Design Parameters

This microscope is designed to be built by students in a few lab periods. In most places, the trade-off between resolution and cost has been tilted toward the cost side. The priority list, from highest to lowest, is:

• Build time of about six hours.
• Setup, troubleshooting, and testing in three hours.
• Cheap components.
• Modest tooling requirements.
• Resolution in the nanometer range.

Part List

One ¾ slide repair coupling – Home Depot part number: 032888605046

Two ½” plug MPT - Home Depot part number: 049081143145

One small magnet (8mm x 3mm) - Home Depot part number: 095421070459

One piece of circuit board material (0.037”, FR4, Single, 1oz) – Ebay

One spool of 30 gauge magnet wire or ribbon cable - Ebay

One 27 mm Piezo Transducer Sound Disc (20mm PZT) - Ebay

One phenolic standoff 3/4” long by 1/4” diameter - Ebay

One DIP socket (any size) - Ebay

One 1¼ to 1½ reducer bushing - Home Depot part number: 034481062271

One NEMA 17 stepper motor - Sparkfun part number: ROB-09238

One brass 2mm to 5 mm motor coupler - Ebay

2-56 threaded rod - Ebay

One 7” Hose Clamp - Home Depot part number: 078575179957

Tooling List

Hand drill or drill press.

3/4” drill bit.

Vise or drill press clamp.

2-56 drill and tap set.

Hot glue gun.

Soldering gun and solder.

Scissors, side cutters, etc.

Hacksaw or bandsaw.

Razor blade.

Multimeter.

1. Housing Preparation.

1. Disassemble the ¾ Slide Repair Coupling into its three component pieces (cap, slider and housing).
   • Try to leave as much grease on the orings and sliding surface as possible since it will be required for normal operation.
   • Clean the grease off any surface that you will be gluing to.
2. Using the drill or drill press and the 3/4” bit, cut the sample access hole just below the threads of the housing.
   • During drilling, use safety glasses, a vise, and observe all safety precautions.
   • In the picture, the hole was drilled a little too close to the flange and cut into it. This configuration still works, but it looks messy.
   • The edges of the hole should be smooth so the orings do not catch on them.

2. Slider.

1. Prepare the plugs.
   1. Cut a rectangle of thin circuit board just smaller than the plug’s outer diameter and hot glue a magnet to the center of the non-copper side.
   2. Solder a six inch length of wire to the circuit board.
   3. Hot glue the circuit board to the plug as shown on the left side of the picture.
   4. Drill and tap a 2-56 hole in the exact center of the other plug as shown on the right side of the picture.
   5. (Optional) Use a saw and cut the hex flange down to ½ its height.
2. Prepare the slider.
   1. Cut the non-o-ring end off the slider so it is 50 mm long and smooth the edges of the cut.
   2. Press the plugs into each end of the slider.
      • The plug with the foil and magnet goes into the end nearest the o-rings.
      • The plugs should fit tightly so they will not need to be glued into position.

3. Piezo and Cap.

1. Use a ruler and razor blade to cut the silver material on the piezo disk into four equal quadrants. The white layer on the piezo disk does not need to be cut. Verify electrical decoupling using an ohmmeter.
2. Solder on five small wires – one to each quadrant and one to the yellow base.
   1. Use magnet wire with each piece about six inches long.
   2. Try to use as small amount of solder and contact time as possible.
   3. All five wires should be connected to the same side.
3. Use hot glue the phenolic standoff to the center of the yellow side of the disk.
4. Attach a tip holder to the end of the standoff.
   1. The tip holder should be made from one section of a DIP socket.
   2. Solder a six inch section of magnet wire to the end of the DIP socket.
5. Hot glue the piezo to the cap.
   1. A small hollow in the cap may need to be cut to allow the piezo to sit flat on the cap.
   2. The five wires from the piezo should feed up through the hole at the top of the cap.

4. Prepare the Motor.

1. Use a 2-56 tap to cut threads in the 2mm end of the motor coupler.
2. Cut a 25 mm long length of 2-56 threaded rod and thread it into the motor coupler.
3. Tighten the setscrews in the coupler to attach it to the motor and the threaded rod.

5. Assemble the STM.

1. Push the slider fully into the housing and feed the wire through the hole you drilled in the housing.
2. Screw the end cap unto the housing and feed the tip wire through the hole.
3. Push the gray reducer bushing onto the housing.
4. Manually thread the motor assembly into slider until the housing until the motor touches the bushing.
5. Place the hose clamp around the STM and tighten it to hold the motor to the slider. Except for the green wire and the black connectors on the magnet wire, the assembly should look like the picture below.
   • The clamp will need to be positioned so that the access hole and the motor wires are not blocked by the clamp.
   • Rotate the gray reducer bushing so that the bumps on it do not hit the hose clamp.

