Difference between revisions of "Spring 2012: Ajoke Jumoke Williams"

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[[Category:Spring 2012]]
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[[Category:20.345]]
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[[Category:20.345 Projects]]
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<h2> Statement of Interest</h2>
 
[[File:Rafikki.jpg|200px|thumb|left|My role model]]
 
[[File:Rafikki.jpg|200px|thumb|left|My role model]]
  
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<h2> Lab 1: Optical Trapping: UI and Instrument Control</h2>
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<h2> Journal Entries </h2>
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All journal entries will be written on my [http://jumoke021.wordpress.com/ personal blog] ( from which I have removed all personal blog related entries =D ). All code related to my final project can be found in my public folder.
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[[http://mit.edu/joke021/public joke021]] and will remain there until May 23 ( after which I will transfer them to the course share).
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<h2> Projects </h2>
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[[Williams: Optical Trapping Lab 1]]<br/>
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[[Williams: PSF and Deconvolution Lab 2]]
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<h2> Final Project </h2>
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[[A.Williams: Objectives and Literature Review]]<br/>
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[[Final Project Proposal Williams]] <br/>
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[[Spring 2012: Williams Key Factors Table]]<br/>
  
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<h4> Diagram of Electronic Control System </h4>
 
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'''''Instruments/Code'''''
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{{Template:20.345 bottom}}
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Instrument Details?
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Matlab : programming language <br/>
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DAQ – <br/>
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Piezoelectric Stages - <br/>
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Bead size : 0.97 um beads used <br/>
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Lasers wavelength `< 1um <br/>
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<h4> Goals: What we set out to accomplish </h4>
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We set out to add functionality to the trap control software, specifically we wanted to automate centering of the DNA-tethered bead using a centering algorithm which we would write in MATLAB. To center the DNA-tethered bead we would need to learn how to talk to different electronics using DAQ and the daqtoolbox in MATLAB, how to test a code which is supposed to provide specific functionality, and a bit about the gui in MATLAB.
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After writing the code, our goals expanded to include writing code to simulate a typical optical trap experiment which would be used to measure the persistence length and the contour length of DNA. <br/>
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<p style="font-family: helvetica; font-size:9pt">
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<h4> How we accomplished the goal(s) </h4>
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<math> F = \frac{k_{B}}{l_{p}}[(\frac{1}{4}(1 - \frac{x}{l_{c}})^{-2} - \frac{1}{4} +\frac{x}{l_{c}}]</math><br/>
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where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length.
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<h4> Project Steps </h4>
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1. Understanding the OTKB code and figuring out how to use the variables that were already defined in OTKB.m to write our code, for ease of integration.<br/>
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2. Writing a skeleton for the data acquisition and then the subsequent update of piezoelectric stage position. <br\>
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3. Determining the relationship between the output piezoelectric voltage and the feedback voltage fed into the piezoelectric motor so that the stage can be centered accordingly.<br/>
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4. Designing a centering algorithm <br/>
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5. Proof of concept - Simulating data and testing results.<br/>
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6. Testing with real DNA-tethers.<br/>
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<h4> Results of Project Steps 1-3 </h4>
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Code
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<a href="http://joke021.scripts.mit.edu/findCenter.html">Centering Algorithm</a>
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<h4> Results of Project Steps 4 </h4>
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<h4> Results of Project Steps 5 </h4>
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Latest revision as of 03:23, 20 May 2012

20.345: Bioinstrumentation Project Lab

Statement of Interest

My role model

Hey, I'm Ajoke(not pronounced -a-joke) Williams and I'm a senior in Biology. I took 20.309 my sophomore year and it was a frightening experience;mostly because the class was really hard for me. Nevertheless the material was awesome. Because of 20.309 I received my first exposure to optics and matlab. Although 20.309 only touched on geometric optics I found thinking about light and its propagation through space and matter exciting. Fast forward to my senior fall year and I found myself taking a Modern Optics class and working in a UROP where I mostly code in matlab, which is pretty ironic since geometric optics was not my friend my sophomore year and I have never before considered myself a "programmer". My expectations for this class are to learn more about optics and how optical components are interfaced with electrical and digital components to make robust biological measurement/imaging systems, to improve my programming skills and learn how to build a PCB board. Right now I think I'm leaning towards working on the STORM imaging method for a final project.


Journal Entries

All journal entries will be written on my personal blog ( from which I have removed all personal blog related entries =D ). All code related to my final project can be found in my public folder. [joke021] and will remain there until May 23 ( after which I will transfer them to the course share).

Projects

Williams: Optical Trapping Lab 1
Williams: PSF and Deconvolution Lab 2

Final Project

A.Williams: Objectives and Literature Review
Final Project Proposal Williams
Spring 2012: Williams Key Factors Table


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