Mass Transfer by

Molecular Diffusion
Ficks law in 1-3 dimensions
1
Why study diffusion

Runs chemical transport inside cells

Runs mass (chemical) transport to all heterotrophs

and autotrophs (This means you!)

A dominant mode of communication in the sea

Almost everything in (biogeo)chemistry is an

advection-diffusion-reaction problem
2
Terminology revisited

Advection or advective motion; engineers call it

convection or convective motion.

Advection or convection is the organized

motion of large groups of molecules, so large
that the uid is treated as a continuum.
3
Advective uxes
L
L
u
Concentration = C (moles or numbers L
-3
)
Advective ux = Area x Velocity x Concentration
mol T
-1
= L
2
x L T
-1
x mol L
-3
Hydrosol ltration: Just because there is a ux
doesnt mean that you can catch much of it.
4
Perspective
The most organized ows are laminar.
The most turbulent ows have the smallest vortices,
but at the scale of the smallest vortices (1-10 mm),
the ow is still organized, and 1 g (approx. 1 cm
3
)
of water contains (6.02 x 10
23
)/18.0153 molecules.
On approach to the scale of a molecule, i.e., in
molecular diffusion, laminar behavior breaks down.
5
Non-intuitive aspects

Very ineffectual at long distance

But, due to viscosity, large relative velocities

(advection) are (is) hard to generate at small
scales.

Molecular diffusion is very fast at sub-

millimeter scales.

Large organisms still rely on diffusion at the

smallest scales.
6
The idea in one
dimension
A molecule can occupy any position.
During one time step it can move one space right or
left.
It moves right or left with equal probability.
After a very long time, the molecule could be
anywhere; there are lots more points away from the
starting point than very near it.
7
Strange things happen
On average, you dont get anywhere.
Over longer times, though, the average distance of
an excursion (starting point to ending point)
increases; even in 1D there are more points far
than near to the origin, and with time they all
become accessible.
Whereas in advection, excursion distance (L) and
time (T) are linearly related (L = Velocity x T), in
diffusion, L = (constant) x T
2
.
8
2D Random Walk on a
Grid
First moves
1/4 of second moves
Occupiable space grows rapidly with
distance from the starting point
9
Example results

0
1
2
3
4
5
6
7
8
9
10
0 5 10 15 20
Bobbi-Jo
Megan
Josh
Laura
Sarah
Nicole
Mean Observed
y
t
i
c
o
l
e
v

t
n
a
t
s
n
o
C
Move #
2
Move Number or Time Step
)
s
p
e
t
s

t
i
n
u
(

e
c
n
a
t
s
i
D
Random Walk
L
2
= T/4

0
5
10
15
20
25
30
35
40
0 5 10 15 20
Bobbi-Jo^2
Megan^2
Josh^2
Laura^2
Sarah^2
Nicole^2
Mean^2
Random Walk
C
o
n
s
t
a
n
t
v
e
l
o
c
i
t
y
)
s
p
e
t
s

t
i
n
u
(
(

d
e
r
a
u
q
S

e
c
n
a
t
s
i
D
2
)
http://lsvr12.kanti-
frauenfeld.ch/KOJ/Java/
Diffusion.html
10
The Diffusion
Coefcient, D

This macroscopic, average constant is called a

diffusion coefcient, and it takes the form D = k
(L
2
/T).

It has no choice if the dimensions are going to

work out.

