The recent big news items are my publication in the Journal of Chemical Theory and Computation and my accepted minisymposium proposal for the mesoscopic modeling of cells for ICIAM 2011 in Vancouver, British Columbia, Canada. If all goes as planned, several experts in cellular modeling and I will be giving talks about our work in Vancouver at the SIAM affiliated ICIAM 2011 conference in July 2011.

As for the publication, it is my first peer-reviewed paper. The focus of the paper concerns the development and implementation of an analytical coarse-graining method (ACG) for the representation of macromolecular particles, such as proteins. We hope to use the ACG method for dynamics simulations in the future. Please watch for future publications.

Visualization of the electrostatically shaded ACG model of OMPDC dimer.
(Red is negative; blue is positive.)

If you are interested, you can find the reference for the paper below.

Michael J. M. Mazack, Alessandro Cembran, Jiali Gao, Internal Dynamics of an Analytically Coarse-Grained Protein, Journal of Chemical Theory and Computation, ASAP, (2010). [doi:10.1021/ct100426m]

Memorial Hall at Harvard University

I gave a talk at the Annual CHARMM Developers' Meeting titled, "Protein Fluctuations without Explicit Atoms" (I'll upload the slides for the talk after the paper is accepted for publication). Harvard is an interesting place -- I didn't find it nearly as intimidating as it is made out to be. Cambridge is a nice area, and it's easily accessible by "the T" (the Boston subway system).

Giving the talk was a good experience. It was my second talk to "the greater scientific community" -- my first was my master's colloquium. I hope to be invited/encouraged to give more talks in the future!

Minneapolis from St. Anthony Falls area

One good news item is that I finished my Ph.D. coursework on May 15th! Essentially, all I need to do now is pass my preliminary exams (which I plan to do pretty soon) and write my dissertation. So I probably have a few years remaining in my program. My software, MACROSHAKER, is coming along well and hopefully the MPI version will be working soon.

As for the website updates, there are now pages about my academic interests and pages about a few types of coins that I have been collecting recently. I have been investing in Silver Eagles, Morgan Silver Dollars, and (fractional) Gold Eagles. They are nice coins and make a good hobby as well as a good and safe investment.

Anyway, enjoy the new pages!

As it turns out, I actually wound up finding time (and motivation) to update this website. The most notable update is the addition of links to my papers, reports, & presentations. These are the same as those on my academic website. However, they have been posted here in order to better circulate them to the public.

I have been programming quite a bit lately. Mainly for my research using OpenGL, OpenMP, and SSE/SIMD. I wound up writing a ray tracer for a class (CSCI 5107) a few months ago. It's amazing how beautiful some of the pictures you can make are. The below for example:

It really looks like it belongs on the cover of a textbook, doesn't it? If you would like to use this image, by all means feel free (in fact, I could even e-mail you a much higher resolution). My only request is that you link to my website or list me in your references if you use this image.

This ray tracer is actually quite beautiful. It's fully interactive in the sense that you can move the geometry around with the mouse, apply textures with an interface, and then render directly overtop of what OpenGL shows. It took a long time to write, but it was worth it.

Anyway, enjoy the updates to the site!

I just finished my first quarter of teaching math 112 at WWU. I feel good having been told that my class had the highest average out of the 1 p.m. math 112 courses, but pretty much all the credit goes to my students.

Teaching has made me learn that I'd probably be best suited working in industry. This isn't because I feel like I'm a bad teacher, but because I'd rather not grade papers and/or work off the clock. Ideally, I'd just like to come home at the end of the day and be done with work. With teaching, this is not the case.

I recently applied for a software engineering internship at Boeing, but haven't heard anything in reply yet. I'm sure that there are a lot of applicants, some of whom are more "qualified" than I am because they got a degree specifically in computer science. Although, ask any one of these kids to write mathematical software and they'll go cry for their mommy. Sure, maybe computer science majors know more about OOP and data structures, but when it comes to mathematics, most of these kids did horrible in linear algebra and can't even integrate simple functions. In other words, I feel that my future career (i.e. programming mathematical software) has job security.

But enough of that. I went to school in Japan again this past summer, and when I went to Odaiba (お台場), I took this picture of Rainbow Bridge (レインボーブリッジ) and Tokyo Tower (東京タワー).

