EXP # 2 ATOMIC FORCE MICROSCOPY

By, Muhammad Sopariwala

Experiment conducted on 5 November 2014

Table of Contents
Abstract .........................................................................................................................1
Introduction ...................................................................................................................1
Theory ...........................................................................................................................1
Method ..........................................................................................................................3
Analysis.........................................................................................................................5
Conclusion ....................................................................................................................8
References .....................................................................................................................8

Table of Figures
Figure 1 - Calibration Grid Colour Map ...................................................................... 4
Figure 2 A Zoomed In Colour Map View of a Calibration Grid Square (Left), And a
Cross-Sectional

Measurement View of the Square (Right) ............................................. 5

Figure 3 - CD Sample Colour Map .............................................................................. 5

Figure 4 - Gold Coated Sample Colour Map at Different Zooms ............................... 6
Figure 5 - Sample Cross-Sectional Measurement Analysis for: CD Pits (Left), CD
Tracks (Right) ..................................................................................................................... 6
Figure 6 Zoomed In Colour Map View of Gold Grain Deposits (Left), a CrossSectional Measurement View of a Large Clump of Deposit (Right) .................................. 7

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Abstract
Atomic Force Microscopy (AFM) is used to study the micro-scale surfaces of various
samples; an AFM calibration grid, a CD sample and a gold coated square. The surfaces of
these samples were found to have beautifully complex structures that we were able to see
in great detail, and make measurements of their various dimensions.

Introduction
Atomic force microscope (AFM) is a common tool which is widely applied to
surface physics, biology and nanotechnology. Invented by Binning in 1986, the AFM is a
high-resolution tool to detect the nanoscale materials, and it can also be used to create
nanoscale structures (Anderson). Different from scanning tunneling microscope (STM),
the AFM can be used to scan both conductors and inductors. The physical, chemical and
spectroscopic property of the ultra-small sample can be obtained and analyzed. Besides,
AFM can reach a higher level of sensitivity compared with STM (Binning & Quate).
In this experiment, we used the new version of commercial software Easyscan 2,
which is a bit different from the edition described in the experiment materials. It is a
highly modular AFM system to control the microscopy functions. We used this software
to control the movement of the probe tip, and analyze the detected sample surface.

Theory
The general principle of AFM is that the image of the scanned object is obtained by
the measurement of the force on the tip, which is generated by the proximity of the
surface. The force is controlled to be small with a feedback mechanism. Forces between
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the tips and the surface can lead to deflection of the cantilever, which follows the Hookes
Law, F=-kx, where k is a constant that represents the characteristic of the spring, and x is
the displacement of the surface. In fact, the forces measured by AFM is complicated,
including mechanical contact force, van der waals forces, magnetic forces, etc. These
forces will all be measured and calculated to generate the image of the sample surfaces,
so the tip is required to be sensitive enough to detect these variations. The force is
controlled to be small with a feedback mechanism.
The sample is connected to three-dimensional piezoelectric drive, so that threedimensional image can be obtained through analyzing the feedback (Binning & Quate).
With different probes and mode, extra quantities can be measured simultaneously. There
are two different modes to detect the surface of an object, static mode and dynamic mode.
In the static mode, a long probe tip is applied to scan the surface of the sample, and the
deflection is directly measured by the laser system. The dynamic mode is mainly applied
to protect the tip when scanning rough surfaces, which used a shorter probe tip. The tip
will oscillate around its resonant frequency near the sample surface, and the change of the
oscillation will be recorded and analyzed by the laser detection system. In addition, two
types of tips are used in this experiment. The SICONA tips are used in the static mode
and the ACLA tip s are used in dynamic mode. They are fragile and protected by laying
the on the bed of gel. In order to protect them, the process to insert them into AFM head
has to be extremely careful.

