Lecture 11

Life in the
low-Reynolds number world

Sources:

Purcell – Life at low Reynolds number (Am. J. Phys 1977)

Nelson – Biological Physics (CH.5)
Tsvi Tlusty, tsvi@unist.ac.kr
 Outline
I. Friction in fluids.

II. Low Reynolds-number world.

III. Biological applications.

• Viscous friction dominates mechanics in the nanoworld.

• Friction is dissipative: converts ordered motion into thermal energy.
• Implications of symmetry.

• Biological Q: Why don't bacteria swim like fish?

• Physical idea: motion in the nanoworld have different symmetry than
motion in the macroworld.
I. Friction in fluids
 Small particles can remain in suspension indefinitely

Suspension of protein
Gravity: mg  Vg
Bouyancy force: mwater g   waterVg
Net force: mnet g   Vg (Archimedes' principle)
mwater g z • What happens after a long time?

dU dP
j   P D  0 (Smoluchowski's
m net geq. for eqilibrium)
dx dx − z
BTr
mg
P( x)  exp   c z =c
 mnet gz 
 (Einstein's
0 relation k BT  D /  )
 k BT  k
•
e
Example: Myoglobin:

Myoglobin mass: m  1.7 104 Da = 2.7 1023 kg

net mass: mnet  m / 4  0.7 1020 kg

k BT 4.2 1023 • Density in test-tube is ~ constant.

scale height z*   20
 60 m
mnet g 0.7 10 10
 Centrifuges can achieve a much higher g
• Centripetal acceleration is by frictional drag:
ω
f centrifugal  mnet 2 r dU
jv   P   f  P(r )   mnet 2 P (r )r
dr
m
• Balanced by diffusion current

dP(r )
jD   D
dr
r
dP
j  jv  jD  0   mnet 2 P (r )r  D 0
dr
 mnet 2 r 2 
P(r )  exp  
 k B T 

• How long does it take to reach equilibrium?

Sedimentation time scale depends on solvent viscosity

• Sedimentation velocity (depends g not intrinsic property)

mnet g
vdrift   mnet g 

• Sedimentation time scale:

vdrift mnet • Unit is Svedberg (10-13 sec)

   mnet 
g 

• The sedimentation scale is determined by the size and mass

of the particles and the viscosity of the surrounding fluid.

• For a sphere
  6 R where  is the viscosity

• The viscosity of water at room temperature is

  103 Pa  s = 102 poise (erg/cm3  s)

 Rheology is useful to study macromolecules
• Example: polymer size scaling. Rg mp
mnet ~ m
• Assuming random walk Random walk: p  0.5
Self-avoiding: p  0.57

k BTk BT
D  ~ m p
 6 Rg s
mnet

mnet m
~ p  m1 p
 6 Rg m

D ~ m 0.57

s ~ m 0.44
 Hard to mix a viscous liquid
• Experiment: ink in glycerin

• The clockwise-counterclockwise experiment: blob will smear out but retracing

make the blob reassemble into nearly original position and shape!

• That's not what happens when you stir cream into your coffee…
 Does reversibility violates 2nd law of TD?
• Ink diffuses but very slowly: D  k BT  k BT
 
• So the blob cannot change much by diffusion     D  0.

• Stirring causes organized motion: fluid layers slide over one another.
• Ink molecules spread out but not randomly (because diffusion is too slow).
• Reversing the wall motion: fluid layers slide back and reassemble the blob.

• Such organized flow is called laminar.

In RGB
 II. Low Reynolds-number world

Quantifying the friction-dominated regime (laminar vs. turbulent)

 Forces in laminar flow

A
f   v
L

• Shear motion: moving plate feels resisting viscous force

stationary plate feels opposite force (entraining force).

• Viscous force f is proportional to area A, and speed v but

decrease with plate separation.

