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Anomalous Diffusion(1)

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You are on page 1of 29

Jan Korbel

Minisymposium on fundamental aspects behind cell systems biology, Nové Hrady

1 / 29

Outline

Diffusion phenomenon

History

Different descriptions of diffusion

Anomalous diffusion models

Fractional Brownian motion

Lévy flights

Interresting processes exhibiting anomalous diffusion

2 / 29

History overview

18th century

First developments were done by Maxwell, Clausius, Boyle...

1827 - discovered Brownian motion

The theoretical description of the Brownian motion was given

by Langevin, Einstein, Smoluchowski...

Many different approaches from different branches

macroscopic vs microscopic approaches

3 / 29

Macroscopic description of diffusion

Fick’s laws

concentration φ

First Fick’s law

∂φ

J = −D (1)

∂x

the flux is proper to concentration change

Second Fick’s law

∂φ ∂J ∂2φ

=− =D 2 (2)

∂t ∂x ∂x

time evolution is given by inhomogeneity of current

the equation is formally the same as heat equation

4 / 29

Microscopic description of diffusion

Langevin equation

heat bath

Newton equation

mẍ(t) − F = 0 (3)

Langevin equation

∂U

mẍ(t)+ +γ ẋ(t) = η(t) (4)

∂x

− ∂U

∂x - external forces

−γ ẋ(t) - friction forces

η(t) - fluctuation forces with hη(t)i = 0, hη(t)η(t 0 )i = 2Dδ(t − t 0 )

5 / 29

Microscopic description of diffusion

Langevin equation

would get nonphysical solution

in the long time limit we get from the relation for velocity

D kB T

hv (t)2 i ' ≡ (5)

γm m

Relation between diffusion coefficient and friction

kB T

D= (6)

γ

√

for long times we get hx 2 (t)i ' t which means that |∆x| ' t

6 / 29

Microscopic description of diffusion

Diffusion equation

probability distribution of the system p(x, t)

for free particle we obtain diffusion equation

∂p(x, t) D ∂ 2 p(x, t)

= 2 . (7)

∂t γ ∂x 2

the equation is formally the same as Fick’s equation for

concentration

for one localized particle at time 0 we get a Gaussian function

(x − x0 )2

1

p(x, t) = √ exp − (8)

4πDt 4Dt

7 / 29

Microscopic description of diffusion

Wiener stochastic process

Definition: A stochastic process W (t) (for t ∈ [0, ∞]) is called

Wiener process, if

a.s.

W (0) = 0

for every t, s are increments W (t) − W (s) stationary process with

distribution: W (t) − W (s) ∼ N (0, |t − s|).

for different values are increments not correlated.

The Wiener process also obeys diffusion equation

All formalisms lead to the main property of diffusion:

1

|∆W (t)| = t 2

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Diffusion in 2D

-100

-200

-300

-400

9 / 29

Anomalous diffusion

and time variables

for space: variance Var (X (t))

for time: correlations Corr (X (t), X (s))

if these quantities do not produce characteristic quantities

(standard deviation, correlation time) , we observe anomalous

diffusion

for long-term correlations we observe fractional Brownian

motion

for infinite variance we observe Lévy flight

10 / 29

Fractional Brownian Motion

we generalize Brownian motion by introduction of non-trivial

correlations

for Brownian motion is the covariance element

1

E[W (t)W (s)] = min{s, t} = (s + t − |s − t|) (9)

2

we introduce a generalization WH (t) with the same properties,

but covariance

1 2H

E(WH (t)WH (s)) = (s + t 2H − |s − t|2H ) (10)

2

Standard deviation scales as |∆WH (t)| ∝ t H

for H = 12 we have Brownian motion, for H < 1

2 sub-diffusion,

for H > 21 super-diffusion

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Sample functions of fBM for H=0.3, 0.5, 0.6, 0.7.

60

60

50

50

40

40

30 30

20 20

10 10

-10 -10

60 60

50 50

40 40

30 30

20 20

10 10

-10 -10

12 / 29

Lévy distributions

distribution

Such distributions are limits in long time for stochastic

processes driven by independent increments with given

distribution

Lévy distributions - class of stable distributions with polynomial

decay

lα

Lα (x) ' for |x| → ∞ (11)

|x|1+α

for α ∈ (0, 2)

the variance for these distributions is infinite

the distribution has sharper peak and fatter tails (= heavy tails)

13 / 29

Difference between Gaussian distribution

and Cauchy distribution (α = 1)

0.4

0.014 Γ=1

Γ=1

0.012 Γ = 0.8

0.3 Γ = 0.8

0.010 Γ = 1.2

Γ = 1.2

0.008 Σ=1

0.2

0.1 0.004

0.002

0.000

-4 -2 0 2 4 5 10 15 20 25 30 35 40

14 / 29

Lévy flights

properties as Brownian motion, but it increments have Lévy

distribution

Because of infiniteness of variance, scaling properties are

expressed via sum of random variables

d

for Brownian motion: a1/2 W (t) + b1/2 W (t) = (a + b)1/2 W (t)

d

for Lévy flight: a1/α Lα (t) + b 1/α Lα (t) = (a + b)1/α Lα (t)

