April Update

It’s been far too long since I’ve posted here, and the more time it was since that last post, the harder it became to post here.

So I’m just going to start again.

Mostly what happened is that I got stuck on some very frustrating bugs with my new hardware design and it took far too long for me to ask for help, so I lost all motivation to work on this project and found other shinier things to play with.

I’m now past that hurdle, and I think I have a way to keep motivation and progress going in the right direction.  I’m going to have a weekly or so meeting where I can ask for help and people can ask me basic questions about my designs, helping me to fix problems as they come up, and readdress all my basic assumptions.

This is basically what most advisers do for their students, keep them on task by asking questions and act as a sounding board for problems.  Maybe that’s something that could/should be used more widely in at-home science arenas?

Another inspiration for me is that ZeFrank came back.  My current favorites are this classic motivation, and this brand new motivation.


General updates since my last post:


Following a series of discussions with my analog adviser (hi Steve) and my physics adviser (hi Lee), I’ve started working on version 0.4 of the electronics (now with actual theoretical chance of working!). I received the (painfully small) surface mount parts from DigiKey and Newark, and managed to solder them to SMD-DIP adapters for breadboarding.

Things I learned:

  • Arduino ints only go to 2^15, that is a problem when dealing with 16-bit DACs.
  • My new DAC’s “write” command only means here’s some information, not do something with the information I’m giving you.


Bart from BuildLog sent some makerslide, a 400-step stepper motor, and other amazing things as part of his Makership project so I can build a solid linear actuator for the rough approach.

Funding and Support:

Wow, thanks so much to all the amazing people who decided to help this project with funding, parts donations, and their generous time:


Chicago Awesome Foundation

Individuals: Nikos G., pdp7, T. Joseph N., David C., Bruce G.


Bart from BuildLog.net

Time and advice:

Steve F., Ian S., Lee

image credit


Chicago Awesome Foundation is Awesome (and hello Make Magazine-ers)

I was notified late Wednesday that I have been awarded the October 2011 grant from the Chicago Awesome Foundation for completing the full prototype of the Scanning-Tunneling Microscope. Their posting is over here. For the record, yes, I officially love the Awesome Foundation.

At nearly the same time, Make magazine blog posted an old video of me playing with the version 0.1 electronics and then Element 14 posted as well (wow, I’ve come a very long way since then – I need to shoot some new video), bringing in a flood of new folks over the past 48 hours. Hello new folks!

For folks who are new, here’s how things stand:

  • The version 0.1 electronics in the video posted on the Make blog was a poor implementation of a good analog design with a microcontroller slapped to the inputs. I’ve since learned that analog is weird compared to digital, and getting those two worlds to talk properly involves a lot more finesse and art than science and equations (equations do get you into the ballpark, however).
  • I’m nearly done with a complete redesign of the digital and analog electronics (now at version 0.3). The new electronics incorporates nearly complete digital control of the STM (I’m working on ways to further increase the control the microchip has over the STM to include gain control of the many op-amps). Thanks to Idea Petri Dish for the assist on analog circuit design and troubleshooting.
  • With new electronics comes new firmware and software of course, which is in-process.
  • I’ve done a very rough draft of the vibration dampening table design.  I’ll be using a classic floating gravestone style table – a heavy slab of material suspended by rubber bands, surrounded by a support structure. It’s not fancy, but it works.
  • I’m working with Bart Dring, of MakerSlide fame to design the rough approach (basically a screw, direct-driven by a 400 step motor and a 1/16th step driver, like the pololus popular with the RepRap folks).
  • I quit my job to pursue my dream of working in the device design industry, so if you’re feeling particularly generous, please purchase a periodic table – 100% of the proceeds goes towards funding this project.
  • If you want to find out when kits are available (soon, I hope), sign up here.

1 year STM project anniversary

It’s now been a year since I first decided to start building an STM in my spare time – this project has taken me all over the country and I’ve learned a huge amount.

I haven’t had much to talk about lately because:

1) I’ve been focusing on hardware upgrades that improve efficiency and speed in not-immediately-obvious ways (look for the teensy at the botom of the picture, and the shiny new chips near it).

2) Since I’m working on signal path stuff, I had a pause while my new DSO nano (at the top of the photo) shipped from overseas.

3) I’ve been completing other projects so I can refocus on the Z signal path with fewer distractions.

Thanks very much to my friends Mitch Altman, Jordan Bunker, Camo, Steve Finklestein, Ian Spielman, and everyone else who took me seriously enough to help me push this project down the road towards reality in 2010!  Here’s to a productive 2011!


