I've had a lot of great news over the past few days. On Wednesday, June 6^th, the Department of Mathematics awarded the Outstanding Ph.D. Dissertation award to Evelyn Lunasin-Manalo and me. I'm trully surprised, thrilled, and honored, because we graduated 10 Ph.D.s with quality dissertations this year. The department also surprised me a with a service award (shared with Nick Alexander for co-founding the mathematics graduate student colloquium (MGSC)) and a teaching/research award (shared with Nick Alexander and Timothy Choi). I'm truly flattered and grateful, and I hope that as an alum that I can make you all proud!

Continuing along the "life is good" theme, I received and accepted my offer letter to work at University of Texas Health Science Center at Houston as an assistant professor under Vittorio Cristini. I'll be working in the School of Health Information Sciences, along with the M.D. Anderson Cancer Center to develop next-generation mathematical and computational models of cancer. I'm very excited at the opportunity to work side-by-side with some of the greatest cancer biologists and oncologists in the world, and the integrated/interdisciplinary aspects are thrilling.

So, life is good. :-) -- Paul

Well, I just traded 2 × 220 heavy pages of dissertation for a single sheet that reads "dissertation manuscript accepted." Whew, what a relief! It's finally done, and the degree should be official in a few days.

It's been an interesting 24 hours or so. I had a burst of energy and motivation around 1:00 this morning, so I decided to print out all the black and white pages of my dissertation on the laser writer at home. At last seeing the light at the end of the tunnel, I filled out all the forms and schlepped myself over to Kinko's at 8 this morning to print the remaining color pages. After spending another hour double-checking the manuscripts, I headed to the University Archives, and that was that! Woohoo! :-)

In other great news, I've been having some great disussions with Vittorio Cristini on my position at the University of Texas Health Science Center in Houston. I'm going to head there as an (non-tenure-track) assistant professor and do some interdisciplinary cancer modeling and simulation with the biologists and doctors there. I'm very excited!

Well, back to work on our joint paper for me. But once again, woohoo! :-) -- Paul

I'm happy to announce that I passed my Ph.D. dissertation defense, and I hope to have my dissertation fully revised within a week or two. The defense was an interesting process with a lot of great (and difficult) questions, but on the whole, it went well, and I'm glad to be done with it.

Ph.D. Dissertation Defense: A snapshot of Paul Macklin giving his talk toward the of the defense.
Photo credit: Angela Macklin

I was really excited to see that many of my great friends were there to support me through the defense. I'm grateful to have so many good friendships here at UCI, and I think it also speaks to what a great community we've built here in the graduate program. Thanks to all who attended! Also, great thanks to Donna McConnell and the department staff who organized a delicious lunch and reception!

I'd like to also thank my committee for agreeing to take time out of their busy schedules to hold the defense today. In particular, I'd like to thank John Lowengrub for being such a great advisor and trusted friend over the past several years. Needless to day, I wouldn't even be here if it weren't for his dedication as an advisor.

I'm grateful for the emotional support I've received from my family and in-laws over the past few years. It has meant so much to me to always receive such encouragement through this long, difficult path.

Last but first, I'd like to thank my wife, Angela, for being so incredibly supportive over the years. She's heard so much about tumor growth, cancer, level set methods, and modeling over the past few years that she really deserves a Ph.D., too. :-) I'm grateful to have such a patient and supportive wife!

Ph.D. Dissertation Defense: Angela and Paul Macklin at the reception following his dissertation defense.
Photo credit: Baochi Nguyen

So, in summary, woohoo! And thanks to all the support I've received from friends and family over the past few years! -- Dr. Macklin (I just couldn't resist!)