R

to

E(|Lα (t1 ) − Lα (t2 )|α ) ∼ |t1 − t2 |. (12)

15 / 29

Lévy flight in 2D

300

200

100

-100

-200

-300

16 / 29

Power Spectrum

power spectrum

it is the absolute value of fourier transform

1

h(∆x(t))2 i ∝ t α ⇒ Px (ω) ∝ (14)

ω 1+α

17 / 29

Examples of anomalous diffusion

Subdiffusive behavior

mRNA molecules in E. coli cells

Lipid granules in yeast cells

Cytoplasmatic molecules

Power law behavior

Power law memory kernel for fluctuations within a single protein

molecule

Persistent cell motion of eukaryotic cells

18 / 29

Physical Nature of Bacterial Cytoplasm

Ido Golding and Edward C. Cox. Physical nature of bacterial cytoplasm.

Phys Rev Lett, 96, 2006

coli is measured

the track of molecules are recorded and fluctuations are

calculated

the fluctuation function hδ(t)2 i scales with an exponent of

α = 0.70 ± 0.007 (for 21 trajectories)

for comparison is done the measurement also in 70% glycerol,

with an exponent of α = 1.04 ± 0.03, which corresponds to

diffusion

Reasons: a) power law distributions, b) time-dependent

viscosity c) time correlations

19 / 29

Physical Nature of Bacterial Cytoplasm

Ido Golding and Edward C. Cox. Physical nature of bacterial cytoplasm.

Phys Rev Lett, 96, 2006

20 / 29

Anomalous Diffusion in Living Yeast Cells

Iva Marija Tolic´-Norrelykke et al. Anomalous diffusion in living yeast cells.

Phys Rev Lett, 93, 2004

investigated

the track is recorded by two methods:

Optical tweezer - short times (∼ 10−4 s), measures frequency

Multiple particle tracking - video based, longer times

(∼ 10−1 − 102 s)

The results were for diffusion in the cell α = 0.737 ± 0.003 for

OT, α = 0.70 ± 0.03 for MPT, about 1 in water

Possible reasons: granules are embedded in a protein polymer

network or mechanically coupled to other structures

21 / 29

Anomalous Diffusion in Living Yeast Cells

Iva Marija Tolic´-Norrelykke et al. Anomalous diffusion in living yeast cells.

Phys Rev Lett, 93, 2004

22 / 29

Anomalous Subdiffusion Is a Measure for

Cytoplasmic Crowding in Living Cells

Matthias Weiss et al. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Biophys J, 87, 2004

correlation spectroscopy

autocorrelation function was measured

we suppose a diffusion coefficienty D(t) = Γt α−1 and obtain

correlation function

1 + fe−τ /τC

C(τ ) ' (15)

1 + (τ /τD )α

for different different masses and hydrodynamic radii were

different α’s obtained, but α < 1 in all cases

23 / 29

Anomalous Subdiffusion Is a Measure for

Cytoplasmic Crowding in Living Cells

Matthias Weiss et al. Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Biophys J, 87, 2004

24 / 29

Power law within protein molecules

X. Sunney Xie et al. Observation of a power-law memory kernel for fluctuations within a single protein molecule.

Phys Rev Lett, 94, 2005

by photoinduced electron transfer

System can be described by generalized Langevin equation,

where we assume non-trivial autocorrelation function

Z t

dU

mẍ(t) = −ζ dτ K (τ )ẋ(τ ) − + F (t) (16)

0 dx

For memory kernel K (t) was measured power decay

K (t) ∼ t −0.51±0.07

25 / 29

Persistent Cell Motion in the Absence of External

Signals

Liang Li et al. Persistent cell motion in the absence of external signals:// a search strategy for eukaryotic cells.

PLoS ONE, 2008

environment with no external signals

it has been shown that the movement is not a simple random

walk

it has persistent behavior in smaller time scales, in larger time

scales (∼ 10min) it becomes a random walk motion

the movement seems to be more complex than simple wiener

process or Lévy flight

cells are able to reach the target very efficiently

26 / 29

Persistent Cell Motion in the Absence of External

Signals

Liang Li et al. Persistent cell motion in the absence of external signals:// a search strategy for eukaryotic cells.

PLoS ONE, 2008

27 / 29

Summary

It can be described through different formalisms

Brownian motion can be generalized in a few different ways -

fBM, Lévy flight

There are examples of subdiffusion and power laws in cell

systems and biology

28 / 29

Ido Golding and Edward C. Cox.

Physical nature of bacterial cytoplasm.

Phys Rev Lett, 96, 2006.

Liang Li et al.

Persistent cell motion in the absence of external signals:// a search strategy for eukaryotic cells.

PLoS ONE, 2008.

Anomalous diffusion in living yeast cells.

Phys Rev Lett, 93, 2004.

Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Biophys J, 87, 2004.

Observation of a power-law memory kernel for fluctuations within a single protein molecule.

Phys Rev Lett, 94, 2005.

29 / 29

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