A double dose of congratulations is in order to our own Markus Dittrich. In addition to being recently named the new Director of the National Resource for Biomedical Supercomputing (NRBSC) at PSC – a huge job in itself – he will also head PSC’s participation in the recently announced Center for Molecular Modeling of Biological Systems (CMMBS), a partnership between the University of Pittsburgh School of Medicine, Carnegie Mellon University (CMU), and PSC.
Markus, who is originally from Germany, came to PSC in 2006 as a post-doctoral researcher with Joel Stiles. He was promoted to senior scientific specialist, and then to group leader of NRBSC before becoming the director. We talked recently about CMMBS, and the NRBSC, software development, and e-books vs. paper books.
Congratulations on your new position in NRBSC!
Thank you. NRBSC is doing well. And as you know, we just became a major partner in the newly funded CMMBS, a Biomedical Technology Research Center from the National Institutes of Health together with the Department of Computational and Systems Biology at Pitt and the Lane Center for Computational Biology at CMU.
How does NRBSC fit into CMMBS?
As part of this new Center, NRBSC will continue its focus on computational biological research. There are multiple levels in our work: first, the atomic and molecular level simulations, then simulations on the level of cells, with many molecules, things like that. Then there are even higher levels, tissues, and larger, organism-level things, and the large-scale volumetric image analysis that comes in there.
Art (Wetzel) and Greg (Hood) are part of the image analysis effort. I personally lead the cell modeling aspect, with MCell development with invaluable work from Jacob Czech.
What else is going on in NRBSC?
There are lots of other research activities going on in NRBSC. For example, I have a successful collaboration with Steve Meriney at the University of Pittsburgh doing cell modeling and trying to understand the structure and function of synapses.
Besides research, we have the MARC program, which is a very successful, very important outreach mechanism, which Hugh (Nicholas) and Alex (Ropelewski) established. It really helps minority institutions get their foot in the door.
We have lots of other outreach and training activities headed by Pallavi (Ishwad).
And there’s Anton. We’ve been doing that for 2 years now and the project has been hugely successful. Very recently, research that used Anton for its computational work was published in Nature.
We were just awarded a 2 year supplementary grant to continue Anton support here at the PSC, and D. E. Shaw has agreed to leave the machine here for at least that long. Hopefully we’ll be able to continue beyond that, of course, but 2 years is a good head start.
There’s lots of other things going on, and hopefully in the future we will continue to get involved in new and exciting collaborations and new projects.
What kind of work are you and Steve Meriney doing with synapses?
We are studying structure and function in synapses. Steve is an experimental neuroscientist at Pitt. So we combine his experimental work and my simulation work to develop models to understand more and more how these systems work.
It’s important for this type of work that you combine simulation and experiment.
How do simulations and experiments work together?
Simulations allow you to get insight that you can’t get using experiments, because many of these synapses are not accessible experimentally. It’s very difficult to look at very detailed events in an experiment, but it’s easy in an MCell simulation.
On the other hand, to make a successful simulation, you need a lot of insight from experiment of how those systems work, to really build a model that you can trust.
It develops in a synergistic way: you build a model, then get input from experiment, and you build from there. Right now, we have a nice model developed that seems to agree quite well with what you see in experiments. It’s really quite predictive. So we are excited to use that, to actually explore new avenues using it.
So your educational background is in biology? or in computer science?
Well, my way, way, background is physics. I went to the University of Regensburg and got a diploma in physics. That’s equivalent to a master’s degree, maybe, here. I focused mostly on theoretical condensed matter physics, understanding materials.
Then I went to the University of Illinois at Urbana-Champaign (UIUC), and joined Klaus Schulten’s group, who is a big name in the field of molecular dynamics simulations. So doing my PhD, that’s where I got into the life sciences, and using computer simulations to understand how living systems work. To me, that was, really, I don’t if it was life-changing, but it was really fantastic to use these physics based approaches to understand living systems. It’s very different than material science, a whole different kind of beast to tackle. So it was really great fun. I enjoyed it a lot, and I’ve been doing biophysics, I guess, ever since.
And that’s when you came to the States?
Well, I went to college in Bavaria, and the University I went to had an exchange program with UIUC. So I went for a year to the States, I believe it was in ’97, and spent a year at the physics department there. I didn’t have any contact with Klaus at this point. But that’s where I actually met my wife, Susan.
I really liked it in Urbana-Champaign, it’s a really nice small town, and a fun town to be in. So I decided that I wanted to go back and do my PhD there.
What brought you to PSC?
Well, when I did my PhD, I mostly focused on enzyme structure and function, particularly on one enzyme called F1-ATP synthase, which is a quite famous protein. It’s a nice machine. A molecular motor. You feed it a chemical called ATP and it converts that chemical energy into mechanical rotations. It’s a wonderful example of something nature has come up with to make life work.
After my PhD, I felt like it would be good for me to also see some other type of approaches to simulate biological systems, so I got in touch with Joel Stiles. I knew I wanted to do some type of cell level simulation, and he was a pretty well-known person in that field.
Once I got here, I went from just studying single molecules to studying whole cells and sub-cellular systems, synapses in this case. It has been great to see different aspects and to learn new tools. It helps you to get a much better view of how to look at systems, to have a repertoire of methodologies that you can draw on to approach them and to try to understand them. It’s really nice to understand how things work.
Between your research and being the director of NRBSC, you must be very busy. Do you do anything for fun?
I do a lot of running, although I’ve been slacking. I used to run every day, but now it’s down to four or five times a week. I’ll get back to every day eventually.
Also, I do a lot of programming just for fun. I enjoy it, so as a hobby, I spend most of my time coding. I do a lot of reading, too.
What are you coding?
All sorts of stuff. My wife is a knitter, so I’ve started writing some software for her to create knitting charts, called sconcho, that’s on SourceForge.
And what are you reading?
I usually go to Project Guttenburg and look at those books. I started re-reading some of the books I read as a child, and right now I’m reading “The Last of the Mohicans” on my Kindle.
Do you still buy physical books?
I do, but I’ve reduced it a little bit. I’m sort of a book nerd. I have a pile of books that are unread. I keep buying them and I keep cursing at myself for doing it.
I still prefer technical books as physical books. I think the Kindle, to just read a novel, it’s fine. But it’s inconvenient on a technical book that you have to flip back and forth a lot, and you have little notes in there and things, it’s hard to work. It’s different from having a physical book in your hands. Then again, you only have so much space in your house, right? It’s good that the e-books are not really taking up any space on your bookshelves.