Difference between revisions of "Spring 2012: Ajoke Jumoke Williams"
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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. | 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. | ||
</p> | </p> | ||
| + | <br/> | ||
| + | ---------------------------------------------------------------------------------------------------------------- | ||
| + | <h2> Lab 1: Optical Trapping: UI and Instrument Control<h3/> | ||
| − | ---- | + | <h4> Diagram of Electronic Control System <h3/> |
| − | < | + | A.<br/> |
| − | <math>F = k_{B} | + | B.<br/> |
| + | C.<br/> | ||
| + | D.<br/> | ||
| + | |||
| + | <h4> Goals: What we set out to accomplish <h4/> | ||
| + | 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. | ||
| + | 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. | ||
| + | |||
| + | <p style="font-family: helvetica; font-size:9pt"> | ||
| + | <h4> How we accomplished the goal(s) <h4/> | ||
| + | |||
| + | |||
| + | <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/> | ||
| + | |||
| + | where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length. | ||
| + | |||
| + | <h4> Project Steps <h4/> | ||
| + | 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/> | ||
| + | 2. Writing a skeleton for the data acquisition and then the subsequent update of piezoelectric stage position. <br\> | ||
| + | 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 | ||
| + | 4. Designing a centering algorithm | ||
| + | 5. Proof of concept - Simulating data and testing results | ||
| + | 6. Testing with real DNA-tethers. | ||
Revision as of 07:51, 28 February 2012
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.
Lab 1: Optical Trapping: UI and Instrument Control<h3/>
Diagram of Electronic Control System <h3/>
A.
B.
C.
D.
<h4> Goals: What we set out to accomplish <h4/>
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.
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.
<h4> How we accomplished the goal(s) <h4/>
$ F = \frac{k_{B}}{l_{p}}[(\frac{1}{4}(1 - \frac{x}{l_{c}})^{-2} - \frac{1}{4} +\frac{x}{l_{c}}] $
where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length.
<h4> Project Steps <h4/>
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.
2. Writing a skeleton for the data acquisition and then the subsequent update of piezoelectric stage position. <br\>
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
4. Designing a centering algorithm
5. Proof of concept - Simulating data and testing results
6. Testing with real DNA-tethers.
B.
C.
D.
<h4> Goals: What we set out to accomplish <h4/> 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. 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.
where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length. <h4> Project Steps <h4/> 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.
2. Writing a skeleton for the data acquisition and then the subsequent update of piezoelectric stage position. <br\> 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 4. Designing a centering algorithm 5. Proof of concept - Simulating data and testing results 6. Testing with real DNA-tethers.
