Here are the slides I made up for the static display of the STM at OSS this weekend:
Here’s the latest:
I’m working to get the STM working as fast as possible, but it’s not 100% – I’ve got basic functionality tested and working, but no images yet – I’m hoping to have images within a month or so.
Current work:
- A new scanning head
- Complete the mechanical supports and approach mechanism (current state photo of the mechanicals, above)
- Programming the arduino and the python script that gathers the image data
- Final electronics testing
- Getting everything prepared for air flight (expect a post in the near future on preparing electronics for TSA inspection)
Here is a video of my latest tests – the digital side talking to the analog side and driving the scanning head (faintly):
If that’s not enough for you, here is some good background info to read about STMs:
Introduction to Scanning Probe Microscopy
Wikipedia Scanning Tunneling Microscope (STM) article
And you may be interested in the ChemHacker youtube channel. It’s a bit sparse now, but keep an eye out for updates as this project proceeds.
A few very quick updates:
- In case you missed the youtube video, the STM is now electronics hardware complete – well, I have a very small change coming in the mail (a two-in-one DAC chip) to replace the two separate DACs. This may improve the code efficiency slightly, but I’m going to wait a while before I implement the change.
- I’m working on the programming right now, and not sleeping much while I do because (see below)…
- I have been invited to display the STM at the Open Science Summit in Berkeley at the end of the month. If you’re there, stop by the Berkeley International House and say hello – I’ll be at the hardware tables.
…I have so much work to do between now and then…
video after the jump:
I’ve been wanting to upgrade the storage in ChemHacker central for a while – but I haven’t found a good, sturdy storage unit that is large, can handle holding a lot of weight, and is chemically resistant.
Until now.
I found this old Faygo-labeled shelving unit in a nearby alley:
After a (lot of) cleaning, here it is holding tools and a wide assortment of chemicals in the underground ChemHacker Lab:
Now that I have Faygo-themed shelving, perhaps I should look into teaching Juggalos some fucking Science?
As I mentioned earlier, I’m working on programming an arduino interface for the ChemHacker STM.
The arduino currently has to handle the following tasks:
- serial control of the five digital potentiometers (amplifier gain control)
- serial control of the 24 bit DAC (signal input to the microscope)
- analog signal processing from the microscope (via built-in ADC lines)
- serial data to the computer of the scanned data (for image processing)
A future task for the arduino may be:
- automated control of a stepper motor (for sample approach and control)
My road map for programming is as follows:
- establish serial control of the potentiometers
- establish serial control of the DAC
- establish signal into the ADCs
- establish serial data line to computer (and figure out some kind of live image processing system)
- interface with microscope circuit(s)
- establish stable scanning
As always, things take more time than you think – I foolishly thought I could get steps 1 and 2 done in a few weeks. After nearly a month of struggling, I finally have (1) accomplished, and with some help from some excellent electronic engineers, I’m quickly closing on (2).
Many many thanks to all the people who publish their SPI code on various Arduino boards, without your examples, I never would have gotten this far…
Here’s what I’ve learned from weeks of banging my head into walls: the entire SPI setup must be used for the arduino’s SPI to activate – that includes declaring pins you don’t intend to use (like the MISO and the SLAVESELECT)
A quick update on where the ChemHacker STM project stands: I’ve completed assembling the electronic components and I’m moving to programming the arduino (well, that’s actually a sanguino in the photo, but I’m moving the whole project to arduino duemilanove based hardware).
What you see in the photo is the red sanguino microcontroller, the green main amplifier board, the tan tunneling current amplifier, and on the breadboard are the digital pots and 24bit DAC I’m using for controlling the microscope. At the top right is the microscope nanopositioning head.
The end result of this project will be an open source STM with modern electronic controls.
My friend Hank K. is working on a safety test for Pumping Station: One‘s new safety system and asked me to contribute a few fun chemistry-related questions. Here is what I came up with (you’ll find the answers after the break):
Questions:
(1) What is the result of mixing concentrated nitric and hydrochloric acids in a 1:3 ratio?
a) the active ingredients in a can of Crunk(TM) energy drink
b) aqua regia
c) nitro glycerine
d) piranha solution
e) piss off, test writer!
**************
(2) A mixture of ice, water, sodium chloride, and ammonium chloride results in what temperature reference?
a) 0 Celsius
b) 273 Kelvin
c) 0 Fahrenheit
d) 32 Kelvin
e) 0 Rankine
**************
(3) You are in a bathroom, and are in process of cleaning it. You have just cleaned the floor, toilet, and bath tub with Soft Scrub(TM) cleaner with the power of Chlorox(TM). You reach for the bottle of Windex(TM) cleaner (now with the power of ammonia!) and proceed to spray it liberally onto the windows, tiles, and mirrors.
Your vision begins to swim.
As your head crashes towards the concrete countertop, towards a severe concussion, likely brain damage due to fume exposure, and your possible death, what is the thought that should be flashing through your mind?
a) holy crap, I’m about to die!
b) d’oh! I’m not supposed to mix bleach and ammonia!
c) am I likely to be eaten by a grue?
d) who cares – I’m about to die on a bathroom floor, how crappy is that?
While we’re taking a short break (tl;dr there’s a lot of stuff cooking behind the scenes – I’ll talk about it shortly), my news feeds are going berserk with chemistry news here’s the highlights:
BP is dumping chemicals in the gulf designed to break up the oil spill, but there are questions about efficacy and how carefully they have been tested. Does this mean that the Gulf of Mexico is now the world’s largest beaker?
Meanwhile, research is showing that chemicals in bananas may be effective against HIV? Take all medical research with a grain of salt, kids.
And on the battlefield, chemistry is making MREs tastier. I suppose that since MREs are a stew of chemistry already, adding more can’t hurt.
I’ve spent a little time thinking about how the lessons of the open source software movement can influence and assist chemical research, but Dr. Matthew Todd is not only cleverer than me, but has spent much more time on the problem – here is what he came up with (presented earlier this month at a Google Tech Talk).
Here are links to a few of the projects he mentions in the talk:
A while back, I decided that I wanted to make all the amazing things in chemistry I never got to learn in school. First on this list is making a ferrofluid.
A ferrofluid is a liquid with the mesmerizing ability to respond to magnetic fields. Descriptions do no justice – videos and images are the best explanation:
[video and more details after the jump] Read the rest of this entry »