Method
In this experiment, we applied the AFM to image several samples, using Easyscan 2
software (which is a little different from the guide materials we had) to control the scan
process. The movement of the probe tip, the video signals, and the output of AFM were
all displayed on the computer screen by the software. Additionally, we used the software
to analyze the features of the given samples.
First, we placed the sample under the cantilever tip, using three leveling screws to
roughly get the tip close to the sample. Then presses the advance button in Easyscan 2
to control the tip to move closer. When the tip almost touched its shadow, press approach
to automatically let the tip contact the surface of the sample without being damaged.
Once the tip contacted the sample, use the SICONA tip in static mode, then we began
to scan the surface by clicking start and finish (where finish was applied to prevent
repeated scan). We obtained an image with an array of raised square surfaces on a lower
background. Use measurement tools to analyze the image and export the data and images.
Then we investigated the CD sample using the same mode and tip. Applying the
similar approach above to establish tip-surface contact, we scanned the surface and used
measurement tools to measure the length of the pits and the average spacing between
tracks of the CD sample.
In the last step, we scanned the gold-coated sample under dynamic mode, and
changed the tip to ACLA tip. The changing process required a high level of precision.
First, we took out the cantilever insertion tool from drop stop, and turned off the
Easyscan controller. Then placed the drop stop to prevent things from falling down. The
cantilever insertion tool was placed into the hole to release the existing tip, then used the
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tweezers to carefully remove the tip and put it back on the gel bed, and placed the new tip
into the cantilever (the tip end was faced to us). The incandescent work light was applied
during the process. Finally we removed the insertion tool to put the tip in place, put the
drop and scan head back to their original place.
Again use the approach technique mentioned previously to establish the tip-sample
contact. When the scan was finished, we used zoom and measurement tools to get the
approximate value of the pillow-shipped gold on the grating surfaces.

Figure 1 - Calibration Grid Colour Map

Figure 2 A Zoomed In Colour Map View of a Calibration Grid Square (Left),

And a Cross-Sectional Measurement View of the Square (Right)

Analysis
The first sample that was analyzed was an AFM calibration grid (Error! Reference
ource not found.). On zooming in, and using the cross-section tool (Figure 2), we were
able to measure the size of the squares of the grid. The length of the base of the square
was measured to be 5.9010.001m, and the length of its upper surface was measured to
be 4.70.001m.
Next, a CD sample was analyzed using the AFM microscope (Figure 3). Multiple
measurements were made of the individual CD pit lengths, and the spacing between the
pit tracks (Figure 5). As can be seen in Figure 3, the pits vary extensively in their sizes.

Figure 3 - CD Sample Colour Map

Figure 4 - Gold Coated Sample Colour Map at Different Zooms

However, the average pit length was found to be 1.20840.0004 m. However, the track
separations were found to be quite consistent, and the average separation distance was
found to be 885.10.07 nm.
Finally, we studied a small square sample on which a gold coating had been
deposited. From Figure 4 we clearly see that the gold has not been uniformly deposited.
On zooming in further (Figure 6), we notice that most of the gold has been deposited in
pillow shaped grains of gold (the background of Figure 6), however some uneven
clumping has occurred, leading to the white dots that are visible in the colour map.
Several sample measurements were done, of both the pillow shaped grains, and the
large clumps (ie. the white dots). In both cases, no clear consistency was observed in

Figure 5 - Sample Cross-Sectional Measurement Analysis for: CD Pits (Left), CD Tracks (Right)
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the sizes, however the average of the pillow shaped grains was found to be
1.6670.00004 m and the average of the larger clumps was found to be
0.51980.0006m. Furthermore, it was noticed that the large prominent clumps were
significantly raised above the surrounding surface .Once again, it is important to
emphasize that the sizes in both cases varied significantly, for instance the largest clump
we measured had a diameter of 7.9590.001m, and the smallest had a diameter of
311.20.1nm, and similarly, the largest pillow we measured had a length of
4.7090.0001m, and the smallest had a length of just 126.20.1nm.

Figure 6 Zoomed In Colour Map View of Gold Grain Deposits (Left), a Cross-Sectional
Measurement View of a Large Clump of Deposit (Right)
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Conclusion
The application of AFM to objects, that on first glance seem to be very mundane and
uniform (such as the gold coated plate), demonstrates the remarkably powerful tool that
AFM truly is; revealing to us the beautifully complex, very small, micro-scale structures
that things have. We were able to successfully determine the base and surface sizes of the
squares of a AFM calibration grid (5.9010.001m and 4.70.001m respectively), the
average lengths of a CDs pits (1.20840.0004 m), the average track separation of a
CD (885.10.07 nm) and finally the average length of the individual gold grain deposits,
that made up a samples gold coating (1.6670.00004 m). Also, we discovered that the
gold was not deposited entirely uniformly, and had in some places formed significantly
raised, roughly circular, clumps of varying sizes (average diameter was
0.51980.0006m).

References
Bustamante, Carlos, David Keller, and Guoliang Yang. "Scanning force microscopy
of nucleic acids and nucleoprotein assemblies." Current Opinion in Structural Biology
3.3 (1993): 363-372.
Anderson, Mark S. "Atomic force microscope mediated chromatography."Review of
Scientific Instruments 84.2 (2013): 025114.