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METAMATERIAL LENS DESIGN FOR ULTRAHIGH RESOLUTION
FLUORESCENT MICROSCOPY
A thesis presented
by
Alexandru Bratu
to
The Department of Physics
in fulfilment of the requirements
for the degree of
MSc of NanoScience
in the subject of
BioPhysics
University College Dublin
Belfield, Dublin 4
August 2009
Thesis advisors Author
Dr. James Rice Alexandru Bratu
Dr. Brian Vohnsen
Page 2
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ABSTRACT
Metamaterials have recently shown great potential in novel lens designs
that allow imaging with resolution beyond the classical limit of diffraction. Here
its potential for ultrahighresolution fluorescent microscopy will be examined
with numerical analysis. Different structures based on surfaceplasmon
polariton excitation on thin metallic films have been examined with even and
uneven distributions of surface scattering elements. The results obtained show
that indeed a resolution beyond the diffraction limit can be obtained with the
novel metamaterial lens designs. This has particular importance in weak signal
fluorescent imaging of biomaterials and possibly for nanotoxicity analyses.
Significant progress has been made in the development of subdiffraction
fluorescence microscopy methods that enable images recorded in the far field
to possess resolution down to the nanometer scale. These methods include
stimulated emission depletion and its related reversible saturable optical
fluorescent transition microscopy, stochastic optical reconstruction microscopy,
structured illumination microscopy, and photoactivated localization
microscopy. However these techniques have limitations requiring either time
consuming pointbypoint scanning or the accumulation of large data sets,
which prevents them from reaching realtime imaging applications.
The application of new lens technology made from metamaterials holds
promise for realtime subdiffraction fluorescence imaging. A metamaterial is a
material that gains its properties from its structure rather than directly from its
composition. In the ideal case unlimited high resolution in the far field has
been found in a theoretical work [1]. Such lenses have been termed
„superlenses‟ or „hyperlenses‟ and are typically made with alternating layers of
materials with careful chosen indices of refraction and dimensions [2, 3].
Recently, they have been applied to optical microscopy and farfield
transmission based imaging with a spatial resolution of <100nm has been
demonstrated [2, 3].
Page 4
Here we outline theoretical work towards a superlens design for
fluorescence based on the proposal of Smolyaninov et al. using surface
Plasmon polaritons (SPPs) [2]. The internal structure of the magnifying
superlens consists of concentric rings of poly(methylmethacrylate) (PMMA)
deposited on a gold film surface. PMMA has a negative index of refraction
2
0 n < , [2]
perceived by the SPPs (the group velocity is opposite to the phase velocity).
The width of as the PMMA rings
2
d is chosen so that
1 1 2 2
n d n d = ÷ , [2]
is satisfied, where
1
d is the width of the goldvacuum portions of the interface.
In our model we first study scattering by ordered nanostructures on a gold film
as shown schematically in Fig. 1. Ideally this can focus the incoming SPP wave
and is an essential first step towards the realization of a 2D subdiffraction
limited lens. We study the SPP scattering and propagation using SPP inplane
scattering based on a Green‟s function propagator formalism. Eventually, our
aim is to convert this theoretical proposal into a workable experimental lens
for fluorescent microscopy.
Page 5
CONTENTS
Metamaterial lens design for ultrahigh resolution fluorescent microscopy ....... 1
Abstract ................................................................................................ 3
List of FIGURES ................................................................................... 7
Chapter 1 – Plasma ............................................................................. 9
Physical properties .............................................................................. 9
SPPs (Surface Plasmon Polaritons) at smooth surfaces ............................ 11
Fundamental Properties ...................................................................... 11
Dispersion Relation ......................................................................... 11
Spatial Extension of the Surface Plasmon Fields .................................. 20
Propagation length of the Surface Plasmons ....................................... 22
Excitation of Surface Plasmons ............................................................ 23
Excitation by electrons .................................................................... 23
Excitation by Light .......................................................................... 24
Internal and Radiation Damping .......................................................... 28
Internal Damping ........................................................................... 28
Radiation Damping ......................................................................... 29
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Chapter 2 – Metamaterials ................................................................ 31
Electromagnetic metamaterials ........................................................... 31
Negative Refractive index ................................................................... 32
Cloaking devices ............................................................................... 34
Chapter 3 – Surface Plasmon Polaritons ............................................ 37
Physical Properties ............................................................................ 37
Theoretical Model .............................................................................. 38
Chapter 4 – NIM (Negative Index Media) .......................................... 47
Time reversal .................................................................................... 49
Negative index makes a perfect lens .................................................... 53
Far Field Imaging .............................................................................. 54
Chapter 5 – MATLAB Code and Simulation Results ............................. 57
Incident electric field SIMULATION ....................................................... 57
Chapter 6 – Conclusion ...................................................................... 75
Acknowledgment .................................................................................. 79
Bibliography ........................................................................................ 81
Appendix ............................................................................................ 85
Page 7
LIST OF FIGURES
1: Scheme of the dispersion of plasmons in a solid
2: The charges and the electromagnetic field of the SP’s propagating on a
surface in the x direction
3: ATR coupler with its respective ( ) , , x y z coordinates and interfaces on the
plane
4: Right Handed Materials (RHM) and Left Handed Materials (LHM) and their
corresponding magnetic, electric and propagation vector
5: External SPP wave propagating under angle  (with respect to the
ellipsoid x – axis) along the dielectric metal interface is scattered by an
ellipsoid particle
6: Holographic technique with a TIR reference wave
7: An NIM flat lens brings all the diverging rays from an object
8: NIM lens enhancing evanescent wave propagation such that the
amplitude of the evanescent waves are identical at the object and the
image plane
9: The dispersion of the wave in a medium with constant velocity ck e =
where c is the speed of light. Both positive and negative frequencies may
be viewed.
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10: Optics of a negative index slab
11: Time – reversing mirrors reproducing similar focusing effect to
subwavelength imaging in the near – field
12: Magnifying optical hyperlens with numerical simulation of imaging of sub
– diffraction limited objects
13: Program 1 diagram  dotted SPP imaging for reference point (1285,
1369)
14: Program 1 diagram  dotted SPP imaging for reference point (0, 0)
15: Program 2 diagram – gradient SPP imaging of the total E – field intensity
16: Theoretical perspective of the diagram for SPP imaging with constant
wavelength of 500nm
17: Theoretical waveguide on the quarter plane (including polarizability
factor to account for extra points)
18: STED apparatus and an intensity distribution graph
19: Microtubules (green) and clathrin – coated pits (red) [X. Zhuang
Research Labs]
20: COS – 7 cell tagged with PA – Fluorescent Protein Kaed
21: Farfield fluorescence methods which enable ultrahigh resolution imaging
Page 9
CHAPTER 1 – PLASMA
PHYSICAL PROPERTIES
This chapter stands out from much of the rest of this thesis in that it
deals with an introductory and numerical method. Each diagram has its
respective reference and listing, hence making it easy to find and understand.
The equations that follow co – work with respect to diagram reference and
those that are harder to find have been carefully addressed to with their own
respective reference.
When we think of plasma we tend to think of an ionized and
macroscopically neutral gas with sufficient amount of free charges to make
electromagnetic forces important to its macroscopic behaviour. The concept of
this fourth state of matter is treated as an electron liquid of very high density
of about
23
10
3
cm
÷
, ignoring the lattice in a first approximation. From this
outlook we have that the longitudinal density fluctuations, plasma oscillations
will propagate through the metal. The quanta of these “volume plasmons” will
carry energy of the order
2
0
4
p
ne
m
t
e = , [4]
where
n
is the electron density of the order of 10eV. They are produced when
electrons hit the surface of the metal [4]. According to Maxwell‟s theory the
EM surface waves can propagate along a metallic surface or film with a broad
Page 10
spectrum of eigen frequencies from 0 e = up to 2 e = depending on the wave
vector k .The dispersion relation
( ) k e lies to the right of light line hence the
surface plasmons have a longer wave vector than light waves of the same
energy e , propagating along the surface.
Figure 1
Scheme of the dispersion of plasmons in a solid. (1) Volume plasmons,
(2) surface plasmons, (3) plasmons in a one – dimensional electron gas, (4)
plasmons in a one – dimensional system. The upper scale is valid for (1) and
(2), the scale below for (3) and (4). ll is the light line. [4]
Page 11
SPPS (SURFACE PLASMON POLARITONS) AT SMOOTH SURFACES
Surface plasmons propagate along the surface of the metal and when
coupled with a photon they create a new quasiparticle called surface plasma
polaritons.
The smooth surfaces along which they travel are not perfectly smooth,
but small enough to be negligible in calculation. The height range is a root
mean square value (r.m.s.) of 5 – 10 Å.
Surface plasmon polaritons (SPP‟s) are confined to electromagnetic
waves that travel along a metal – dielectric interface with an exponentially
decaying amplitude into the nearby media.
FUNDAMENTAL PROPERTIES
DISPERSION RELATION
When an electron on a metal boundary is charged energy oscillations are
given. Their existence was proven by electron energy – loss experiments by
Powell & Swan. The frequency e of the fluctuations are dependent of the wave
vector by a dispersion relation. The localization of these fluctuations is done in
the z – plane with Thomas – Fermi screening length which is approximately
about 1Å, accompanied along with a mixture of the transversal and the
longitudinal EM waves which decay completely as z ÷·.By considering the
description of the electric field
Page 12
( )
0
exp
x z
E E i k x k z t e
±
= + ± ÷ (
¸ ¸
, [4]
where + for > z 0 , – for s z 0 , an imaginary
z
k would cause an exponential
decay for
z
E . The equation gives that direction
x
k x ¬ ÷ ;
2
x
p
k
t
ì
=
where
p
ì is the
wavelength of the plasma oscillation [4]. An illustration of the field would show
a maximum in the surfacez =0 , which is normal for surface waves.
Figure 2
The charges and the electromagnetic field of the SP’s propagating on a
surface in the x direction are shown schematically. The exponential
dependence of the field
z
E is seen on the right.
y
H shows the magnetic field in
the y – direction of this p – polarized wave. [4]
With the use of Maxwell‟s equations the retarded dispersion relation for a
plane surface semi – infinite metal along with the dielectric function
Page 13
( )
' '
1 1 2
c c c = + when close enough to the medium
2
c as air or vacuum:
1 2
0
1 2
0
z z
k k
D
c c
= + = , [4]
together with
2
2 2
i x zi
k k
c
e
c
 
