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2 Brownian Motion
2 Brownian Motion
1
Brownian Motion
Nelson; Dill and Bromberg
2
Brownian Motion
Jones
• Forces are random so each • We can also use the identity
direction behaves in the same way 2
d dx dx d 2x
and x x 2
dt dt dt dt
x 2 y 2 z 2
2 2 • Thus
R 3 x 2
2
•
d dx dx d ( x )
Work in 1D for simplicity m x m xFrandom
dt dt dt 2 dt
d 2x dx
m 2 Frandom
dt dt • Rearranging and taking an average
yields
• Use the substitution
d (x2 )
d (x2 ) dx
2x 2 dt
dt dt d dx
2
dx
xF m x
random dt dt dt
• Then d 2 x d (x2 )
m 2 Frandom
dt 2 x dt
3
Brownian Motion cont
d (x2 )
• And hence the total squared
2 dt
displacement in 3D is
d dx dx
2
xF m x
random dt dt dt 6 k BT
R 2
3 x 2
t
• The direction of the random force on
the particle is not correlated with the
• The motion is diffusive with a
particle's position, so the first term is
diffusion coefficient given by the
zero. Similarly, there is no
Einstein relation
correlation between the particle's
position and its velocity, so the D=kBT/
second term is also zero.
• The third term can be rewritten via
• We will explore the implications of
the theorem for equipartition of
this later, but note the inverse
energy, since
relation between drag () and the
• mvx2/2=kBT/2 or vx2=kT/m diffusion constant D.
d x 2 2 k BT
dt 4
Aside on Ensembles
(for the theoretically inclined)
Waldram:The theory of thermodynamics
• On the previous slide we saw averages • If the system obeys this Principle, then an
<….>. average over the probabilities of the
• What are we averaging over? system being in a particular configuration
• is the same as the average over time.
Those of you who took TP1 will
probably assume this is a time average • But, formally, one should always specify
– and it may be. what sort of average is being taken by the
• But the ensemble average can also be <…..>.
over a set of replicas at a given instant. • Frequently is is simply referred to as an
• ensemble average, which could mean
In your Thermal Physics course you
either.
have been taught about the different
types of ensembles. • Underlying all this is the ergodic
• You have also been taught about the assumption – that the system can go
anywhere within the allowed energy range.
Principle of Equal Equilibrium
Probability,namely that for an isolated • In which case in equilibrium, the
system, all microstates compatible with fluctuation distribution is identical with the
the given constraints are equally likely ensemble average distribution.
to occur.
5
The Diffusion Coefficient
• When the diffusing particle is a sphere,
• For a molecule such as a protein, the
Stokes Law gives
radius R may not equate to the actual,
=6r, so physical size.
k BT • A hydrodynamic radius RH can be
D
6r defined, which is the effective radius
presented to the fluid by the molecule.
• This is known as the Stokes- Einstein Additionally, the molecule may or may
equation. not permit the fluid to drain through it,
• For other shapes the drag coefficient, and depending on the density of chain
hence diffusion constant, take different packing.
forms. • Thus the detailed hydrodynamics of e.g.
• E.g. disc moving randomly globular proteins diffusing through a fluid
= 12r can be complex.
• Ellipsoid (major and minor axes a and b) • We will return to these concepts when
=6a/ ln(2a/b) for random rotation discussing proteins and polymers in more
detail.
(other expressions for motion sideways
or lengthwise)
6
Typical values for D in water
7
Diffusion Equation
Dill and Bromberg
• Fick's first law states that the flux J of • Specific solutions depend on
particles is proportional to the boundary conditions (recall your
concentration gradient. 2nd year maths!).
• e.g for point source diffusing in 1D
J Dc along x, starting at x=0
• And conservation of particles requires
c
.J
t
• Hence in 1D and assuming D is a
constant, then
c 2c
D 2
t x
• which is Fick's second law in its
Numbers
simplest form.
correspond
to values of
8
Dt
Diffusion Equation cont
• Compare with data from Wall Street • Note that D need not be a constant,
although in many simple situations
it is.
