Chapter 4 Lecture

Biological Physics
Nelson
Updated 1st Edition

Random Walks, Friction &

Diffusion (part II)

Slide 1-1

Important Dates
Extra class
Wednesday May 6th (Self Study)

Midterm report presentation

Tuesday May 12th (5th Period)
Presentation on Chapter 5 in book
See next slide
Final Report
Topic of you choice based on research
papers related to biophysics
Slide 1-2

Announcement: Midterm Presentations

Midterm presentation are Week 7/8
May 12th, 5th period (1620-1800)
Each group (3 students) will give a short 30
min. prezi from 3 subsections:5.1+5.3.x1; 5.2+5.3x2; and
5.3.1, 5.3.2, 5.3.3, 5.3.4, 5.3.5
(choose 3 x1,x2)
Each student ~10 min. (template on GDrive)
Make mini-group-report (ShareLaTeX)
Deadline May 26th
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Biophysics quote
Humans are to a large degree sensitive to energy fluxes rather
than temperatures, which you can verify for yourself on a cold,
dark morning in the outhouse of a mountain cabin equipped with
wooden and metal toilet seats. Both seats are at the same
temperature, but your backside, which is not a very good
thermometer, is nevertheless very effective at telling you which is
which.

-Craig F. Bohren and Bruce A. Albrecht, Atmospheric

Thermodynamics (Oxford University Press, New York, 1998).

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Summary: Random Walks

1961. Used by permission of Dover Publications.

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Outline

Brownian motion
Random walks
Diffusion
Friction

Three important equations, leading to the

Fluctuation-Dissipation relation

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Homework
1. Read 4.1.3:- Understand statement: Random
Walk is model independent!
2. Read 4.2:- What Einstein did?
3. Make a diagram for 1D case of four steps
4. Extra:- Are two elevator shafts better when
stopping at odd and even floors only?
Assume the cost of the elevator is only to
start and stop ~ 50 Yen per ride

Slide 1-7

4.3 Other Random Walks (Discussion)

If we synthesize polymers made from various numbers of the

same units, then the coil size increases proportionally as the
square root of the molar mass.
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Polymer Diffusion

Slide 1-9

Polymer Random Walks (Problem 7.9*)

Figure 4.8 (Schematic; experimental data; photomicrograph.) Caption: See text.

1999. Used by permission of the American Physical Society.

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Random Walks on Wall Street*

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4.4 4.6 Equations Summary

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4.4 The diffusion equations: Ficks 1st Law

First lets derive Ficks first law: consider 4.10
and release a trillion random walkers and
compare P(x,0) with P(x,t) at time steps t
Flow from L > R is
and when bin size is shrunk we get

No. density c(x) is just N(x) in a slot divided by

LYZ (vol. of slot) = N/(LYZ) implies

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4.4 Diffusion cartoon

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4.4 Ficks Law (1st Law)

From last time we know D = L2/t so we have

Q:- What drives the flux?

Slide 1-15

4.4 Ficks Law (1st Law)

From last time we know D = L2/t so we have

Q:- What drives the flux?

Mere probability is pushing the particles (cf.
entropic forces)
Ficks (1st law) is not enough. We need his 2nd
law; otherwise known as the Diffusion Equation

Slide 1-16

4.4. Diffusion Equation

Lets look at how N(x) and hence c(x) vary in
time:
Now dividing by LYZ gives the continuity
equation

Now take derivative of

w.r.t. time and use continuity to show that

Later our goal will be to solve this equation

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4.5 Functions and Derivatives

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And Snakes Under the Rug

Try to use Wolfram to make some plots

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4.6.1 Membrane Diffusion*

Imagine a long thin membrane/tube of Length L,
with one end in ink C(0)=c0 and in water C(L)=0
This leads to a quasi-steady state so we set
dc/dt =0 and hence d2c/dx2=0
This means that c is constant and js=-Dc/L
where c0=cL-c0 and subscript s means the flux
of solute not water
Now define js=-Psc where Ps is the permeability
of the membrane. In simple cases Ps roughly
relates to the width of the pore and thickness of
the membrane (length of pore)
Using dN/dt=-Ajs leads to (next slide)
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4.6.1 Membrane Diffusion

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4.6.2 Diffusion sets fundamental limit on

bacterial metabolism
In class exercise:
Example on pg. 138 of book
Follow steps and present your derivation
And also try to do Your Turn 4F
a) Find I (mass per unit time) ...
b) Estimating metabolic rate <= I/m =
3Dc0/(R2) = ...
c) use the actual metabolic activity of a
bacterium is 0.001 mole kg-1s-1 to estimate
size of bacterium (ans: - 24 m)
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4.6.3 Nernst relation

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4.6.3 Nernst relation & scale of cell

membrane potentials
Consider now a charged situation like many cell
membranes in biology (see Fig. 4.14)
The electric field E = V/l and hence the drift
velocity is
Now consider a flux trough area A (Fig. 4.14)
and we argue that j = c vdrift (check units) which
implies that
Now including dissipation in Ficks law we find

and using the Einstein relation we find

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The Nernst-Planck Formula

FQ:- what electric field will cancel out nonuniformity in a solution?

Ans:- Set j=0 implies
which has
solution

where V = Ex
Using real values we estimate V~58 mV. Not
far off voltages observed in real cell membranes
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4.6.3 Comment (from Nelson)

D has dropped out because we are considering
an equilibrium problem

In reality in cell membranes are non-equilibrium

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4.6.4 Electrical Resistivity from Nernst

Show that electrical resistance in solution is due
to dissipation D of random walkers (amazing)
In Fig. 4.14 now consider placing electrodes in
NaCl solution separation d
Now the ions in the solution wont pile up and we
will assume c(x) is uniform which from NernstPlanck means that E=V/d= kBT/(Dqc) j (check)
and since j is no. of ions per unit time we have
current I = qAj and hence
Ohms law V=IR with electrical conductivity
=d/(RA) where
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Homework: Section 4.6.5

Read Section 4.6.5 and do Your Turn 4G
Also Your Turn 4F on bacterium

Solution of diffusion equation is a Gaussian

profile (Gaussians again)
In 1D the solution is
In 3D follow Your Turn 4G or do 1D case.
Homework question 4.7:- Vascular Design
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