Soft Condensed Matter and Biophysics

Athene Donald

•Liquids and Complex Fluids

•Brownian Motion
•Self Assembly
•Surface Energy
•Polymers and Biological Macromolecules
•Liquid Crystals

•http://www.bss.phy.cam.ac.uk/~amd3/lectures_2007
•Material will be put here after each section is completed
1
 Pierre-Gilles de Gennes
Nobel Prize Winner in Physics 1991
• In his Nobel Prize lecture he
identifies the following key
topics as the central players in
soft condensed matter:
• Polymers
• Surfactants
• Liquid crystals
• Colloids

• They will be playing a key role

in our course.

2
What do we mean by Soft Condensed Matter?
• The term usually refers to states of matter which are neither simple liquids nor
crystalline solids.
• Includes many familiar types of matter – soap, yoghurt, paint, liquid crystals,
putty….but also much of our bodies including cell membranes and the
cytoplasm inside.
• In general we will be dealing with lengthscales intermediate between atomic
and macroscopic; these are often known as mesoscopic.
• Quantum mechanics will not therefore be useful; the predominant techniques
we will use will be statistical.
• Mean field theories will be found to be useful, as you have seen before, to
describe the behaviour of large numbers of molecules.
• Although dealing with ensembles of molecules, we will find that thermal
energy is comparable with the energies giving rise to distortion and interaction
energies, so Brownian motion and fluctuations are very important.
• This is a key difference with 'hard condensed matter' for which thermal
fluctuations are not important.

3
 What do we mean by Biophysics?
• The term is used in different ways by different communities eg in Physiology
you will find it referring to the study of electrical impulses across cell
membranes.
• ‘Many regard biophysics as a discipline still waiting to be adequately defined’
(Cotterill – Biophysics an Introduction).
• Biophysics courses in Life Science degrees often cover topics where physics
can be applied to biology, with the physics being kept simple.
• In this course we will be looking at where our detailed physics understanding,
possibly gained from quite other systems, can be applied to study the
complexity of biological systems.
• A key example is self-assembly.
• Biology (unlike physicists) is very good at this.

TMV Cell
Membrane
4
 Useful Books
• RAL Jones Soft Condensed Matter OUP 2002
• D Tabor Gases, Liquids and Solids, 3rd ed CUP 1991
• M Daoud and CE Williams, Soft Matter Physics, Springer 1999
• IW Hamley, Introduction to Soft Matter, Wiley 2000
• P Nelson, Biological Physics, Freeman 2003
• KW Dill and S Bromberg, Molecular Driving Forces, Garland Science 2003

• Advanced Texts
• M Kleman and OD Lavrentovich Soft Matter Physics, an Introduction, Springer
2003
PM Chaikin and TC Lubensky, Principles of Condensed Matter Physics, CUP
1995
SA Safran, Statistical Thermodynamics of Surfaces, Interfaces and Membranes,
Addison Wesley 1994
M Daune, Molecular Biophysics, OUP 1999
JN Israelachvili Intermolecular and Surface Forces, Academic 1985
M Rubenstein and R Colby Polymer Physics,OUP 2003
PG de Gennes, F Brochard-Wyart and D Quéré, Capillarity and Wetting
Phenomena Springer 2002
5
 Additional Texts
• ME Cates and MR Evans, Soft and Fragile Matter, IoP 2000
• IM Ward Mechanical Properties of Solid Polymers, Wiley 1983
• IM Ward and J Sweeney, An Introduction to the Mechanical Properties of
Solid Polymers, Wiley 2004
• S Vogel Life in Moving Fluids Princeton 1994
• RAL Jones Soft Machines OUP 2004
• J Goodwin Colloids and Interfaces with Surfactants and Polymers Wiley 2004
• M Doi Introduction to Polymer Physics OUP 1992
• R Balescu Statistical Dynamics, Imperial College Press 1997
• D Boal Mechanics of the Cell, CUP 2002
• DC Bassett Principles of Polymer Morphology CUP 1981
• AM Donald, AH Windle and S Hanna, Liquid Crystalline Polymers, CUP
2006
• JR Waldram, The theory of thermodynamics
• WCK Poon and D Andelman, eds, Soft Condensed Matter Physics in
Molecular and Cell Biology, Taylor and Francis 2006