I just finished my Ph.D. dissertation revisions and sent a copy to my committee. It's a little surreal, but I'm nearly done! :-) -- Paul

John Lowengrub and I just submitted an invited paper for an upcoming special issue of the Journal of Scientific Computing on level set methods. I'm very excited! I'll update the publications page page shortly to reflect the change. -- Paul

At long last, my dissertation defense has been scheduled. Here are the details:

• Date: Tuesday, May 15^th, 2007
• Time: 12:00 noon to 2:00 pm
• Room: MSTB 254
• Title: Nonlinear simulation of centimeter-scale tumor growth into heterogeneous tissue
• Committee:
  • Natalia Komarova (Mathematics)
  • John Lowengrub (Mathematics, chair)
  • Hongkai Zhao (Mathematics)

More details and an abstract / title to follow! -- Paul

We just wrapped up the Mathematical Modelling and Analysis of Cancer Invasion of Tissues workshop in Dundee, Scotland. It was a fantastic workshop, with a great mixture of mathematical modelers and biologists. I got to meet many new friends and colleagues from the European and U.S. cancer modeling community, and I look forward to keeping in touch with them.

In spite of initial jitters, my talk (Nonlinear simulation of centimeter-scale tumor growth into realistic tissue) went very well on Tuesday. The audience asked some great questions, and in further discussions, I received a lot of helpful feedback that I will use to improve the model and the numerics. I'm very excited for the future of our work, and the insightful comments from my new friends will help me quite a lot!

John Lowengrub and I had a chance to catch up on work with our collaborators (Sandy Anderson, Mark Chaplain, and Steven McDougall), and we hope to make rapid progress on our first joint paper. To that end, I'm working in Edinburgh this week with Steven McDougall to complete the coupling of our angiogenesis and cancer invasion software packages. It should be a very exciting few days!

Of course, work also continues on our J. Sci. Comput. and J. Math. Biol. papers. I hope to get those drafts done pretty soon, particularly given the fact that they are the next two chapters of my dissertation!!! :-)

I'll be attending the Mathematical Modelling and Analysis of Cancer Invasion of Tissues workshop in Dundee, Scotland from March 26th to March 30th (my birthday). The workshop is organized by Mark Chaplain and hosted by the International Centre for Mathematical Sciences. Although I have yet to receive email confirmation, it looks like I'll be giving a thirty minute contributed talk on our most recent centimeter-scale glioblastoma simulations. I'm very excited!

In the following week, I'll be working with Steven McDougall in Edinburgh to put the finishing touches on our joint tumor growth-angiogenesis software. After that, we'll be ready to start writing our joint papers.

On the dissertation front, I'm making slow progress on the writing. I spent some time tracking down subtle behavior in my code and improving the accuracy of our ghost fluid method extension. We should be submitting a paper on that to the Journal of Scientific Computing pretty soon. Next up: writing up our tumor growth model for the Journal of Mathematical Biology. After that, I can finally return to my dissertation writing for real.

Lastly, as a goofy web programming aside, I fixed some bugs in my PHP code that inaccurately displayed times in the noon and midnight hours, as well as single-digit minutes. (I accidentally appended a 0, rather than inserting it.)

Update: March 18, 2007: My contributed talk has been confirmed for Tuesday, March 27th at 3:30 pm. I guess I'd better get to work on that PowerPoint!

I just received word that my proposal for the NSF Mathematical Sciences Postdoctoral Research Fellowship was declined. However, there was a silver lining: most of those who were declined received word earlier than February 12^th, and so my application was most likely in the running until the very end. Given that 151 applications were received this year and only about 30 are awarded, this was a very competitive process. So, it was a good experience, and we must not have been very far off.

I'd like to give special thanks to my recommenders (Mark Chaplain, Natalia Komarova, and John Lowengrub), as well as Vittorio Cristini and Robert Gatenby for the generous time and help that they provided in the application process! -- Paul

John and I decided to delay my dissertation defense until next quarter. This will allow me to finish up a couple of papers and remain in graduate student housing a little longer. More details to come on the two papers. Essentially, John and I decided that chapter 5 of my dissertation could be separated into two publications: a ghost fluid/level set method paper, and a modeling paper on our latest tumor growth/tissue model. Publishing these results as separate modeling and method papers will greatly assist as we start publishing results with our collaboration with Mark Chaplain, Steven McDougall, and Sandy Anderson.

