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Researcher of the Month
Biomedical Engineering & Physics majors, Class of 2013
Research Mentor(s): Dr. Carlos Simmerling, Chemistry; BME Senior Design: Dr. Balaji Sitharaman, BME
Research focus : Use of graphical interfaces to represent molecular dyanimics; developing new algorithms for novel ways of simulating RNA in AMBER
Neville Bethel wasn’t trained in Hollywood or film school but does he ever have a talent for moviemaking! The visual stories he tells are developed from the Simmerling group's work on simulated biomolecular systems. From creating TCL scripts, to making custom movies in Visual Molecular Dynamics that reveal the energy landscapes across a protein, to his latest project on RNA simulations in AMBER, Neville has steadily built his skills in molecular animations and optimizing software. His work with Prof. Simmerling on VMD graphical use interface is currently being submitted to the VMD development team for inclusion in the next release. A double major in biomedical engineering and physics, Neville remembers the first day of Chem 131 (Fall 08) when he heard Prof. Carlos Simmerling talk about his research, and thought: “That’s the research I want to do!” Soon after emailing Prof. Simmerling, Neville got his wish—an invitation to start working in the Simmerling Group! Even though he was a freshman, had no prior background in research or even in programming, Neville emphasizes that “If you have a good amount of passion for what you’re studying, you can start whenever you want. You just have to have the willingness and inspiration to look into things yourself rather than be taught to you. Self motivation is key.”
The commitment to doing research early on has provided invaluable training: Neville
is currently making great progress on developing new algorithms for simulating RNA,
his latest project. Recently, Neville was among the students selected to receive theMinority
Access to Research Career (MARC) fellowship which will support his work with Dr. Simmerling
during the academic year and ease his financial burden (he has been working ~20 hours
a week at a local Stony Brook restaurant, while pursuing full time studies). Neville
also enjoys working with fellow BME students on his senior design project directed
by Prof. Balaji Sitharaman. He has presented at URECA’s campus wide poster symposium;
and will be presenting a poster at the ICB&DD 5th annual symposium on Friday, October
14th, in the Wang Center, titled: "The Development of an Advanced Rendering Program to Create Movies That Illustrate
Macromolecular Dynamics and Interactions." In his spare time, Neville volunteers at Sweetbriar Nature Center, Smithtown, where
he helps care for various animals undergoing rehabilitation. A graduate ofSt. Anthony’s
High School in S. Huntington, Neville is tremendously appreciative of the resources
and opportunities that have opened up to him as a student at Stony Brook, particularly
through his work with Dr. Simmerling. Below are excerpts of his interview with Karen
Kernan, URECA Director.
Photo (right): Image of protein fpg in the process of pulling out a mutated base pair on a DNA helix (provided courtesy of N.Bethel).
Karen: Tell me about your area of research.
Neville: The Simmerling lab works in computational biology, simulating macromolecules such as DNA, protein and other small peptides; and building inferences off of the molecular dynamic simulations that they make in AMBER (a molecular dynamics program package, developed/run by a collaborative of professors across the US, including Dr. Simmerling). I’ve been working with another program called VMD (Visual Molecular Dynamics) that takes the trajectories – the frame by frame snapshot pictures of the molecules going through pico second scale time ... I take these trajectories and I make movies out of them.
The VMD software package is somewhat limited (e.g. it can only show separate rotations, for instance rotation by one axis). So when I started working on generating animations of the molecular motions–and making scripts to do things like zooming in, rotating, and doing multiple things at once, changing representations of the proteins– I started making different scripts, making more advanced algorithms to show things such as the energy landscape across a protein. When simulating HIV-1 protease, for instance, I was able to create an algorithm that would color each amino acid in the protein to show that the energies for the flaps would decrease in energy as they would open. The animations I worked on have been used by Prof. Simmerling and members of the research group for conferences and for presentations.
Was this complicated to learn? Did you have any background in this area?
I didn’t know much about computational biology before I went in. And I had absolutely no background in programming. So it was a steep learning curve. I didn’t know anything to start. Then, as I went to more meetings, and listened to Ph.D. students talk about what they’re working on, I learned more and more as I went along.
I first had to go into VMD and actually learn basic commands, the TCL commands (that’s the language it runs in) to transfer it to base C programming. I had to learn to develop loops and different coding blocks to be able to tell the program exactly what to do. The more I go along, the more I learn how exactly each parameter goes into VMD. I was then able to customize certain parameters, certain codes, and commands to enable us to do more than you could do within the VMD graphical user interface–such as different coloring schemes for energies, and forces.
How did you find out about the Simmerling research group?
I took Chemistry 131. And in Prof. Simmerling’s first day of lecture, he told us the research he does. I was very interested in it. Once he gave his introduction, I thought: That’s the research I want to do! So I sent him an email.
What is the Simmerling research environment like?