6
 Style of Course
• We will be looking at a wide range of concepts, from diverse areas.
• The ideas behind the systems are as important as the maths.
• This means the course has an uneven theoretical content; this is to some extent
the nature of the topic.
• If you only deal with equations in this field, you do not develop your intuition.
• Statistical ideas dominate (you may want to look over what you know about
partition functions, free energy, fluctuations and chemical potential).
• By considering a range of different classes of systems, you should aim to look
for similarities of behaviour.
• Do not consider the topics as independent; they share principles and the field
is generally treated – in texts and by researchers – as unified. And so should
you!
• Applications should be perceived in our every day world – and not just in
technological developments.
• Next year's Part III course will develop some of the topics in more depth.
7
 Style of Handouts

• The handout consists of these lecture notes.

• They are in bullet point form, and you should expect to annotate them during
the lectures.
• They will also be put on the web, at the end of each section, so that if you
want to see the text in full colour for additional clarity you can.
• You are expected to read around the subject, using the books listed, to flesh
out ideas you may not have picked up first time around.
• I will try to indicate, for each substantive section, which books are likely to be
most useful for that part of the course.
• However, the handout will cover all concepts required for the exam.
• Where proofs are not given rigorously in the lectures, that means that is all
you are expected to know.
• Often arguments are only semi-quantitative, and that is the nature of the
subject.

8
 Flow and Viscosity
• Viscosity  defined by
Shear flow down a pipe
dv x vx
 
dy dv x y
dy
• where  is the shear stress and x

dv x is the velocity gradient.

dy
• Viscosity has the units of kg m-1s-1 or Pa s
(old fashioned unit the Poise, after Poiseuille, ux is the displacement in the x direction.
where 1 P = 0.1 Pa s).
• This so-called constitutive equation can be Compare this with the behaviour of
rewritten in terms of the strain rate

elastic solids
  E


dv x d du x d du x d
  
dy dy dt dt dy dt where E is Young’s modulus.
d
  
dt 9
 Newtonian and non-Newtonian Fluids

• For a Newtonian fluid, the viscosity is strictly a constant.

• However many complex fluids, unlike water, do not obey this simple linearity.
• Examples of different types of fluids:

Newtonian

• There is a great richness of behaviour

• Some materials behave like solids at high strain rates, but liquids at low.
• Such materials are known as viscoelastic, and their response depends on the
conditions under which deformation is applied.

10
 Examples of Different Classes of Liquids
• Non-drip paint is a Bingham Fluid – also known as thixotropic.
– Has a yield stress
– Spreads easily when brushed on with finite shear stress
– Does not drip when brush stops.
• Dispersions of particles (colloidal dispersions) often shear thin
– As shear is applied, the particles can line up into 'strings' which line up and
hence interact less with neighbouring particles, reducing viscosity (and
dissipation).
• Shear-thickening fluids are important for lubrication.
– As two components move faster and faster to each other, one does not want
the lubricant being squeezed out causing high friction.
– A shear-thickening fluid will remain in place, maintaining a low-friction
environment.

• For non-Newtonian liquids, the viscosity is therefore a function of time or

equivalently shear rate.
• It is not a simple constant.
11
 Flow down a Pipe
see standard fluid dynamics texts, and Nelson

• Rearrange and integrate,

remembering the velocity is zero at
the wall (‘no-slip’ boundary
R
conditions).
v r
P P
P1 r P2   dv  1 2  rdr
flow 0
2 L R
Viscous drag force
P1  P2 2 2
v  R  r 
4 L
L
• Entrance and exit pressures P1 and P2 • This implies a parabolic flow
profile,
respectively.
• Viscous drag force acting at radius r
dr
F   2rL
dv

