used to compute intermolecular interactions. He is developing a new model incorporating electrostatic polarizability using the
uctuating charge model, parameterized by tting to density
functional theory calculations of small molecules in both gas and crystalline phases, which represent extremes of the degree of intermolecular interaction. During the spring, Biochemistry and Biophysics graduate student Joshua Horn did a rotation in the group, running molecular dynamics simulations of a small oligonucleotide to examine vibrational relaxation aer photo- excitation, which is being studied in Dave McCamant’s group. Harry has also enjoyed collaborating with ILYAS YILDIRIM
PH.D. ’09 in Doug Turner’s group on free energy calcula-
tions and molecular dynamics simulations of oligonucleotides. Ilyas defended last August and published a paper in the Journal of Chemical eory and Computation.
On the home front Eva and Danny are keeping their parents busy. Eva is on her way to becoming an accomplished visual art- ist (mixed media) and has a permanent installation on our re- frigerator as well as several traveling exhibitions throughout the house. She likes music as well, as long as her dad is not singing it. Much of our parenting time is spent chasing Danny around and trying to take things out of his mouth before he can eat them.
e list is extensive and includes not only traditional comfort
food such as crayons, chalk, garden soil, woodchips, and sand, but more cosmopolitan tastes including ladybugs (dried),
band-aids (used), sticks of butter (straight up), and hand soap. He also enjoys sprinting down our driveway towards Brunswick Street, tearing a hard right, and taking o down the sidewalk towards Park Ave. is is especially rewarding if being chased by a parent and even better, if the parent is yelling.
The Eastman Theatre
Douglas H. Turner
Professor of Chemistry
Ph.D. 1972, Columbia University
RESEARCH INTERESTS Biophysical chemistry: nucleic acid structure and function, prediction of RNA structure from sequence, RNA folding, and design of therapeutics that target RNA.
is year's science continued the steady progress in understand-
i n g R N A . J i m H a r t ' s p a p e r o n N M R A s s i s t e d P r e d i c t i o n o Secondary Structure (NAPSS - Doug's favorite hobby) was published. Jim collaborated with Scott Kennedy and DAVE MATHEWS PH.D. ’02, M.D. ’03 in the Department of Biochemistry and Biophysics and then returned to Medical School. e NAPSS method revealed an unusual 74 nucleotide pseudoknot in a retrotransposon discovered by Tom Eickbush in UR's Biology Department. In collaboration with the Eick- bush group, Ela Kierzek and Walter Moss, respectively, provid- ed experimental and bioinformatic support for the pseudoknot and for other conserved secondary structures in a 320 nucle- otide segment in ve retrotransposons. Walter also noticed an f
interesting progression in the sequence from a region coding for conserved RNA secondary structure to one conserving both RNA secondary structure and protein sequence to one conserving only protein sequence. Insights into RNA thermo- dynamics were provided by the Kierzek group's work on locked nucleic acids (LNA) and GANG CHEN’S PH.D. ’06 work on CA pairs, which are extra stable in certain contexts. ILYAS YILDIRIM PH.D. ’09 collaborated with Harry Stern and the Sponer group in the Czech Republic to test the ability of com- putational approaches to predict NMR structures previously determined by JOHN SANTALUCIA PH.D. ’91, MING WU PH.D. ’96, Gang Chen, and Scott Kennedy. e bot- tom line is that computational approaches need to be improved
continued on next page