Procedures for Imaging of Standards at Atomic-Scale
Resolution Using the Digital Instruments Multimode AFM
Ortiz Nanomechanics Laboratory@MIT F01
I. Sample Producers and Preparation
? Muscovite Mica is a yellowish, light-colored, transparent to translucent silicate (subclass :
phyllosilicates) mineral with the following chemistry : KAlSiAlO(OH,F), Potassium 2462204aluminum silicate hydroxide fluoride. It is a hard, layered, crystalline (monoclinic 2/m)
material that fractures along weak atomic planes ("cleavage" planes), thus easily producing
atomically flat surfaces of atoms having a regular lattice structure which are excellent for use
in high-resolution AFM piezo calibration and as substrates for imaging of biological samples.
Muscovite has a layered structure of aluminum silicate sheets weakly bonded together by
layers of potassium ions. The potassium ions occupy large holes between 12 oxygen atoms, 6
from the layer above and 6 from the layer below; the resulting K-O ionic bonds are rather
weak and easily broken. The cleavage sheets fairly flexible and elastic, hydrophilic, and
negatively charged in water. Muscovite Mica has low iron content is a good electrical and
thermal insulator. More detailed information on Muscovite Mica can be found here :
Another typical AFM substrate is Highly Ordered Pyrolytic Graphite (HOPG) which is described in detail here : http://www.2spi.com/new/hopgsub.html ? A few suppliers include the following companies :
1) Bioforce Lab (http://www.bioforce.com)
2) Structure-Probe Inc. (*http://www.2spi.com/catalog/afmstm.html),
3) Microscopy Mart / Pelco International (*http://www.pelcoint.com/AFM.htm) ? Cleavage directions are detailed here : http://www.2spi.com/catalog/submat/mica-disk.html
? Attach to metal puck and then to piezo scanner cap.
II. Real Time Parameter Settings
? contact mode, air or fluid cantilever holder (it is typically much easier to obtain images in
water or buffer than in air)
? use stiffest spring constant cantilever; on DI V-shaped cantilever chips this is the shortest
one with fattest legs
? use oxide-sharpened SiN probe tips, e.g. Model NPS which has the following 34
specifications (http://www.di).com/products2/NewProbeGuide/ContactModeProbes.html :
spring constant 0.58 N/m
nominal tip radius of 5-40nm
cantilever leg length 100?m
cantilever configuration V-shaped
reflective coating Au
shape of tip square pyramidal
tip half angle 35o
? use piezo scanner with smallest distance range available, A or EV scanner, E scanner
should also work (the difference is the engagement mechanism).
? load sample, turn microscope and vibration table on, and then focus the laser as far out on
the cantilever as possible to obtain the highest sensitivity
? let the system stabilize thermally for 30 minutes (with hood on)
? laser focusing (find maximum): the laser should never been switched off, i.e. turn the
system on and off and all manipulations done with the laser on
PANEL PARAMETER SETTING Scan Controls Scan size 1 ?m
X offset 0.00 nm
Y offset 0.00 nm
Scan angle 0.00 deg
Scan rate 61.00 Hz
Number of samples 512
Slow scan axis enabled
Z limit between 55V-440V Feedback Controls Integral gain 0.001
Proportional gain 0.00
Lookahead gain 0.00
Setpoint 0 V Other Controls AFM mode Contact
Input attenuation 1x Interleave Controls Interleave mode Disabled Channel 1 Data type Height*
(*setting this parameter to
deflection is typically easier)
Highpass filter OFF, 3-4
2 Lowpass filter OFF, 1
? Engage the surface. Make sure you are not false engaged (*see Section 10.10.1 of the DI
? Reduce Scan Size to ~12 nm.
? Engage with the Scan Size set to zero and slowly increase.
? Increase Scan Rate to 60Hz. Notice that if the Scan Rate is set much higher for atomic scale images to defeat some of the noise due to thermal drift.
