Using the Atomic Force Microscope

Equipment
Menu/Part
Process
Computer
Main Menu
  • Set “Scan Size” – usually 3 mm to start for DNA but larger if needed
  • Set Rate – usually 1 Hz
  • Set Points – Usually 512
  • Set Lines – Usually 512
  • Set Gain to 3 (This allows the computer to multiply the input to 3 so the cantilever is not broken during adjusting.)
Atomic Force Microscope (AFM)
Laser
  • Turn on light
  • Adjust mirror so the cantilever can be seen with the video camera. (Image of TV on screen)
  • Adjust x-axis of laser so it will hit the cantilever.
  • Adjust y-axis of laser to the maximum “Sum” measurement.
  • Adjust x axis to the tip of the cantilever so that about 75% of the diameter of the laser is hitting.
  • Adjust the photodetector (PD) so that the deflection is less than 0.1.
Computer
Tune Menu
  • Go to the Tune Menu to auto tune the cantilever.
  • Note: resonance frequencies of the cantilever vary between about 1 kHz and about 400 kHz for different kinds of cantilevers. Get the range of values from the box of cantilevers.
  • Set the lower and upper limits for frequency, being sure the value is between them.
  • Set the Target Amp to 1.00 V
  • Set the Target % to -10%.
    • This is the area with the largest slope, meaning as the cantilever interacts with the surface it will cause the greatest change in amplitude.
Computer
Sum Menu
  • Hit “Engage” button to extend piezo for vertical motion of the cantilever.
AFM
Legs
  • Lower unit very slowly keeping the leveling, until the amplitude is at 0.8 and the z-voltage drops to about 70.
  • Once the amplitude begins to change, use only the front leg wheel to adjust the AFM.
AFM
Light
  • Turn off the light
  • Remove the light from the box and seal the hole it was in.
  • Place front cover over microscope to dampen sound interference.
Computer
Main Menu
  • Change Integral Gain to 1.0 for DNA
    • This is done to make the microscope less sensitive to noise.
  • Hit “Do Scan” to start the scan.

Additional comments:
If nothing shows up, enlarge the scan to 5 mm and slow the scan to 0.5 Hz.

There are several adjustments that can be made to help an image come out clearer. These include adjusting the image size, adjusting the frequency, and adjusting the set point.