Biophysics 2A03/LifeSci 2BP3 Fall 2023

Molecular Motion, Transport

and Diffusion
These notes make use of Phillips et al. – Physical Biology of the Cell
Chapter 13 – A Statistical View of Biological Dynamics
From last class…
An E. coli cell is rod-shaped and about 2 micrometers long. E. coli can
divide every 20 mins if sufficient nutrients are available.
If the cells continue to divide at this rate, how long would it take for one
cell to fill an Olympic sized swimming pool?

Exponential Growth: 2! where x is the number of doubling times

Number of cells is then 𝑁"#$$% = 2! where x is the number of doubling times

Olympic Pool:
𝑉&''$ ~50 𝑚 × 25 𝑚 × 2 𝑚 = 2500 𝑚(

E.coli cell:
𝑉"#$$ ~2 𝜇𝑚 × 1 𝜇𝑚 × 1 𝜇𝑚 = 2×10)*+ 𝑚(

Number of cells to fill pool:

𝑉&''$ 2500 𝑚( ,*
𝑁"#$$% = = = 1.25×10
𝑉"#$$ 2×10)*+ 𝑚(
How many divisions does E.coli need to undergo to fill the pool, i.e. what is x?
𝑁"#$$% = 2! = 1.25×10,*

Take log of both sides

log(2! ) = log(1.25×10,* )
𝑥 log 2 = log (1.25×10,* )
log 1.25×10,*
𝑥=
log 2
𝑥 = 70

How long does it take for 70 divisions to occur?

Time for 1 division = 20 min, so 3 divisions per hour
Time to fill pool = 70/3 = 23.3 h
 Introduction and History – Brownian Motion
• Scottish botanist and microscopist (1773-1858).
• Contributed detailed descriptions of the cell nucleus, and of
cytoplasmic streaming.
• Visited Australia (1801-1805) and described many new plant
species.
• Interested in pollination.
• Best know for his observation of what is now known as
Brownian motion (1827). Robert Brown in 1855
National Portrait Gallery, London

“... the particles have a manifest motion. This motion is only visible to my lens which magnifies
370 times. The motion is obscure but yet certain...” Brown’s lab notebook, June 12, 1827.

Pollen of Clarkia pulchella Bursting pollen Amyloplasts and spherosomes

Pearle, P., Collett, B., Bart, K., Bilderback, D., Newman, D., and Samuels, S. (2010) What Brown saw and you can too. Am. J. Phys. 78: 1278-1289.
 Introduction and History – Brownian Motion
• Brown reported on the “jittery
motion” of the particles released by C.
Pulchella and then other pollens.
• Idea 1: the motion of the particles is due to
an active force generated by a living
organism.

• Idea 2: the smaller particles are the

“building blocks of life” (“same” particles
observed for all kinds of plant cells).
Brownian motion of contents of Clarkia pulchella pollen
physerver.hamilton.edu/Research/Brownian/index.html

• He observed the same particles and their

motion for inorganic matter, which
convinced him that both ideas were
incorrect.
• He eventually concluded: “... motions
for which I am unable to account. “

Pearle, P., Collett, B., Bart, K., Bilderback, D., Newman, D., and Samuels, S. (2010) What Brown saw and you can too. Am. J. Phys. 78: 1278-1289.
Brown, R. (1828) A brief account of microscopical observations made in the pollen of plants, Edinburgh New Philos. J. 5, 358-371.
 Brownian Motion of Cells

Magnetotactic bacteria swimming in a magnetic field

Bacteria swim along the direction of the applied magnetic field (B). However, small deviations from a linear trajectory
demonstrate the influence of Brownian motion.
Movie credit: Rohan Nadkarni.
 Brownian Motion of Macromolecules

Bacterial cytoplasm
Molecular dynamics simulation of a model of the bacterial cytoplasm.
McGuffee & Elcock, 2010.
 Brownian Motion of Atoms in Proteins

Major histocompatibilty complex (mhc) protein

The molecular dynamics software used for this simulation is Gromacs and the result is visualized using the software VMD.
Both can be downloaded free from the web.
http://www.youtube.com/watch?v=Y79Xl0LfYI4
Membrane Transport – Passive Mechanisms

Simple Diffusion:
• Particles cross the membrane without the aid of a protein
• Must be able to penetrate the hydrophobic core of the bilayer
Facilitated Diffusion:
• Spontaneous passage of molecule or ions across a biological membrane
passing through specific transmembrane integral proteins
Membrane Transport – Active Mechanisms

Cooper & Hausman The Cell

Active Transport:
• Requires energy
• Particles are moved against their concentration gradient (i.e. from low to
high concentration)
• If process uses chemical energy for example from ATP it is called primary
active transport
Example of Diffusive Motion
• Ions enter a cell when an ion channel
protein opens.
• Initially they are close to the channel.
• By random diffusive motion, they
eventually spread over the whole
cell.
How long does it take?
Why does it happen?

