Margaret Putney is a senior physics major with a minor in rhetoric and composition. This column marks the first in her new series of science-related articles for the Review.

This summer, the sciences at Oberlin College got a new resource thanks to a proposal composed by several of our faculty members. Professors of chemistry Manish Mehta and Matthew Elrod, Professor of physics and astronomy Dan Stinebring and Professor of computer science John Karro wrote the proposal to the National Science Federation for the brand new parallel cluster supercomputer that is now residing on the second floor of the chemistry department.

“One of the long-term goals of the project is to make this a campus-wide resource,” Mehta said.

This is already evident as the computer is running a lot of research, and even more is expected. Senior physics major Ben Sulman was able to discover a pulsar when he ran the first large data set from a sky search he did this summer on the supercomputer.

“Projects in data analysis and modeling will benefit enormously from a computer like this,” Sulman said.

Since Physics and Astronomy Professor Chris Martin and Mathematics Professor Peter Thomas have joined the faculty, the scene is shifting.

Unlike large research universities that optimize a cluster only for a certain type of calculation, Oberlin’s will be used as a much more general-purpose instrument, allowing more students and professors to benefit from it in their higher-level classes and research.

Currently, Mehta is working with honors student Rob Hartley on modeling work to understand how water molecules interact with proteins and how they help determine the three-dimensional structure.

In chemistry, the equations can be easy to write down but nearly impossible to solve when made even the least bit complicated, such as the addition of any molecule above the element helium. The new software on the computer solves the equations and gives the structure of the molecule along with its energy, showing how the protein will interact with water; this is something that is very important to understand but extremely hard to determine experimentally.

Elrod is running simulations on the computer of chemical reactions in the atmosphere to understand smog formation more accurately, and Stinebring is using the cluster to reduce large data sets of pulsar observations down to more manageable sizes.

Some students will feel the immediate result of the new cluster in the spring. In Chemistry 339: Quantum Chemistry and Kinetics, students previously had to wait to use a single processor to solve a simple Schrödinger application on the element helium.

“Because the supercomputer is actually 64 separate computers wired together. Each student in Chemistry 339 will essentially have their own powerful computer to perform the quantum calculations,” Elrod said.

“This aspect will allow each student to perform the calculations simultaneously during the class period, which will allow me to actually incorporate the student results directly into the class discussion.”

Another example of an implication for the new resource is the work that biology professor Laura Romberg plans to do on the computer. By understanding a certain protein in bacterial cell division, she hopes to find new ways to prevent the spread of the bacteria that may be used to create new antibiotics. The computer plays a key role when one tries to understand the mechanisms of the particular protein that helps prevent the bacteria cell from dividing, which includes the protein assembling into polymers.

“Because we’re working with polymers, we cannot easily model this system using differential equations,” Romberg said. “Polymers can be infinite lengths, so we would have an infinite number of differential equations to solve. This is why we are doing the simulation instead.”

The cluster will speed up the calculations immensely.

Other ideas include climate modeling in the geology department, having students use an entire genome in their problems in biology and more real-world situations in science.

“The resource is there for faculty to incorporate into their teaching,” Mehta said.

With future faculty hires and creative Obies working alongside their professors, there is no doubt Oberlin College will get the most out of this resource.