= +

\ .
, [4]
or
1
2
2
2
, 1, 2
zi i x
k k i
c
e
c
(
 
= ÷ =
(

\ .
(
¸ ¸
, [4]
The wave vector
x
k is continuous through the interface hence we can
rewrite
0
D :
1
2
1 2
1 2
x
k
c
c c e
c c
 
=

+
\ .
, [4]
However if we assume besides
2
, e c e and
'' '
1 1
c c < , we obtain a complex
' ''
x x x
k k ik = + , [4]
with
( )
3
' ' ''
2
' '' 1 2 1 2 1
2 ' '
'
1 2 1 2
1
&
2
x x
k k
c e c
c c c c c e e
c c c
c
   
= =
 
+ +
\ . \ .
, [4]
For
'
x
k e one needs
' '
1 1 2
0& c c c < > , this may be accomplished in a metal
Page 14
and also in a doped semiconductor near the eigen frequency. From this we can
also use a Thomas – Fermi wavenumber theory to deduce the relationship
between the wavelength of the incident electric field and the dielectric constant
of the metal with the presumptions that the density of the plasma oscillations
is constant throughout.
Consider a metal that has a relative absorbance, hence a complex
dielectric constant component. By using the work of Y.C. Lee and S.E. Ulloa [5]
we could find a beginning to such a theory of wavelength – dependent
dielectric constant that could later be used to calculate the incident electric
field with cumulative point – dependence:
( )
2
2
1
FT
metal
k
q
q
c = + , [5, 10]
where
dielectric constant of the metal, thomas fermi wavenumber, wavenumber
metal FT
k q c ÷ ÷ ÷ ÷
which is derived from Lindhard‟s formula [6] for the longitudinal dielectric
function given by
( )
( )
, 1
k q k
q
k
k q k
f f
q V
i
c e
e o c c
÷
÷
÷
= ÷
+ + ÷
¿
, [6]
with
( ) ( )
q eff ind
V V q V q = ÷ and
carrier distribution function,aka the Fermi  Dirac distribution
function for electrons under stable thermodynamic equilibrium
k
f
 
÷

\ .
Page 15
We must also study the formula under the limiting case. Lindhard‟s formula
will be studied under 3D since the density applies only to 3D.
Consider the long wavelength limit ( ) 0 q ÷ for the denominator and
numerator
( )
2 2 2 2
2 2
2 ,
2 2
...
k q k
k q k k k k k k k
k k q
E E k k q q
m m m
f f f q f f q f
÷
÷
·
÷ = ÷ · + ÷ ÷
÷ = ÷ · V + ÷ ÷ · V
, [6, 39]
Substituting and letting 0 o ÷ we get
( )
2
,
0
,
0 0
2
2
0
2
0
2 2
2 3 2
0 0
2
2
0
0, 1
1 1
1
1
4
1
1
k
i
i
q
k i
q
k
i
k i
i
q k
k
q
pl
f
q
k
V
k q
m
V
f k q
q
k m
q
V f
m
q N
V
m
e q N
q L m
c e
e
e e
e
e
t
c e
e
e
c
c
+
·
÷
 
c ·
+ +

c
\ .
= ÷
= ÷
= ÷
= ÷
¿
¿
¿ , [6, 39]
where we have that
2 2
2
2 3 3
0 0
4 4
, &
k k q pl
e e N
E V
q L L m
t t
c e
c c
= = = , [6, 39]
Now consider the static limit 0 i e o + ÷ where Lindhard‟s formula takes
the following shape:
Page 16
( )
2 2
, ,
, 0 1 1
i i
i i
q q
k i k i
f f
q q
k k
q V V
k q k q
m m
c
c c
÷
c c
= ÷ = ÷
· ·
÷
¿ ¿
, [6, 39]
Hence using the equation above we get that for a thermal Fermi – Dirac
thermal equilibrium
2
k k k k
i i i i
i i i
i i
f f f
q q q k
k k m
c
µ µ
c c c c
= ÷ = ÷
c c c c
¿ ¿ ¿
, [6, 39]
where
2 2 2
&
2
k i
k
i
k k
m k m
c
c
c
= =
c
, [6, 39]
Therefore
( )
2
2
2 3 2
,
0
2 2 2
2 3 2 2
0 0
4 1
, 0 1 1 1
4 4
1 1 1
k
i i
q q k
k i k k
f
q k
f e m
q V V f
q L k q
m
e N e n
q L q q
t µ
c
µ c µ
t t k
c µ c µ
c
c c c
= + = + = +
c c ·
c c
= + = + ÷ +
c c
¿ ¿ ¿
, [6, 39]
( ) is a 3D screening wave number 3D inverse screening length defined as k
2
0
4 e n t
k
c µ
c
=
c
, [6, 39]
But thinking in terms of the statistics of the parameter we get that the
Coulomb screening potential is given by
Page 17
( )
( )
2 3 2
0
2 2 3 2 2
0
2
4 1
, 0
, 0
q
s
e
V
q L e
V q
q q L q
q
t
c t
e
k c e c k
2
4
= = = =
+ = +
, [6, 39]
By applying a linear Fourier transform of the equation above we get
( )
( )
2 2
3 2 2
0 0
4
iq r r
s
q
e e
V r e e
r L q
k
t
c c k
· ÷
= =
+
¿
, [6, 39]
which is similar to the Yukawa potential.
Now by considering a degenerating ideal Bose – Einstein gas at which
0
T 0 K = , the Fermi energy becomes
( )
2 2
2
3
3
2
f
E n
m
t = , [6, 39]
Hence the density n is given by
3
2
2 2
1 2
3
f
m
n E
t
 
=

\ .
, [6, 39]
At
0
3
T 0 K E
2
f
f
n n
=
E
µ
µ
c
÷ ÷ ¬ =
c
. Substituting this result into the screening
wave number equation we obtain:
2 2
0
6
f
e n e n
E
t t
k
c µ c
4 c
= =
c
, [6, 39]
and the answer given is the 3D Thomas – Fermi screening wave number.
Proceeding further we get that for the general metal:
Page 18
( )
( ) ( )
( )
( ) ( )
2 2 2 2
2 2 2 2
2 2 2 0
3 3
0 0
2 2
2 2
2 2 2 2
3 3
0 0
6 1 6 1 6
1 1 1 1
3 3
2
2
6 2 12
1 1
1
3 3
FT
metal
f
metal
k e n e n e n
q
q E q q
q n n
m
m
e n m e mn
q
q n q n
t t t
c
c
c t c t
t t
c
c t c t
= + = + = + = +
 

\ .
= + = +
, [6, 39]
But from simple theory we have that
( )
2
q wavenumber
t
ì
= , [5]
My simulation data will use a typical green laser wavelength of 500nm,
hence I had to also consider at what density such a wavelength would
propagate through a medium [7]. By considering an experimental
demonstration of Nd:YAG laser where we have
Nd:YAG
1064nm ì = , almost about
1000nm which corresponds to a density of
21 3
Nd:YAG
10 cm n
÷ ÷
= . However we have
that the wavelength is inversely proportional to the density of the volume of
the ionic distribution in the medium, thus
( )
21 3
500
2 10 cm
green nm
n
÷ ÷
× . [7]
Now substituting in the equation for the wavelength – dependent
dielectric constant we get that:
( )
( ) ( )
2 2
2 2
2 2 2 2
3 3
0 0
12 6
1 1
2
3 3
metal
e mn e mn
q
n n
t ì
c
t
c t c t
ì
= + = +
 

\ .
. [6, 39]
By inserting the values for gold we have that the inner density for the
metal may vary slightly but not much. Thus:
Page 19
( )
( )
( )( )( )( )
( ) ( )( ) ( )
2
2
2 2
3
0
19 31
2
34 2 1
2
12 1 21 3
6
1
3
6 1.602 10 9.109 10 500
1
6.626 10
8.854 10 3 3.14 2 10
3.14
gold
e mn
q
n
C kg nm
m kg s
F m cm
ì
c
c t
÷
÷ ÷
÷ ÷ ÷ ÷
+
÷ × ×
+
  ×
(
× ×

¸ ¸
\ .
. [6, 39]
By converting the SI units throughout the equation we get that
0.24
gold
c .To verify our answer we must carry out a much simpler calculation
to verify that in the long – wavelength region the screening wave number is
correct when considering an ideal Bose – Einstein gas. Using gold as our metal
we have that by international standards its refractive index is given by [8]:
0.47
gold
n = . [8]
From electro – optics we know that:
( )
2
2 2
0.47 0.2209
gold gold
n n c c = ÷ = = = . [8]
By comparing this with the general case in the long – wavelength range
we just evaluated we have that the local error is about
4
0.24
1.08 10
0.2209
Theoretical
Experimental
÷
e= = = × , [general]
hence almost negligible.
Now returning back to our plasma retardation we have that the
dispersion relation
0
D approaches the light line
2
@
x
k small
c
c e
÷ , but remains
Page 20
further away than
2
c
c e
such that the surface plasmons cannot convert into
light. However at larger values of
x
k or
'
1 2
c c ÷÷ , we have that
2
lim
1 x
p
SP
k
e
e e
c
÷·
= =
+
, [4]
where the
p
e corresponds to the plasma frequency, given by
2
4
p
e n
m
t
e = ,
with n the electron bulk density.
As
x
k gets larger we also have that
( )
( )
lim 0
lim 0
x
x
k
k
group velocity
k
d
phase velocity
dk
e
e
÷·
÷·
¦
÷ =
¦
¦
´
¦
÷ =
¦
¹
, [4]
such that the surface plasmon matches a localized fluctuation of the electron
plasma.
SPATIAL EXTENSION OF THE SURFACE PLASMON FIELDS
From definitions we are aware that the wave vectors
2 1
&
z z
k k , [4]
are imaginary due the fact that
'
1
& 0
x
k
c
e
c < < , [4]
so that the amplitude of the surface plasmons have an exponential decay
Page 21
zi
k z
e
÷
normal to the surface. From this information we gather that the depth value of
the field falls to 1/e, becomes
1
ˆ
zi
z
k
= or
1
'
2
1 2
2 2
2
'
1 2
1 ' 2
1
ˆ in the medium:
2
ˆ in the metal:
2
z
z
c c ì
t c
c c ì
t c
  +
=