Easiest 3D example is of gas molecules

They have a velocity [L T

-1
] and mean free path
[L], so D = k x Velocity x L.
11
One interpretation
D =
6 ! r
0
k
B
K
=
Driving Potential
Resistance
=
Chemical Potential Gradient
Stokes Drag Terms
K = temperature in Kelvin
k
B
= Boltzmanns constant = 1.38054 x 10
-23
J K
-1
r
0
= molecular radius of the solute
12
Driver is (Average) Kinetic
Energy of a Molecule
m u
2
2
=
3 k
B
K
2
Molecules move fast, but in liquids they
are so densely packed that collisions are
very frequent, and it is impractical to
measure the molecular velocity. The velocity
is the same, however, in air or water if the
temperature is the same.
13
In water, D for most small
molecules is similar
Molecular velocity at room temperature in both
air and water for a small molecule (e.g., O
2
) is
roughly 5 x 10
2
m s
-1
.
It is collisions with water that set the drag.
Whereas in air at 1 atm a mean free path is
typically about 10
-7
m (comparable to the
wavelength of visible light) in water it is 10
-11
m
(about 0.1 x radius of a hydrogen atom).
The value of D for a small solute in water is
typically (1-2) x 10
-9
m
2
s
-1
.
14
Some simple manipulations
2D
T =
L
2
L
2
2T
D =
It is most consistent to
use k = 1/2 because a
diffusing molecule has a
50% chance of going in
one direction or its
opposite. For 2 and 3D,
the k changes to 1/4
and 1/6, respectively, by
analogous reasoning.
For D = 2 x 10
-9
m
2
s
-1
Distance (L) Time
1 m 0.25 ms
10 m 0.025 s
100 m 2.5 s
1 mm 4 min
1 cm 7 h
10 cm 1 mo
1 m 8 y
15
Its not so strange
A molecule cant go very far in a straight line by
this mechanism (molecular diffusion). In a single
step in a straight line, nothing is out of the
ordinary.
It takes longer to get from point A to point B if you
dont go straight from A to B.
In a random walk, time increases with the square
of the (straight-line) distance and (straight-line)
distance increases with the square root of time.
16
Now, what else can we
do with D?
With advection the amount of a chemical passing
through a surface is simply the area of that surface
times the concentration times the velocity (L
2
x
mol L
-3
x L T
-1
= mol T
-1
).
With diffusion, the amount of a chemical passing a
surface is the area times D times the gradient in
concentration = L
2
x L
2
T
-1
x mol L
-3
L
-1
= mol T
-1
).
17
Ficks First Law
J
x
= ux per unit of area
(area perpendicular to x)
J
x
= -D
"C
"x
18
Transport through 1D
diffusive sublayers
Concentration
Diffusive sublayer
Direction of diffusional
transport?
What happens above
the diffusive sublayer?
If the same amount of material is owing by diffusion through
each plane, then the prole cant change: "
2
C/"z
2
= 0, so "C/"t = 0.
19
Transport through 1D
diffusive sublayers
Concentration
Diffusive sublayer
Direction of diffusional
transport?
What happens above
the diffusive sublayer?
How much material
is owing by diffusion
through each plane?
If the same amount of material is owing by diffusion through
each plane, then the prole cant change: "
2
C/"z
2
= 0, so "C/"t = 0.
19
Diffusion in 1, 2 & 3D
20
21
What happens with a
sphere?
With steady uptake, the same amount of material must cross
each spherical shell per unit of time, so the gradient driving
the ux must get steeper closer to the sphere: "C/"r = k/r
2
This is a
no-ow
case
(diffusion
only)
22
23
Concentration vs. distance
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
0
r
r
0
0
!
C
C
0
C
-
C
-
Because "C/"r
2
= k, C must vary as k/r.
There is no advective uid motion involved, just geometry & diffusion.
24
Absolute limit in
stagnant water
Total ux to the cell = -4 ! r
0
D (C
inf
- C
0
)
J
r
= -D
C
inf
- C
0
r
0
J
r
= ux per unit area of cell surface
25
How big should a
bacterium be?
r r
L H
G
ro
ss g
a
ln
a
t lo
w

G
r
o
s
s

g
a
l
n

a
t

b
l
g
b

n
u
t
r
l
e
n
t

c
o
n
c
e
n
t
r
a
t
l
o
n

G
r
o
s
s

l
o
s
s

n
u
trle
n
t c
o
n
c
e
n
tra
tlo
n

Cell radius (r
0
)
G
r
o
s
s

g
a
i
n

o
r

l
o
s
s
(
m
o
l

c
e
l
l
-
1

t
i
m
e
-
1
)
26
Cylindrical diffusion
Oblique view
Top view
"C/"r = k/r
So C is proportional to k/lnr,
specically to ln(r
0
/r).
E.g.: lamentous or chain-forming phytoplankter,
vicinity of a worm tube in sediments,
vicinity of a blood vessel in an organism
27
28
Equations
C(z) =
l
C
1
- C
1
z + C
2
z
C(r) =
ln
a
b
aC
1
ln
r
b
- C
2
ln
a
r
C(r) =
r (b - a)
aC
1
(b - r) - bC
2
(r - a)
1D
2D
3D
C
1
= Concentration at surface, z = 0 or r = a
C
2
= Concentration at distance z (1D) or b (2 or 3D)
Slightly modied from Crank (1975)
29
1, 2 and 3D
Flat plate Cylinder Sphere
30
Graphical view
Boundary conditions: Surface at zero; concentration = 1 at distance 100
31
Worm tube in the seabed (conc of oxygen)
32
A ciliate demonstration (Fenchel)
33
Shape matters

Spheres have the most space to diffuse to (waste

removal) or from (nutrients), but do have an
absolute limit of diffusive delivery.

