Difference between revisions of "Team:UMaryland/Design"

<p> The PCR machine is a quintessential component of any biological laboratory that needs to amplify or extend fragments of DNA for subsequent experiments. This tool is especially relevant to iGEM and SynBio labs who pave the way to vaster applications of genetic engineering.

Although the process of PCR, the necessary hardware needed to do it is relatively simple. While different templates, primers, and polymerases can be used, a thermocycler capable of maintaining temperatures between 4 and 95 degrees is absolutely required. Current thermocyclers cost thousands of dollars, which is often prohibitively expensive for a DIY Bio effort. Making the device cheaper would give more people accessibility to this valuable lab tool, enabling breakthrough research in more places around the globe.

<p>After significant soldering and reworking the internal safety measures inside the hairdryer, we were able to wire the system so that we could turn the heat on and off while running the fan continuously. Using tape, we secured a sheet of aluminium foil to the top of the heating unit of the hairdryer. The outer casing of the hairdryer had been removed. We placed a heat sensor inside the tin to measure the temperature of the air inside the machine.  By wiring the heat sensor to the Arduino, we were able to receive input/feedback from the sensor and adjust the heating of the device to maintain our desired setpoints and produce proper thermocycling.

<p>At this point, we tried to perform our first PCR reaction. Unfortunately, we soon found that we had melted our tube. We learned that the machine had difficulty with evenly distributing the heat. To better distribute the heat, we removed our tinfoil lid and replaced it with with a cut soda can. This can was designed with evenly spaced holes enabling for better heat distribution. Although we did not and still have not modeled the heat transfer of between the can's surface and the convection heating generated by the hair dryer, we were able to experimentally conclude that the heat distribution was more even across the can than the tin foil.

 

<p>The working internals of our PCR machine are comprised of hairdryer elements. With the exception of the hairdryers outer housing, the thermal fuse and bimetallic circuit breaker all other working components remain intact. The thermal fuse and bimetallic circuit breaker were shorted using copper wire in order to reach temperatures up to 95 within our machine. The outer plastic housing of the hairdryer was also removed to enable our machine to stand upright and fit PCR tubes. The hairdryers heating mechanism which utilizes a bank of nichrome wires and fan that distributes the heat remained untouched.

  The relays convert the low wattage outputs of the Arduino into a high wattage output needed to power the hairdryer. The relays are switches that can be triggered by the milliwatt output of the Arduino and can handle the 1.8 kilowatt power of the hairdryer.  

<b>Closing the loop.</b>With both the temperature sensor and the relays we are able to provide the micro-controller with the ability to regulate and cycle the machine at various temperatures. To allow for tight temperature regulation within the machine a proportional integral derivative control scheme was adopted. This scheme enabled the controller to take temperature readings and calculate rate at which the temperature is increasing, the constant error of the machine found through the integral term, and the proportional error which compares current temperature to a set point. The way our code is designed and implemented utilizes three setpoints, 95,70, and 50 degrees C, all of these are variable and able to be adjusted but for convince we will define the three with these set of temperature values. A any given time only one of these setpoints is active, and the PID control scheme regulates temperature at that specific value. Since the machine needs to cycle and hit at least 3 different temperatures our code also logs time after each setpoint is hit, thus allowing us to define a time interval after which the setpoint is altered. What this means is that if we define the first setpoint to be 95 degrees C that our code will execute and tell the machine to heat to 95 and once that temperature is reached it will trigger a timing function which after a defined period will reset the setpoint to 50 degrees which will then force the machine to cool down to the new setpoint.                   

<img src="https://static.igem.org/mediawiki/2015/d/d5/IGEMCYCDATAGRAPH.png" style="width:800px;height:400px;">

<img src="https://static.igem.org/mediawiki/2015/e/e8/IGEMUMDPCR.png" style="width:450px;height:450px;float:left;">

<p> We have had one successful amplification with our machine; however, we still struggle to replicate these results with an updated housing design (essentially, a new soda can with appropriately sized holes). Our trials still suggest that our temperature sensor and the liquid reaction housed within the tube are not at the same temperature, with a discrepancy of over 10 degrees Celsius. We are currently working of milling a block of aluminum with better and more consistent heat transfer properties, and modeling the heat transfer within the can. Our hope is that modeling the heat transfer will facilitate better control of temperature within the device.