Building Virtual Bridges across the Borders of Science
Coray Colina, associate professor of Materials Science and Engineering; co-director, Center for the Study of Polymeric Systems
Prof. Coray Colina embodies the transnational and multidisciplinary nature of modern research. A chemica l engineer by training in her native Venezuela, a petroleum engineer for industry, a Ph.D. in polymers at North Carolina State, post doctoral research in biochemistry at UNC Chapel Hill, and now using computational methods to study materials as an associate professor in the Materials Science and Engineering Department at Penn State, she looks at scientific puzzles from many perspectives and encourages her students to embrace a cross-disciplinary and internationalist approach in their style of research.
“My dream is to bridge not only biophysics and materials, but to incorporate all of the disciplines: materials science, chemical engineering, chemistry, biophysics, biochemistry, and computational science,” Colina says. Her own group is a mix of different disciplines, and she encourages her students to interact among themselves and with other groups, here and abroad.
Her research involves collaborations with labs both within the U.S. and around the world. In the last year she has had visitors from the U.S., the UK, the Czech Republic, and Venezuela working side by side with her students, giving them a sense of how research is performed in other countries.
Packing hydrogen or CO2 into a novel polymer
One international collaboration is with a lab at Manchester University in the UK, where researchers have developed a nanoporous polymer that is extremely promising for applications involving gas storage and fluid filtration. Called polymers of intrinsic microporosity (PIMs), these macromolecules with pores sizes less than 2 nm have gained a great deal of attention recently as a possible storage medium for hydrogen and CO2.
One of the major roadblocks to the widespread use of hydrogen as a fuel for vehicles is the lack of a suitable on-board storage system. Current storage methods include compressed gas tanks and cryogenic liquid hydrogen tanks, both of which have a large energy cost and safety concerns. Metal hydrides have also been intensively explored as likely candidates, but to date, none have reached the Dept. of Energy goals for storage capacity, price, longevity, and fueling time. PIMs are a new, promising material that might meet the DOE goals with further improvements.
PIMs owe their high storage capacity to their structure, a rigid framework of contorted monomers that cannot pack tightly, creating nanopores with high surface areas. Rigid at a nanometer length scale, these large molecules are flexible at a macroscopic scale and exhibit swelling properties due to their polymeric nature.
Prof. Colina and her grad student Greg Larsen are developing the computational procedures that will help the experimentalists in Manchester to understand the structure of the nanoporous materials and increase the storage capacity. A colleague in her department, Prof. James Runt, will be characterizing the new materials with broadband dielectric spectroscopy.
PIMs also lend themselves to CO2 sequestration, an area of widespread interest as atmospheric CO2 is a leading greenhouse gas implicated in climate change. PIMs functionalized to capture and hold CO2 are an option for obtaining large scale greenhouse gas reductions at the source, such as coal-fired power plants, oil refineries, and petrochemical plants. Today’s methods of industrial CO2 capture are both expensive and energy intensive, Colina, says. PIMs can be easily functionalized, for instance, by adding amine groups that don’t react with CO2. “We can change the functional groups and see what happens; we can increase the length of the polymer and see what happens; and then, in collaboration with our experimentalists, we can guide them with the molecular simulations that seem the best.”
Modeling deadly viruses
As a post-doc at UNC, Colina had taken part in work that investigated a new way of understanding blood coagulation diseases based on the movement of proteins. Using molecular dynamics, she was able to show that a protein called Factor VIIa has to be in contact with another protein called Tissue Factor to stop VIIa’s motion long enough for the clotting cascade to begin. The work gave her insight into how the motion of proteins can affect the active sites on proteins and viruses that new drugs are designed to attack, sometimes making the drugs lose their effectiveness
Now at Penn State she is doing similar work with biochemist Craig Cameron to understand the relationship between movement and function in an enzyme called polymerase, which helps viruses replicate and mutate. The Cameron lab has recently developed a model poliovirus to study how interfering with the speed and accuracy of replication in a virus can cause it to weaken dramatically.