• Must balance force due to pressure

difference
• It is obeyed for Newtonian fluids in
( P1  P2 )r 2 long narrow pipes.
12
 Example – Blood Flow
• Rate Q of volume flow down a
‘pipe’, in this case an artery, is 8L
Z
given by R 4
R
P P
R • This shows a very strong (inverse)
Q   v 2rdr  1 2  ( R 2  r 2 )rdr dependence of resistance on
0
2 L 0
dimension of the artery.
( P1  P2 )R 4
 • If R is only decreased by ~6% the
8 L
change in Q ie blood flow, is
nearly 30% reduction.
• This is known as Poiseuille’s • Thus, small clogging of arteries has
equation (or sometimes Hagen –
Poiseuille) extremely detrimental effect on
• force required to pump blood.
It can also be expressed as
• Q=p/Z where Z is the • Alternatively, tiny dilations or
hydrodynamic resistance and p the contractions can significantly affect
driving force (ie pressure blood flow eg to prevent heat loss
difference). from extremities on a cold day.

13
 Drag on Particles and Stokes Law
Streamlines
• Streamlines show the simultaneous
instantaneous motions of the fluid
at each point in the fluid.
• For a fluid moving with uniform
velocity the streamlines will be straight
lines.
• They are perturbed around a particle.
• In the ideal case (as in diagram) the
perturbation will be symmetrical
and there is no net force.
• For a viscous fluid there is a net
drag force
• Stokes’ Law for particle of radius r
F  6rv
• This applies either if particle is
stationary and fluid flows past, or
for a particle falling through
stationary fluid.
• In general a falling particle will
reach a terminal velocity when the
drag force equals the pull due to
gravity.
14
 Sedimentation under Gravity
• Net force due to gravity is • In practice this approach forms the
meff g, where meff is given by basis of simple viscometers for
measuring the viscosity of fluids by
4 measurement of the terminal velocity
meff  r 3 (  p   l )
3 of a standard sphere falling through
where p and l are respectively the the fluid.
densities of the particle and liquid.
• Terminal velocity vT is given by
the balance of drag and
gravitational forces so that

meff g 2r 2 (  p   l ) g
vT   • Although this is very crude, and relies
6r 9
on various assumptions about the
motion, it does permit ready ranking
of different fluids.

15
 Sedimentation in Practice
Ludwig Boltzmann
• Boltzmann distribution tells you how
1844-1906
particles will distribute with height.

n( z )  no exp(meff gz / kT )

• In an ultracentrifuge can apply

accelerations many times g and speed
up the sedimentation even for quite
small particles/molecules.
• By examining either the rate of
sedimentation or the equilibrium
distribution of molecules can get an
estimate of size.
• Issues arise from need to account for
detailed hydrodynamic shape of
molecules.
16
 A Quick Look at Colloids
Jones, Hamley
• Whether or not particles stay in
suspension will therefore depend
on their meff and temperature.
• If particles are small enough – and
do not aggregate/clump – then
suspensions can be stable
indefinitely.
• Colloids fit into this category:
micron or smaller particles
designed so that interparticle forces
keep them apart.
• Because they are small, Brownian
motion is sufficient to counteract
the sedimentation, as we will see
later.
• For macroscopic particles as well
as for molecules, fluctuations in
polarisation leads to an attractive
potential.
• For isolated molecules this leads to
the 1/r6 van der Waals attraction.
• For particles, we have to integrate
over all the pairwise interactions.
• Approximate potential
A 1
 2 V
U  dx1dx2
r 6
1V2 12
• A is known as the Hamaker
constant and depends on the
polarisability of the particles.
17
 Interactions between Colloidal Particles

• Two main routes to prevent

Hard core aggregation in the ‘primary
Repulsion minimum’, by introducing a
Interaction energy

distance
Van der
Waals
attraction
• Van der Waals force (also known
as the dispersion force) leads to a
long range attraction.
• At very short distances there is a
hard core repulsion
• So why don’t colloidal particles
always stick together?
repulsion force.
1. By introduction of an
electrostatic repulsion.
2. By steric repulsion.
• Both these routes are of great
practical importance.
• Colloids turn up in many
situations: ink, ferrofluids, milk,
clay, blood….
• We will return to stabilisation
methods later.