Prof. Simmerling is a great mentor! He’s extremely nice and extremely inspiring. His life story is amazing. He’s also very good at teaching me new things about computational biology, going in depth and showing me exactly what he wants. Right now, I’m the only undergrad. I work very closely with Prof. Simmerling, but also with different graduate students, working on movies for upcoming conferences & presentations. They’ll come to me saying what they want to show, how they want to show it…and I’ll go into it and try to develop new scripts to show what they want to show.
Has your project changed significantly developed over time?
Now I’m actually working on doing my own simulations and programming AMBER instead of VMD…So now, instead of making movies, I m making the movies, making the trajectories to make movies from. I’m working on programming AMBER to simulate RNA properly. Currently, protein and DNA simulations work well but RNA models aren’t accurate. So we’re working on developing new algorithms, and hard coding it into AMBER so that we can simulate and get better structures.
How many hours a week do you normally dedicate to research?
I do have another job, working at a restaurant in Stony Brook. So I normally put in ~20 hours a week to research during the summer, and about 10-15 hours during the school year.
What’s most challenging about the work you do?
The most difficult part is just understanding new languages that I haven’t worked with before – such as TCL, TK, C++, or FORTRAN. Fortran is what AMBER is run in. So I would typically have to go into these scripts and reverse engineer them to see how they work. There are different variables that are under-explained. I look into the manual, the coding, the source coding…it’s like a puzzle, working through everything, being able to go into a program and being able to understand it to the point where I can make my own scripts.
Do you ever get frustrated by the work?
In my old project, I would be making mistakes here and there. Sometimes I would realize after the fact that maybe I forgot to put a flag here, or I’d put a “1” instead of a zero when I was working in VMD, rendering movies. But it’s a lot more frustrating when it comes to programming AMBER. Because AMBER takes time to compile. The simulations take days and days and days rather than just a day. If you compile AMBER for a day and run a simulation for two weeks and then realize that you forgot to do something (forgot to put in a particular command, or a 1 instead of zero) then you wasted two weeks of work! That can be extremely frustrating.
You said previously that you had no background in this work. Yet you do seem to have
a knack for making movies, for visual presentation.
I think I’m fairly good with transferring numbers into 3-D objects. Multivariable calculus wasn’t as hard for me because I was able to see the rotations in my head. With the animations I work on, I find that I am able to see what kind of angles, what kind of factors I would need, to fully rotate the proteins to a certain point. When I had a huge array of numbers that were representative of the energies for each residue, I was able to see how to properly program them and calibrate them to show the energies within a reasonable spectrum.
Is it difficult to balance academics and research?
This is another thing that makes me happy about working with Prof. Simmerling. He’s very understanding, especially when I have a lot of coursework or midterms to study for, and I can be somewhat flexible with my schedule.
What are your long term goals?
I want to get a Ph.D in biomedical engineering and do work in nanotechnology.
How do you think being involved with research enhances your education, or complements
I’m a double major, in physics and biomedical engineering. Both majors offer classes in the computational side of biomedical engineering and physics, but doing research — the research I'm doing with Prof. Simmerling— allows you to go into much more depth. Working with Carlos Simmerling bridges the gap between my learning very basic commands and actually being able to apply it to computational science.
Sounds like you have really valued the opportunity to do research at SB.
I’ve been very happy with coming to SB because of the amount of resources that have been offered to me— and opportunities such as coming into contact with Carlos Simmerling. The BME program is also really great! I have my own advisor in BME , Prof. Sitharaman, who this year is my mentor for our senior design (group) project. It’s perfect for me because I’m also interested in nanotechnology. . . . . . It’s been fun too, just the range of classes I’ve been able to take at SB! There have been so many classes that I’ve had a lot of fun taking, such as my mathematics class in chaos which helps me describe dynamical systems I’m able to apply. Or some of the physics classes I’ve taken where I’ve learned a lot about electrical circuits, thermodyamics. That’s why I thought physics would be a good second major because of the thermodyamics I have to learn. It gives me a very good background, in the fundamentals of what nanotechnology is. I feel like I can solve more problems right because of having dual majors in physics and bioengineering. I feel like I’m being trained to know the theoretical side and the engineering side and I can go from both ends to be able to solve problems.
Have you presented before at any meetings?
I presented at URECA (2010). I had never done it before. It was interesting to take what I had learned and actually put it into laymen’s terms, to be able to explain it to other people. It was interesting figuring out how to give enough background, but also be able to condense it so that it could be understood quickly & easily….I’m hoping to present my new project at the URECA symposium next April.
What advice do you have for other students?
Start doing research as soon as possible! The more time that you have in the lab, the more things you can do. It will pay off in the end! Prof Simmerling stressed even in our first meeting that research isn’t about what you learned in your classes. If you have a good amount of passion for what you’re studying, you can start whenever you want. You just have to have the willingness and inspiration to look into things yourself rather than be taught to you. Self motivation is key. That’s the biggest thing to be successful in research. You don’t learn from someone telling you what to do.