Finding new vaccines to combat deadly viruses such as SARS or West Nile, or viruses that could be used as biological weapons, such as Ebola or smallpox, requires the production of an attenuated virus, a process involving slow, random mutations. With his model virus, Prof. Cameron hopes to create a universal strategy to speed up vaccine discovery and virus attenuation.
To help in that development, Colina models the polymerase process within the virus to gather information that is not available experimentally. Using x-rays of the frozen crystal structure of the virus, she can simulate the large proteins as they move. To test the validity of her simulation, she compares it to similar but smaller proteins that can be seen in motion using nuclear magnetic resonance imaging. Pulling the two techniques together, Colina can extrapolate the movement of the large proteins.
The Center for the Study of Polymeric Systems
Prof. Colina co-directs the Center for the Study of Polymeric Systems (CSPS) along with Ronald P. Danner, professor of chemical engineering. CSPS grew out of a previous Center in the Department of Chemical Engineering co-directed by Danner and the late Larry Duda. The new Center began operation in conjunction with Materials Day 2007, and quickly grew to include 14 faculty, 50 students and 15 post docs, along with a growing industry partnership.
The Center includes synthesis, characterization, and modeling of polymer systems, as well as software development and short courses. “We’ve had a good response from industry, because they feel that we are offering the whole package. They know they can come to Penn State and we will hopefully be able to solve their problem in any area,” Colina says.
There are challenges to simulating large molecules such as polymers. The complexity of polymer interactions, polymer composites, entanglements, and the sheer size of some polymer molecules make modeling computationally intensive. For that reason, some of the already established techniques in the protein research community could be transferable to polymer simulation. Proteins and polymers have a lot in common; in fact, a protein is a big polymer, a chain of amino acids. “With the techniques developed in the last 15 years in the polymer area, and the knowledge developed by the protein community, we’re at a great moment to move forward the research,” she says.
The Computational Biophysics and Soft Materials Group
The Colina lab is a room with several desktop computer stations located down the hall from her office. Although there are no fume hoods or prep sinks, lasers or electron microscopes, her students are performing experiments, developing and studying new materials and processes at a molecular level. Although they might just as easily be working from home, today her group is all seated at their computer terminals.
Colina says that one of the elements that connects virtual experiments to real life experiments is that both need to be taken care of on a regular basis. She advises her students to check up on their experiments every couple of hours and as soon as they wake up in the morning to be sure that their experiment hasn’t blown up overnight.
That no one gets hurt in virtual explosions makes computational modeling ideal for experiments that involve extreme temperatures, high pressure, or dangerous chemicals or biological samples. Computers can also simulate processes that are too dangerous or hard to replicate in a lab, but that could be suitable for large scale industrial applications.
In the lab, the Colina group, also known as the Computational Biophysics and Soft Materials Group, are connected to computer clusters on campus or to the Pittsburgh Supercomputer Center, part of the National Science Foundation's Shared Cyberinfrastructure program. On the Cray supercomputer, called Big Ben, computations that once might take four months, such as achieving one nanosecond of movement in a protein, can now be done in eight hours using 200 to 250 nodes of the Cray’s approximately 2000 nodes. The high computational power puts her group in position to answer questions they would not have thought to ask only a few years before.
But not all her projects are funded to use the PSC, which has a competitive grant process similar to NIH and NSF. In 2008 her group is joining the Materials Simulation Center, the Materials Research Institute’s computational center run by Jorge Sofo and Ping Lin. Through the MSC, her group will have access to Penn State’s Research Computing and Cyberinfrastructure resources, run by Vijay Agarwala and his team.
About the university-wide facilities Colina says, “I’ve had experience in groups that maintained their own computer clusters and groups that had university staff maintaining the clusters. I do believe it’s five times better to let the university maintain the computers and let my students do the research.”
For her students, the ability to run a simulation in a few hours that might once have taken months, and check on it while they sip a mocha grande in a coffee shop, is taken for granted. For Prof. Colina, whose Master’s thesis calculations took her almost two years to complete, and which she now gives to her students as a week’s homework project, it is a virtual bridge to the future.
Contact information:
Coray Colina – e-mail
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CSPS Web site- www.polymercenter.cheme.psu.edu/