\ .
  +
=

\ .
, [4]
By using 2 metals with internal absorption such as gold and silver, we
get:
2
1
2
1
ˆ 390
:
ˆ 240
600
ˆ 280
:
ˆ 310
z nm
silver
z nm
At nm
z nm
gold
z nm
ì
¦ = 
¦
=
¦ \
= ¬
´
= 
¦
¦
=
\ ¹
, [4]
since
1
ˆ lim
x
i
k
x
z
k
÷·
, [4]
this leads to a strong field concentration at the interface between the two
media. But for lower
x
k values or bigger
'
1
c the field has a more powerful
transverse component
z
E compared to the longitudinal component
x
E , as
'
1
z
x
E i
E
c
= ÷ , [4]
Page 22
leading to a guided photon field from a Zenneck – Sommerfeld wave, which in
theory gives guided propagation with no radiation field to waste energy.
But in a metal
z x
E E < since
'
1
z
x
E i
E
c
= + . [4]
The theory can be validated from Maxwell‟s theory in vacuum
0 or 0
y
x z
E
E E
E
x y z
c   c c
V· = + + =

c c c
\ .
, [4]
however it suffices only outside the surface of the air/metal interface and at
large
x
k value the z and x – component would suffice:
:
:
z x
air i
E iE
metal i
+  
= ±

÷
\ .
.
PROPAGATION LENGTH OF THE SURFACE PLASMONS
Considering a smooth surface the intensity of the surface plasmons
decay exponentially as
( )
''
3
' ''
2
2 ''
1 2 1
2 '
'
1 2
1
@
2
x
k x
x
e k
c
c c c e
c c
c
÷
(
 
(
=

(
+
\ .
(
¸ ¸
. [4]
The length after which the intensity decays to 1/e is given by
''
1
2
i
x
L
k
=
.
Now consider in the visible region( ) 400 700 nm nm ì = ÷ we have that
Page 23
( ) 22 @ 514.5
i
L m silver nm µ ì = = , [4]
while at 1060 500
i
nm L m ì µ = ÷ = .
Using the temporal decay
i
T instead of the spatial coordinate decay
along the x – axis we have that the values of the propagation and length and
temporal decay are inter – connected by:
g
i i g
g
v group velocity
L Tv
v
k
e
÷ ÷  

=

=

\ .
.
By using a complex frequency ' '' i e e e = ÷ and
'
x
k e with
2
''
i
T
t
e
= we obtain
( )
'' '
' 1 1 2
2 '
'
1 2
1
1 2
'
1 2
1 2 '
'
1 2
''
2
@
'
x
x
x
k c
k
c
k c
c c c
e
c c
c
c c e
c c
c c
e
c c
¹ ·
=
¦
+
¦
=
`
+
¦ +
=
¦
)
. [4]
EXCITATION OF SURFACE PLASMONS
EXCITATION BY ELECTRONS
When electrons hit a solid surface they have an energy loss of E e A =
after penetration. They transfer a momentum q and energy
0
E A to the
electrons of the solid material. The wave vector
x
k is determined from the
projection of q upon the surface of the film. The electrons are scattered at
different angles u and they transfer different momenta
'
sin
x el el
k k k u u = ~ with
2
el
el
k
t
ì
= . [4]
Page 24
To observe a successful excitation the use of fast electrons is highly
recommended such as to study the dispersion relation at larger
p
x x
k k
c
e  
>

\ .
,
since a small value irrespective of the electrons velocities will cause the
aperture of the electron beam to be sufficiently reduced. And during the
electron transmission in thin films, the dispersion relation determines the
energy e of the surface plasmons, while the choice of
( )
'
el
k u fixes
x
k and
e respectively.
EXCITATION BY LIGHT
To excite the surface plasmons photons are used, however they face the
difficulty of having the dispersion relation to lie right of the right line, i.e.
larger x – component wave vector. To achieve this “conversion” of photons to
SPs the photon energy e must be increased by a factor of
x
k A . 2 suitable
methods to achieve this increase are:
1. Grating Coupler [4]
The principle of this method is that if light penetrates the grating with a
grating constant a at an angle
0
u the surface component has wave vector
0 0
sin sin
1
x g SP x g
w
k v k k with v
c c c k
e e c e
u u
c
 
= ± = = = ± A =

+
\ .
, [4]
where
x
k A rises from the perturbation along the smooth surface. We observe
that the resonance can be observed as the reflected light minimum. For the
Page 25
surface plasmons to be turned into light their propagation along the grating or
a rough surface should result in a reduction in their wave vector component
x
k
by
x
k A . Radiation is used to detect the presence of the SPs, because if the SP
is excited to a maximum value, the emitted intensity is excited as well to a
maximum.
2. ATR (attenuated total reflection) coupler [4, 24]
If light is reflected at a metal surface covered with a dielectric medium
( )
1
pr
c > then:
sin sin
cos cos
pr
x pr pr pr pr
pr
z pr pr pr pr
k n
c c
k n
c c
e e
c u u
e e
c u u
¦
= =
¦
¦
´
¦
= =
¦
¹
. [4, 24]
Figure 3
ATR coupler with its respective ( ) , , x y z coordinates and interfaces on the
plane. [4, 9]
The resonance condition for the light in the prism with SP at metal (1)
air (2) interface (Kretschmann – Raether configuration) is:
Page 26
pr sp
x x
pr prism
k k
sp surface plasmon
÷  
=

÷ ÷
\ .
[4, 24]
1 2
1 2
sin
pr pr
c c
c c e e
c u
c c
 
=

+
\ .
[4, 24]
The reflected intensity R may be given by Fresnel‟s equations of the
prism from the prism  metal  air – 3 layer system:
2 2
2 2
cos cos
cos cos
zi zk k zi i zk zi zk zi zk
k i
p p k i i k i k i k i k i k
ik ki
zi zk k zi i zk zi zk zi zk
k i i k
k i
i k i k i k i k
k k n k c n k c k k k k
n n
n n k k n n n n
r r
k k n k c n k c k k k k
n n
n n
k k n n n n
u u e e c c
u u
e e c c
÷ ÷ ÷ ÷
÷
= = = = = = ÷
+
+ + + +
. [4, 24]
For transmission however:
( )
( ) ( )
( )( )
1
1 1
1 1
p p i
ik ik
k
p p p k k
ki ki ik
i i
p p p p
ik ki ik ik
n
t r
n
n n
t r r
n n
t t r r
= +
= + = ÷
= + ÷
. [4, 24]
Hence the total reflection for the 3 – layer system becomes:
1 1
1 1
2
2
2
1 12
12 2
1 12
1
cos cos
cos cos
cos cos
cos cos
z
z
ik d p p
pr p
pr ik d p p
pr
i k
p k i i k i k
ik
i k
k i i k
i k
r r e
R r
r r e
n n n n
r
n n
n n
u u
u u
u u
u u
+
= =
+
÷
÷
= =
+
+
, [4, 24]
1 1 2 2
sin sin sin
pr pr
n n n u u u
¹
= = , [4, 24]
Page 27
2 2
2 2 2 2
2
2 2 2 2
2 2 2 2
2 2
1
1
1
2
1
sin
cos 1 sin 1 sin
sin sin
sin sin
sin cos
sin cos
pr pr
k k k k k k pr pr
k
i pr pr k pr pr
p i k
ik
i pr pr k pr pr
i k
pr pr pr
pr p
pr
pr pr
pr
n
n n n n n
n
n n
r
n n
n
n
r
n
n
u
u u u
c u c u
c c
c u c u
c c
c u u
c
c u
 
= ÷ = ÷ = ÷


\ .
÷ ÷
÷
=
÷ ÷
+
÷
÷
=
÷
+
2
1
pr
u
c
. [4, 24]
The last term can be understood better by the following expansion,
( ) ( ) ( )
( )
( ) ( ) ( ) ( )
1 1
1 1
1 1 1 1 1 1
1 1 1 1 1 1 1 1
2
1 12
12 2
1 12
2 2
2 2 4
1 12 1 12 1 12
2 2 3 2
2 2 4 4
1 12 1 12 1 12 1 12
1 1
1
1 ...
...
1
z
z
z z z
z z z z
ik d p p
pr p
pr i k d p p
pr
ik d ik d ik d p p p p p p
pr pr pr
ik d ik d ik d ik d p p p p p p p p
pr pr pr pr
p
pr pr
r r e
r
r r e
r r e r r e r r e
r r e r r e r r e r r e
r r
+
=
+
+ ÷ + ÷
= + ÷ ÷ + +
= + ÷
( ) ( ) ( )
( ) ( ) ( ) ( ) ( )
1 1 1 1
1 1 1 1
1 12 1 1 12 1 12 1
2 2 2
2 4
12 1 1 12
2 4
1 1 12 1 1 12 1 12 1
1 1 12 1
1 ...
1 1 1 1
z z
z z
p p p p p p p p
pr pr pr pr pr
ik d ik d p p p p p
pr pr
ik d ik d p p p p p p p p p
pr pr pr pr pr pr
t r t t r r r t
p p p
pr pr pr
r e r r r e
r r r r e r r r r r e
r t r t
(
+ ÷ +
(
¸ ¸
= + + ÷ + + ÷ ÷
= +
1 1 1 1
2 4
1 12 1 12 1
z z
ik d ik d p p p p p p
pr pr pr
e t r r r t e +
, [4, 24]
where the phase factor ( )
1 1 1 1 1
cos
z
k d k d u = is the optical length.
Thus the detailed phase factor becomes
2
2 2 2
1 1 1 1 1 1 1 1 1 2
1
cos 1 sin sin
pr
z pr pr pr
n
k d k d n d d n
c n c
e e
u u c u = = ÷ = ÷ . [4, 24]
Please note that I have expanded and shown every term to its full extent
for clearer understanding. Thanks also to the R. Adams calculus book. [22]
Page 28
INTERNAL AND RADIATION DAMPING
INTERNAL DAMPING
From the extended dispersion relations we have that the internal
absorption is given by
( )
3
' ''
2
''
1 2 1
2 '
'
1 2
1
2
x
k
c
e c c c
c c
c
 
