Molecular Description of Water
![Page 11: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/11.jpg)
Velocity Field Formalism
![Page 12: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/12.jpg)
Fluid Viscosity Measurement
F
A= η vd
η = viscosity of fl uidA=area of platev = velocity d = distance between plates
![Page 13: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/13.jpg)
Acceleration of Small Fluid Parcel
![Page 14: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/14.jpg)
Forces Acting on Fluid Element
Fluid velocity
Pressure Viscous
![Page 15: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/15.jpg)
Forces
• Pressure Forces (FP)
• Viscous stress forces
![Page 16: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/16.jpg)
Incompressible Flow- Newtonian Fluid
![Page 17: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/17.jpg)
Newtonian Fluids
![Page 18: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/18.jpg)
Navier-Stokes Equation
![Page 19: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/19.jpg)
Blood Circulation
• Blood vessel sizes: 1 cm to 2 µm• RBCs: 5 µm (human)
![Page 20: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/20.jpg)
Fluid Dynamics of Pipe Flow
Cylindrical fl uid elementFlow through a pipe of diameter d andLength L
Velocity profi le varies along radius
Viscous forces balancedby
pressure forces
![Page 21: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/21.jpg)
Velocity of Flow
• Pressure and viscous forces balanced• Derive Fp and Fv in z-direction• Get expression for v(r) velocity• Volume fl ux rate
![Page 22: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/22.jpg)
• What is the expression for maximal velocity?
![Page 23: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/23.jpg)
Speed of Blood
Different animal capillaries
d=5 µm
∆ p � 20 mm Hg � 3000 Pa
Length of capillary l � 1 cm
Avg. fl ow velocity?
η = ?
![Page 24: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/24.jpg)
Hagen-Poisuelle’s Equation
Q= volumetric fl ow rate (dV/dt)
� p= pressure difference across the pipe
d= diameter of the pipe
� = kinematic viscosity
l = length of the vessel
![Page 25: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/25.jpg)
Hemodynamics
VESSELTYPE DIAMETER(mm ) FUNCTIONAorta 25 Pulsedampeningand
distributionLargeArteries 1.0-4.0 Distributionofarterial
bloodSmallArteries 0.2-1.0 Distributionand
resistanceArterioles 0.01-0.20 Resistance(pressure&
flowregulation)Capillaries 0.006-0.010 ExchangeVenules 0.01-0.20 Exchange,collection,and
capacitanceVeins 0.2-5.0 Capacitancefunction
(bloodvolume)VenaCava 35 Collectionofvenousblood
![Page 26: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/26.jpg)
Distribution of Pressure
Pressure vs vessel diameter?
![Page 27: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/27.jpg)
Flow and Resistivity• Ohm’s law V=IR, V=potential difference,
I=current, R=resistance• D’arcy’s law ∆ P=QR (for low reynold’s
numbers) where ∆ P is the pressure difference, Q is fl ow rate and R is resistivity
![Page 28: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/28.jpg)
Leukocyte Invasion into a Tissue
Leu
kocy
te
adhe
rent
to a
n en
doth
elia
l cel
l
Ext
ra-v
asat
ion
acro
ss e
ndot
heli
al
cell
barr
ier
Leukocytes:
Flow
Infection
Adhesive forces
Rolling
![Page 29: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/29.jpg)
The 100-year Experiment• 1927 Australia• Flow under gravity• 8 drops
Edgeworth, Dalton, Parnell (1927) The Pitch Drop Experimenthttp://www.physics.uq.edu.au/physics_museum/pitchdrop.shtml
![Page 30: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/30.jpg)
Stoke’s Formula for Drag Force on a Sphere
Flow types away from the wall at constant velocity vFundamental solution for sphere in a fl ow-Solve Stokes Equation
![Page 31: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/31.jpg)
Stokes Drag
• Cylinder• Arbitrary shapes• Movement of Bacteria in Re<<
![Page 32: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/32.jpg)
Stokes Drag in Single Molecule Experiments
