This project is no longer active

Hello and thanks for visiting!

Unfortunately, you’re looking at an archive of projects I worked on and/or completed.  I’m leaving this all up for now for historical purposes, but if you want to see the latest things I’m working on, Chemhacker isn’t the best place any more.

There are a lot of reasons for the change, but the biggest two are:

1) “Chemhacker” doesn’t really describe me.  I work on a lot more things than just chemistry and science, and I found the title to be stifling to blog under.

2) “Chemhacker” kinda came to mean that STM project I stopped working on quite some time ago.  I stopped working on it because STMs are really difficult to do well and I found other problems that interested me more, and so I moved elsewhere.

If you’re interested in seeing the things I work on now, here are places where I’m publishing my projects:

Blog  << primary outlet of things I do

Twitter << side outlet, thoughts, what I’m reading, etc




January 29, 2014 | Posted in: Announcement | Comments Closed

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

Time and advice:

Steve F., Ian S., Lee

image credit


Open Notebook 1

This is an experiment with opening my research notebook to the web.  I’m keeping my notes in an Evernote notebook, but I’m going to post lightly edited (i.e. remove personally identifiable information from people I talk to unless they give me specific permission).

Keep in mind that these are my raw thoughts for the past two months, with no editing for accuracy.  Follow these notes at your own risk.

11/03/2011 (Purchase Notes)
Purchased from Newark ($62.46 + shipping):
* 3 DAC8554 (TSSOP-16 packages)  quad 16 bit DAC
* 3 REF02 (DIP-8 packages) precision 5v reference
Purchased from eCrater user fcpcb ($11.44):
* 5 TSSOP-16 to DIP adapters

10/31/2011 (Denver/Boulder Notes)
met L. M. (physicist) at Solid State Depot hackerspace meeting – he built an STM as part of his PhD work:
* L. M.’s STM had a higher cost (and precision) than the chemhacker STM, but a lot of his designs and thoughts can be adapted to fit a cheaper device. Also, he’s excited by the idea of an open source STM project.
* need more bits on the Z DAC
* * 10 bits gives ~17.59 mV/step which is ~2.81 nm /step (at ~0.16 um/volt) that’s so large that the needle will pass into and out of tunneling in only one step.
* * 16 bits gives ~0.2747 mV/step which is ~43.9 pm/step, small enough that you can control tunneling with more than one step.
* * 16bit DAC notes:
* * * DAC8554 from TI is a 4-channel ultralow glitch DAC
* * * $10-15 each: pricey, but handles all four channels at once, not much more expensive than 4 of the microchip DACs I’m using
* * * SPI interface, unsure if it differs from the microchip SPI standard
* * * TI recommends a REF02 precision 5V voltage reference (~$3-4 each) – probably a good idea to try this out
* * * downside: no DIP package available – surface mount only
* probably need a better/faster micro controller
* * suggest that PID loop be accomplished at about 20MHz
* * suggest the Maple from Leaf Labs
* * * 12 bit ADCs (versus 10 bit for arduino/teensy)!
* * * 47 MHz versus 16MHz for arduino/teensy
* * * the IDE looks almost exactly like the arduino IDE.
* * * I’ve spoken to Leaf Labs folks in the past, they’re a good group of quality-focused engineers/artists.
* * * purchased on 10/30/2011 should arrive in a day or so via USPS
* thoughts on the sample bias voltage
* * since sample needs only ~10 millivolts, it’s probably best to just pass the DAC output through a pair of unity inverting amps (don’t remove the DC bias).
* * then, put the two outputs (positive and negative outputs) to a manual switch so the user can choose a positive or negative sample bias (allows future expansion to negative sample bias)
* * with a 16 bit DAC, it’s pretty easy to select ~10mV (just set DAC to ~4 and leave it there)

10/20/2011 (Nanotech conference notes)
Questions for people who know more about SPM than I:
* Is Gwyddion well-regarded in the microscopy arena?
* How do you make HOPG / graphene? Is it at all easy?
* What is an appropriate sample bias for starting? I saw ~10mV today, but I was going to use ~1-2V, that’s bad.
* Is there a market for STM tip-making machines?
* What is the process for making an AFM tip?

10/19/2011 (prototyping notes)
* added 2.5V and 5V voltage regulators to clean up voltage signals
* fixed clipping problems by lowering the gain resistor from 36k (predicted by the formulae) to 27k (as determined experimentally)
* fixed non-symmetrical behavior by applying correct ground to the 2.5v and 5v regulators (their grounds were floating a little higher than true ground)

10/10/2011 (Purchase Notes)
Purchased from Newark ($43.69)
* +9v, -9v, +5v, +2.5v voltage regulators
* piezo elements
* 0.1uf, 1uf, 0.33uf capacitors
* tunneling op-amps

CHEN chapter 11.1: desirable tunneling amp design: 1V/1nA

Idea: change op amp gains such that the electronics use ground, +5v, +12v, -12v >>same as supplied by ATX power supply
Test: test ATX power supply with oscilloscope to check cleanliness of signal (should be pretty clean, right?)