This is a picture of Shinjuku (新宿), one of Tokyo's 23 wards. This picture was taken around 6:30AM on a Saturday. Shinjuku can get very crowded around this area (near Alta Studio) later in the day -- especially at Shinjuku station. The Shinjuku Station has over 200 entrances/exits, and is the busiest train station in the world. All that being said, I love Shinjuku.

-Michael

This summer I took two linguistics courses (an introductory linguistics course and a course in English syntax), and I now feel comfortable reading linguistic literature about Japanese. One book, in particular, that I find useful is a book titled An Introduction to Japanese Linguistics. It's amazing how much easier a language is to learn from a linguistic perspective. In foreign language courses I have taken in the past, there was absolutely no presupposition of any linguistic knowledge whatsoever. Language learning was done in a rote manner of memorization rather than in the logical manner presented by linguistics. I find that the linguistic approach to learning a language is much easier.

So in the month before I go to Japan, I'll likely be reading my first-year Japanese text, Foundations of Japanese Language (which I highly recommend), while trying to learn as many kanji as I can. Vocabulary will also be an important component to focus on since the Japanese classes I have taken focused on grammar -- not vocabulary development. There are many basic words that I do not know (many, many). This vacation will also be a good opportunity to review linear algebra and multivariate calculus -- two crucial subject areas of mathematics which I forgot, probably due to overload with other things to learn.

Learning is fun and important, but one should only do so much at a time. If you learn too much at once, you're bound to forget most of what you just learned -- if not all of it.

I wrote maztrix so that I could have a fully portable program to row reduce matricies, find determinants, and give LaTeX output for matricies. Of course, I did all of this with only a community college education ... that is, no formal knowledge of numerical analysis.

It's been about a year and a half since I wrote maztrix . I have since taken much more sophisticated math courses and I now have formal knowledge of numerical analysis. Thus, I have decided to rewrite maztrix from the ground up. The software will have the same features (and more), but it will be written in C this time (instead of C++) and will be placed under a much more liberal license than LGPL.

I'd really like to see this software become useful to someone or something important, and I'd really like to see it used in embedded environemnts ... possibly even placed directly on chips. Ha ha! I think that I'm dreaming, but the new license will allow for this type of setup without any legal trouble. If you have ever used maztrix, and you want to tell me a success story, please e-mail me. I would love to hear how it has been of use.

This page has been updated. I realized that my web hosting provider allows the use of PHP on my service plan. Thus, I renamed all .html documents to .php so that I can make use of PHP if I so desire.

Second, you will notice the blog is now on the front page. I was debating whether or not to put it here, but in the end I decided to have it on the front page. It's not really all that important though.

Anyway, if you have any bookmarks to pages on this site, or if you have linked to pages on this site, please update your URLs so that your links will not be broken.

Date and time stamps were entered manually before. Now, the blog does this automatically, which I think is a lot better. The date and time on the stamps seems to be eastern standard time (or eastern daylight time).

The most annoying bug in this blog code has been fixed. New blog entries are now prepended (albeit in a rather inelegant fashion) instead of appended. I'm sure that there was a better way to solve the problem, but as it is with perl, TMTOWTDI.

Hopefully I'll have something worthwhile to say here, eventually. However, today there is nothing really all that important to say.

I finally decided to start a blog. The purpose of this blog will be to record pointless stuff. However, there are probably people who will want to read it for some crazy reason. It really has no point, and it was only put up here so that when I go to Japan, people can sort of stay in touch with me.

One of the things you should notice about this blog is that I wrote the code myself. I wrote all of the code in perl in about eight hours. Some things don't work the way I want them to, but that's probably the way it's going to be. Hopefully I'll be able to fix the issue with the newest entry being put on the bottom of the page. Well, that's for another day.

It's also important that Japanese and HTML work on this blog. mazack.org ... yep, looks like HTML works ... and now for some Japanese ... この日本語は見えますか。 ... Hmm, possibly.

That's all the pointless rambling I have for today. I'm already not liking writing about this stuff. It feels too much like MySpace or some other stupid social networking thing. Hmm ... who knows.