The Colvin Group
at Rice University presents its on-line

TappingModeTM - Atomic Force Microscope Manual

for the Digital Instruments NanoScope® Multi-Mode AFM

Manual Version 1.1, August 1997

Manual by
Stephen Prilliman and Prof. Vicki Colvin

Editing and HTML Coding by
Stephen Prilliman and Steve Robertson

Rice University
Department of Chemistry, MS-60

WWW: http://nanonet.rice.edu

Disclaimer, as requested by Digital Instruments:   Nanoscope is a registered trademark of Digital Instruments, Inc., and TappingMode, AutoTune, and are tradmarks of Digital Instruments.  Although this manual is for DI products, DI is not responsible for its content, so if you break your AFM using one of these procedures, its not their fault, (and for that matter it's not the Colvin Group's either). Questions about this disclaimer may be forwarded to Bobbie Offen, BobbieO@di.com.

Table of Contents

I. Introduction
II. TM-AFM Theory
    A. Review of Simple Harmonic Oscillators
    B. Modeling the AFM Cantilever
    C. Lessons to be Learned from the Model
III. Setting Up the AFM
    A. Turning the Instrument On
    B. Loading a Tip in the Microscope
    C. Loading a Sample into the Microscope
    D. Aligning the Tip for Operation
IV. Getting and Utilizing Data
    A. Description of Data Types
    B. Basics of Data Acquisition
    C. Optimization of Scan Parameters
    D. Data Analysis and Output
V. Trouble-shooting and Helpful Hints
    A. Preserving Your Investment
    B. Trouble-Shooting

Note: Our group uses Digital Instruments TESP tips (fo between 200 and 350 KHz). If you do not use TESP's, the procedure for optimizing your TM-AFM may very slightly, and the value of parameters that you should use will also vary. 

I. Introduction:

Tapping ModeTM Atomic Force Microscopy (TM-AFM) works by vibrating a tip which is at the end of a cantilever and bringing the tip into intermittent contact with a sample surface. When the tip interacts with a surface feature, its amplitude is decreased from its previous amplitude of oscillation. The AFM senses this decrease, and the tip is raised away from the sample in order to re-attain the previous amplitude of oscillation. In this way, the tip can be rastered across the sample to generate topographical images. Because the reaction of the tip is sensitive to sample mechanical properties, such as viscoelasticity, we can also gain an understanding of these quantities through TM-AFM.

TM-AFM has a number of advantages over other microscopic techniques. One is the ability to image soft samples without damaging them, and for this reason TM-AFM is very useful for imaging biological and polymer samples. It also has the advantage of being fairly easy to use and requires little sample preparation.. The resolution of TM-AFM is arguable though it is certainly less than contact mode AFM. It is probably about 5 nm..

II. TM-AFM Theory

In order to understand TM-AFM, it is necessary to understand oscillators. We will therefore first do a little review.

A. Review of Harmonic Oscillators

The most simple expression for springs is Hooke's Law.

By Newton's Second Law, this is equal to

As is usual with physics, this is a gross oversimplification of anything we would encounter in real life. There are two additional forces besides the tension in the spring which effect the motion of most oscillators one encounters, including the AFM cantilever. These forces are damping and driving.

Damping is a frictional force, and like the friction of a piece of wood being pushed across a floor, the damping force is proportional to the negative of the velocity (i.e., it opposes the motion). Thus,

The expression for the driving force depends (oddly enough) on how you drive it. Since it is generally nice for oscillators to oscillate, a typical driving force is

Thus the driving force has some maximum amplitude Fo and a frequency omega (not to be confused with omegao, the resonance frequency of the free, undamped oscillator).Summing the forces, we get the equation for damped, driven oscillators.

Most textbooks or articles are not content to leave the equation in this form, however. A common term which is substituted is Q, the quality factor of the spring. Q is defined as

Where omegaR is the resonance frequency of the damped driven oscillator,

and Beta = b/2m. If you do a lot of algebra, you can find that

Usually we can ignore the ½, (Q >> 1) so we get

Thus, we can substitute the above into Eq. 5 for b, and obtain another form of the equation of motion

It is also common for textbooks to divide this equation through by m, then using the definition of undamped resonance frequency,


B. Modeling the AFM Cantilever

Since the cantilever is essentially, as Science (v.207, p.1983) calls it, "a wee diving board", i.e., a driven damped oscillator, J. Tomayo and R. Garcia (Langmuir, v.12, pp.4430 - 4435) had the neat idea of modeling it using Eq.6.  However, now one must consider another force, that of the surface.


If the system is set-up as in Figure 1, then the differential equation of motion is:

which is just Eq. 6 with an F(zc,z) term inserted to account for the surface interactions. This term depends on whether or not the tip in contact with the surface (i.e., zc+z > ao) or not (zc+ z <= ao)

where parameters are defined in Table 1.

