Difference between revisions of "Arsenic Prototype 4.0"

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* 12x M3 nuts
* 12x M3 nuts
* 10x M3 washers
* 10x M3 washers
==Before Starting==
[http://mightyohm.com/files/soldercomic/FullSolderComic_EN.pdf Soldering is easy!] Learn it!

Revision as of 15:02, 19 January 2016


The Arsenic prototype v4.0 is the Winter School 2016 kit version of prototype 3.0.

The basis of the prototype remains the same - the bioreporter, a GMO bacteria expressing eGFP (Green Fluorescent Protein) is incubated with a water sample, where the fluorescence is detected optically and can be quantified in order to measure the concentration of Arsenic in the water

  • A vial containing the water sample we want to test is positioned on a socket through which a fluorescent excitation LED (blue 488nm for eGFP) passes.
  • GFP absorbs this blue light (λ=475 nm) and emits green light (λ=504 nm) which is detected by a photosensor on which the light is concentrated with the help of two lenses that avoid loss of intensity
  • A long-pass filter allow only the signal eGFP fluorescence to reach the photosensor

Moreover, a red LED was added to measure the transmittance, which can be converted into turbidity. The measurement of turbidity will allow us to normalize our results.

  • A red LED is placed in-line with the photosensor

We use an arduino to take the measurements, and we have a liquid crystal display (LCD) to read out the numbers.
With these measures, compared against a standard curve of water containing known arsenic concentrations, one can determine the concentration of arsenic in the sample and so know if the water is drinkable or not.

In summary, the most current version consists of:

   lasercut chassis
   blue LED for eGFP fluorescence excitation at 90 degrees from detector
   red LED for transmittance measurements in line with detector
   vial holder matching the vial approved by the Swiss authorities
   light to frequency detector
   a filter to block excitation light
   LCD screen read out
   based on the arduino


  • Soldering iron
  • Tin
  • Knippers
  • Plier
  • Screwdriver phillips #1
  • Vice (for crimping the ribbon cable)


  • Don't burn the wires on the table with the soldering iron
  • Mind your fingers
  • When knipping the legs of the components, hold the loose end so that it doesn't fly into someone's eye.
  • Apply common sense


You can find the bill of materials here:

For the full BOM including reference numbers see this sheet.

LCD Shield

  • 1x LCD 8x2 HDM08216L-3-L30S
  • 1x resistor 1K (R1)
  • 1x Trimpot 10K
  • 2x Tactile switch 17mm (S1, S2)
  • 1x Potentiometer
  • 1x Micromatch connector 10 pin SMD female 8-338069-0
  • 1x 1x40 pin header straight long (17mm)
  • 1x 2x8 pin header straight

LED Driver board

  • 1x LED 485nm (blue) SMD XPEBBL-L1-0000-00Z01
  • 1x P-channel MOSFET TO-220
  • 1x P-channel MOSFET TO-92
  • 1x Micromatch connector 10 pin SMD female 8-338069-0
  • 1x Resistor 5 ohm 3W
  • 1x Resistor 150 Ohms 1/4W
  • 1x 1x3 pin header 90 degree bent
  • 1x 1x2 pin header 90 degree bent

Optical density (red LED)

  • 1x red LED 5mm
  • 1x 1x2 pin header straight

Light sensor

  • 1x Light To Frequency Converter – TSL235R
  • 1x 1x3 pin header straight


  • 2x Plastic Biconvex Lenses LPP1009
  • 1x Plastic long pass filter 510FAP5050


  • 1x Arduino UNO Rev 3
  • 1x 2.1mm DC barrel jack
  • 1x 9V battery snap and contact connector
  • 5x Jumper cables female-to-female 10 cm
  • 1x 9V Battery
  • 20cm Ribbon cables 1.27 10 wires
  • 2x Micromatch connector 10 pin male 8-215083-0


  • 12x M3 screws 10mm
  • 12x M3 nuts
  • 10x M3 washers

Before Starting

Soldering is easy! Learn it!

Step by Step Buildling

Laser Cutting the Inner Scaffold Pieces

at chez hackuarium neighboring @make space of univercité - laser cutter model: Keyland KQG-1060 120W CO2 laser cutter

Cutting Parameters for Material: HDF (MDF)
mode speed power scan mode interval
Groove LED (fluo) scan 50 (100) 35 x_unilat 0.1
3mm board cut 20 100
Text and Logo scan 250 (100) 25 x_unilat 0.3
Groove Lens scan 50 12 x_unilat 0.1
2mm board cut 35 100

With these parameters, the 3mm thickness pieces take 5 min to cut, and the 2mm thickness pieces take min.


Assembling the Electronics

There are four PCBs for:

  1. Blue LED (for the eGFP excitation)
  2. LCD screen
  3. Red LED (for the transmittance)
  4. Light to frequency meter (to detect the light)

TIP: if this is your first time soldering, we suggest to start with the LCD screen
Each of the PCBs except the LCD screen PCB are fixed onto the lasercut fiber boards using M3 screws.

Soldering and Mounting

Blue LED

Blue LED PCB and parts.png

Soldering the pieces:

Blue LED 10.jpg
10. ready for mounting

Now mounting onto the particle board:

LCD screen

This LCD screen / arduino shield will connect to the blue LED PCB with a ribbon cable
LCD PCB and parts.png

Soldering the pieces:

LCD 09.jpg
9. done soldering this board, onto the next


Red LED PCB and parts.png

light to frequency meter

LFD PCB and parts.png

Battery connector

Lens assembly

  1. Place the two sides next to each other. They should be both marked with the *same* letter (A/A or B/B).
  2. Place the lens in the groove on one side.
  3. Place the second side on top, with letters towards the inside for both sides.
  4. Fix together with 2 screws and 2 bolts.

Final Assembly

Finally, the Red LED and light to frequency meter will be plugged into the Blue LED board with connectors.
Final assembly 1.JPG

Then the LCD screen is plugged into the Blue LED board with a ribbon cable.
Final assembly 2.JPG

The LCD screen board is ready to be mounted on the arduino.

We are now ready to test it out.

Testing the Electronics

Uploading the arduino code

If you have not done so already, download the arduino open software.
The firmware is in our github repository for the FluoMeter.

Reading the measurements

First test the firmware and the hardware without sample.

  • When you push the start button, does the blue LED go on?
  • Do you see the measurement on the LCD screen?
  • Do you then see the red LED go on?

Then try it with sample with fluorescence

  • Do you see changes in the measurement?

Now we are ready for the actual bacterial samples.

Transmittance and absorbance

What we actually measure with the red LEDis the transmittance - how much of the red LED light goes through the sample and reaches the other side.
Absorbance (optical density) is then calculated.
A = - log10 T
where T = (Red LED captured by the light to frequency meter with sample / with buffers (no bacteria))

Making the Outer Housing

What we have built so far leaves the samples exposed to ambient light.
So we need to make outer housing that can mount the LCD screen, house the battery, enclose the scaffold inside, and have easy access to put the samples in and out while keeping the light and optics dark.

Links other References