Research with STEM Pathways
Summer 2023
For the summer of 2023, STEM Pathways provided me an opportunity to work as a research assistant to a PhD candidate in the Khalil Lab, which is a Boston University affiliated lab which is focused on building biological systems using complex cellular functions to achieve a desired outcome.
A very notable resource used by the lab is the eVOLVER, a modular and automated framework which consists of individually controlled and monitored bioreactors used for automated cell growth and evolution. This played a huge role in my summer research since my mentor's research was primarily focused on improving the throughput capabilities of the eVOLVER and running cell evolution experiments with the modified system. My role in this project was to help with all the necessary hardware changes that are being made to the system. I also worked with the software by creating Python scripts to automate calibration of hardware parts and translate cell culture protocols into computer code.
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Although much of my research was not experiment based, I was able to develop many practical engineering skills, such as learning how to design a PCB from scratch using KiCAD and how to develop my own hardware calibration protocols. I was also able to get some experience with wet-lab work, whcih was a very insightful experience. Overall, this was a very informativew and fun experience and I am very grateful for STEM Pathways and Khalil Labs for giving me this opportunity to gain experience and widen my professional skillset.
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Below are some key highlights from the research I did in Khalil Lab.
Hardware and PCB Design
My research journey started with me using CAD tools such as KiCAD and Onshape to design the necessary PCBs and enclosures needed for the modified eVOLVER. The tiny proportions of the cellular organisms used cell culture experiments meant I had to take painstaking care to ensure that error bounds for the hardware were kept as small as possible.
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The photo to the right shows the 3D enclosure and base I printed for LED testing, with my designed PCB resting between the two parts.
Hardware Calibration
One interesting capability my mentor and I were hoping to make to the eVOLVER was for the enabling of optogenetic experiments. In order to achieve this, I researched and selected various LEDs that could be assimilated onto a board and into the final design.
After the PCBs and enclosures were designed and fabricated and LEDs were soldered onto the boards, the next step was ensuring that these LEDs were properly calibrated to account for any manufacturing inconsistencies. This was a surprisingly tedious process since the scale of light intensity was a lot smaller than I had initially expected, which caused larger error bounds with relatively tiny changes in light intensity between measurements. Nevertheless, I was able to finish testing and calibrating various LEDs, which, with the help of my mentor, allowed me to select appropriate LEDs for cellular experimentation.
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The photo to the left shows one of my initial setups for calibrating the LEDs, which are underneath the black enclosure, using a ThorLabs photodiode and Matlab, along with the eVOLVER motherboard and my printed PCB.
More Research Documentation
Some finalized CAD designs for an enclosure for one of the test PCBs.
Graphs representing measured light intensity during the calibration of the LEDs on each PCB
Calibration in progress; automated with Arduino and Python scripts
Thorlab photodiode and enclosure used for calibrating PCB
PCBs for testing out LEDs
Here are some results and additional images from my research experience, with attached descriptions