? Adjust Integral Gain, Setpoint, Scan Rate, and Scan Angle to obtain a good image. Initially, the Setpoint should be kept as low as possible initially and then increased to obtain
an image. The Z-center position should be close to 0V. The Scan Angle is known to have
a huge effect, with optimal imaging conditions if the sample is rotated until the atoms are
oriented vertically or when the fast scan axis is parallel to the a or b crystallographic axis.
The Proportional Gain should stay at zero except for large scan sizes (~70% of the scanner
range). The system determines the minimum value of the Integral Gain. If you start with a
value less than the system's minimum, you wont get an image.
?Filters, you should be able to obtain an image with the filters off. In general, the filters
should be set to off since filtering during data acquisition affects raw data and height values.
? If difficulty is experienced obtaining and image Withdraw and try a different location on the sample surface, then Engage again. See Section 15.10.1 of the Multimode AFM Manual
for Troubleshooting Contact Mode imaging.
? Once an adequate image of the surface is obtained (see Figures 1-4), make sure the image
is real by varying the Scan Size. The spots observed should scale with Scan Size. The image
you will obtain is based on the "stick-slip" frictional motion of the probe tip (which is why
there needs a certain amount of force to be applied) determined by the spatial periodic
corregations on the crystalline lattice surface.
? If you notice a bright vertical band on either end of the image, this is due to the abrupt
reversal of direction of the scanner at the end of each scan line. You can eliminate this by
using the following procedure :
1) select Microscope/Calibrate/Scanner
2) A window will open with the scanner calibration files and in the lower right hand
corner is the "rounding coefficient" which is the percentage of the last portion of
each scan line that is not displayed. This should initially be set equal to 0.0. Increase
this to ~0.2 (while not exceeding 0.5) and this will cut off the last 20% of each scan
3) Reset this value back to 0.0 when finished.
? Capture the image.
? Sometime a good image can suddenly vanish, possibly due to adsorption of surface
contaminants. Try different XY locations on the same cleaved plane and cleaving the sample
a few other times.
Figure 1. AFM High-Resolution Contact Mode Image of Mica from A.Belyayev, State
Research Institute of Physical Problems & NT-MDT, Moscow, Russia.
(unpublished) (*downloaded from :
Figure 2. AFM High-Resolution Contact Mode Image of HOPG (*downloaded from :
Figure 3. AFM High-Resolution Contact Mode Image of HOPG (*downloaded from :
Figure 4. AFM High-Resolution Contact Mode Image of HOPG
IV. Off-line Image Analysis.
? Go to Off-line / View / Top View option and measure the spacings between atoms. The spacings should be as follows (as shown in Figure 5) :
MICA : A=0.519 nm, B=0.900 nm, C=1.37 nm
HOPG : A=0.255 nm, B=0.433 nm, C=0.666 nm
hexagonal atomic latticehexagonal atomic lattice
Figure 5. Hexagonal Atomic Lattice
Record the spacings for ~ 10 atoms observed in a captured image and average them. This
can be done by alternatively "walking" the cursor line from atom to atom; the average
distance will be shown on the bottom right hand corner of the display monitor's status bar.
If the measurements vary by more than 2 percent from the dimensions shown above, a
correction should be made as follows.
V. X and Y Axis Corrections
? See Sections 15-7.2-15-7.3 of the DI Multimode manual. The only difference is that the
known distances must be adjusted for the smaller atomic spacings of the atoms.
Furthermore, the sensitivity parameters are adjusted for atomic-scale imaging as follows :
oX fast sens 0 Scan Angle
oX slow sens 0 Scan Angle oY fast sens 90 Scan Angle oY slow sens 90 Scan Angle
The derate parameters are not changed for atomic scale imaging including ; x fast derate, x
slow derate, Y fast derate, Y slow derate, retracted offset der, extended offset der.
As stated in section 15-7.9 in the DI Multimode manual, the sensitivity parameters must be
calibrated with the Scan angle set at both 0 degrees and 90 degrees. Z-axis calibration is done
the normal way using a silicon calibration reference (see Section 15.8 of the Multimode
Manual for detailed instructions).
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