Computer Data Acquisition

Back when the Scanning Tunneling Microscope was invented in 1981, the CPU in most computers was very slow. The feedback loop needs a bandwidth of about 5 kHz and the CPU couldn’t deliver that speed. The only way to get the desired bandwidth was to build the feedback system using analog electronics. By the 1990s, Digital Signal Processors (DSPs) were available and allowed the most of the feedback loop to be built in software. This allowed much greater flexibility in customizing the feedback system, but was expensive since DSP-based systems cost over $2500.00. In the last 10 years, the speed of the CPU in most computers have increased to the point that the CPU can run the feedback loop in addition to running the operating system, displaying data, and getting input from the user. The requirements for the computer CPU for this microscope are not very demanding by today’s standards. A computer with a dual or quad core CPU should work for this project.

The heavy lifting from the data standpoint is taken care of by the data acquisition card. Although the cost is reduced by not needed a DSP-based system, the data acquisition card is still the most expensive part of the project. Ideally the card should have the following features:

• 4 voltage output channels (DACs) with a voltage range of -10 to +10 volts at a minimum of 14 bit resolution (16 bit resolution is preferred).
• 1 voltage input channel (ADC) with a voltage range of -10 to +10 volts at a minimum of 14 bit resolution (16 bit resolution is preferred).
• 2 digital out channels.
• Ability to read and write DC voltages (sound cards don’t do this).
• Ability to read a single value and write a single value and repeat this combination at a minimum of 1000 times per second (2000 times per second is preferred).

This feature list is out of the range of most low-cost solutions but the National Instruments Corporation makes boards that fit both the minimum and preferred requirement list.

Part List - Option 1: Slow but Simple.

The minimum option costs $378 and is based around the NI USB-6001 device. Each device only has two voltage outputs, so two have to be purchased for this project. Each device includes screw terminals so connection to the microscope is easy. Because the USB interface is not optimized for the single read /single write operations that a feedback loop needs, the bandwidth of the feedback look is slow so image acquisition will take longer.

Part List - Option 2: Fast and Expensive.

The preferred option costs $1800 and is based around the NI PCIe-6323 card. This card is available from National Instruments for about $900.00. To connect the card to the electronics, two cables and two breakout boards are needed which add another $900.00 to the total cost. In the picture below, the connections from breakout boards to the microscope are shown.

There are a couple of ways to lower this bill. The company DaqStuff.com sells cableshttp://www.daqstuff.com/100768_vhdci_mm_cable.htm and breakout boardswww.daqstuff.com/400057_400058_vhdci_m_series_breakout.htm that are much cheaper. Two of these cables and breakout boards have a total cost of $220. Another method to lower the cost is to use the older National Instruments PCI-6229 card. This card uses the older PCI bus and can be found used on Ebay for about $500.00. There does not seem to be a difference in STM operation between the PCI and PCIe cards.

Part List

One TI Quad Op-Amp (TL074CN) – Ebay

Four 10 kΩ Resistors – Ebay

One 10 MΩ Resistor – Ebay

One Stepper Motor Controller – Sparkfun part number: ROB-11699

One 12V/1A power supply – Ebay

Four 9V battery plugs – Ebay

Four 9V batteries – Ebay

Breadboard – Ebay

Part List - Optional

One 14 pin DIP IC socket – Ebay

One custom printed circuit board (Amp Rev B) – OSH Park or similar.

24 Female Headers – Sparkfun part number: PRT-00115

24 Break Away Headers – Sparkfun part number: PRT-00116

Assorted Grommets – Home Depot part number: 032076074746

By using a good data acquisition system, the electrical system is simplified. There are only three amplifiers needed and they all are on a single chip. Two of them invert the X and Y scan voltages and the last one converts the tunnel current into a voltage. A stepper motor controller board is also needed.

The circuit diagram below shows all the connections. On the left, connections will be made to either the PCIe-6323 card or the USB-6001 device. The pin number for the PCIe card is before the slash and the pin name for the USB device is after the slash.For the best noise results, the amplifier is powered by four 9-volt batteries – two wired in series to provide -18 V and two wired in series to provide +18 V. 

