Newswise — Daniel Aalberts, associate professor of physics at Williams College, was recently awarded grants from the National Science Foundation (NSF) and the National Institutes of Health (NIH).

Aalberts uses statistical and computational physics methods to study biological polymers. His research focuses on RNA, single-stranded nucleic acids that play a variety of roles, including supplying cells with the information needed to build proteins and catalyzing key chemical reactions.

The NSF Research in Undergraduate Institutions grant, in the amount of $260,000, will support a three-year project "Improving RNA Pseudoknot Models and Algorithms." RNA is a long, thin molecule that folds into complex, compact shapes through complementary base paring.

One such shape, the pseudoknot, is the rare but highly functional stacked structure that most RNA enzymes take on. Most traditional RNA prediction methods exclude pseudoknots. To bridge that gap, Aalberts and his undergraduate collaborators have been developing and improving mathematical models to explain pseudoknot structures and calculate their abundance.

A $226,000 NIH Academic Research Enrichment Award grant, also a three-year award, will support a project titled "Binding and Splicing mRNA." Splice junctions in messenger RNA indicate the boundaries of sequences that intervene in genetic information. As these sequences must be edited away to locate gene signals, predicting these junctions is crucial. While statistical models for this processing step are still incomplete, one effective approach on the cellular level is preferentially binding a small RNA molecule to these splice junctions.

Students in Aalberts' laboratory this year include Teng Jian Khoo '09 from Penang, Malaysia, and Sandy Nandagopal '09 from New Delhi, India. Among the students who have previously worked with Aalberts on pseudoknot structures are Nathan Hodas '04, winner of the American Physical Society's Apker Award for outstanding undergraduate research, Evan Miller '06, and Alex Zaliznyak '07. Past undergraduate collaborators on his binding and splicing projects include Jeff Garland '03, Hodas, Eric Daub '04, Jesse Dill '04, Rob Cooper '06, and Will Parker '08.

Aalberts joined the Williams faculty in 1997. He teaches classes in computational biology, mathematical methods for science, and modern physics. His work has been published in several peer-reviewed journals, including Bioinformatics, Nucleic Acid Research, and Physical Review E.

He received his S.B. in physics and Ph.D. in theoretical statistical & condensed matter physics from the Massachusetts Institute of Technology.

Founded in 1793, Williams College is the second oldest institution of higher learning in Massachusetts. The college's 2,000 students are taught by a faculty noted for the quality of their teaching and research, and the achievement of academic goals includes active participation of students with faculty in their research. Students' educational experience is enriched by the residential campus environment in Williamstown, Mass., which provides a host of opportunities for interaction with one another and with faculty beyond the classroom. Admission decisions are made regardless of a student's financial ability, and the college provides grants and other assistance to meet the demonstrated needs of all who are admitted. To visit the college on the Internet: http://www.williams.edu

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