![Page 33: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/33.jpg)
Viscous Forces In Optical Tweezer Experiments
• Bead diameter ~500 nm
• Motor speed 1 micron/s
![Page 34: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/34.jpg)
Vesicle Transport
Motion enhanced differential interference contrast (MEDIC) movies of living NT2 (neuron-committed teratocarcinoma) velocity (v), radius (a), and effective cytoplasmic viscosity (� ')
DIC ME-DIC
![Page 35: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/35.jpg)
Time Scales of Movement
• Viscous time scale • Inertial time scale
• u=velocity, a=characteristic length
τv=ρ a2/ ητi=a /u
![Page 36: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/36.jpg)
Viscous timeInertial time
![Page 37: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/37.jpg)
Viscosity� = dynamic viscosity (Pa-s = N-s/m2), absolute viscosity
1 Poise = 0.1 Pa-s
For water η = from 0.1 to 0.01 Pa-s
At 293K,� =1 mPa-s = 1x10-3 Pa-s
At 300K, η=0.798 mPa-s = 0.798x10-3 Pa-s
� = kinematic viscosity = ρ/η (1 Stokes = 10-4 m2/s)
For water at 293K, � =10-6 m2/s
ρ= density (kg/m3)
![Page 38: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/38.jpg)
Swimming E. coli
Fuorescently-labeled cells with strobed laser illumination, using an ordinary CCD camera at These cells where grown on T-broth. They are about 1 µm in diameter by 2 µm long and swim at about 30 µm/s
Turner et al. (2000) J. Bacteriol. 182( 10) 2793-2801
![Page 39: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/39.jpg)
Velocity Components of E. coli Swimming
Rotation of E. coli fl agellum: Length L=10 � m
Frequency f=100Hz
Pitch P=2 � m
Diameter D=0.5 � m
![Page 40: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/40.jpg)
Drag Coeffi cients• Small segment of length l• Angle with z-direction• Linear velocity v=� Df• Angle tan� =� D/P • Forces- viscous drag and propulsive• Propulsive force components:
perpendicular, parallel
![Page 41: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/41.jpg)
Velocity of Swimming
Since
Where v = linear velocity along z-direction
D = diameter, f = frequency of rotation
Estimate V ~?
V =v cosθsin θ=πD f sinθcosθ
v=πDf
![Page 42: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/42.jpg)
Reciprocal DeformationScallop
swimming
E.M. Purcell (1977) Life at Low Reynolds Numbers. Am. J. Phys. Vol 45, No. 1
water
Motion
Fast closing, slow openingSingle hinge
At low Re a bacterium-sized clam-like mechanisms will go nowhere!
![Page 43: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/43.jpg)
Purcell’s Simple Swimmer
3 plates, 2 hinges can avoid reciprocal motion- so long as order of folding up and opening (LR) is the same
![Page 44: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/44.jpg)
Oars In a Submarine in Molasses
Rigid Oars: reciprocal motion
Flexible oars: Propulsion
![Page 45: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/45.jpg)
Application
Centrifugation and separation• Fractionation (cells, organelles, chromatin)• Separation of proteins• Purifi cation
![Page 46: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/46.jpg)
CentrifugationCentrifugal force on each molecule ~ mω2r
If particle size << distance from axis,Force per unit mass approx. constant
Frictional force � drift velocity
gc = centrifugal force/mass, � = friction coeff.
vdrift=mgc / γ
![Page 47: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/47.jpg)
Size Depedent Separation
• Spherical particle frictional coeff • Svedberg (const)
1S = 10-13 s for globular protein 1nm radius
Dependent on particle and nature of medium
γ=6πηRS=m / γ
![Page 48: Physical Biology of the Cell - IISER Punecathale/lects/2012spring/slides/...Physical Biology of the Cell Author Phillips et al. Created Date 2/12/2012 10:27:21 PM](https://reader034.vdocuments.us/reader034/viewer/2022043010/5fa027612bed19535a083d53/html5/thumbnails/48.jpg)
Paper Reading
• E. M. Purcell (1977) Life at Low Reynolds Numbers. Am. J. Phys.
• Chen and Springer (1999) An Automatic Braking System That Stabilizes Leukocyte Rolling by an Increase in Selectin Bond Number with Shear. J.Cell.Biol.