=

+
\ .
. [4]
The EM field of the SPs excites pairs of electron – holes at the Fermi
level,
( )
1
1
e
kT
F
e
c µ
c
÷
=
+
, [10]
µ chemical potential at the Fermi – Dirac Distribution function.
The de – excitation that follows produces the phonons and hence the
heating. The energy can also be lost by the emission of photoelectrons, if
( )
photoelectric work function e   > ÷ ÷ ÷ [11], with the heat measured with a
photo – acoustic cell. A small exception is that of silver for which the periodic
heating of the film can be registered by the periodic pressure variations in a
microphone. Experimentally the energy lacking in the reflected light is
measured with the photo – acoustic cell as the heat energy in the silver film.
The power lost by light decaying from surface plasmons can be detected
assuming we have a smooth surface with 5 o Å.
Page 29
RADIATION DAMPING
If the SPs propagate along the smooth surface interface of air/metal with
a dielectric material 1
o
c > as in the ATR device, the SPs, the evanescent wave,
with an imaginary
1 z
k ,
( )
2
1 1 1
0
z x
k k
c
e
c c
 
= ÷ <

\ .
, [4]
transform the in the medium
0
c into a plane wave due to the real
2 z
k ,
since
0 x
k
c
e
c s . Hence radiation damping, which is characteristic to an
asymmetric 2 – interface system.
The electrons excite the SPs which emit light into the dielectric
( )
0
c to
produce 2 intense tip – like plasma radiation peaks with an angular width and
a corresponding intensity usually about 100 times stronger than the transition
radiation. The peaks arise from 2 differently valued scattering angles and due
to these angular dispersions and intense light circle around the film
perpendicular plane normal is produced.
By analyzing the phase factor for the ATR coupler we have that the
internal damping is given by
{ }
0
Im
x
k I = where
( )
0
1
3
'
2
2
1
0
1
' '
1 1
2
1 1
x
k d
p
x pr x
k e r k
c
c
e
c c
÷
(
 
(
 A =
(

+ ÷
\ . (
¸ ¸
, [4]
Page 30
with
1
p
pr
r given by /
p zi zk zi zk
ik
i k i k
k k k k
r
c c c c
   
= ÷ +
 
\ . \ .
. In the MATLAB simulation we shall
later discover that also from experiment that for a wavelength of 500nm a
silver film gives that the minimum reflectance R
( )
2
12
p
pr
r is equal to zero
corresponding to a minimum thickness of 55nm. The evaluation of the
minimum thickness depends on the dielectric function c just like we showed
the dependence of the wavelength in the steps above, but it varies by at least
10%. We must also remember that the energy conservation satisfies:
1
R relative reflection
R A T A relative absorption
T relative transmission
÷ ÷
 

+ + = ÷ ÷


÷ ÷
\ .
. [4]
Hence at T = 0 and with
min
d we have that R = 0 A = 1, i.e. the whole
energy is absorbed in the metal film. The case of R = 0 also gives that
{ } { }
0
Im Im
x
k k = , i.e. where internal damping = radiation damping.
Now we can determine the function
( )
c e in situ using the ATR minimum.
Data shows that a detailed an accurate formula matches the experimental data
by analyzing the reflection minimum. In situ shows the variation of e with
respect to the dielectric function for many absorbing metals such as silver, e.g.
( )
2
5.7 81 0.4
silver
i c e e
÷
= ÷ + [1].
Page 31
CHAPTER 2 – METAMATERIALS
ELECTROMAGNETIC METAMATERIALS
Metamaterials are materials that gain their properties from its structure
rather than its composition. They are artificially subwavelength composites
which possess extraordinary optical properties that do not exist in nature. [12]
Their importance is vastly used in the field of electromagnetism, in
particular for optics and photonics. Uses include microwave applications such
as new types of beam steerers, modulators, band – pass filters, lenses
(superlenses and hyperlenses), microwave couplers and antenna radomes.
A metamaterial has structural features smaller than the wavelength of
the electromagnetic radiation it interacts with. Instinctively for the material to
act homogenously (have size feature close to wavelength size) it must be
described by an effective refractive index. An example would be visible light
from sunlight, wavelength about 560nm for which the structures would have a
size about halfway or even smaller. For microwave structures however they
must have structures in the order of 1 decimeter.
They usually have periodic structures such as photonic crystals and
frequency selective surfaces, but they differ from metamaterials as their
features size almost matches that of the wavelength.
Page 32
NEGATIVE REFRACTIVE INDEX
Study of the exotic nature of metamaterials is studied to investigate the
possibility to create a structure with negative refractive index, since this
property is not found in any naturally occurring material. Typical optical
mediums and substances like glass or water have a positive refractive index,
with glass about 1.5 and small deviations for crown glass and clear water
about 1.33. These positive indexes of refraction have their permittivity c and
permeability µ > 0 as well since
n cµ = . [1]
But there are metals with light absorption abilities such gold and silver
which have negative permittivity c at visible wavelengths 400 700 nm nm ì = ÷
By using the work of Vohnsen and Veselago [13, 14] we have the
following formulas to properly indicate how the sign of the refractive index
behaves with respect to the correspondent material:
2
0
0
n
n
n
cµ
cµ
cµ
¦
= >
¦
= ÷ v
´
¦
= ÷ <
¹
&
0
0
0 ,
0
dielectrics
dielectrics
metals plasmas absorption
metamaterials
c
µ
c
µ
>
>
< ¬
<
. [13, 14]
No materials with 0 µ < are known in nature. All known transparent
materials posses positive values for c and µ . The positive square root is taken
by convention. Some materials have both values negative and it is then
Page 33
necessary to take the negative square root. Veselago proved that such
substances can transmit light [14, 15]. For special metals such as gold and
silver we have values such as
( )
( )
2
26.15 1.85 800 
5.7 81 0.4 560 
gold
silver
i nm gold air interface
i nm silver air interface
c
c e
÷
= ÷ + ÷ ÷ (
¸ ¸
= ÷ + ÷ ÷ (
¸ ¸
. [14, 15]
Numerous physical properties of metamaterials have stormed the
imagination of physicists for years. The most important ones are:
1. Snell‟s Law
By definition we have that
1 1 2 2
sin sin N N u u = , but since
2
0 N < , the rays of
light will be refracted on the same side of the normal (perpendicular
axis to the light plane) on entering the material.
2. Doppler Shift
The effect is reserved such that if a light source is moving towards an
observer it appears to reduce its frequency
3. Cherenkov radiation
Cherenkov radiation changes direction and thus points the other way
4. Poynting vector, S = E x H
Poynting vector is anti – parallel to the phase velocity, hence unlike a
right –handed material, the wave fronts move in the direction opposite
to the flow of energy. By making a diagram of energy flow we have that:
Page 34
Figure 4
Diagram showing the Right Handed Materials (RHM) and Left Handed
Materials (LHM) and their corresponding magnetic, electric and propagation
vector. LHM were first introduced by Victor Veselago in 1967. [14, 15]
CLOAKING DEVICES
Once a dream, now a possibility metamaterials are now being considered
to create optical illusions such as invisibility or more commonly referred to as
„cloaking‟. The mechanism of this physical concept involves surrounding the
object with a shell such as to prevent light to bounce off of it. First proposals
for such an amazing technology was given on the 14
th
of February 2005 at the
Page 35
University of Pennsylvania by Andrea Alü and Nader Engheta who announced
that plasmons can cancel out the visible light on radiation coming from an
object. This „plasmonic cover‟ would in theory suppress light scattering by
resonating with illuminated light, which could render objects „nearly invisible to
an observer‟.
The first successful „cloaking‟ approach was done by a US – British team
of scientists which created a metamaterial that made an object invisible to
microwave radiation. Since this was not visible light, this proved as a stepping
stone towards more advanced nano – engineering techniques.
Page 36
Page 37
CHAPTER 3 – SURFACE PLASMON POLARITONS
PHYSICAL PROPERTIES
Surface plasmons coupled with a photon create a quasiparticle called
polaritons, thus they become surface plasmon polaritons (SPPs). They are
confined to electromagnetic waves that propagate along a dielectric – metal
interface with amplitudes which decay exponentially into both neighboring
media.
Their physical nature allows them to concentrate and guide
electromagnetic radiation using wavelength structures such as metamaterials.
Typical uses of SPPs occur in micro – optical components that may be used as
mirrors, beam splitters, micro – scatterrers and efficient SPP interferometer.
Currently SPP analysis involves the use of point – dipole system
approximation and an anisotropic free – space polarizability component that is
dependent of the of the ellipsoid major axes and hence on the particle shape.
The system involves the use of a dielectric constant
p
c for the particle in
the region z < 0 with dielectric constant 0
r
c > and a metal in the region z < 0
with dielectric constant
m
c . The particle is positioned above the metal surface
in the dielectric ½  space with its center located at
( )
0,0,
p p
z = r . To support
SPP propagation requires that we must have the metal dielectric interface with
the condition
m r
c c < ÷ [16]. For this scattering system we get:
Page 38
Figure 5
Schematic of the scattering system: an external SPP wave propagating
under angle  (with respect to the ellipsoid x – axis) along the dielectric metal
interface is scattered by an ellipsoid particle. [16]
THEORETICAL MODEL
However the MATLAB model for our scattering system will involve also
contributory work given by Evlyukhin and Bozhevolnyi[18] we have that for
the point – dipole approximation using a holographic technique along with a
TIR(total internal reflection) configuration. Like in the scattering case above
we consider a point dipole located at
( )
0,0,
d d
z = r , [17, 18, 19]
in an air medium above a flat surface of a glass substrate(n typically 1.5
depending on the type of glass used) with dielectric constant
2
2.25 n c = = .
Page 39
Figure 6
Schematic view of the holographic technique with a TIR reference wave
[17]
The dipole has an electric monochromatic field
( )
0 d
E r with wavelengthì .
A holographic image of the dipole is obtained at the height due to the
interference between the induced dipole field
( )
d
E r and reference wave
( )
r
E r . Further detailed study of the near – field above the surface
( )
d
z ì ,
gives that the coupling is not negligible, hence an increase in the magnitude of
the dipole [20, 21]. To consider these couplings we must have the polarization
of a spherical nanoparticle with volume given by
( )
3
4
3
d
V a a particle radius t = ÷ ÷ , [22]
and a dielectric permittivity
d
c with external optical field with wavelength
bigger than the particle‟s size hence not limiting the analysis to metamaterials.
Page 40
We now obtain a dipole moment p:
( ) ( )
1
2
0
, 0
0
ˆ ˆ
ˆ ˆ I ,
S
d d d
k
G o o
c
÷
(
= ÷
(
¸ ¸
p r r E r [23]
where
ˆ
ˆˆ ˆˆ ˆˆ I xx yy zz = + + (in spherical coordinates)[22] is the unit dyadic tensor,
o
k is the wave number in vacuum,
0
c is the vacuum permittivity,
( )
ˆ
, '
S
G r r is
the surface part of the Green‟s tensor of the substrate – air interface system,
where we have & ' r r located in the air medium. Now considering the
polarizability tensor ˆ o as the dipolar polarizability of the spherical nanoparticle
in the free space along the long – wavelength electrostatic approximation we
have
0
1
ˆ
ˆ 3I
2
d
d
d
V
c
o c
c
÷
=
+
. [23]
The dipole electric field
d
E
( ) ( ) ( )
2
0
0
0
ˆ ˆ
, ,
S
d ob ob d ob d
k
G G
c
(
= +
¸ ¸
E r r r r r p, [23, 24, 25]
at the point – dipole
ob
r on the parallel plane to the substrate surface (i.e. P –
polarized field) now takes the contribution first of all from the Green‟s tensor
of free space that determines the direct electric dipole field
( )
0
ˆ
,
ob d
G r r and
secondly from the scattering part of the Green‟s tensor accounting for the
secondary electric field which is related to reflection from the interface
Page 41
( )
ˆ
,
S
ob d
G r r . The last Green‟s tensor is calculated with Sommerfeld integrals
[23, 24, 25]. To calculate these integrals the use of the Lommel function,
incomplete Weber integrals and incomplete Lipschitz – Hankel integral along
with a zero – order Hankel function of the first kind. Intense numerical analysis
is required, thus a smaller substitute may be to acquire Maple and input the
functions desired and where the error function occurs use an approximation.
To do so use the first desired terms from the Taylor expansion of the error
function, remembering that the error function is an entire function(it has no
singularity except that at infinity). For completion the expansion formula would
take the following shape [22]:
( )
( )
( )
2