…actually, can use these power supplies now without changing the gains…


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.

Your support did this!

To everyone who purchased a periodic table to help support this project:

Many, many thanks!  I can’t easily express how grateful I am for your generous support!  I’ve chosen to quit my job to pursue my passion of open source scientific devices, and your support goes directly towards furthering this project.

I just received the first visible result of your help – a shipment of components.  These are mostly op-amps, voltage regulators (silver bags on the left), capacitors, and piezo disks (clear bags on the right).  This shipment will solve several power supply and signal issues – - the +2.5V signal will actually be +2.5V now, significant improvement over the unreliable voltage divider I was using previously.voltage regulators, op-amps, piezo disks, and capacitors


STM Physical Design Basics

I’ve been mulling over a simple physical design for the STM.

My primary design goals are ease of finding parts and ease of assembly.

The support structure is an outer support frame with a heavy inner platform suspended by rubber strips for vibration isolation.

The rough approach of the microscope will have a stepper motor driving the scanning head towards the sample.  I’d like to use gearing to reduce the distance driven per step, and I’ll be using a stepper motor driver capable of providing 16th steps (that’s 0.1125 degrees on a typical 1.8 degrees per step motor).

I’ll probably need help in designing the rough approach – any mechanical engineers out there? I have access to a laser cutter and a 3D printer for making gears.

basic physical design of the STM


Would you like to support the Chemhacker STM project?

Chemhacker periodic tableI’ve been asked this question a few times in the past week – how can someone support the Chemhacker STM project?

Here’s the easiest way: purchase a periodic table! I designed them myself, they are accurate to 5 significant figures and even contain Copernicium, the newest element! You can’t do chemistry without a periodic table.

So if you’re having trouble combating sentient grey goo, you should support the Chemhacker STM project by purchasing a periodic table!

$25 and ship worldwide for free.


Please Vote! Open Hardware Scholarship Applicant!

OSHW logoHello everyone,

I’m delighted to announce that I’m an applicant to the Open Hardware Scholarship. It’s a grant of over $2000 for the completion of an open hardware project.  Without going into boring personal finance details, $2000 will allow me to more rapidly push the Open Source Scanning Tunneling Microscope project to the public beta stage.

The scholarship award will be chosen by votes, so please visit the Open Hardware Scholarship voting page (I’m the fifth one down on the left side of the page) in the next 24 hours  (voting ends September 15th 6pm EST) and vote for the project you feel is most deserving of a grant (hopefully this one).

Here is my 30 second application video (no, it’s not easy explaining this project with only 30 seconds and 500 characters):

Many thanks,

Sacha (Chemhacker)


UPDATE 2: thanks so very much for all the votes everyone! Sadly, microscopes lose to hydroponics. Winners list at

UPDATE: fixed the voting link, please go here:





What would you do with an STM?

When I started this project, I had only one idea for using an STM: looking at nanoparticles.

Since then, I created this sign-up form where people are asked the simple question above.  Here are some of the fantastic answers I received (actual quotes):

  • “I have a project of a small semiconductor fuel cell that I want to experiment with”
  • “A perfect research tool for a homeschooler or small school!”
  • “I am neuroscience student at Keele University (Staffordshire, UK), I will use it for my research.”
  • “Scan for micro-fractures on radio-controlled helicopter and aircraft load bearing components and bearings.”
  • “Look at cancer cells and experiment with magnetic frequencies and cancer cell destruction.”
  • “Hi! I’d like to examine the morphology of bees when subjected to the insecticide imidacloprid.”
  • “I am working as assistant professor in VIT university, Vellore, India. I am interested to do surface probe microscopy (SPM) with an STM.”



STM Version 0.3 electronics on the way

This is just a quick note: I’m currently breadboarding version 0.3 of the STM electronics – Hopefully I’ll have photos and results shortly thereafter.

New features of this version:

  • 100% of John Alexanders’ analog STM design has been replaced with all-digital controls
  • Greatly simplified electronics (but more complicated firmware)
  • Microcontroller manages four channels: X, Y, Z movement, plus sample bias
  • Teensy microcontroller (though the design is pretty microcontroller-agnostic at this point)
  • Firmware tunneling current detection and PID control of Z height

Thanks to Steve F., and Efrain O. for their extremely valuable input to this revision.