X-Y redesign

In version 0.1, there was a pretty major design flaw: instead of sending -9 to +9v to the scanner head, the design I used actually sent 0 to +5v, this was noticeable in that the scanning head made almost no noise.

I’ve just completed a full redesign of the X-Y signal path and here is video (with oscilloscope proof) of the vastly improved signal output to the scanner head.

So just in time for Thanksgiving, we are a major step closer to the beta!


v.0.1.5: rebuild and bug fixes

I just finished building the version 0.1.5 machine.

Here’s what I’ve been working on during the past month and a half:


  • Fixed EAGLE routing flaws (thanks Dorkbot Chicago for a very timely EAGLE CAD class!)
  • Fixed part specification flaws (it turns out that the digital pots I originally used can’t handle much more than 8V, I was giving them 18V – oops!)
  • Built a completely new test machine from scratch, by hand (not as bad as I originally feared)
  • Started an arduino shield based design (using adafruit’s excellent protoshield as a starting point)
  • Started testing the MCP4912 DAC as a replacement for the dual 4911s, I’m currently using.
  • Switched from arduino duemilanove to freeduino/boarduino for physical design improvements (I’d like to use the UNO, but I’m waiting/hoping for improvements in the USB functionality of that board before switching).
  • Added a fast prototyping area for experiments.


  • Stopped using magnets as fasteners for the scanning head – those were awful.
  • Built a completely new physical support with improved tripd geometry and stability.

Next up:

  • Redesign the X/Y signal pathway to use the full +/- 9V range and be flexible enough to handle +/- 18V via switch and/or gain adjust (I’m only using +/- 5V now, and it’s not flexible at all).
  • Redesign the transimpedance amp pathway to improve signal/noise ratio and gain.
  • Investigate alternative approach mechanism designs.

Reminder: I’ll be showing the ChemHackerSTM version 0.1.5 at the Armand Hammer Museum in LA on Saturday afternoon/evening as part of CRITTER Salon’s Enormous Microscopic Evening.


Pining for the fjords

HELLLLOOOO POLLY!This project is not dead, it’s just pining for the fjords!

Actually, I’ve been up to my neck in:

  • rebuilding the circuit from scratch
  • debugging software
  • debugging hardware
  • redesigning circuitry

This is all stuff that is slow and relatively unglamorous.

I’ve been working frantically because I’ll be in LA next weekend showing the microscope at the Enormous Microscopic Evening at the Armand Hammer Museum in UCLA on November  6th at 4pm, and I’d really like to have version 0.2 ready for the exhibit.

I’ve learned a lot in the past month – notably that I had made a few poor design assumptions (now thankfully corrected).

Many thanks to everyone for being patient, everyone who has helped me with debugging and redesign, and to CRITTER salon for inviting me to the Enormous Microscopic Evening!


ChemHackerSTM 0.1 Schematics and Source Released w/GPL3

With a lot of help, I’ve hit the 0.1 milestone (proof of concept), so it’s time to release version 0.1 of the ChemHackerSTM designs and source code.  As the version number indicates, this is a proof of concept device — if you follow these plans, you’ll get an STM that sort-of works – no promises.

All designs and source code in version 0.1 is hereby released under GPL 3.

The physical microscope is built and works.  It’s still fiddly – I have several design improvements in mind.

The microscope’s electronics work, and will probably not change only moderately between now and version 1.

Video and source code after the jump. Read the rest of this entry »


How I etch STM tips

If you’ve been following the chemhacker twitter feed, you’ll know that I promised video of the etching I accomplished last weekend.

The video does a much better job of explaining the process than my words can:

A few notes: I made a few mistakes on the narration (it was late!):

1. The drop of “water” suspended in that steel plate is actually 2 molar sodium hydroxide (yikes)

2. Yes, those resistors are clearly in parallel, not series (gimme a break, I was tired)


Laser testing: movement!

I just completed a new (much better) scanning head in preparation for final build and testing, but how do you know if the head is actually moving back and forth?

The answer I came up with is to use reflected laser light to amplify the movement of the scanning head.

To test the new head, I mounted a small mirror (actually a sequin, they’re lighter) in the needle mounting point, shined (shone?) a laser at the mirror to see if I could see movement in the reflected laser point as the scanning head moves back and forth.  What I saw was a little movement, but the laser reflection was so diffuse and the movement was so much smaller than the laser reflection that the movement didn’t show well on the video I shot, so you’re going to have to put up with still photos until I acquire better mirrors and/or a more focused laser.

Laser and sequin

Diffuse, reflected laser light