2 1
0
3 5 7 9
2
1
2
! 2 1
2
...
3 10 42 216
x
t dt
o
n
n
n
erf x e
x
n n
x x x x
x
+
·
=
=
÷
=
+
 
= ÷ + ÷ + ÷

\ .
}
¿
.
, [22]
The tensor
( )
ˆ
, '
S
G r r also includes the excitation of SPPs for a dielectric – metal
interface. Hence the electric reference field is
( )
t ob
i
r ob t
Ee =
k r
E r , [23]
where
( )
2
0
sin ,0, sin 1
t
k k i c u c u = ÷ , [23]
Page 42
withu , the incident angle being larger that the critical one for the TIR which is
given by
1 1 0
1 1
sin sin 41.8
1.5
critical
glass
n
u
÷ ÷
 
 
= = =



\ .
\ .
. [22]
The amplitudes
t
E are linearly connected to the incident amplitude and
can be found by using the transfer matrix of Fresnel coefficients.
The Fresnel reflection coefficient for p – polarized waves
( )
( )
p
r satisfies:
( )
2
2
2
2
2
2
cos 1 sin
1 1
cos sin 1 0 0
lim lim lim 1
1 1
cos 1 sin
cos sin 1 0 0
p
r
u u u
u c u
u c u
u c u u
c c
u c u
u c u
c c
u c u u
÷· ÷· ÷·
 
÷ ÷
 ÷ ÷ ÷ ÷
\ .
= = = =
  + ÷ + ÷
+ ÷

\ .
,
[26]
since
cos
lim lim 1
cos
u u
u u
u u
÷· ÷·
= = ,
sin
lim lim 0
sin
u u
u u
u u
÷· ÷·
= = and
1
lim 0
u
u
÷·
= [22] by using
the general infinity  delta for evaluating limits.
Having a p – polarized electric field we have a component parallel and
perpendicular to the field. The parallel component disappears as the angle u
reaches 90 degrees because the electric field for these waves is perpendicular
to the direction of propagation. We also notice that by inserting our theoretical
values from above we have first of all that
Page 43
2
1 2 2 5
sin cos 1 sin 1
1.5 3 3 3
u u u = = ¬ = ÷ = ÷ = ,
then also by substituting the value for the glass dielectric constant we have
( )
2
2
1
cos sin
3 2 9
@ cos ,sin ,
1
5 3 4
cos sin
p
r
u c u
c
u u c
u c u
c
÷ ÷
¦
¦
= = = =
´
¦
¹
+ ÷
( )
( )
( )
( ) ( )
( )
( )
( )
2
2 2
3 4 9 4
3 4 65 3 65
81 3 5 65
5 9 4 9
5 9 36 5 81
3 4 9 4 3 4 65 3 65 81 3 5 65
5 9 4 9 5 9 36 5 81
81 3 5 65
81 3 5 65 81 3 5 65
81 3 5 65 81 3 5 65
81 3 5 65
19683 810 195 1625
19683 1625
21308 810 195
18058
0.55
p
p
p
p
p
r
r
r
r
r
÷ ÷
÷ ÷
÷
= = = =
+
+ ÷ + +
÷
÷ ÷
= =
+ ÷
÷
÷ +
=
÷
÷
=
.
Hence 55% reflection from the surface. Depending on the material
surface properties the remaining 45% goes to the transmission and absorption
factors as we have seen in chapter one on plasmas.
Finally by illuminating the nanoparticle by a reconstructing plane wave
( )
c
E r starting off from the substrate surface at an incident angle u , the
holographic image of the dipole source is obtained. This wave shall construct a
transmitted field
( )
'
t ob
i
ct ob t
e =
k r
E r E that propagates in the direction opposite to
Page 44
the reference wave
( )
t ob
i
r ob t
Ee =
k r
E r , with its respective wave number
( )
' 2
0
sin ,0, sin 1
t
k k i c u c u = ÷ ÷ . [23]
To evaluate the dipole momenta of the nanoparticle the full momentum
must be considered as a summation of the i
th
point:
( ) ( ) ( ) ( )
2 2
0
0 0
0 0
ˆ ˆ ˆ
ˆ ˆ ˆ , , ,
N
S S
i ct i i i i i j i j j
j i
k k
G G G o o o
c c
=
(
= + + +
¸ ¸
¿
p E r r r p r r r r p , [23]
where
( )
, ,
i i i i
x y z = r and
( )
, ,
j j j j
x y z = r are the radius  vectors of the center of
the particles with number i and j respectively. The other parameters were
defined above and N is the total number of particles in the nanoparticle array.
The reference wave acts as an SPP Gaussian beam excited on the
surface of the metal substrate with propagation along the x – axis. By
considering the electric field at the substrate – air interface, the reference
beam propagating along the x – axis may be given by:
( )
( )
( )
( )
( ) ( ) ( ) ( )
( )
( ) ( )
2
2
2
2 2 2
2
2
2 1
ˆ ˆ ˆ 1
ob
SPP ob z ob
ob
y
i k x k z
W f x
r ob
ob
SPP ob
ob z z
SPP
SPP ob SPP ob
SPP ob
e
f x
k y
y k k
z yi x
k
k W f x k W f x
k W f x
+ ÷
=
¦ ¹
(
 
 
¦ ¦ ÷ ÷ ( 
× + + + ÷ 
´ `
( 

(
¦ ¦  \ .
(
¸ ¸
\ .
¸ ¸
¹ )
E r
,
[12]
with
( )
, ,
ob ob ob ob
x y z = r , W is the beam waist, ˆ ˆ ˆ , , x y z are the unit coordinate
Page 45
vectors given by the unit dyadic tensor
ˆ
I ,
0 SPP
k k
c
c
=
1+
is the SPP wave
number ,
2 2
0 z SPP
k k k = ÷ and
( )
2
2
1
ob
ob
SPP
x
f x i
k W
 
= +

\ .
. By further detailing on
these terms we have that:
2 2 2 2
0 0 0 0 0
1
1
1 1 1
z SPP
k k k k k k k
c c
c c c
= ÷ = ÷ = ÷ =
+ + +
Considering our Gaussian beam propagating in free space with the
function
( )
w z with a minimum
0
w at one place along the beam axis, known as
the beam waist. Now for a wavelength ì at a distance z along the beam waist,
the variation of the spot size function is given by
( )
2
1
o
R
z
w z w
z
 