• Empirically, for small v, many fluids follow simple law:

 Newtonian fluid

y
 f dxdz y  dy
v  dv
v( y )
x v y

Uniform flow along x Force applied on y+dy layer by y layer

dv
 f  
dy (Newtonian viscous formula)

Coefficient of viscosity
Critical force demarcates the friction-dominated regime

• Intuitively, flow is laminar when viscosity η is large and turbulent if η is

small. But “small” or “large” w.r.t. what?

force M M
• Dimensional analysis for Newtonian fluid: [ ]   ; [ ]  3
velocity x length LT L

• No dimensionless quantity from η and ρ.

• But we can make a characteristic quantity. 2

f crit  critical viscous force


 no intrinsic length scale: cannot tell “thick” from “thin” fluids.

Newtonian fluid is scale invariant.

2
f  f crit  .
• Situation dependent: fluid motion is viscous if 
 Aquatic cellular environment is viscous

• For macroscopic bodies and forces water is turbulent.

• For pN forces in the cell, water is viscous…

• For f < fcrit, fluid is thick: friction quickly damps out

inertial effects. Flow is dominated by friction.
The Reynolds number quantifies the relative
importance of friction and inertia
Flow past a sphere:
 Velocity changes direction during t ~ R / v.
 Acceleration magnitude a ~ v / t ~ v 2 / R

 Newton's law f ext  f frict  f tot  ma

(f ext is by fluid pressure)

v2
 finertia = ma   l 3

R
f dv
 friction force:  
A dx

 Net force on fluid: f  f ( x0  l )  f ( x0 )

df d 2v v
f friction  f ~ l   Al 2   l 3 2
dx dx R
• Small Re: friction dominates; flow stops
Reynolds number immediately when force stops ("creeping flow“).
finertia  l 3v 2 / R  vR • Big Re: inertial effects dominate, coffee keeps
  3 
f friction  l v / R 2

swirling; flow is turbulent.
 Microbiology is viscous (low Re)

10 3
kg m 3   30 m 10 m/s 
 3 108 1
10 3
Pa s 


10 3
kg m 3 106 m  30 106 m/s 
 3 105 1
10 Pa s 
3
 Tuning Re

• Australian Pitch drop

experiment running from 1927

• Viscosity ~ 1012 of water

 Time-reversal properties of a dynamical law
signal its dissipative character
 Sheets move uniformly  forces balance out:
dv x
 const.  v  v0
dx d

 Time depndent motion: f f crit  finertia negligible

x
v ( x, t )  v0 (t )
d

 Unmixing:
f dv
friction force:  
 x, y, z    x  
x
v0 : v0t , y, z  A dx
 d 
 x   x x 
v0 :  x  v0t , y, z    x  v0t  v0t , y, z    x, y, z 
 d   d d 

• Once the top plate has

returned to its initial position,
each fluid element has also
returned, regardless of the
dynamics of the return stroke.
 Time reversal: Newtonian mechanics
dz 2 dU
m 2  f   mg • In Newtonian physics, the time-
dt dz reversed process is a solution to the
equations of motion with the same
dz 2 solution 1 2
2
 g z (t )  v0t  gt sign of force as the original motion.
dt 2

 Time reversal:
t  t

dz 2 solution 1 2
2
 g z (t )  v0t  gt • Time-reversed trajectory solves
dt 2
Newton's law with inverse v0.
 Time reversal: Diffusion

dc d c 2 solution 1  x2 
D 2 c ( x, t )  exp   
dt dx 4 Dt  4 Dt 

 Time reversal:
t  t

dc d 2c solution 1  x2 
 D 2 c ( x, t )  exp   
dt dx i 4 Dt  4 Dt 

• Diffusion equation is
• Time-reversed solution does not
not time invariant.
solve original diffusion equation.
Viscous friction is not time reversal invariant
A ball in highly viscous fluid

solution:
f dz f
 f
dt  z  z0  t
 Time-reversed solution does not
solve original friction equation,

solution: unless force is inversed

f
dz f
  f
dt  z  z0  t


Frictional motion is irreversible because friction dissipates ordered motion into heat.

