Craig L. Zirbel, Ph.D., Department of Mathematics & Statistics
I am an applied mathematician who enjoys working with scientists on models of physical systems. For the last six years, I have been collaborating with Neocles Leontis in the BGSU Chemistry department on probabilistic models of RNA sequence variability. As a data-collection step, we developed a program to search RNA crystal structures for instances of recurrent motifs, so we could study their sequence variability. There are many individual motifs waiting to be studied, which provides an excellent entry into biochemistry for mathematics students, and an entry into algorithmics for chemistry students. Appropriate project titles would be "Automated RNA motif library generation through geometric search and cluster analysis" and "Efficient geometric search for RNA motifs in 3D structure files". More recently, with an undergraduate researcher doing the coding in Java, we have developed programs to align RNA sequences according to models built from RNA 3D structures, the first time this has been done, and the start of a long-term subfield due to the growing number of crystal structures and the faster-growing number of RNA sequences. There is much for chemistry, computer science, and mathematics to do in this area. An appropriate project title would be "RNA multiple sequence alignment by aligning sequences to 3D structures".
438 Math Science Building