# User:Pfitzg

## Contents

## Personal Information

I study Computer Science and Physics as an undergraduate student at Purdue University. I will be a junior in the Fall of 2011. I am working this summer under Dr. Anne Clough on a project to model the kinetics of 99mTc-HMPAO in the lungs of rats.

## Goals and Milestones

**Week 1**

- Become familiar with the project

**Week 2**

- Modify the input function to the model to be a Random Walk Function
- Add subroutines to the MATLAB code
- Add recirculation to the model
- Modify the distribution of transit times
- Complete a first draft of the Materials and Methods section of the final paper
- Forward model should be mostly completed

**Week 3**

- Complete a first version of the new program for the inverse problem
- Complete a first draft of the Introduction section of the paper

**Week 4**

- Complete an updated version of the program for the inverse problem
- Complete a second draft of the Introduction section of the paper

**Week 5**

- Complete a second draft of the Materials and Methods section of the paper with the inverse problem included

**Week 7**

- Conduct simulations of control and hyperoxia data
- Complete a first draft of the Results section of the paper

**Week 8**

- Apply the model to real data
- Complete the Results section of the paper

**Week 9**

- Complete the discussion section of the paper

**Week 10**

- Final edit of the paper
- Presentations

## Progress Log

## Week 1

**Monday, May 30**

- Moved in

**Tuesday, May 31**

- Orientation Day
- Had lunch with mentors
- Paper work

**Wednesday, June 1**

- Discussed project overview and goals for the week with mentor
- Obtained the MATLAB code and became familiar with its workings
- Read Lesson 37 in
*Partial Differential Equations for Scientists and Engineers*to understand the method used to solve a system of PDEs

**Thursday, June 2**

- Performed a literature search for papers relating to the project
- Talk by Dr. Factor on good research practices
- Had a tour of the library

**Friday, June 3**

- Met with mentor to discuss goals and milestones for the ten week project
- Added these goals and milestones to the wiki
- Read
*MATLAB: An Introduction With Applications*in preparation to begin editing the MATLAB code

## Week 2

**Monday, June 6**

- Read papers about modeling the distribution of capillary transit times and input functions
- Read a chapter on ordinary differential equations
- Began implementing subroutines in the MATLAB code

**Tuesday, June 7**

- Changed the input function in the MATLAB code from a Normal Distribution to a Random Walk Function
- Continued adding subroutines to the MATLAB code
- Discussed numerical methods for approximating differential equations
- Met with mentor to discuss progress and the inverse problem

**Wednesday, June 8**

- Changed the distribution of transit times function in the MATLAB code to a Random Walk function
- Documented the new MATLAB code
- Forward model is now mostly complete
- Began work on the first draft of the Materials and Methods section of the paper

**Thursday, June 9**

- Working lunch with other REU students
- Finished a project description
- Continued work on the first draft of the Materials and Methods section of the paper.

**Friday, June 10**

- Began reading on the use of a nonlinear least squares regression
- Finished a first draft of the materials and methods section of the paper.

## Week 3

**Monday, June 13**

- Met with mentor to look over the forward model
- Began fixing a few bugs in the MATLAB code for the forward model

**Tuesday, June 14**

- Continued working on bugs in the MATLAB code for the forward model
- Talk on research papers/presentations by Dr. Brylow

**Wednesday, June 15**

- Began working on the first version of the inverse program
- Successfully added noise to the simulated data

**Thursday, June 16**

- Met with mentor to review bugs in the code and discuss the inverse model
- Working lunch with REU students and mentors
- Responsible conduct of research training
- Finished the first working version of the Inverse program

**Friday, June 17**

- Developed a MATLAB GUI for the forward and inverse programs
- Worked on the Introduction section of the final paper

## Week 4

**Monday, June 20**

- Continued debugging of the forward model.
- Added rate constant labels to the graphs for the forward model.
- Read papers and continued writing the Introduction

**Tuesday, June 21**

- Met with mentor to discuss progress on the inverse model
- Modified the inverse GUI to allow for variable numbers of rate constants
- Modified the inverse program to display graphs of forward model simulation

**Wednesday, June 22**

- Ran tests on the forward model to determine the effect of each rate constant on the output
- Documented the new code

**Thursday, June 23**

- Working lunch with other REU students
- Continued running tests to determine the effect of each rate constant
- Read papers to try to get an idea as to which rate constants can be assumed to be zero or fixed at some other value.

**Friday, June 24**

- Met with mentor to discuss changes to the inverse model
- Continued reading papers for the Introduction section of the final paper

## Week 5

**Monday, June 27**

- Wrote a MATLAB script to test the sensitivity of R, Hb, Ht, Lb, and Lt to the six rate constants.
- Worked on slides for the midway presentation.