When the tip is not in contact, the only force it feels from the sample is van der Waals, which is attractive.  When in contact, there is the attractive van der Waals force over the interatomic distances, and the repulsive force due to sample hardness (the Young's modulus term). The third term is due to viscosity and acts like a friction force, opposing the motion of the tip.  While the terms involving Young's modulus and viscosity make the model more difficult, if we model the system correctly, we can obtain these two sample parameters that cannot be obtained by other microscopic techniques.

C. Lessons to be Learned from the Model

The most important thing to get from theoretical modeling is that the tip does not simply push itself into a surface it comes in contact with.Such behavior would not be consistent with the differential equations. Instead, it decreases its amplitude of oscillation in a nearly linear manner, which allows it to continue to satisfy the equations.

III. Getting Started in TM-AFM

A. Turning the Instrument On

The power switch is on the back right of the main computer. Also turn on the optical microscope lamp (Cream colored box with black switch to back right of microscope) and the monitor for the video camera (switch on front). The video camera is usually on. You will know you turned on the machine because you'll see numbers appear on the AFM.

B. Loading a Tip in the Microscope

1) Prepare a sophisticated tip holder. Use a 5 inch piece of copper wire. Cut a small piece of double sticky tape and press one end of the Cu wire down against the tape -- it should stick to the wire.

2) Move the actual AFM tip off of the storage cases' sticky tape. The AFM tips come packaged in plastic containers with a sticky tape area used for stabilizing the tips. Using a pair of tweezers move one of these tips off the sticky tape area.

3) Place the tip under the tab on the tip holder piece. Using your special copper wire device from (1), touch the tip just to the right of the line running vertically to the long axis. Don't put it too far to the right or you will hurt the AFM tip. Too far to the left and you'll block the electronics. Lift the tip up into the air. With the tip holder assembly upside down, press down on it -- this will cause a small tab of metal to come up and you can then slide the left part of the AFM tip in. Stop pressing on the tip holder and the metal tab should be securing the tip in place.

4) Readjust slightly the tip position if it is really crooked. It doesn't matter too much that the tip be set at a perfect right angle to the tip holder; however, you can set it in well and ensure electrical contact by using a pair of tweezers to rotate the tip slightly to align it coarsely. If you need to adjust the position of the tip in the holder, you can push the tip around by inserting the tweezer tip into the intersection of the grooves on the tip.

C. Loading a Sample into the Microscope.

1) Put sample on holder and slide stage into microscope. The sample holder is a circular metallic disk which is magnetic and sticks to the magnetic stage. Use double sticky tape to hold down the sample to the puck.  Place a piece of mica on top of this and use scotch tape to take off the first layer. You can then apply your sample. The sample/puck assembly can be easily placed in the AFM using a pair of tweezers.

2) Put the Tip Holder Assembly Into the Microscope. Use the "Tip Up" toggle switch to bring the tip away from the sample.   If you do not do this you risk breaking your tip.  Flip the tip holder over so the metal rod is out and the copper tabs face up and the tip down. Slide the tip holder into the microscope and let it gently come to rest on the two ball points in the scanner head.  Watch through the optical microscope as you twist the large knob (See Figure 4) directly behind the sample stage to lower the electrical connectors down onto the tip holder. If the tip looks shiny STOP! The tip has come in contact with the sample. Do a tip up immediately, and you may salvage the tip.

D. Aligning the Tip for Operation

1) Get the optical microscope working. First make sure that you have light on the system (turn on the black knob #1 in Figure 2). Next, look through the eyepiece- you should see light. If not, then move shutter3 to put the view to the eyepiece. It may not look in focus. You should generally be able to focus on the sample area using the focus knob (#4). If you have trouble bringing anything into focus it may be that the optical microscope is lifted up and away from the AFM. Lower the whole microscope by turning the largest black knob in the back right- make sure you support the microscope, and never turn the two black knobs on either side of the microscope.  If the optical microscope falls it could crush the very expensive AFM and you will have your salary garnished for the rest of your life.

2) Centering Tip and Sample in Field of View. Using the lower knobs (See Figure 1) on the stage that supports the whole AFM, bring the tip and sample into view (See Figure 3). You can use the eyepiece first to grossly get the tip into the center, then switch to the video screen using the shutter (#3 in Figure 2).

3) Get tip close to surface. You want to bring the tip close enough to the surface that your alignment procedures work well, but not to close as to crash it into the surface. Begin by using the focus knob to focus on the sample surface. Go past (or "up") the sample focus to comeback to your tip. Then reverse from this position -- you should bring the sample surface back into focus again, then go past this focus to bring the back reflection of the tip into focus. Then move back to the sample focus. This exercise is important, because you'll know that you are indeed looking at the sample surface, not its virtual image.  Now, use the black lever (Figure 4) to push the tip down until it gets into better focus.DON'T BRING THE TIP INTO COMPLETE FOCUS(this will crash it)- instead just make its shape distinct.