Cylinders have the next most space (2-D

objects)

1D diffusion characterizes diffusive uxes to

and from the seabed, with tubes acting as short
circuits.
34
Structure of a Bacterium
35
Tumble and Run (as observed in E. coli)
A more-or-less straight swimming path is a run.
In a tumble, the
motor reverses,
the agellar
bers splay out
uselessly, and
orientation is
randomized.
Then the cell
runs in a new
direction.
The result is a biased random
walk. Its like diffusion but
sends the cell up a food gradient.
36
Ways that a bacterium
might get small, dissolved
molecules

Without the aid of hydrolytic enzymes; wait for them

to arrive; go hunting or grazing

Wear hydrolytic enzymes on its

sleeves (immobilized enzymes)

Send hydrolytic enzymes out on their own (freely

released exoenzymes); collect the products

Send out a recognizable chelator to catch them and

make them both recognizable and transportable across
the cell membrane (called a siderophore)
37
Could a bacterium get more
small nutrients by swimming?
Typical swimming speed, u = 50 m s
-1
Swimming encounter ux is !r
0
2
C
inf
u
Ratio of swimming encounter/diffusional ux < 6.25 x 10
-3
An organism of this size cannot outrun diffusion.
<http://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html>
38
But an unknown fraction of
bacteria do swim. Why?

To nd a region of higher C
inf
, e.g., to colonize an
aggregate (marine snow particle) settling through
the water.
But how?
Onboard sensors measure arrival rate of molecules,
which is proportional to C
inf
If arrival rate is increasing, continue to run
If arrival rate is not increasing, tumble (change
direction at random), then run
39
Open problems
In what forms, at what scales and under what
conditions of uid motion do dissolved, small
molecules become available?
What movement rules work best?
Candidate sources include autolysis and leakage.
Mean concentration may mean little, and
remember that a cell cannot measure
concentration, only arrival rate.
40
What if there are not
enough small molecules
Immobilize enzymes
either on your surface
or in a permeable
layer near your surface
(< a few radii away).
For large polymers, advective
supply may be important
because D is so small.
41
(Micrographs from Cowen, 1992, Marine Biology)
42
Likelihood that product will hit the cell when
produced at a distance
43
Freely released enzymes
Bacterium
Sediment grain
Adsorbed or
particulate food
Enzyme
Hydrolysate
In the xed reference frame of aggregates or sediments
44
What about freely releasing
enzymes to diffuse away?
Can work in particle aggregates and sediments if the
enzyme does not go too far away (# 5 cell radii)
Vetter et al. 1998
Microbial Ecol.
The enzyme adsorbs
tightly to particles and
most tightly to its substrate
45
Container: a space
in anoxic sediment
or rock or an
animals gut
Or free release can work
if there is a container
Enzyme 2
Ideal setup for
evolution of
mutualism
With a heterogeneous food, like
detritus, each can make products
useful to the other.
Enzyme 1
Product 2
Product 1
Solid Food
46
Siderophores

Molecules that go out and bind particular

substrates, e.g., iron and can be recognized and
used to haul it in across active uptake sites

Free release can work if the siderophore is cheap

and local competition is not intense

Siderophores can work in a planktonic but likely

not benthic setting
Grifn, A.S., S.A. West and A. Buckling. 2004.
Cooperation and competition in pathogenic bacteria.
Nature 430: 1024-1027.
47
Short Break
48
Larger organisms