In an unrelated vein, I'm going to try to keep this website better updated. I may roll out some home-grown XML/PHP software I wrote to make it a bit more "blog" like. :-)

My advancement to Ph.D. dissertation is scheduled! The details:

• Date: Wednesday, February 28^th, 2007
• Time: 2:00pm to 4:00pm
• Room: MSTB 254
• Topic: Nonlinear Simulation of Cancer / Computational Oncology
• Committee:
  • Natalia Komarova (Mathematics)
  • John Lowengrub (Mathematics, chair)
  • Hongkai Zhao (Mathematics)

More details to come in a later posting.

I just got word this week that our microenvironment paper has been accepted to the Journal of Theoretical Biology. I'd like to thank the reviewers for their insightful comments, as they were helpful in strenghtening the paper. We should be receiving proofs around Dec. 28^th, which I suppose means the paper will come out in final form in early 2007. Please follow this link to read the most current draft.

This week, I applied for a NSF mathematical sciences postdoctoral research fellowship, or MSPRF. It was a very educational experience for me, in that the application format was that of a short grant proposal. Regardless of how this turns out, it was a great experience in what shall surely be an integral part of my life as a scientist.

I can't go into too much detail on the proposal itself, but it involves some exciting research on a next-generation tissue-level cancer model. I also got to learn more details on my coming post-doc next year at the University of Texas Health Science Center at Houston, which is closely tied to the M.D. Anderson Cancer Center. More to come later. -- Paul

The MGSC is off to a great start! Timothy Choi gave the first talk, and it was well-attended, with about 25 graduate students present. I'm very excited about the future of the MGSC, and I hope that it develops into a positive, community-building tradition.

It's been a long time since I've posted an update on my Ph.D. work. Things are going well! In August, I spent two weeks working with Steven McDougall in Edinburgh on our joint tumor-angiogenesis code. We made great progress, ultimately linking two separate codes with data sharing, etc. The tumor releases pro-angiogenic growth factors that diffusion into the microenvironment and promote / guide angiogenesis. The resulting blood vessels provide nutrient to the growing tumor. This next-generation computational framework includes fully heterogeneous coefficients, which allow us to model the tissue structure and tumor microenvironment in rich detail, as well as investigate some of the functional relationships between the microenvironment and the microphysical parameters. Steven and I met with Sandy Anderson and Mark Chaplain, and we hope to begin work on an exciting paper very, very soon!

As for our joint project with Natalia Komarova, we have finished validating the code by verifying her theoretical results for 1D and mass action tissue invasion, and so now we're moving on to new investigations.

On another note, I've begun writing my dissertation. Part of that process includes learning BibTeX, which has also proven useful in paper revisions. (John and I received our JTB paper reviews, which included a lot of useful comments and suggestions for improvement.) At the moment, a December 2006 graduation is still a possibility, but a March 2007 graduation looks more likely.

It's been awhile since I've posted an update. First off, John Lowengrub and I submitted a new paper (Nonlinear Simulation of the Effect of Microenvironment on Tumor Growth) to the Journal of Theoretical Biology in the last week of June. The article is still under review, but we're pretty excited about the results!

In other news, I've begun writing my dissertation in earnest. As my recent coding starts to settle out and I find my last bugs, I hope to devote more of my attention to that coding, and perhaps graduate in December!

Lastly, I'm going to Heriot-Watt on August 19^th for two weeks of joint coding on our tumor growth-angiogenesis project. Early results are good, and I hope to post an animation on that soon. Now, if only the UK travel restrictions can calm down ... An LAX-LHR flight with no hand baggage sounds incredibly long! :-(

From June 5^th to June 9^th, John Lowengrub and I attended a Cancer Modeling Workshop at Dundee University in Scotland. The workshop was very interesting, and John and I had some extra opportunities to continue our collaboration with Mark Chaplain and Steven McDougall. Things are really starting to come together on this project, and I'm very enthusiastic!

I also got to visit Edinburgh for the first time, which was a lot of fun. I hope to update this posting later with some pictures.