Difference between revisions of "Team:UMaryland/Design"

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<p style="font-size:64px"><b>UMD DIY PCR</b></style>

<p style="text-align:center;font-size:24;"><i> How we created a dual purpose PCR machine and incubator out of a hair dryer.</i></p>

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<p style = "font-size:18px;">Construction Hazard. Jumping hairdryer safety measures will cause rapid heating of the machine, without proper control the machine may cause fires. Proceed with caution. </p>

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<p>Our initial prototype for a DIY PCR machine was modeled in the fashion of most readily available commercial machines, relying on on two Peltier units stacked on top of each other to heat a customized aluminum block in which PCR tubes would sit. In order for the system to be informed by accurate feedback on temperature fluctuations, we embedded a temperature sensor in the aluminum block. The sensor reported the temperature to an Arduino UNO, which responded by regulating the energy flow to the Peltier units, thereby controlling the temperature of the block and tubes.

 

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.

Another consequence of expensive conventional thermocycling is the financial difficulty of bringing these machines into the classroom. PCR is an extremely important topic in biotechnology, but it is typically also one that requires one to "see it to believe it." However, schools often cannot afford to purchase thermocyclers due to their high cost. By manufacturing a cheap, DIY thermocycler that can be assembled at a low cost, we can help bring this technology into schools that would otherwise be unable to afford it.

<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Electronics</b>

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<b>Closing the loop.</b> With the combination of the temperature sensor and the relays, we imbued the micro-controller with the ability to regulate and cycle the machine at various temperatures. To better facilitate tight cycling control, a proportional integral derivative control scheme was adopted. This scheme enabled the controller calculate the rate at which the temperature is increasing while also determining the constant error of the machine (derived from the integral term) and the proportional error (which compares the current temperature to a set point). Our code utilizes three setpoints, 95,70, and 50 degrees C, all of which are variable and may be adjusted depending on the reaction set up. At 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 the time at which each setpoint is hit, thus allowing us to define a time interval after which the setpoint is altered. The net result is that if we define the first setpoint to be 95 degrees C, our code will execute and tell the machine to heat to 95; once that temperature is reached, it will trigger a timing function that after a defined period will reset the setpoint to 50 degrees, forcing 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 style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>Problems and Current issues </b>

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<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.    

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<p style="text-align:center;font-size:32px;font-family: Tahoma, Geneva, sans-serif;"><b>CODE</b></p>

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<font color="#434f54">//The PID functions by adjusting a certain output in order to &nbsp;</font>

<font color="#434f54">// minimize the error between two values, which are the setpoint </font>

<font color="#434f54">// and the input.</font>

<font color="#434f54">// The PID function itself creates a PID controller and takes </font>

<font color="#434f54">// five parameters:</font>

<font color="#434f54">// Input: The value that needs to be controlled</font>

<font color="#434f54">// Output: The value that the PID will adjust</font>

<font color="#434f54">// Setpoint: The value that the input will be maintained at</font>

<font color="#434f54">// Kp,Ki,KD: Parameters that will affect how the output is adjusted</font>

<font color="#434f54">// Direct: Defines which direction the output will proceed given an error</font>

  &nbsp;&nbsp;&nbsp;<font color="#434f54">//The following code is only implemented once as the first cycle of the PCR</font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// This allows for the user to set conditions which may be different from the subsequent </font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// cycles. The code, however, works in much the same way as the other cycles</font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// at the most basic level. It divides each cycle into subcycles: activation, pcr and extension</font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// and enters each step based on stepnow(which denotes how many subcyles the program has entered) divisiblity by 3. </font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// The remainder for activation will always be 1, </font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">// the remainder for pcr will be 2 and the remainder for extension will be 3</font>

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  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">//If the pcr has maintained the setpoint for the desired amount </font>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">//of time, it will enter this loop and begin cooling</font>

  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">//checks if the machine has maintained the temperature for </font>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">//the desired amount of time, and begins the next step</font>

  &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">//checks if the machine has maintained the temperature </font>

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<font color="#434f54">// for the desired amount of time, and begins the next step</font>

 

<font color="#434f54">//Begins the intermediate steps which work in an identical manner to the startup cycle </font>

<font color="#434f54">//and may differ only in the alloted temperatures and times for each subcycle</font>

 

  &nbsp;<font color="#434f54">// Begins the last step, which again works in a similar fashion </font>

&nbsp;<font color="#434f54">// to the other steps, but may differ in the final extension temperature</font>

&nbsp;&nbsp;

  &nbsp;

&nbsp;&nbsp;<font color="#434f54">// Once the last step has been completed, determined by </font>

&nbsp;&nbsp;<font color="#434f54">// stepnow being greater than cyclenum+2,the code will tell the </font>

&nbsp;&nbsp;<font color="#434f54">// pcr to hold at 4 C. It will continue looping at this step indefinitely</font>

&nbsp;&nbsp;<font color="#434f54">// because the conditions will no longer satisfy any of the other if statement</font>

&nbsp;&nbsp;

  &nbsp;&nbsp;&nbsp;<font color="#434f54">//Once the pcr has reached 37 C, the pcr will </font>

&nbsp;&nbsp;&nbsp;<font color="#434f54">//print out that the pcr has shutt off</font>

  <font color="#434f54">// if the pcr machine's temperature reaches 97, cooling will </font>

<font color="#434f54">// &nbsp;&nbsp;automatically be initiated and a death message will be displayed</font>

<font color="#434f54">// these two statements work on the maintaining the temperature, by </font>

<font color="#434f54">// controlling heating and cooling when there is overshoot or undershoot </font>

<font color="#434f54">// in the temperature</font>