= +

\ .
, [27]
where the origin of the z axis is defined, without loss of generality, to coincide
with the beam waist W, and where
2
0
R
w
z
t
ì
= , [27]
is defined as the Rayleigh range. Thus by inspecting the Gaussian distribution
on a 3D medium we can interpret the equation for the SPP reference wave in
an easier to understand manner.
Page 46
Page 47
CHAPTER 4 – NIM (NEGATIVE INDEX MEDIA)
An NIM (Negative Index Media) refers to medium which possess
negative refractive index and in time are subject to negative refraction. The
idea was originally brought out by Veselago in 1967, where as we discussed
earlier, anomalies occur such as reverse physical equivalents of Snell‟s Law,
Doppler Shift and Cerenkov radiation. The idea of negative refraction at the
interface of a negative and positive refractive index medium allows a flat slab
of NIM to focus all the diverging light from one inside and one outside of the
slab.
Figure 7
An NIM flat lens brings all the diverging rays from an object [28]
Light when emitted or scattered from an object includes not just
propagating waves but also evanescent waves, which carry the subwavelength
detail of the object, and they are sometimes referred to as the image “lost
treasures”. The evanescent waves decay exponentially in a medium with
Page 48
positive refractive index, thus their image cannot be identified in the plane by
a normal lens. But if the lens were made of an NIM placed close enough to the
object, the near – field evanescent waves can be strongly enhanced across the
lens.
Figure 8
NIM lens enhancing evanescent wave propagation such that the
amplitude of the evanescent waves are identical at the object and the image
plane [28]
After escaping the NIM lens the evanescent waves decay again till their
amplitudes reach their original level at the image plane. In the meantime the
propagating waves go through the NIM lens with a negative refraction and a
reversed phase front, ultimately leading to a phase change by the image
plane. The ultimate goal is to apply this to far – field imaging.
Page 49
TIME REVERSAL
NIM media have also established a link between time reversal and
negative refraction. The concept of negative refraction implies that as a pulse
wave moves forward, the phase evolves in the opposite direction, hence the
groups and phase velocity progress through the medium in opposite directions,
0 ,
group phase
d d
v v
k dk k dk
e e e e
 
< = =

\ .
, [31]
leading eventually to phase reversal.
Considering a medium that can have both a positive and negatively
refracting state where like in graphene the pseudo – spin of an electron close
to the Fermi energy controls the phase evolution [29, 30]. Media with
properties such as these are referred to as “self – conjugate”. This self –
conjugation establishes the link between time reversal and negative refraction.
Let us have a wave of the form:
( )
0 0
ˆ e
i t
E E e
e ÷
=
k r
, [31]
where E is the electric field component,
0
E is a constant,
0
ˆ e is a polarization
unit vector, r is a position vector and t is the time.
Shifting the frequency by 2 oe e = gives the shifted electric field E‟ as:
( )
0 0
ˆ ' e
i k r t
E e
e +
= E , [31]
demonstrating that reversing frequency is the same as reversing time. It may
Page 50
be viewed schematically as the following diagram:
Figure 9
The dispersion of the wave in a medium with constant velocity ck e =
where c is the speed of light, (c = 299792458m/s). Both positive and negative
frequencies may be viewed. Time reversal may be understood as vertical
transition between positive and negative frequencies [31].
Now think of a system having 2 time – reversing sheets separated by a
distance d. Waves are reversed by the first sheet and reversed again by the
second sheet, i.e. switching between positive and negative frequency. To
understand it better we shall make a transmission – reflection typical
coefficient analysis, but in this case we assume that the coefficients are
identical, i.e. T = R. Since the sources are in 2D, they become mirror –
symmetrical about the plane and thus give the same transmitted and reflected
fields. To solve the wave further we must first consider the wave vector
component that is perpendicular to the sheets, i.e.
Page 51
2
2 2
2
0
z x y
k k k
c
e
= + ÷ ÷ , [31]
when
z
k e and
2
2 2
2
0
z x y
k i k k
c
e
= + + ÷ , [31]
when \
z
k e .
Thanks to J.B. Pendry‟s formulae [31] we observed that the waves are
allowed to emerge from the end of the cavity. For real
z
k
( ) 2
2
0
2
ˆ e ,
1
z
i k r k z d t
R e
E E d z
R
e ( + ÷ ÷
¸ ¸
= <
÷
, [32]
while for imaginary
z
k
2
0 2 2
ˆ e ,
1
z
z
i k r k z t
ik d
R e
E E d z
R e
e ( + ÷
¸ ¸
= <
÷
. [33]
The limit of very large transmission and reflection coefficients would give
( ) 2
0
ˆ lim e
z
i k r k z d t
R
E e
e ( + ÷ ÷
¸ ¸
÷·
= ÷ E , [33]
given that T = R whether
z
k is real or imaginary. From the equation above all
Fourier components contribute respectively to the image, and in the infinite
limit the image tends to perfection, i.e.
z
ik d
R e .
Page 52
Figure 10
Optics of a negative index slab [13]
By considering this concept we thus have the idea of a superlens, which
bases itself on negative refraction. The main problem of these lenses is not the
loss since the fields are translated trough loss – less vacuum but the ability of
the time – reversing sheet to give enough resolution
max
1
ln
d
k R
A ~ ~ .
Like in the theoretical model we discussed the idea would be to create
the following subwavelength – enhancing resolution diagram:
Figure 11
Time – reversing mirrors reproducing similar focusing effect to
subwavelength imaging in the near – field [31]
Page 53
Such a 2D hologram is challenging to build but it is possible by
considering the Fourier coefficients & the work of Bozhevolnyi and Pendry.
Later I will show how such an idea may be modeled by MATLAB.
NEGATIVE INDEX MAKES A PERFECT LENS
The idea of Fourier components of a 2D image has been shown in terms
of transmission and reflection components for a p – polarized field, i.e.
1
1
1
1
lim
&
lim 0
z
ik d
P polarized
P polarized
T e
R
µ
c
µ
c
÷
÷
÷÷
÷÷
÷
÷÷
÷÷
=
=
. [31]
What makes the perfect lens more “realizable” is that for a P – polarized
fields, where the electrostatics claim ownership, the dependence of µ
vanishes and only the dielectric constant takes effect. Hence by further
analysis the transmission coefficient of the slab in the electrostatic limit gives
that the 1 c = ÷ condition satisfies the existence for a surface plasmon as we‟ve
seen in chapter 1. The condition was also shown by R.H. Ritchie [34]. As
Pendry demonstrated, in silver the dielectric function finite imaginary part
prevents ideal reconstruction but a considerable focusing is achieved
throughout. The focusing idea remains valid as we have seen the use of the
quasi – electrostatic limit applied in our earlier theoretical model of a point –
dipole source.
Page 54
FAR FIELD IMAGING
Near – field imaging has shown good prospectus but to achieve the
greater goal we must also consider the far – field subwavelength imaging [12].
To do so we use a hyperlens, works like a superlens and uses cylindrical
coordinates for its analysis. The slab of material on which far – field was
proposed was a magnifying optical hyperlens which had a curved periodic
stack of gold(Au) and aluminium oxide(
2 3
Al O ) both of 35nm deposited on a
half – cylindrical cavity fabricated on a quartz substrate. The material had sub
– diffraction – limited objects inscribed into a 50nm – thick chrome layer
located at the inner surface (air side).
Figure 12
Magnifying optical hyperlens with numerical simulation of imaging of sub
– diffraction limited objects. [3, 35]
Page 55
This demonstrated the capability of a hyperlens for sub – diffraction –
limited resolution imaging. The same simulation ideals will be involved in my
MATLAB coding where we have that the propagation will satisfy the condition
give by the evanescent waves, i.e.
2
oblique incidence
ì
ì
 
A< ÷ ÷

\ .
, [13]
with the wavelength as given by several experiments such as 495, 500 and
515 nm.
Page 56
Page 57
CHAPTER 5 – MATLAB CODE AND SIMULATION
RESULTS
The coding provides detailed explanations and programming comments
to ease reading along with the following main equations for simulation of the
incident electric field.
INCIDENT ELECTRIC FIELD SIMULATION
To calculate in 2D I have made the following assumptions:
( ) 1 The polarizability factor ˆ 1 o = since it requires the evaluation of the volume of
the nanoparticle which is impossible in 2D, i.e. as
0
1
ˆ
ˆ 3I
2
dielectric
d
dielectric
e
V
e
o c
÷
=
+
where
( )
3
4
, radius of spherical nanoparticle, not 2D
3
d
V a a t = ÷ ÷ 3Donly
( ) 2 The electric field is Ppolarized
( ) 3 The Green‟s function is the wave propagator exhibiting Huygens wavelet
behaviour,
( ) ( )
2 2
1 1
,
ii jj
ii jj
G r r ii jj
r r
x y
= = =
÷
+
Page 58
( )
( ) ( ) ( ) ( ) ( )
( ) ( )
( )
2 2
2 2 2 2
2 2
2 2
, ,
Re Re cos sin cos
cos
Re , Re , ,
z z
z
z z
ik x y ik y
incident ii ii jj jj
jj
ik y
ii z z z
z
ik x y ik x y
ii jj jj ii jj jj
jj jj jj
E e G r r e ii jj
e k y i k y k y
k x y
G r r e G r r e ii jj
x y
+
+ +
= + =
= + =
+
   