4) Get laser on tip. Turn down the microscope light using knob#1 on the cream box. On the video you should see a wash of red light which is the laser. Using the 2 laser positioning knobs (X and Y in Figure 4),move the laser so that it is centered on the tip (see Figure 3).

5) Alignment- fine adjust in intensity. Look at the bar that wraps around the large oval circle on the bottom of the microscope. Adjust the mirror position using the lever (#1 in Fig. 4) in the back of the microscope to maximize the bar. For a TESP tip the bar reading should be between 2 and 3 after alignment.

6) Focusing laser. Use the Align-O-Gadget© (which is just a Q-Tip with a piece of paper taped to one side of the soft end) to see what the laser beam looks like near the photo-diode. Adjust the laser knobs (X and Y in Fig. 4) to make this beam look as sharp as possible. The laser will not look like a point, but rather a bar through a diffuse circle (Fig.5)

7) Photo-diode adjustment. Now you want to get the light centered on the position sensitive detector. Your goal is to make the number in the oval equal to zero (+/- 1 is OK). You will be moving the two knobs (A and B in Figure 4) which control the position of the detector while watching the number in the oval. Using A, turn the knob counter-clockwise to make it decrease, or clockwise to make it increase.  Usually this should do it.  However, if you notice the bar graph decreasing, turn A back to where it was and use B.

8) Isolation Platform and the Seuss Hat. At some point, you may need extra vibrational and acoustical isolation of the AFM from the surroundings. In this case, you can use the isolation table, which is just a piece of granite suspended from a tripod by bungee cords, and the Seuss hat, a felt cylindrical cover. Vewy vewy cewfuwy move the very very expensive AFM over to the isolation table.  Make sure that the cord that looks like a SCSI cord does not catch on the base of the adjustment table (Todd Day at DI has asked me to note that the cord is not a SCSI, so please don't try to hook it up to anything like a zip drive as the 440V that the cord carries will fry it instantaneously). Place the Seuss hat over the AFM. Note: you need not do this for standard imaging conditions,just when things are really noisy or you are trying to see something very small. Make sure you have a working tip before you do this, because it is a pain to have to move it back to the table and realign or replace the tip.

IV. Data Acquisition

A. Description of Data Types

There are two types of data that are commonly used, height and phase. Other data types are available, such as deflection, but are not included here.

1) Height Data. Height data, or topography, is often the most useful and reliable data that can be obtained from the AFM. In TM-AFM, when the cantilever encounters a surface feature, its amplitude of oscillation is decreased from its set-point value (Fig. 6, top). This decrease is noted by the sensor and the tip is moved up away from the sample to re-attain the set-point amplitude (Fig. 6, middle). When the tip moves past the feature, its amplitude will increase, and the tip will be moved down again so that the amplitude is once again brought back to the set-point (Fig. 6, bottom).

2) Phase Data. Phase data is obtained from the difference between the driven and the actual oscillations of the cantilever.

Figure 7 (DI publication "Phase Imaging: Beyond Topography") illustrates how phase data is obtained. The tip is driven with Focos(wt- phid), but the actual response of the tip is Focos(wt - phir). The phase offset caused by interaction with the surface is then phid - phir. Phase is useful because different materials will cause different offsets in phase, due to the fact that it depends on differences in adhesion, friction and viscoelasticity. In Fig. 7, Sample 1 has a much smaller phase offset than Sample 2, so they will be very distinguishable in phase imaging. Phase images will also display great sensitivity to fine ridges in materials, often helping the user to locate areas of interest.

B. Basics of Data Acquisition

1) Start the program: Hit "Z" to start from Windows 95

2) Tune the tip. Hit the little tuning fork icon. Because other users will utilize different scan parameters than you, you should hit the "Manual" button to see that the parameters are acceptable for use with TESP tips. Typical settings are listed in Table 2.

Table 2. Quick Reference for Scan Parameters*
Parameter Definition Typical Value Range of Values Effect on Image Quality
Setpoint The value of the RMS of the 
cantilever vibration amplitude that the feedback loop maintains. (Setpoint is thus proportional to force applied to surface)
2.00 V 1.00 V - 5.00 V Reducing setpoint often leads to better quality images
Drive Amplitude The amplitude of the force at which the cantilever is driven (Foin Eq. 6) 50 mV 30 mV - 1.00 V Increasing drive amplitude often gives better phase data, up to a point
Proportional and Integral Gains Determine how sensitive the feedback loop is to variations in the tip's amplitude of oscillation 0.400/4.00 0-0.600/0-6.00 Increasing gains often helps obtain better images (especially height)but only up to a point, above which high 
frequency noise is observed
Scan Rate Controls the rate at which the cantilever scans across the sample area 2.00 Hz 1.00 Hz - 4.00 Hz A slower scan rate generally leads to better images, but not always. Decease until you get the best image
Number of Samples The number of pixels used to create the image 256 128-512 Increasing leads to better image quality, but there is a trade-off with time

* For more information on scan parameters, see Section IV.C.

