Alumni Profile: Mark Nelson

Mark Nelson is a leading software architect at Oracle who made an important contribution as a graduate student at Beckman.

University of Illinois alumnus Mark Nelson doesn’t work with biologists or physicists in his job at information technology giant Oracle. But his involvement with those scientists and their fields at the Beckman Institute helped pave the way for his current position as a software architect.

Nelson was an original author of the code for the hugely successful NAMD molecular dynamics simulation software developed at Beckman’s Theoretical and Computational Biophysics (TCB) group. The TCB program has been used by more than 30,000 scientists from around the world to simulate atomic scale processes such as mutations in viral proteins. 

Nelson was a graduate student in computer science at Illinois in 1993 when he joined TCB to help write a new software program to replace one that had code consisting of two-letter abbreviations in German.

“Not speaking German, it pretty much made the code completely unreadable to me,” Nelson said. “So we decided we needed to have another program that was written from the ground up to be a platform for us to try what we wanted to try, and hence, NAMD was born.”

The lessons I learned at Illinois and being in the Theoretical and Computational Biophysics group were certainly the ability to dive in and learn an applied problem and build a platform where that problem can be solved.
– Mark Nelson

Today, NAMD’s ability to simulate molecules doing the kinds of intricate dances involved in biological processes is providing unprecedented, atomic-scale insight for scientists in a variety of fields. Even though he says his old code is probably gone by the wayside, Nelson says the experience taught him a lot.     

“The lessons I learned at Illinois and being in the Theoretical and Computational Biophysics group were certainly the ability to dive in and learn an applied problem and build a platform where that problem can be solved,” Nelson said. “For me, the interesting thing about computer science is not necessarily computer science itself; it’s the fact that you can apply it to just about any problem in the world.

This was kind of my first large scale ‘diving in’ and using computer science to solve a problem. It happened to be theoretical biophysics, but the basic process is still the same. You spend six months learning what the problem was, and then developing software to solve it.”

And that problem-solving aspect is what still drives Nelson today as a senior software architect for a number of different products, including Oracle Public Cloud. 

“That’s the interesting part of computer science to me,” Nelson said. “I have gone on to use that same basic principle of learning what people want and need their software to do and designing software to meet those needs. That is my job. It’s on a different scale and a different problem space, but it’s still the fundamental problem.”

At Oracle, Nelson sets the technical direction for several groups writing software for different projects, using the analogy of a building architect to describe his role.

“I help build the blueprints for the software that is being built here at Oracle for a number of products, most notably Oracle Public Cloud and Fusion Middleware,” he said.

Their target customers are in the business world but the goal is the same as when he worked at Beckman: providing a tool that meets the user’s needs. Nelson said he and his collaborators on the NAMD code did that by working with TCB Director Klaus Schulten and others and by making the code adaptable.

“For the physicist, the number one rule was to be able to do real research with it,” Nelson said. “Klaus and his students at the end of the day needed to do research and get real results. The way to get better results was to be able to quickly incorporate new ideas from the computer science professors and from Klaus on the physics side of things, because they were also trying out new techniques and new algorithms.

“So the key to success was to be able to plug in the new algorithms without every time saying, ‘oh, I have to start a new program and write a new program every time.’ I think NAMD is still around because it’s become this platform that has good features where people are able to innovate on top of it very quickly. And I think that idea, whether any of my code lives on or not, that purpose of NAMD specifically as a platform to try these things out, that’s clearly why it has been successful. It has become this bed of innovation for both the physicists and the computer science investigators.”

That type of collaboration across disciplines is what Beckman is known for, and something Nelson appreciated during his time here in the early 1990s.

“What I learned, certainly, from TCB and being in Beckman in general, was that the strength of Beckman was this mish mash of different disciplines in one place,” he said. “I thought that was awesome. I had a great experience learning biophysics and half of my time was not really doing computer science; it was learning biophysics so I could apply my computer science problem to it.

“Whereas if I had been purely in the computer science department doing something purely computer science related, I might not have had that chance. I think that it’s great and NAMD proves that there are great things that can come from this type of collaboration, where the departments really mix together.”

This article is part of the Spring 2012 Synergy Issue, a publication of the Communications Office of the Beckman Institute.