?
Fluids and solids differ in time-reversal symmetry
(displacement)

f du
G y
u
A dy
• No explicit time dependence: invariant. x

• Solids have “memory” of position.

f d  du 
   v
A dy  dt  y

• Not invariant. x
Fluids and solids differ in time-reversal symmetry

k
d 2u
m 2  ku f  ku
dt
• 2nd order time derivative: invariant.

• Solids have “memory” of position.

du f f

dt 

• 1st order time derivative: Not invariant. 

  6 R
 Viscous flow have other symmetry properties

Stokes flow: The reversed flow with

v  v p   p
 p   v 2
obeys the same equation.

Low Re flow around a stationary object

having a plane of symmetry is symmetric.
Proof: Symmetry plane x  0.
 Flow reversal: v( x, y, z )  v( x, y, z ).
 Mirror symmetry:
v x ( x, y , z )  v x (  x , y , z )  v x ( x , y , z )
v y , z ( x, y , z )  v y , z (  x, y , z )  v y , z ( x, y , z )

• Sensitive test for small Re flows

 upon reversal, fluid follows the identical
streamlines in the opposite direction.
Stokes flow:
 p   v
2

• In low Re we can blow out a candle

either by blowing or suction.

• In high Re, we cannot blow out a

candle by suction
 Streamlines are invariant to rate of flow

Stokes flow:
 (  p )   (  v )
2
 p   v 2

• Follows form linearity of the flow.

• No notion of explicit time.

v1 (r , t ) and v2 (r , t ) solutions
 1v1  2 v2 is also a solution
with p  1p1  2p2
III. Biological applications
 Swimming and pumping
• In the low Re world: a motion can be canceled completely by applying minus the time-

reversed force. What are the implications for microorganisms?

• Flapping back and forth returns every fluid element to its original position:

No net motion!
 Swimming of microorganisms: reciprocal motion

a. paddles move backward at b. paddles move forward at c. Repeat…

speed v relative to the body  v' relative to the body 
forward motion of the body at backward motion of body at u'
speed u relative to water. relative to water.

Any net motion? [Cartoon by Jun Zhang.]

 relative velocity of paddles w.r.t. fluid: v  u

 drage force on paddles: f paddle   p (v  u )

 drag force on body: f b  b u

 force balance: f p  fb

p
 body velocity: u  v
b   p

p
Total displacement: x  ut  vt
b   p
 Similarly: relative velocity of paddles w.r.t. fluid: v ' u '

 drage force on paddles: f paddle   p (v ' u ')

 drag force on body: f b  bu 

p
 body velocity: u   v
b   p

p
Total displacement: x  u t   vt 
b   p
 In reciprocal motion the paddles return to their original position:
vt  vt 

 Hence:

p p
x  u t   vt   vt  ut  x
b   p b   p

NO NET MOTION!
 Scallop theorem forbids strictly reciprocal motion

• Scallop theorem:
Strictly reciprocating
motion won’t work for
swimming in the low-
Reynolds world [Purcell
(1977) Am. J. Phys.]

What other options a microorganism has?

Motion must be periodic (to be repeated).

It can’t be of the reciprocal.

Ciliary propulsion is periodic
not reciprocal
• Many cells use cilia to generate net thrust.
• Each cilium contains internal filaments and motors.
• Cilia can be used for translocation and pumping
(in stationary cells).

• The difference is in the additional degrees of freedom.

Net motion requires breaking the back and forth symmetry

Large drag in forward motion. Smaller drag in backward motion:  p   p

Displacement: Displacement:
p vt  p vt 
x  ut  vt  x  u t   vt  
b   p 1  b /  p b   p 1  b /  p


Total displacement:
vt vt  b  p   p 
x  x    vt 0
1  b /  p 1  b /  p b   p b   p 
Cilia break symmetry by changing the direction of motion

• Effective stroke: high drag (perpendicular)

• Recovery stroke: low drag (parallel)

 Bacteria use rotating
flagella for locomotion
 Flagella break shape symmetry for locomotion

f
f┴=-ζ┴v┴

f║ =-ζ║v║

v║
v┴
v
• The drag coefficients parallel and perpendicular
   to the cylinder (helix) are not equal.
 f  f   f    v   v  Although the velocity is in y-x plane, there is a
f not parallel to v z-component of the force.