General Notes

• Never unplug or plug in the motor while the stepper motor controller’s power supply is on. It will burn out the stepper controller. Make sure you don’t reverse the connections and connect 12 volts to GND.
• Always unplug the batteries when you are not using them so they do not discharge.
• Unplug the stepper motor power supply when you are not using the motor so it doesn’t heat up too much.

Optional Improvement

To avoid crashing the tip into the sample, it is recommended that the half-step mode be used rather than the full-step mode on the stepper motor. This change is made on the stepper motor controller board by connecting the MS1 pin to +5 volts and leaving the MS2 & MS3 pins connected to ground. In this configuration, four half-steps move the sample through the vertical piezo range. The quarter-step mode could also be used, but the reduced risk of crash does not seem to justify the slower approach speed.

Build Option 1 – Fast and Noisy.

The fastest build will run direct wires to each component and build the circuit on a bread board. The best results are obtained by making the wire from the sample to the amplifier as short as possible. A typical system is shown below. The STM is placed on foam to minimize vibrations. The connections to a PCIe card are made through the green and blue breakout boards purchased from DaqStuff. The problem with the above configuration is that it picks up too much noise on the wire from the sample for good resolution.

Build Option 2 – Custom PCB.

A better build option is to use a printed circuit board and removable headers. The PCB can be placed closer to the sample which reduces noise and the headers make trouble-shooting the system much easier. The PCB board file can be downloaded from this link and sent to a vendor such as OSH Park for fabrication. In the pictures below, the board and schematic are shown.

The components should be on the side with the labels and all the soldering should be done on the opposite side. All the headers are identified by a “J” label. Pin 1 of each header is the one closest to the “J” label. The connections to each header are listed below:

J1	Tip		J5 Port 0 - Analog Connection
			1	21/AO1: Z from Computer
J2 Port 1 – Analog Connection			2	55/AO-GND: Ground
1	22/AO0: X from Computer		3	68/AI0+: Tunnel Current
2	21/AO1: Y from Computer		4	34/AI0-: Tunnel Current Ground
			5	22/AO0: Bias
J3 Power
1	Ground		J6 Piezo Connection
2	+V		1	+X
3	-V		2	-X
			3	-Y
J4 Oscilloscope Connection			4	+Y
1	Z from Computer		5	+Z
2	Ground
3	Tunnel Current		J7	Sample
4	Ground

This circuit board can be attached to the housing of the STM right by the sample. The board can be glued to the housing or attached to grommets. In the picture below, the grommets are glued to the housing and hold the board tight enough during operation, but allow it to be removed if needed.

Software Overview

The STM control software used to drive the studentSTM was written in Visual Studio in C++ using Microsoft Foundation Classes.  It has been tested both as 32 bit code and 64 bit code.  The 64 bit code did not show any speed improvement, so only the 32 bit version is available as a compiled download.

This program requires drivers from National Instruments to interface with the National Instruments PCIe-6323 or the USB-6001 data acquisition cards.  The “NI-DAQmx” software is the preferred option.  The “NI-DAQmx Base” software does not include all the necessary features.

Using a Dell Optiplex 745, several combinations of Windows and the NI-DAQmx software have been tested to determine the maximum speed possible for a read/write combination used in the feedback loop.  The feedback loop ideally would run with a speed just below the piezo resonance (4.6 kHz).  The feedback loop speed is limited by the card, the card drivers, and the Windows OS.  The loop reads a single value from the card, processes it, and writes it out to the card.  The Speed Test results will be displayed on the status bar at the start of each image acquisition.

Windows 7 and Windows 8.1 both work with 32 and 64 bit versions of studentSTM with no difference in speed.  For the USB-6001 device, the maximum speed is about 1000 Hz.  For the PCIe-6323 card, NI-DAQmx V14.2 is the slowest at 800 Hz, V9.7 has a speed of 1800 Hz, and V9.1 is even faster at 2100 Hz but does not have stated support for Windows 8.1.

Software Download

For the PCIe-6323 card, version 1.0.1 of the compiled 32 bit code can be downloaded. Once the NI-DAQmx driver installed, it should work without further programming.

Version 1.0.1 of the source code for use with Visual Studio can be downloaded here.  To compile it, the files NIDAQmx.lib and NIDAQmx.h must be copied from the default location where the NI installer puts them to the same directory where the rest of this code resides.

For the USB-6001 device, the compiled code and the source code can be downloaded.

A Description of Each Field in the Software

Feedback Loop Group

Feedback On:  The feedback loop is on if this is checked.  This is normally checked.