3) Approach the Surface. Hit the down green arrow icon, which will cause the tip to approach the surface of the sample. You can monitor the progress of the tip engagement by watching the bottom of the control screen.

C. Optimization of Scan Parameters

Do not try to optimize the image by observing the image!  Instead, hit the "Scope mode" icon (looks like an oscilloscope). You'll see a graph of z-position versus xy positions. The white and yellow lines represent the trace and retrace of the tip as it is rastered across the sample. Since the difference in space between the trace and retrace is small, these two should closely agree, so the white and yellow lines should overlap. If the white and yellow lines do not overlap, follow this procedure:

1) Decrease the Set Point. Do this until the image improves or until you reach 1.0 V

2) Increase the Drive Amplitude. Often times there will be a significant amount of strong noise. Increasing the Drive Amplitude will take care of this. Once you have a good picture, back off on Drive Amplitude as much as you can without coming off the surface. The following set of images is ordered by drive amplitude, from lowest to highest (60 to 200mV).

As you can see, the best quality images are at the lower drive amplitudes.

3) Change the gains. High values of gain may cause high frequency noise, so it is often necessary to reduce their value, keeping them in approximately a 1:10 integral to proportional ratio. However, the gains should be kept as high as possible, since they control how fast the cantilever will respond to changes in topography.

4) Change the scan rate. If reducing the gains does not eliminate noise, this can help. Scan rate values that are too low as well as too high will cause poor images. You should try a range of values while in image mode to obtain the best one.

5) Adjust the Z Range. Although this can be changed later (e.g., in Flatten), it is often important to have the most contrast available while in you are imaging. Thus, you should set the Z Range in such a way that the scope mode picture just fits within the Z Range.

D. Data Analysis and Output

1) Capturing data. In order to save your image files and to be able to do data analysis, you must first capture the image. First go to the Capture menu, and select "Capture Filename". Name the file something that makes sense to you, but try to keep it systematic (e.g., your initials, a date and another letter) as you will eventually take large numbers of images. Once you have done this, you can capture any picture by clicking the camera icon. You can monitor the status of your capture by looking at the bottom of the control screen. If you are in the middle of an image, it will probably give you the message, "Capture: Next". In this case, hit either the arrow up or arrow down icon, which will start your scan from the bottom or the top. Be sure that while you are trying to capture an image you do not adjust the scan parameters. Doing so will reset the capture to take the next image. When the capture is complete, it will say "Capture: Done".

2) Data Analysis. Once you have captured an image, you can analyze it with the many tools supplied by the DI software. First, click on the TV screen at the left of the control screen. Now go to the "Image" menu, and select right or left image. Full details of data convolution and analysis will be included in the next version of this manual. For now, let it be said that it is generally necessary to "Flatten" the image before it can be used. This is done by hitting the rolling pin icon.

A very useful data analysis tool is "Section". Select this from the "Analysis" menu. By clicking on the image and drawing a line between points, you can see a plot of Z versus the axis you have drawn. This is handy in determining the size (width) of nanoparticles, for example.

3) Output. You now probably want to get your data off the machine so you can show your family and friends. To simply get an image, go to the "Utility" menu and select "Tiff Export". This will give you a dialogue box. It is important that you choose "Reverse" under background, because if you print these out, you do not want a lot of black surrounding your image - that will significantly slow down your printing time. Select a filename somewhere on the C:\ drive.

If you want to get another picture, e.g., a section analysis, you must choose "Print" from the dialogue box and set destination to "TIFF".

To copy your files to a portable disk (floppy, zip, etc.) you must exit the AFM program and return to Windows. If you need to zip up your files, you can use the DOS version of pkzip which is installed on the CNST's AFM.

V. Helpful Hints and Trouble-shooting

A. Protecting Your Investment, or, Stupid Ways to Break Tips

The biggest cost involved in day-to-day AFM-ing is for cantilever tips. A box of 10 TESP tips from Digital Instruments runs $400. Thus, it is important to be careful and not break these precious commodities. Here is a list of things to avoid doing while handling the tips.

B. Trouble-Shooting

Here are a few problems you may encounter in the course of doing AFM.

1) AutoTuneTM will not work.

2) Sample seems to move when lowering the tip. 3) Getting poor images. 4) Tip will not engage. 5) Z Center Position reaches limit