**Tuesday, June 28**

- Continued work on the sensitivity analysis MATLAB script
- Finished the slides for the midway presentation

**Wednesday, June 29**

- Met with mentor the discuss the sensitivity analysis and review the presentation slides.
- Finished a final revision of the slides for the midway presentation.
- Practiced the presentation

**Thursday, June 30**

- Midway presentations
- Completed a MATLAB script to varying the rate constants by 1% to test sensitivity of R, Lt, Lb, Ht, Hb.

**Friday, July 1**

- Worked on a journal of progress I have made up until this point.
- Created an annotated bibliography of the papers I have read thus far.
- Edited the sensitivity script so k2 will permanently be held at 0

## Week 6

**Monday, July 4**

- Added the Inverse Model to the Materials and Methods draft
- Ran the sensitivity script with N=150, T=20, and k2=0
- Ran the One_percent script with N=200, T=20, and k2=0
- Continued work on the progress journal
- Continued work on the annotated bibliography

**Tuesday, July 5**

- Continued work on the annotated bibliography
- Ran the One_percent script with N=300, T=20, and k2=0
- Attended a talk on good poster presentations
- Met with mentor to discuss the sensitivity analysis

**Wednesday, July 6**

- Created a MATLAB script to fit the parameters of the input function to the simulated mass (R) curve.

**Thursday, July 7**

- Went to the Zablocki VA Medical Center with Dr. Clough to observe the experiments on rats.
- Attended the weekly working lunch and a talk by Dr. Struble on his work with Tandem.
- Obtained the experimental data and began working with it in the MATLAB models.

**Friday, July 8**

- Documented new MATLAB code
- Completed the progress journal up to the present
- Re-ran the sensitivity analysis with an incorrect absolute value operation removed and k2=0

## Week 7

**Monday, July 11**

- Read papers dealing with the previous uses of HMPAO in the lungs
- Updated the Introduction of the final paper to include a review of the lung literature

**Tuesday, July 12**

- Worked on a few bugs in the function that determines the input function given the mass curve (R).

**Wednesday, July 13**

- Met with Dr. Audi and Dr. Clough to discuss problems and progress so far
- Dr. Audi recommended that I exchange velocity for a flow parameter and run sensitivity tests on the input curve and the flow parameter.
- Made a trip to the library to find a few papers

**Thursday, July 14**

- Finished an annotated bibliography
- Began writing a MATLAB script to estimate model parameters after computing the input function using the experimental data
- Began thinking about how to incorporate a flow parameter into the model.

**Friday, July 15**

- Continued a new version of the program that combines all three scripts (Forward, Inverse, and the Input Function Calculation).
- Learned how to use the MATLAB function interp1() to interpolate the experimental data so it can be used in this new version.

## Week 8

**Monday, July 18**

- Removed repetitive code from the latest version of the combined Forward/Inverse program
- Debugged the combined Forward/Inverse program

**Tuesday, July 19**

- Searched the literature for papers on the relationship between HMPAO and glutathione.
- Finished debugging the combined Forward/Inverse program

**Wednesday, July 20**

- Wrote a MATLAB script to test the sensitivities of the outputs to the input function.
- Met with mentor and discussed improvements to the inverse model
- Modified the code that generates an input function and tested and integrated it into the main program

**Thursday, July 21**

- Working lunch with REU students
- Created a script to perform a sensitivity analysis on the volumes
- Continued working on bugs in the input curve fitting program
- Began work on the poster

**Friday, July 22**

- Continued working on the poster
- Continued working on bugs in the inverse model
- Met with mentor to discuss these bugs and discuss the poster

## Week 9

**Monday, July 25**

- Continued work on the input function generation algorithm
- Fixed a scaling issue in the inverse model. The model now produces reasonable output.
- Met with mentor to discuss the poster and input function problems
- Finished a draft of the poster

**Tuesday, July 26**

- Sent a draft of the poster to mentor for review
- Met with mentor to review the poster
- Began creating a version of the program with K5=K6

**Wednesday, July 27**

- Finished a final draft of the poster
- Completed a version of the program where K5 is always equal to K6
- Met with mentor for the final time. Discussed poster, presentation slides and things to complete before leaving.
- Worked on documenting and cleaning up code.

**Thursday, July 28**

- Final lunch with other REU students
- Worked on documenting and cleaning up code.

**Friday, July 29**

- Continued documenting code.

**Saturday, July 30**

- Created readme files for the MATLAB code.
- Continued working on the final paper.

**Sunday, July 31**

- Created slides for the final presentation.

## Week 10

**Monday, August 1**

- Finished slides
- Worked on the final paper

**Tuesday, August 2**

- Poster Session
- Worked on the final paper

**Wednesday, August 3**

- Attended the first half of the final presentations
- Worked on the final paper.
- Practiced presentation.

**Thursday, August 4**

- Formal Presentation

**Friday, August 5**

- Paper Due