18
 Complex Viscosity and Viscoelasticity
Jones, Ward
Creep
A constant load is applied and the
• A viscoelastic material is, as the
resulting strain is measured.
name suggests, one which shows a
combination of viscous and elastic
Load applied
effects.
0
• Polymeric fluids and some solids time
are examples.
• The elastic term leads to energy
Strain response 1

storage. 1 
• Its contribution to a shape change
will be lost once the stress is immediate elastic deformation
removed.
• The viscous term leads to energy delayed elastic deformation
dissipation, and irreversible shape  Newtonian flow (i.e. permanent
changes associated with the flow. deformation
• Rate effects are very important for
Define creep compliance
these materials.
 (t)
J(t)  19
o
Stress Relaxation
• A fixed extension (strain) is • Thus both the shear modulus and the
compliance are functions of time.
applied

strain applied • One can talk about relaxed (long time) and
unrelaxed moduli.
time

modulus
effective
stress  measured

time
• Define stress relaxation modulus
 (t ) max dissipation

G (t ) 

dissipation
o

• If no viscous flow occurs, stress
drops to finite value at infinite
times  relaxed modulus.
• If there is viscous flow, stress can
drop to zero.
energy
time
• But associated with flow will always be
dissipation.
• This is a maximum at intermediate times.
• So the effective viscosity is also a function of
time – or equivalently shear rate.. 20
 Boltzmann Superposition Principle
Input 

Stress
3
• To describe the general response of a 
2

system, must allow for details of Response
1

loading history. e3(t)

Strain
• This can be done using the
e2(t)
Boltzmann superposition theory.
e1(t)
  
Boltzmann proposed: 1 2 3 Time
1. Creep is a function of the whole
sample loading history. In general, for a creep experiment,
2. Each loading step makes increments of stress d at times tn
independent contribution to total t d (u)
loading history.  (t)   J(t  u) du
 du
3. Total final deformation is the sum of
each contribution. For stress relaxation, incremental additions
of strain d at times tn

t d (u)
 (t)   G(t  u) du
 du 21
 Complex Modulus and Viscosity
• For a steady state shear rate
• However what happens to Newton’s law if
d (u )
t
the stress and strain are not in phase?
 (t )   G (t  u ) du

du • Think of an LCR circuit analogy, with the
stress  as the driving force and the strain
can be rewritten as as the ‘current’.
(t) = od/dt • In that case will have a complex
• i.e.Newton's law of viscosity impedance, and by analogy we will now
have complex viscosity or equivalently
where

complex moduli
 o   G (t )dt
0
 *   'i "
(by change of variable) G*  G 'iG"
• where * is the complex viscosity and G*
the complex modulus

22
 Complex Moduli and Viscosity cont
• Example Torsional Rod Method
• If there is an oscillatory driving force, then rod end
one rigidly clamped at
• real part G'= storage modulus one end
(This gives the part of the strain in phase cylindrical rod of polymer
with the driving force) radius r, length l
• imaginary part G" = loss modulus
inertia disc,
(This represents the out of phase moment of inertia I
component).
• Set in oscillatory motion
This is a general description for all • Let phase angle be , apply
viscoelastic materials. sinusoidal strain
• There are various methods of measuring
•  = oexpit
both real and imaginary parts, which use
oscillatory approaches.  = oexpi(t+)
• By solving the appropriate equations of
 o
motion it is possible to relate G' to the  G*  exp i
energy storage (natural frequency), and G"  o
to the energy dissipation.
• The moduli will in general be both time and
23
temperature dependent.
 Example of Viscoelastic Behaviour
• Polymers are typical viscoelastic
materials.
Polyisobutylene data • Their moduli depends on the relevant
Glassy timescale.
Rubbery • At short times/high frequency the
chains cannot respond (we will look in
more detail at the chain dynamics
later).
• The storage modulus is high, and the
material is said to be glassy.
• But there is little dissipation.
• At long times the chains can move
easily, and the storage modulus is low.
• There can be many decades difference
in these two values.
• Loss processes/dissipation are low at
each end of the spectrum, and pass
through a maximum in between.
24
 Reynold's Number for Flow
Nelson