All molecules jostling one another

continually. Thermal motion –
molecules not at rest.
Entropy is increasing – more
configurations with the ions spread
out than with them all together.
Diffusive vs Directed Motion

• Compare the diffusive and directed motions of an RNA

polymerase protein within a cell
• 1D directed motion along the DNA is much faster than diffusion
• Why?
• How does it know which way to go?
Diffusive vs Directed Motion
Motion of a swimming E.coli

Large scale à random walk Small scale à directed

• Motion can be directed at some scales and diffusive at other

scales
When is Diffusion Effective?
The time taken to diffuse a distance x is proportional to the square
of the distance.

t = x2 / D

slope is 2 on this
log-log plot
When is Diffusion Effective?
• Typical time it takes a particle to diffuse distance x is
𝑥!
𝑡=
𝐷

• D is the diffusion constant which has dimensions (units) of

length squared per time, and depends on factors such as
particle size, temperature, and viscosity of surrounding fluid

• Here time grows as the square of distance! Our previous

experience in kinematics was with objects moving at a
constant velocity where the time to travel a distance x grows
linearly with distance.
When is Diffusion Effective?
The time taken to diffuse a distance x is proportional to the square
of the distance.

For a typical globular protein at

room temperature in water
𝜇𝑚!
𝐷~100
𝑠
How long does the protein take
to diffuse 1 m (106 μm)?
10" 𝜇𝑚 ! #$ 𝑠
𝑡~ ~10
𝜇𝑚!
100 𝑠
~300 𝑦𝑒𝑎𝑟𝑠

Diffusion is not effective at large length scales.

When is Diffusion Effective?
Let’s look at transport within a nerve cell

Passive transport

Active transport

(A) Passive transport by diffusion would only be effective in a small

region of the cell.
(B) Active transport by a molecular motor would be necessary to
move something all the way along the cell.
Experimental Techniques to Probe Diffusion

FRAP: Fluorescence
Recovery After
Photobleaching

DOI: 10.1017/S0033583515000013
Example of FRAP

GFP = green fluorescent protein ER = endoplasmic reticulum

A protein in the ER membrane is labelled with a GFP tag so it can be
seen in an optical microscope.
Molecules in the black region are bleached by a laser.
New molecules diffuse into this region by moving within the
membrane. measure the time for the fluorescence intensity to
recover.
 Experimental Techniques to Probe Diffusion

FCS: Fluorescence
Correlation
Spectroscopy
DOI: 10.3390/ijms19040964

Single Particle Tracking

DOI: 10.1007/s00253-007-1007-8
Mathematical Pictures of Diffusion
%!
• Where does the 𝑡~ & relationship come from?
• Can approach this from two perspectives that both lead to
the same diffusion equation in the end
1. Macroscopic
• Collection of diffusing molecules can be used to describe a
‘concentration field’
• Write macroscopic evolution equations for how
concentration changes over space and time
2. Microscopic
• Consider trajectory of individual diffusing particles (hopping
events) à random walk through volume of interest
• Bringing these two notions together: when you sum up
many randomly wandering molecules, together their
collective motion gives the macroscopic appearance of
directed motion that is driven by concentration gradients
Random Walk Model of Diffusion in 1D

step size a
x0 = 0 xt-1 xt = xt-1+dxt

Amount moved on one step: dx = +a or -a

Mean: 𝛿𝑥 = 0
Mean square displacement: 𝛿𝑥 ! = 𝑎!
At time, t: xt = dx1 + dx2 + ... + dxt

xt = å dx
i
i =0 average position is at 0 (equally likely to go forwards
or backwards)
mean square distance is
xt2 = å
i
dxi2 + åå dx dx
i j ¹i
i j =a t 2
proportional to time

this part is zero because steps are uncorrelated

 Models of Diffusion in 2D
x 2 = dx 2 t
mean square distance
moved in x direction in t mean square distance moved in
time steps x direction in one step

Square lattice model Off-lattice model with fixed step length

(see Assignment 1)

a 𝛿𝑦 a
𝜃
𝛿𝑥

moves in one of 4 directions

𝛿𝑥 , + 𝛿𝑦 , = 𝑎,
1 , 𝑎, 𝑎,
𝛿𝑥 , , , ,
= 𝑎 +𝑎 +0 +0 = ,
𝛿𝑥 =
4 2 2
Models of Diffusion in 2D
In both the 2D models
𝑎!
𝑥! = 𝑡
2

𝑎!
𝑦! = 𝑡
2

𝑟 ! = 𝑥 ! + 𝑦 ! = 𝑎!𝑡
r

Again, mean square distance moved is proportional to time

What’s next?
• We will continue to explore diffusion next class
• We will also spend time working with NetLogo for
Assignment 1
• Download NetLogo
• Read through assignment 1
• Start exploring the NetLogo programs provided