Difference between revisions of "Spring 2012: Ajoke Jumoke Williams"
| Line 15: | Line 15: | ||
C.<br/> | C.<br/> | ||
D.<br/> | D.<br/> | ||
| + | |||
| + | '''''Instruments/Code''''' | ||
| + | Instrument Details? | ||
| + | Matlab : programming language <br/> | ||
| + | DAQ – <br/> | ||
| + | Piezoelectric Stages - <br/> | ||
| + | Bead size : 0.97 um beads used <br/> | ||
| + | Lasers wavelength `< 1um <br/> | ||
| + | |||
<h4> Goals: What we set out to accomplish </h4> | <h4> Goals: What we set out to accomplish </h4> | ||
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<p style="font-family: helvetica; font-size:9pt"> | <p style="font-family: helvetica; font-size:9pt"> | ||
| − | <h4> How we accomplished the goal(s) < | + | <h4> How we accomplished the goal(s) </h4> |
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where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length. | where k_{B} is the Boltzmann constant, l_{c} is the contour length and l_{p} is the persistence length. | ||
| − | <h4> Project Steps < | + | <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/> | 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\> | 2. Writing a skeleton for the data acquisition and then the subsequent update of piezoelectric stage position. <br\> | ||
| Line 35: | Line 44: | ||
5. Proof of concept - Simulating data and testing results.<br/> | 5. Proof of concept - Simulating data and testing results.<br/> | ||
6. Testing with real DNA-tethers.<br/> | 6. Testing with real DNA-tethers.<br/> | ||
| + | |||
| + | <h4> Results of Project Steps 1-3 </h4> | ||
| + | Code | ||
| + | |||
| + | [[Centering Algorithm:C:/Users/Owner/Documents/MATLAB/Optical Trapping/html/findCenter.html]] | ||
| + | |||
| + | <h4> Results of Project Steps 4 </h4> | ||
| + | |||
| + | <h4> Results of Project Steps 5 </h4> | ||
Revision as of 08:03, 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.
Contents
Lab 1: Optical Trapping: UI and Instrument Control
Diagram of Electronic Control System
A.
B.
C.
D.
Instruments/Code
Instrument Details?
Matlab : programming language
DAQ –
Piezoelectric Stages -
Bead size : 0.97 um beads used
Lasers wavelength `< 1um
Goals: What we set out to accomplish
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.
How we accomplished the goal(s)
$ 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.
Project Steps
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.
Results of Project Steps 1-3
Code
Centering Algorithm:C:/Users/Owner/Documents/MATLAB/Optical Trapping/html/findCenter.html