 The net force on the helix is in z direction.

 How bacteria avoid rotating by torque?

• Bacteria are large enough

such that friction slows
down rotation

• Bacteria may also have

pairs of flagella rotating in
opposite directions.
 Two coupled scallops can move

Single pair of paddles Dimer of 2 pairs of paddles

Strictly reciprocal Single pair: strictly reciprocal

 No net motion Dimer: nonreciprocal
 Net motion!

[Lauga and Bartolo (2008) PRE]

 Why should bacteria move and stir?

• Eating? It’s anyhow hard to mix: Streamlines around Volvox (protozoa)

-- Only a few streamlines reach a moving object.

• Solution: use diffusion.

• Why stir?

-- Cilia of length d refreshes its volume every tstir = d/v

-- diffusion time scale is tdiff = d2/D

• Only if tstir < tdiff this is worthwhile.

• Peclet number:
tdiffusion d  v
• For D = 1000 μm2/s and d =1 μm, v = 1000 μm/s… Pe  
tstir D

• Bacteria swim for other reasons, like food gradient…

 Vesicular delivery networks are essential for
macroscopic organisms that cannot rely on diffusion

2R

Constraints:   103 kg/m3 ; R  10  m

v( R)  0 (non-slip) v  10 cm/s ;  =103 Pa  s
v(0)  
 vR 103 101 105
   1 (within low Re)
 10 3
Balancing the forces:

2R

 Pressure applies force: df p   2 rdr  p

 Viscous force from inner shell pushes shell forward:
dv(r )
dfin    2 rL  (dv / dr  0)
dr r
 Viscous force from outer shell pulls shell backward:
dv(r )  dv(r ) d 2v(r ) 
df out    2  r  dr  L     2  r  dr  L    dr 
dr r  dr  dr dr 2
 r r 
df  df p  dfin  df out 
dv  d 2v  p 1 dv d 2 v
 2 r  pdr    2 L  dr    2 rL   r 2 dr   0 df  0    2 0
dr  dr 
 L r dr dr
Poiseuille flow:

2R

p 1 dv d 2 v
df  0    2 0 General solution:
 L r dr dr
p 2
v(r )  A  B ln r  r
4 L
Flux
Boundary conditions:
R
R p 4
Q   2 rdrv(r )  v(r ) 
p
 R2  r 2 
0
8 L 4 L

• The flow is laminar in most blood vessels in the human body except for
the largest veins and arteries.

• Q ~ R4 flow can be controlled by small variation of radius.

 Viscous force at DNA replication fork

Since the two single strands cannot pass through

each other, the original must continually rotate.

Would frictional force resisting this rotation

be enormous?

2R

Y-shaped junction
 Viscous force at DNA replication fork

The torque scales like:

2R
  r  f  R  RL

The dissipation work

P     2 R 2 L

per turn of  :
W  2  2 R 2 L
ω

Replication rate: 1000 bp/s

DNA period: 10.5 bp/turn
1000
   2  600 rad/s
10.5
W  (2 )(600 s 1 )(103 Pa s)(1 nm 2 ) L ~ 0.01 L k BT /  m

• Small friction compared to energy consumed

by DNA helicase which unzips DNA.
Y-shaped junction
Summary
• Viscosity dominates the nano-world . vdrift mnet
   mnet 
g 
• Suspension is stabilized by diffusion at time scale:

• Hard to mix viscous fluids

Reynolds number
• Reynolds number: finertia  l 3v 2 / R  vR
  
– Inertia/friction f friction  l 3v / R 2 
– Force/critical force

• Symmetry:
– Newtonian dynamics: time-reversal invariant

– Viscous friction: not time-reversal invariant

• Swimming of microorganisms:
– Strictly reciprocal motion cannot translocate

– Periodic but not reciprocal motion work

in ciliary and flagellar propulsion

• Viscosity dominates flow in blood vessels.