= = =
 
+
\ . \ .
¿
¿ ¿ ¿
with
2 2 2 2
0 0 0 0 0
1
1
1 1
z SPP
k k k k k k k
c c
c c c
= ÷ = ÷ = ÷ =
1+ + +
The result obtained shows only the real part of the dielectric
function for the metal gold since a different formula for wavelength – dielectric
function is used for semiconductors like Si and Ge, where we usually consider
a measurement of the thickness of the slab and the screening Coulomb effect
that comes into action.
Now that the SPP group and phase velocities may have opposite signs
then ( ) ( )
gold dielectric
c e c e ~ ÷ which describes the condition for exceeding the
resonant frequency e where ( ) ( ) &
gold dielectric
c e c e are the frequency dependent
dielectric constants of the metal and the dielectric, respectively [2].
But by using
2
n c = wherec ÷dielectric constant andn ÷refractive index,
refractive index tables have that ( )
2
0.47 0.47 0.2209
gold gold gold
n c c = ÷ = ¬ = .
Then by substituting in all the necessary values we have that the
incident electric field takes the form
Page 59
( )
( ) { }
( ) { }
( )
0
0 0 0
2 2
2 2
2 2
0
1 2 1 2 10000 200 1
1 1 0.2209 12209 12209
0, if and only if 0
,
, 0 ,
cos
cos ,
200
cos
200
, cos
12209
z
z
jj
incident z
ii
ij
incident
ii
k k
x y
z x y
x y x y
k x y
E k y ii jj
x y
E x y y
t t t
c ì ì ì
t
ì
t
ì
= = = =
+ +
= = ¦
¦
=
´
+ + < < +·
¦
¹
+
= + =
+
¦ ¹  
¦ ¦
= +
 ´ `