• If it is not, then the equation must
be modified to allow for the fact
that D can be a function of
position.
a a
c(r ) c (1 )
r
• We will model as spherically
symmetric, so work in spherical
coordinates.
• Assume steady state so dc/dt=0. • For such a concentration profile, the flux
• Diffusion equation becomes is given by
2 1 d 2 (rc ) dc Dc a
c 0
r dr 2 J (r ) D 2
dr r
• Solution depends on boundary 10
conditions.
Diffusion Controlled Collisions and Reactions
• Hence the number of collisions at the 2 Growth of particles post-nucleation
surface per unit time I(a) is
• In this case the molecules diffusing to
the surface are causing growth of the
I (a) J (a)4a 2 4Dc a particle – a process known as Ostwald
• Minus sign implies flux is towards ripening or coarsening.
particle (-r direction). • Flux J(r) as before but now we have
• This is the fastest possible rate at which
any process can occur, i.e. when it is 1 dr
J (r )
limited by diffusion. r2 dt
• If the reaction at the surface itself is rate
• Integration yields
limiting, a process will be slower.
• If the diffusing molecule is a nutrient to r3 t or
an organism, then we also have to think
about its consumption and this will be r t 1/ 3
proportional to the volume. • This is known as the Lifshitz-Slyozov
• Thus if the bacterium etc is too large, law, and is empirically found to hold as
cannot get sufficient supply of the long as diffusion is the limiting factor.
nutrient by diffusion, and so this will set
an upper limit on size.
11
Diffusion Controlled Aggregation
• During colloidal aggregation, can have either
diffusion or 'reaction' being the limiting factor.
No salt • Which is dominant depends on the conditions
of aggregation
• E.g. in the examples shown here of 250nm
polymethyl methylacrylate particles, it is the
salt concentration which is changing.
• This changes the interparticle potential.
With salt
• The shape of the aggregates can provide
insight into the processes occurring.
• Very often fractal structures form.
• In these the structure is the same at all
lengthscales
1/ d f
R~M
Watching paint
dry; a new paint
formulation; • Where R is the size, M is the mass and the
fractal structures fractal dimension 1<df3 (equality for compact
again visible, object)
but clearly with 12
rearrangement
Aside on Fractals
Jones
• This is known
dv as the Langevin equation • Example: For a sphere of radius 10nm
(strictlymthe A-Langevin v
f (t ) equation, as dealing (typical size for a large polymer) in water,
dt
with acceleration). this leads to ~10-10 s.
14
Velocity Correlation Function
(Doi, Balescu – see the latter for a rigorous and general discussion)
• More generally, look at the velocity • For so-called stationary stochastic processes,
correlation function defined as any autocorrelation function only depends on
<v(0)v(t)>. the time interval involved
• Recall the <…> imply a suitable ensemble i.e <v(t1)v(t2)> = Cv(t1- t2) with Cv a function
average.
• Thus more specifically we can write
• Correlation functions in general measure
the extent to which there is any correlation v(t )v(0) 2 D (t )
between a function at two separate times.
• It can be applied to position, force, • Where D is the diffusion coefficient.
velocity etc, and can be defined in the
same way as for the velocity correlation • This can be seen by considering, the mean
function. square displacement (MSD) in 1 dimension
• The larger the value of the function is, the about an average position x = 0 for diffusive
greater the extent of correlation. motion is
t t
• For random motion, the velocity • x(t ) dt1 dt2 v(t1 )v(t 2 )
2
0 0
15
Velocity Correlation Function cont
• Returning to the Langevin equation • By equipartition of energy
1 1
m v 2 (0) k BT
dv 2 2
m f (t ) v kT
dt v(0)v(t ) B exp ( t / m)
m
multiply by v(0) and take the ensemble average
Velocity correlation function
dv(t )
m v ( 0) v(0) f (t ) v(0)v(t ) <v2(0)>
<v(0)v(t)>
dt
<v2(0)>e-t/m
• Now v(0) and f(t) are uncorrelated so that the
first term on RHS = 0, and
t
d • The figure confirms that the longer the
v(0)v(t ) v(0)v(t ) 0
dt m time interval, the less the correlation
v(0)v(t ) v 2 (0) exp ( t / m) between v(0) and v(t) .
