Michael Zuker

Biography

Dr. Zuker works on the development and implementation of algorithms to predict nucleic acid folding and hybridization by free energy minimization using empirically derived thermodynamic parameters. Modeling and algorithm development have been closely coupled with the derivation of nearest neighbor and related energy rules. Current work is focused on the computation of partition functions for systems containing two molecules in solution that can fold as well as hybridize with each other. Ensemble free energies, mole fractions of different monomer and dimer species and base pair probabilities are computed over a range of temperatures. These computations lead to the prediction of UV absorbance (optical density) and heat capacity (Cp) melting profiles that can be directly compared with experimental data. A related project is the development of an algorithm named FASTH that searches RNA or DNA sequence databases for optimal hybridization sites for nucleic acid query sequences. Unlike traditional search algorithms, such as BLASTN and FASTA, FASTH uses hybridization free energy as the criterion for selection

Research Interest

Experimental study of light-matter interactions at the single-molecule level, Design and characterization of plasmonic nanostructures