Hardware Objectives

We designed and created two types of hardware: one to support the wet project, and the other to be specific to our project by adding additional functions to it. The former was designed to tune the system by measuring multiple series in a wet experiment to determine the optimal incubation time and light intensity, and was made using only commercially available products to make it inexpensive and easy for anyone to reproduce. The latter is a specialized system for "security," which is one of the key objectives of Optopass, and was constructed to be able to detect the destruction of hardware and to detect whether the final output is produced or not.

Device Breakdown

Wet Supporting Hardware

We designed and built hardware that can simultaneously run three incubators, each capable of producing a single color of light at a set intensity and time interval, completely independently and in parallel. Both the microcontroller and the LEDs in the incubators are powered by an AC outlet, and the size of the incubators, excluding the power supply unit, is 15 cm^3 cubic, allowing them to be placed directly inside an incubator for shaking and culturing. Schematics, workflow, and photos of the actual device are below. The source code is available at the following link.

Main hardware "Optocoder".

We designed the hardware "Optocoder" to protect the useful microorganisms’ strains, mainly from the perspective of security protection of Optopass. The main functions we intended to introduce are shown below.

• Independently shines four colors of light at set times and intensities
• Measure absorbance at 590 nm light and calculate OD
• Pre-cultured test tubes can be inserted and cultured as is
• Detects hardware breakdown and shines light on the yeast inside to activate the wrong circuit and stop the normal synthesis
• Adjust the temperature of liquid medium to a pre-set constant
• Displays the status of the synthesis in progress and the production of the final product.

The functions in the design were determined by referring to the following human practices in addition to those necessary to break the encryption and to perform the culture itself.

ASTEC Co., Ltd. (Technology)
Kaneka Corporation

Since our yeast is designed to be inactivated by exposure to light if it is taken out of the device before finishing shining the light in the correct order. In order to culture and propagate yeast, it must be transferred to a larger device for production after you finish shining the light. Therefore, the amount of yeast needed for the main pre-locking device is not so large, and it should be about the same size as a test tube.

Now function a-d above were drawn up in the design, and for e and f, we are still considering how to design it.

Components and Technology

• Components
  • Microcontroller Development Kit 　"ESP32" [ESP32-DevkitC]
    • Very inexpensive and has a wifi/bluetooth module, one-chip microcontroller, flash memory, and various interfaces such as SPI, UART, I2C, PWM, GPIO, and AD converters
  • Power Supply Module (Included in ELEGOO uno super starter kit)
    • A total of six incubators and two microcontrollers were stably powered in the test device.
  • Slide Switch [SS-12D00G3]
  • LEDs
    • Red: 3mm Round Red LED [OSR7CA3131A] peak: 660 nm
    • Blue: T4.4 Midpower LED Blue [LP-T4.4CDSB] peak: 455-460 nm
    • Green: 3mm Round Pure Green LED [OSG5TA3Z74A] peak: 525 nm
    • Far Red: Tops 3 Power Red LED [OSR9XAT3C1E] peak: 730 nm
    • Yellow: 3mm Round Yellow LED [OSY5JA3E34B] peak: 590 nm
  • Phototransistor [NJL7502R] peak: 590 nm
  • Resisters
  • Prototyping Board (used only in Wet-supporting device)
  • Wires
• Technology: learned through HP to iGEM UPenn [link]
  • Pulse Width Modulation (PWM)
    • Pulse-width modulation (PWM) is a technique for lowering the average power produced by an electrical signal by essentially breaking an electrical signal up into discrete pieces. Rapidly flicking the switch between supply and load on and off, the average value of voltage (and current) provided to the load is regulated. The resulting signal will consist of a train of square-wavelike pulses. That is, the wave will either be high or low at any given time.
    • Both Amplitude modulation, which changes the amplitude (signal strength) of the wave in proportion to power you want, and PWM can regulate the brightness of LED, but PWM enables easier adjust of brightness voltage control, and regarding the ESP32 microcontroller we used, the number of pins that can do PWM control is greater than the number of pins that can analog output. We searched for a paper on that issue and confirmed that PWM control can provide the same stimulus as amplitude control in regard to optogenetics .
  • Multiplexer
    • A circuit element that selects and outputs one of several signals by means of a selection signal.
    • By using it, the microcontroller will require only n outputs and 1 input to handle $2^n$ inputs. This greatly reduces the number of pins used, allowing a single board to handle a larger number of inputs.
    • This will be necessary when you want to handle more colors of light, or when you want to be able to control multiple series simultaneously for application to optogenetics in general.

Future Prospect

As mentioned above, the design of "Optocoder" is not yet complete (as of October 12), and the actual full-function device is still in the design stage, so it needs to be tuned after completion. In addition, it would be easier to use if the system has a function that allows automatic substitution to withstand long-term storage and a function that allows purification and retrieval of biosynthesized products as samples from the hardware.