• The Reynold's number Re gives a measure l

of the relative importance of inertial and v
viscous forces.
R
• In general different behaviour is found at
low and high Reynolds number.
• It also indicates when turbulence will set in.
• We will consider a heuristic argument to • Consider motion of volume
get a feel for this number for a simple element of fluid (density ) side l
geometry of a spherical particle. around obstacle radius R.
• It can also be obtained in a more rigorous • The inertial term for this volume
way from the Navier Stokes equation, for element is
those of you who have come across this 2
equation, where all the different forces v
acting on a body are considered. ~ l 3
R
Mass acceleration
25
 Reynold's Number cont
• Hence Re= inertial/viscous forces
• The viscous force is
dv l 3 v 2
 vR
dx Re  R 
l 3 v 
• So on this volume element of side l R2
there is a net force across it of
• More generally (i.e. not for a sphere) R will
d dv be some characteristic lengthscale of the
l 2 l object.
dx dx • When Re is low, viscous forces dominate.
• Stirring has least effect
• The flow stops as soon as the external force
is removed.
~v/R2 • In contrast at high Re, inertial forces
dominate and it can take a long time
fordisturbances to die away.
• Turbulence becomes important
26
 Properties of the Reynold's number
• Reynold's number is
Cylinder Re =41
dimensionless.
• Although evaluated here for a
specific situation, its general
properties are the same regardless
of geometry. Fluid flow
• At a sufficiently high Reynolds
number, flow will always become
turbulent; the precise number
depends on geometry.
• At low Re (<<1) have symmetry
upstream and downstream of an
obstacle.
• This is broken at higher numbers, Sphere Re =116
when fluid leaves the obstacle
before reaching rear point of
symmetry – eddies form.

27
 Consequences
DJ Tritton Physical Fluid Dynamics

• Flow patterns become very • Drag coefficient CD a non-dimensional way

complex of representing drag as f(Re).
D D
Re~30 CD  
1 / 2 v 2 R 1 / 2v Re

where D is the drag/unit length

Re~40
CD for circular cylinder

Re~47

CD
Onset of turbulence

Re~55

• At low Re, CD  1/Re (precise for a sphere)

Re~67 • When CD constant, then D  v2; often a
characteristic of flow at high speeds.
• At CD ~3 x105 dramatic drop as flow becomes
Re~100
turbulent.
28
 Life in Moving Fluids
Re

Need to keep drag down-

Large whale swimming at 10 ms-1 300,000,000 by design of shape and
material characteristics.
Duck flying at 20 ms-1 300,000

Large dragonfly going 7 ms-1 30,000 Increasing effect of viscosity

Flapping wings of smallest flying 30

insects
Invertebrate larva 0.3mm going at 1 0.3
mms-1 Problem of propulsion – use
1 m bacterium swimming at 30 0.00003 cilia and flagella ie anisotropic
ms-1 shapes and hence anisotropic
drag forces.

29
Motion of E Coli cells
• E Coli cells examined by video-
enhanced differential-interference
contrast microscopy.
Some cells are shown de-energised
near the bottom of the preparation.
• They exhibit a variety of wave
forms: normal, colied , semic-
coiled etc.
• The mobile cells show the strongly
beating flagellae, which propel
them forward.

30
 Implications for Nanotechnology

• What is wrong with this?

• What drag will the nanobot feel?
• How easily will it move through
the blood vessel?
• What will be the effect of random
buffeting (in other words Brownian
motion)?
• Do we know what design criteria to
use to make this work?

• The dynamics at this lengthscale

"A microscopic, computerised robot, also
known as a nanobot, looks for life threatening
blockages in a human blood vessel, as
imagined in this artist's futuristic illustration."
From Encarta
are totally different from our
everyday experience (although
bacteria have probably got it right!)
31
 Implications for Nanotechnology cont

For a good discussion of some of these issues see

Soft Machines by RAL Jones (2004)

"If we were making a submarine that operated in treacle, we would have to use a
completely different design for the propulsion system than we would for water…..
[and] if we were shrunk by a factor of 10000 then water would no longer feel like
the free-flowing fluid we are familiar with, but instead it would take on the
consistency of treacle."

Twisting motion is much more effective than e.g our normal swimming strokes in
high viscosity situations. And this is how bacteria swim around, by twisting
cilia/flagellae.

32
'Nanobot swimming'

33