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

9/23/2011
CHEN chapter 11.1: desirable tunneling amp design: 1V/1nA

9/10/2011
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…

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.

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.

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.

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.

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 openhardwaresummit.org.

UPDATE: fixed the voting link, please go here: http://www.openhardwaresummit.org/scholarship/

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.”

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.

Below is the original post:

Open source hardware saved Campfire #1

I know there are case studies of Open Source Software helping businesses with their day-to-day tasks, but how many case studies are there of Open Source Hardware helping a business solve problems?

Here is my example of how the Open Source Hardware community saved the launch of my company’s first product.

I’ve also included all the theory, technical schematics, and details towards the end.

Here is the video we did for Pumping Station: One and Element 14:

Transmissometer from Pumping Station: One on Vimeo.

How did I get here:

My idea for a campfire scented cologne won the business plan competition at barcamp Chicago 2010, and on May 10, 2011, nearly a year later, I’m ready to launch my product-RuggedScents’ Campfire. Unfortunately, less than four weeks to launch, I discovered a major process flaw: gigantic inconsistencies between the longevity of the fragrance’s smell on the user’s skin from batch to batch-some batches lasted three to four hours, some barely made it past 30 minutes!

<pictures, schematics, and video after the jump>

After some experimenting, I discovered that longevity is directly proportional to concentration of my main ingredient, but I didn’t have a good way of measuring concentration.

Luckily, my main ingredient has a very strong color, so I thought about using transmissivity.

Transmissivity is a measure of the light that passes (is transmitted) through a sample.  This is pretty easily seen visually. In the photo below are samples of the fragrance concentrate in 2.5%, 5%, 7.5%, and 10% concentrations from left to right.

My plan: pass a laser through the sample and measure the amount of light that makes it through the sample with an optical sensor and display the results on some 7-segment LED displays.

This is where the open source community’s love of sharing information rescued me and completely saved my launch timetable:

Using open source hardware and freely available code and tutorials, I was able to interface an optical sensor with an arduino, and send the data to a display of three 7-segment LED units.

To get the device to it’s current finished state took about $40 in parts and about 16 hours of soldering, fabricating, and coding. I was able to create the data I needed to proceed with my product launch in about four days in my spare time.

The alternative to using open source hardware would have been to purchase a UV-Vis spectrometer (in the $3,000 range).

By using Open Source Hardware, not only did I save money and time, I have exactly the device I need – a rugged, portable tool I can use during production, not a sensitive piece of lab equipment that requires tethering to a computer and gives me more information than is I need to continue with my launch.

A little grounding in theory:

Just by looking at these vials you can visually tell that concentration and transmissivity are related, but how are they related? Here is the Beer-Lambert law for absorbance of light in a sample:

• Io = the intensity when I use a vial filled with alcohol only
• I = the intensity when passing through a sample of fragrance in alcohol
• c = concentration
• epsilon is a constant, so we’ll ingore it
• L = distance the light travels through the sample – also a constant (all my samples are in the same kind of sample vial), so we’ll ignore it
• When you actually use the transmissometer, you get data in the form of I, in volts (explained in the electronics section), which on its own is a meaningless value, so I record all the data as the dimensionless %Transmissivity (%T) which is I / Io.

If you rearrange the Beer-Lambert law, you’ll see that %T is proportional to 10^-c.

If you graph %T versus c, you’ll see the following relationship:

(Image from reference 1)

Note: I know the graph says %Transmittance versus Absorbance, but if you look back at Beer-Lambert’s law, Absorbance is directly proportional to Concentration.

The important thing to see here is that when %T is between 30% and 60%, you get a linear behavior.  Below 30%, large changes in c have a nonlinear effect on %T, and above 60%, huge changes in c cause little changes in %T.

Here is a graph of some actual data I gathered (yes, it’s a little sparse). You can see that between 30% and 60%, the relationship between %T and concentration is linear. However, below that region, the relationship between %T and concentration is much less useful.

References:
1. http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/beers1.htm
2. http://en.wikipedia.org/wiki/Beer%E2%80%93Lambert_law
3. http://www.chemguide.co.uk/analysis/uvvisible/beerlambert.html

How I actually made this thing:

Components:

• (1) red laser pointer (5v)
• (1) CdS optical sensor
• (1) 10k ohm resistor
• (3) common ground 7-segment displays
• (7) 220 ohm resistors
• (1) arduino
• rigid foam
• aluminum tape
• aluminum foil
• hot glue + hot glue gun
• lots of wire
• some solder
• heat shrink tubing
• project box for the electronics
• battery holder/batteries
• spst switch (I used a nice red on/off push button)

Tools:

• Soldering iron
• Multimeter
• Various knives for cutting and shaping the foam

Below is a basic schematic of how the transmissometer was wired together – you can see that it is a pretty simple device:

If you’re interested, the arduino code for reading the optocell and displaying to the 7-segment displays is here.

I’m releasing my transmissometer schematic and software code under the Creative Commons 3.0 attribution license.

Thanks to Limor Fried and Adafruit for the extremely useful and detailed photocell tutorial, thanks to the Arduino forum community for 7-segment tips and tricks, and thanks to my friends Steve Finklestein, Ishmael Rufus, Nathan Witt, Jordan Bunker, Dan Dumitrescu, and everyone at Pumping Station: One for helping me.

Here is a blog post with details, schematics, photos, and source code.

Here is a video we shot (with the support of Element 14) to show how the device works:

Transmissometer from Pumping Station: One on Vimeo.