Set Point (V):  The voltage as measured by the card that it tries to hold using the feedback loop.

Feedback Gain:  How strongly the feedback loop responds to perturbation.

Stepper Motor Group

Move Closer:  This moves the sample closer until it is stopped by the user.

Auto Approach:  This moves the sample into tunneling range while monitoring the tunnel current.  It will stop by itself once tunneling is established.

Move Further:  This moves the sample further until it is stopped by the user.

Data Acquisition Group

Take Image:  This starts the image acquisition.  It can be stopped by pushing the button again.

X Offset (nm):  This entry offsets the next image in the x-axis relative to the center position.

Y Offset (nm):  This entry offsets the next image in the y-axis relative to the center position.

Bias (mV):  This entry sets the bias applied to the tunneling tip.

Image Width (nm):  This entry sets the size of the image in nanometers.

Time (mS)/Line:  This entry sets the image acquisition speed.

Calibrations Group

(PCIe-6323 option)  Card Number:  This entry sets the number of the card to match the number assigned by the driver.

(USB-6001 option)  Card Number TZ and Card Number XY:  This entry sets the number of the devices to match the number assigned by the driver.

Piezo Range (nm):  This entry calibrates the scan size in each axis.

Piezo Sign:  This entry allows sign reversal of the voltage going to the z-axis.  If the feedback loop drives the system out of tunneling range instead of holding it in tunneling range, this sign needs to be reversed.

On the dropdown menu is a way to load images, save images, and save the parameters from the ribbon.

Part List

#10 Flat Washers – Home Depot part number: 887480024715

Pt/Ir tip wire (50 cm) – nanoScience part number: 20105

Conductive carbon tape or conductive silver glue – Ebay

Prepare a tunneling tip. For initial tests, the tip wire can be regular copper wire, but for the best results a Pt/Ir wire should be used. The tunneling tip wire should be cut using scissors or side cutters held at a 45 degree angle. The cut wire should be about 1 cm long. Load the tunneling tip into the tip holder (the section of DIP socket) using a pair of tweezers.

Prepare a sample to image. For early testing, the circuit board of the sample holder can be used, but the best practise is to use a section of DVD. Cut into a DVD-R disk with a pair of scissors. Try to remove the clear plastic layer from the DVD, leaving the top of the disk with that label and the foil layer on it. Cut a section out just smaller than the #10 washer. Place it, foil side up, on the washer. Attach it down using conductive tape or glue. Make a good electrical connection between the foil and the washer. In the picture below, the DVD section is in the foreground and has been attached with silver paint. The sample in the background has been attached with conductive tape. Load the sample into the microscope where the magnet in the sample holder should hold the #10 washer down tightly.

Start the software. Click on the question mark on the extreme right side of the screen. This will open a program information screen. It will show the electrical connections that the software requires. At the bottom of the window, it will show all NI cards in the system. Look for the 6323 card entry or the 6001 device entries and make a note of the device number(s). Enter the device number(s) in the “Card Number” field in the “Calibrations” group.

Check all electrical connections to the computer shown in the program information screen. Use an oscilloscope to monitor the z-axis voltage and the tunnel current output from the transimpedance amplifier. If you do not have an oscilloscope handy, two multimeters can be used instead. They will not capture the quick changes in voltage but they will register trends. Plug in the batteries for the amplifier and plug in the stepper motor power supply.

Click the “Feedback On” button. If no error messages show up on the status bar at the bottom of the screen, the feedback loop is on. As soon as the feedback loop is turned on, the z-axis voltage monitored on the oscilloscope should move quickly to +10 V or -10 V. The tunnel current output monitored on the oscilloscope should be 0 V. Use the “Closer” and “Further” buttons to verify that the stepper motor can move the sample holder.

Next click the “Auto Approach” button. The sample should begin moving slowly toward the tip. At each motor step, the computer will monitor feedback loop. Once the sample has moving into tunneling range, the stepper motor should stop moving.

Once the motor stops, the z-axis voltage monitored on the oscilloscope should be between +10 V and -10 V but not at either extreme. The tunnel current output monitored on the oscilloscope should be at value given in the “Set Point (V)” edit box in the software. If these voltages are right, press the “Take Image” button and the first image acquisition will start. A typical image of a DVD sample is shown in the picture below for a scan width of about 4000 nm. It should have ridges every 740 nm.

It is best to withdraw the tip for a few seconds before turning off the system. This prevents the tip from crashing into the surface when the feedback loop is turned off. Remember to unplug the batteries and the motor power supply.