¦ ¦ \ . ¹ )
¿
2 2
0
2 2
12209
,
j
jj
x y
ii jj
x y
¦ ¹  
¦ ¦
+
 ´ `
¦ ¦ \ . ¹ )
=
+
¿
The indexes ii and jj were chosen such to distinguish between MATLAB‟s
complex i and j.
Where the summation of the
th
j components involves the adding of the
respectively cumulative points along the waveguide from the surface, the
measurement will give a theoretically accurate description of the field
intensity.
To account for the ultra – high image resolution we must also include the
approximation for the SPP propagator with the complex parts. Thus the
equation for the electric field becomes:
0
0 2
0
ik z
ik y
e
E E e
z
= +
¿
where
( ) ( ) ( )
2 2
2 2
, 1, 2,3,..., number of points on graph
i i
z x x y y i N N= = ÷ + ÷ =
Page 60
Hence z is always positive with
( )
2 2
, x y the reference point for evaluating the
intensity of the electric field along all the points.
Now consider the actual E  field as an SPP dotted waveguide with
uniform wavelength and even distribution.
MATLAB Codes:
Program 1
% Alexandru Bratu, Bio Science Masters
% Program #1  Generate point spread field for polarization equation, take
% polarizability tensor alpha as = 1, then proceed with E field equation
% approximation to the Sommerfeld Integrals. I did so by using exponential and
% arithmetic equations. At very high numbers(N > 100,000 for example) the
equation may be evaluated
% using Sterling's approximation to obtain a more accurate result.
%Sterling's equation > ln N! = N * Ln(N)  N, where Ln is the natural log
close all;
clear all;
format short g
diary Superlens22.out
disp([' SPP Imaging with Reference Point
(X2,Y2) '])
diary off
%1.Wavelength
%"Wavelength" choice of 495,500,515nm; as used in observed experiments
wavelength_choice = questdlg('Please select the value for the wavelength in nm
you wish to choose :', ...
'Wavelength  Menu', ...
'495','500','515','515');
% Handle response
switch wavelength_choice
case '495'
lambda = 495;
case '500'
lambda = 500;
Page 61
case '515'
lambda = 515;
end
%store wavelength in nm to data file
wavelength = num2str(lambda);
diary Superlens22.out
disp(['Wavelength is ' wavelength ' nm,'])
disp([' '])
diary off
%2.Number of graphs
%"Number of graph(s)" choice of 1  10; for accurate analysis later and
%faster image processing
number_of_graphs_choice = questdlg('Please select the number of graphs you wish
to choose :', ...
'Number of Graphs  Menu', ...
'2  4','5  7','8  10','8  10');
% Handle response
switch number_of_graphs_choice
case '2  4'
%2  4 graphs range choice
first_range_choice = questdlg('Please select in the range 2  4 :', ...
'2  4 graphs range', ...
'2','3','4','4');
% Handle response
switch first_range_choice
case '2'
number_graphs = 2;
case '3'
number_graphs = 3;
case '4'
number_graphs = 4;
end
case '5  7'
number_of_graphs = 2;
%5  7 graphs range choice
second_range_choice = questdlg('Please select in the range 5  7 :', ...
Page 62
'5  7 graphs range', ...
'5','6','7','7');
% Handle response
switch second_range_choice
case '5'
number_graphs = 5;
case '6'
number_graphs = 6;
case '7'
number_graphs = 7;
end
case '8  10'
%8  10 graphs range choice
third_range_choice = questdlg('Please select in the range 8  10 :', ...
'8  10 graphs range', ...
'8','9','10','10');
% Handle response
switch third_range_choice
case '8'
number_graphs = 8;
case '9'
number_graphs = 9;
case '10'
number_graphs = 10;
end
end
%store number of graphs to data file
graph_number = num2str(number_graphs);
diary Superlens22.out
disp(['Graph has ' graph_number ' curves,'])
disp([' '])
diary off
%3.Step size
%"Step size" choice 0.025,0.05,0.1; as these numbers when divided by
Page 63
%generate finite rational numbers
step_size_choice = questdlg('Please select the value for the angular  step_size
you wish to choose :', ...
'Step size Menu', ...
'0.025','0.05','0.1','0.1');
% Handle response
switch step_size_choice
case '0.025'
step_size = 0.025;
case '0.05'
step_size = 0.05;
case '0.1'
step_size = 0.1;
end
%store number of graphs to data file
size_of_step = num2str(step_size);
diary Superlens22.out
disp(['Graph has step size of ' size_of_step ])
disp([' '])
diary off
%4.Diagram of the SPP Dotted Waveguide in a P  polarized field
%wave vector constant
k = (200 * pi)/(lambda * sqrt(12209));
%store wave vector constant to data file
kappa = num2str(k);
diary Superlens22.out
disp(['Wave vector constant is ' kappa ' nm^1'])
disp([' '])
diary off
%total number of points on graph
N = 20 * number_graphs^2 + number_graphs;
diary Superlens22.out
num = num2str(N);
disp(['The graph has ' num ' points in total'])
disp([' '])
diary off
Page 64
%Reference point value x_2
x_2 = input('Reference X  Value > ','s');
X2 = str2num(x_2);
%Reference point value y_2
y_2 = input('Reference Y  Value > ','s');
Y2 = str2num(y_2);
%store the reference point(X2,Y2) at which the electric field intensity is
%calculated to data file
diary Superlens22.out
disp(['Reference point for E  field is (' x_2 ',' y_2 ')'])
disp([' '])
diary off
%storage of diagram code to data file
diary Superlens22.out
disp(['Reference graph showing evenly spread point distribution with respect to
focus reference point (X2,Y2)'])
%initial step before point  to  point uniform distribution
disp(['initial step before point  to  point uniform distribution'])
ii = 0;
disp([' '])
%initial value for sigma summation to used later for calculating total
%electric field intensity
disp(['initial value for Gaussian propagator summation used later for
calculating total electric field intensity'])
E_sum(1) = 0;
disp(['
'])
diary off
%storage of E field calculations and respective diagrams to data file
diary Superlens22.out
disp(['ii a b z E_total'])
for n = [ 1 : number_graphs ] %10 curves drawn for default research
for theta = pi * [ 1 : step_size/number_graphs : 1 ];
ii = ii + 1;
%create a radius that encompasses lambda(/2,/1,/0.5,etc...) by using
%the the angle theta, pi <= theta <= pi x = 0.5 * lambda *
%cos(theta), y = 0.5 * lambda * sin(theta)
%x  coordinate
a = 0.5 * n * lambda * cos(theta);
Page 65
%y  coordinate
b = abs(0.5 * n * lambda * sin(theta));
%line  trace the point with respect to other coordinates
line([a X2],[b Y2])
%z  coordinate
%z = sqrt([X2  a(N)]^2+[Y2  b(N)]^2)
z = sqrt([X2  a]^2 + [Y2  b]^2);
%Gaussian propagator function E_sum
E_sum = (exp(i * k * z))/z + E_sum;
%E_total = E_sum + incident E field with initial amplitude
%E_0 = 0
E_total = exp(i * k * Y2) + E_sum;
%point number,its with respective xy coordinates and electric field
%intensity
disp([ii a b z E_total])
plot ( a , b ,'g*')
figure(1), xlabel('a()'), ylabel('b()'),title('SPP Dotted Imaging
with 1 Reference Point (X2,Y2)')
hold on
end
end
for r = 1:1
plot(X2, Y2 , 'ro')
end
gtext('(X2,Y2)')
%intensity field value at (X2,Y2)
E_field = num2str(E_total);
disp(['The value of E at (' x_2 ',' y_2 ') is ' E_field ' Joules'])
diary off
warndlg('The point spread xy coordinate values generate a hectic gradient E 
field, run the second program please.','Warning')
% N.B. DISCUSSION of Figure (1):
% 
% Since the (a,b) coordinates would not give an accurate gradient
% field, the E  field intensity must taken over the entire plane,i.e. from
% [a_min b_min]<=>[a_max b_max] to show the variation, however the ultra 
% high focusing may be viewed from the intensity of the blue lines as the
% reference point reaches the semi  circular located points. The necessity
% of a second program to evaluate the entire gradient E field was therefore
% a requirement.
% 
Page 66
The program is very flexible and it allows for proper choice of values
including number of curves(precision), wavelength values of 495,500 and 515
nm(which are mentioned in [1,2,12,16]), which also determines the number of
points N (= 20 x number_graphs
2
+ number_graphs). For N > 100,000 it
comes to within a good estimate of Sterling‟s equation and within a few digits
away from the exact Sommerfeld equations. In terms of wavelength I
preferred 500nm cause it was a more exact value. And finally in terms of
step_size I have chosen 0.025 and 0.05 and 0.1 because they increase from
0.025 gradually and also due to the fact that when divided by they produce
finite numbers.
The data that follows is taken from the external file produced from
Superlens11.
Program 1 Results
Wavelength is 500 nm,
Graph has 10 curves,
Graph has step size of 0.1
Wave vector constant is 0.011373 nm^1
The graph has 2010 points in total
Reference X  Value > 1285
Reference Y  Value > 1369
Reference point for E  field is (1285, 1369)
Reference graph showing evenly spread point distribution with respect to focus
reference point (X2, Y2).
The (x, y, z) coordinates and their correspondent E – field SPP
calculations are located in the appendix(end) of the paper.
Page 67
Figure 13
Program 1 diagram  dotted SPP imaging for reference point (1285, 1369)
Figure 14
Program 1 diagram  dotted SPP imaging for reference point (0, 0)
Page 68
Program 2
% Alexandru Bratu, NanoBio Science Masters
% Program #1  Generate gradient SPP diagram
%
% Warning  Due to the processsing power of my computer i have halved the
% components of the y  axis coordinate!
clear all;
close all;
%second program is made such to avoid the overwhelming amount of
%calculations fomr the first one
%by choosing for 10 graphs we have that the range of the x,y coordinates is
%given by
%1. a = [2500,2500]
%2. b = [0,5000]
I_sum = 0;
k = (200 * pi)/(500 * sqrt(12209));
X2 = 1285;
Y2 = 1369;
% since we have 2010 points on program 1 we now split this up to achieve
% the same effect by having x = [1005:1:1005]
for x = 1005 : 1 : 1005
for y = 0 : 1 : 2010
%Now we include indexes positive bigger than or equal to 1 since
%Matlab indexing requires positive integers and not nonnegative
%i.e. integers including zero
%translation index for x
c = x + 1006;
%translation index for y
d = y + 1;
t = sqrt([X2  x]^2 + [Y2  y]^2);
I_sum = (exp(i * k * t))/t + I_sum;
I_total(c,d) = exp(i * k * Y2) + I_sum;
end
end
Page 69
figure(2), imagesc(abs(I_total)), xlabel('X(number of points)'),ylabel('Y(number
of points)'),title('SPP imaging  Electric field intensity for 2010 points'),
colorbar;
Program 2 results
Figure 15
Program 2 diagram – gradient SPP imaging of the total E – field intensity
Along the entire spectrum of colours we can observe the total electric
field intensity since I had included indexing in the “for”  loop by translation of
the original coordinates. The grading shows that the most intense E  field is at
the base of the since it almost approximates a function of the form
Page 70
( ) ( )
( ) ( )
2 2
2 2
1, 2,...2010,
1
, ,
, 1285,1369
i i
i
E z x x y y
x y z
=
¦
= = ÷ + ÷
´
=
¹
The high focusing could not be achieved from the first diagram since
there were too many points and on more powerful computers the field
achieved a chaotic structure in the form of pylons packed closely together.
The ultra high focusing was however observed in program 1 from the
intensity of the blue colour near (X2,Y2) but I did not include the effect of the
polarizability tensor ˆ o to achieve the calculation due to more points and show
the intensity gathering even at these points. To account for this I created the
following theoretical program to illustrate my idea.
Program 3
% Alexandru Bratu, NanoBio Science Masters
% program 3  SPP intensity gradient in the 1st quarter  plane
%wavelength chosen from the range 490,500,515
lambda = 500;
for p = 1:2010
for q = 1:2010
E(p,q)= p*q/lambda + 1;
end
end
figure(3), imagesc(abs(E)), xlabel('p(number of points)'),ylabel('q(number of
points)'),title('SPP imaging  theoretical constant wavelength of 500nm'),
colorbar;
Page 71
Program 3 results
Figure 16
SPP imaging – theoretical constant wavelength of 500nm
Page 72
Program 4
Since the first program involved the evolution of the point – focus the
following coding that was inspired with the help of my supervisors showed the
theoretical perspective of the SPP beam imaging for ultra – high resolution.
The only problem with program number 1 is that the polarization field equation
did not show the “true” gradient envelope I expected. Even after about 160
tests the expected gradient was not achieved by the equations but perhaps an
accurate solution to the Sommerfeld integrals would have achieved this. The
analysis of Smolyaninov‟s work showed that successful simulations involved
study of the beam waist
0
w , a much denser and a more accurate complex
equation describing the SPP Gaussian beam. Since my computer simply did not
have such power, computations even over an square array of 1,000,000 still
took several minutes and those above it simply froze and made MATLAB crash
at times. What proved successful however was that the physical concept was
well understood with respect to coordinating the field with the dotted SPP
image. Nonetheless a theoretical model of the waveguide would something
along the following lines of code (with polarizability tensor factor of course):
% Alexandru Bratu, NanoBio Science Masters
% program 4  theoretical image, conversion from dotted to purely gradient
% coding inspiration by Dr. Brian Vohnsen
clear all;
close all;
pixels = 2010;% < polarizability tensor included,hence another 100 factors
for x = 1:2010,
for y = 1:2010,
E(x,y)= cos(x*y*2*pi/(pixels*pixels));
Page 73
end;
end;
figure(4), imagesc(abs(E)), axis square, xlabel('X(number of points'),
ylabel('Y(number of points)'), title('SPP amplitude(with polarizability factor
included)'), colorbar;
Program 4 results
Figure 17
Theoretical waveguide on the quarter plane (including polarizability
factor to account for extra points).
The diagram shows how the polarizability factor affects the overall effect
on the P – polarized plane. The desired effect was using the original equations
to create for a reference point of (0,0) the gradient field along the dotted path,
Page 74
i.e. start off with source at zero and create a constant waveguide along it with
wavelength of 500nm or 495 or 515(as discussed by Smolyaninov and his
fellow researchers). The high – resolution diagram was supposed to include a
even more complex outlook since the polarizability tensor created an
interaction between all the points such as in a numerical chain of alpha –
carbons chain – interaction. The calculations would have involved an extra
2010 points and at that stage my computer simply could not cope with 2010 *
2010 * 2010 = 8120601000 such a vast number of computations.
Page 75
CHAPTER 6 – CONCLUSION
The coding provides theoretical evidence for creating a 2D hologram for
sub – wavelength imaging. To achieve ultra – high resolution one needs a low
density of excited fluorescent molecules. It may be achieved by:
1. De – exciting most molecules before imaging (STED): [13, 38]
Stimulated emission depletion microscopy (STED)
Excite fluorophores (here with green light just like in our
simulation, we had values of 495, 500 and 515 nm)
De – excite with STED (here red light, 625 740 nm)
This emission [13] can be stimulated with the STED
beam(see below)
Delayed STED reduces the PSF (Point Spread Function), where the
PSF is ideally constructed by a full converging spherical
wave(4Pi)[38] . [13]
Page 76
Figure 18
STED apparatus and an intensity distribution graph [13, 36]
2. Exciting only a few molecules at a time (STORM, PALM): [13, 38]
Stochastic Optical Reconstruction Microscopy (STORM)
Multicolored probes to see multiple cellular components at the
same time, such as these microtubules (green) and small hollows
called clathrin – coated pits (red)
Figure 19
Microtubules (green) and clathrin – coated pits (red) [X. Zhuang
Research Labs]
Page 77
PhotoActivitable Localization Microscopy (PALM)
Thin section from a COS – 7 cell expressing the lysosomal trans –
membrane protein CD63 tagged with the PA – Fluorescent Protein
Kaed
Precision was set at the 50nm section by E. Betzig‟s experimental
data as seen below
Figure 20
COS – 7 cell tagged with PA – Fluorescent Protein Kaed [37]
In terms of biological purposes we have methods like Fluorescence
imaging with one nanometre accuracy (FIONA), Standing wave fluorescence
microscopy (SWFM), 4Pi microscopy, and saturated structured–illumination
microscopy. There are also mathematically derivable methods such as point
accumulation for imaging in nanoscale topography (PAINT), i.e.:
Page 78
Figure 21
Farfield fluorescence methods which enable ultrahigh resolution
imaging. [38, 39]
Page 79
ACKNOWLEDGMENT
I would like to personally thank my supervisors/thesis – advisors
Dr. Brian Vohnsen and Dr. James Rice for participating in this project.
Dr. Nicolae Viorel Buchete for inspirational ideas from molecular simulations in Unix,
Dr. Vladimir Lobaskin for notes on manipulating 2
nd
order Fourier transforms,
Dr. Gareth Redmond for notes on physical concept of microscopy,
Dr. Padraig Dunne especially for his last end of the year lecture notes on lasers,
Professor Nick Quirke for original methods from his papers to handle exponentials,
Dr. Dominic Zerulla for his book on Raether & surface plasmonics,
Dr. Brian Vohnsen for his papers on plasmonics and the 3 lecture notes on
BioPhotonics which helped me design my 1
st
, 3
rd
and 4
th
program,
Dr. James Rice for his own paper on fluorescence microscopy and for helping me to
provide accurate techniques for ultra high imaging and create 2
nd
program
Dr. Suzi.Jarvis for her papers on biomimicry and the field of lipid bilayers that are used in
fluoresce microscopy analysis
Dr. Gerry O’Sullivan for his 3
rd
year notes on Advanced Quantum Mechanics
Dr. Joachim Raedler for his concepts on fluorescent microscopy
& my colleagues Codrin Andrei, Andrzej S. Pitek and JiaJun Li.
Page 80
Page 81
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Page 84
Page 85
APPENDIX
Results from program 1 data are displayed below for reference point
(X2, Y2) = (1285, 1369).
They include evaluation for the following:
( ) ( ) ( )
( )
0
0
2 2
0
1
1, 2,..., 2010 of points on graph
x  coordinate
y  coordinate
1285 1369
_ ,
ii
ii
ik z
ik Y2
ii number
a
b
z a,b a b
e z
E total a b E e
z
=
¦
¦
¦
= ÷
¦
÷
¦
¦
¦
÷
´
¦
¦
÷ ÷ + ÷
¦
¦
= +
¦
¦
¹
¿
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