• For timescales shorter than the
characteristic time) the velocity retains
• So we have obtained an equation for the correlation, but not for time scales much
velocity autocorrelation function. longer than this.
16
Fluctuation-Dissipation Theorem
Dill and Bromsgrove
<v(0)v(t)>
0
v(0)v(t ) dt
m 0 exp ( t / m ) dt
D
18
Further thoughts on the Fluctuation
Dissipation Theorem cont
• Further Examples of how the FDT applies
• Consider a pendulum moving about an
equilibrium position, due to fluctuations in air • Nyquist's formula in electrical circuits
compared with its motion in a viscous fluid. says that the larger the resistance (giving
• At a fixed temperature, the mean square rise to dissipation) the larger the
displacement will be the same in both cases, (thermal) noise emf present.
corresponding to the magnitude of the
fluctuation in the displacement. • Thus this theorem translates into many
• However since the damping in the second case different situations where fluctuations
is much greater, then the random forces f(t)
giving rise to the fluctuations must be greater
and dissipation are present.
too.
• An alternative form of the equation expressing • BUT It only applies to equilibrium
this relationship is given by systems.
• Recent work has been directed at trying
to understand how far it can be pushed
e.g. for glasses which have quenched in
force correlation function disorder
1
2 k BT
f (0) f (t ) dt
19
Using Brownian Motion to obtain Local
Viscosities
• Beads moving around in viscous
fluids provide a means of probing
local viscosities.
• In some materials (e.g. liquid
crystals, see later) these may be
anisotropic.
• Other systems (e.g gels) may be
heterogeneous.
• A generalised version of the Stokes
Einstein equation allows the
complex moduli to be determined
by tracking the motion of the
particles.
20
Using Particle Tracking in Practice
• The mean square displacement as a function
of time can be followed eg. during some
process.
m
2 dk BT
r ( )
3a
• (d is dimensionality, a is particle radius, is
lag time)
m • Data for hectorite clay 1 hour and 24 hours
after the start of the experiment, showing how
Brownian motion becomes restricted as the
systems 'sets' or 'gels'.
m
• From the displacements the viscoelastic
moduli can be determined (via Laplace
transforms).
dk BT
G ( s)
m 3as r ( s ) 2 21
Chemical Potential and Free Energy
• • Model situation:
Recall the definition of the Helmholtz free
energy F for a simple system
F=U-TS A B
• If one has a reservoir containing N
atoms/molecules, the chemical potential
is defined as • Particle (species i) and energy
exchange is possible between two
F boxes A and B.
N T ,V • Total change in entropy
• The chemical potential is the change in
free energy when one particle moves from S S
one position, phase etc to another. dS tot A dE A B dE B
• Equivalently E A E B
S A S B
G
U
H S
T i N dN Ai i N dN Bi
N T , P N S ,V N S ,P N E ,V Ai Bi
1 1
dE A Ai Bi dN Ai 0 dF SdT pdV i dN i
TA TB i TA TB i
dH TdS Vdp i dN i
and this must be true for all the species. i
A =B
23
Aside on the Clausius Clapeyron Equation
T
• But across the boundary T and p
• Recall this tells us about how must be equal so
properties change along the phase
boundary, eg between gas and dp S L
liquid.
dT V TV
24
Chemical Potential of a Perfect Gas
• Recall F= -kBTlnZ • Now z/N can be written in terms of the
pressure as
where Z is the partition function.
z zk BT
• For N indistinguishable particles, as in a
N pV
perfect gas,
Z = zN/N! • Thus = o + kBTlnP
where z is the individual particle partition where o represents the chemical
function. potential of a standard state.
25
Membranes
• Membranes are the envelopes
around all our cells in our bodies.
• They are complex, dynamic
structures comprising so-called
lipid bilayers (see later).
• They have to be able to respond to Vesicles – simple
significant shape changes as our approximation to
bodies move or an organism biological cells - easily
crawls.
distort to allow for shape
• Initially let us treat the membrane changes, but do not
as a simple fluid interface with
associated surface tension, and exhibit short wavelength
look at its fluctuations. fluctuations as these cost a
• This is far too simple, because in lot of energy.
fact there is a curvature elasticity to
be taken into account (to be
discussed later).