Combine advection and diffusion

Circulatory/respiratory and digestive systems

in large organisms advect over large distances
and diffuse over small ones
49
Two nondimensional
numbers
Pclet number = Pe =
u r
0
D
Sherwood number = Sh =
Q
Q
D
Ratio of advection to diffusion over a length scale in the uid
Caution: Net diffusion may not be in the same direction
A snap to calculate, but not very useful
Ratio of total mass ux to or from an object to purely diffusive ux,
i.e., Q/(4 ! D r
0
(C
inf
- C
0
)) for a sphere (range is one to innity)
A great idea, but how do you nd Q?
50
An engineering solution
0.01 0.001 0.1 1
1
10 100 1000
1.5
2
3
5
7
10
Sh
Pe
Sinking or Steady Swimming
Sh =
1
2
( )
1 + (1 + 2Pe)
1/3
Calculate Pe, measure Sh, and t an equation
Easy
Hard
Pretty Easy
51
Effect of Shear from
Turbulence
u = ("/#)
1/2

r
0
0.01 0.1 1 10 100 1000
1
1.5
2
3
5
7
10
0.7
0.001

S
i
n
k
i
n
g

o
r

S
t
e
a
d
y

S
w
i
m
m
i
n
g
She
a
r fr
o
m

D
i
s
s
i
p
a
t
i
n
g

T
u
r
b
u
l
e
n
c
e
" = kinetic energy dissipation rate of the ow [L
2
T
-3
]
Karp-Boss,
Boss &
Jumars
1996,
Oceanogr.
Mar. Biol.
Ann. Rev.
52
From similar Sh-Pe regressions
Sh > 1.5 requires
Cell radius > 20 m for swimming or sinking
Cell radius > 60 m to gain from shear arising
from decaying turbulence
Conclusion: An advective contribution can be
important for large dinoagellates and diatoms or
for smaller osmotrophs relying on large molecular-
weight compounds (small D).
53
Pe = 0; Sh =1 Pe = 1; Sh = 1.21 Pe = 1; Sh = 1.44
Karp-Boss,
Boss &
Jumars
1996,
Oceanogr.
Mar. Biol.
Ann. Rev.
54
An interesting advection-
diffusion problem
Chemoautotrophic bacterial mutualists that supply
organic carbon use highly reduced compounds,
such as hydrogen sulde, as energy sources.
Their hosts require oxygen.
Advection is the solution to the non-coexistence of
oxygen and powerful reductants, although
diffusion gets the material to and across the tissue-
water boundary.
55
East Pacic Rise at 9 50' N.
Note the yellowish mussels surrounding the group of tube worms.
Deep Submergence Operations Group, Dan Fornari)
56
Redox Sequence in
Marine Sediments
(Aller 1982)
57
Various means of advection
Ott, J.A., M. Bright
& F. Schiemer. 1998.
Mar. Ecol., P.S.Z.N.
58
Ciliate colonies
(Zoothamnium)
Ott, J.A., M. Bright
and F. Schiemer. 1998.
The ecology of a novel
symbiosis between a
marine peritrich ciliate
and chemoautotrophic
bacteria. Mar. Ecol.
-P.S.Z.N. 19: 229-243.
(also the source of the
previous gure with
worms and clams)
59
Gradients and surface area
J
x
= -D
"C
"x
Flux per unit of area to the organism; advection
supplies the concentration and sharpens the gradient
To provide a high supply rate, the animal moves the
uid or sits where uid movement is high and presents
large surface area; this solution is widespread for respiration.
Here we are looking at solutions for nutrition (& resp.).
60
Bacteria (Thioploca)
Figure II.C.4. 150 trichomes of the sulfide-
oxidizing bacterium Thioploca with a total
length of 1 m extend from one square cm of
sediment, doubling the surface area for
exchange. Figure courtesy of Markus Huettel.
61
Thioploca make sheaths
62
And they shuttle
Fossing et al.
1995.
Concentration and
transport of nitrate
by the mat-forming
sulphur bacterium
Thioploca Nature
374: 713-715.
63
Generalized gut, with
idealizations
Product ()
P
Absorbed Product ()
Food ()
Enzyme ()
nitial food
concentration,

0
Final ( ) food and
product concentrations,

Generalized
Gut

A
PFR
CSTR
o

64
Wash and Rinse Cycle (Mayer)
65
Unfortunate
consequences

Surfactants also solubilize hydrophobic

pollutants.

The high dissolved peptide concentrations

in the gut dissolve heavy metals.
66
Digestion summary

There is an intermediate, optimal rate of

ingestion.
Advection, mixing, hydrolysis and
absorption interact.
Faster ingestion yields higher rates of
hydrolysis, but not necessarily higher rates
of absorption.
67
Take-home message

Most large organisms obtain their mass

through a combination of advection and
diffusion (plus reaction)

Advection dominates large-distance

transport

Diffusion dominates transport to and

through the last barrier between the
external and the internal environments.
68