26
Monge Representation of a Membrane Surface
Boal
• The Monge representation is a common • We can construct tangent vectors
way of representing an undulating along x and y, represented by rx
surface, such as a membrane. and ry by taking a unit step in the x
• A point r on a surface is represented by (or y) direction, and a step
• r = (x,y, h(x,y)) h h
hx or hy
x y
27
constrained to be single-valued.
Monge Representation cont
• The surface can also be defined by
n rydy its curvature – these are simply
z dA geometrical relationships,
hx rxdx discussed in maths texts.
• The curvature of a surface is
1 defined as
x
2r
• The element of area dA is defined
C n. 2
s
by
where s is the arc length.
dA rx ry dxdy 1 h h
2
x y
2 1/ 2
dxdy • In general there will be two
principal curvatures (the two
• And the metric g of the surface is
extremal values) C1 and C2.
defined by
• The combination (C1+ C2) is the
mean curvature .
g (1 hx2 hy2 )
• And C1. C2 is the Gaussian
curvature .
So that dA=g dx dy
28
Fluctuations in Membranes treated as a
Simple Fluid
Safran
• Hence, writing the undulations as a
Fourier sum
h(r ) h(q)e iq.r
h(x,y) q
2 k BT
• In two dimensions the logarithm of
| h(q) | 2
q
the integral diverges at small q,
and so we must think carefully small wavelength fluctuations in
about the limits. real space (ie large q) have far
smaller fluctuations associated with
• Set the upper limit as/a, where a them than large wavelength (small
is the atomic size. q) fluctuations.
• Set the lower limit as /L, where L • Or equivalently higher energy is
is the size of the interface. associated with small wavelength
• Then fluctuations.
k T L • Thus largescale distortions of
2
h (r ) B log membranes are more favourable
2 a than local rumpling.
30
Real Cells
• Example: Bovine pulmonary arterial endothelial
cells imaged in the confocal laser scanning
microscope
• Dual labeled with a green stain for actin
microfilaments (FITC-Phalloidoin) and a red stain
for mitochondria.
• The stain for actin is actually derived from a toxic
compound found in mushrooms.
• The stain for mitochondria only becomes
fluorescent when the stain is activated by enzymes
which reside in the mitochondria.
• For this reason, only the mitochondria appear red,
Bone cells not the other organelles.
• Example: Bone cells imaged in the environmental
scanning electron microscope (ESEM).
• Normal scanning electron microscopes work in high
vacuum, and so require cells to be dehydrated.
• The ESEM does not, and so potentially provides a
new route to high resolution examination of cells.
31
Real Cells cont
• Real cells are a lot more complex than simply an interface undergoing
fluctuations, but the basic ideas are correct.
• Have to take into account
– The physical structure of the membrane
– The (bio)chemical structure of the membrane
– The contents of the cell, particularly the cytoskeleton.
– What is surrounding the cell
– Osmotic effects
Example: what happens
when the cell is placed in
different media which
cause different degrees of
stress? The example shown is for
changing the osmolarity of the
surrounding medium, when the cell
shrinks or stretches according to
whether molecules have flowed in or
out.
32
Aside on Osmotic Pressure
• The osmotic pressure, , is the pressure which
• The comment on osmolarity will just stop the flow occurring.
introduces the idea of osmotic • In general
pressure.
• You will be familiar with this V RT ci
through the idea of what happens • Which for low concentrations approximates to
with a semi-permeable membrane. N
RT
V
• This has a form equivalent to the case of a perfect
A B gas.
• This effect is crucial in maintaining cells healthy.
• For instance, when a plant 'wilts' it has lost water
• If there is solute in A, then water will from its cells and the external pressure causes the
flow across the semi-permeable cells to collapse.
membrane until the chemical • By watering the plant, water is sucked back into
potentials on the two sides are equal. the cells to return the plant to full 'turgor' (in this
context one talks about 'turgor pressure', and the
mixture (T , p , ci ) pure (T , p,0) cells are then said to be turgid).
33
Brownian Motion within Cells- current (and
preliminary!) Research
35