Computational Biomolecular Design

NILES PIERCE
Applied and Computational Mathematics, Bioengineering, and Biochemistry California Institute of Technology
Pasadena, CA 91125, USA
niles@caltech.edu

Abstract:

This talk will describe our efforts to develop computational algorithms for encoding mechanical or chemical function in biopolymer sequences (DNA, RNA, and protein). A useful computational algorithm must identify molecular sequences for experimental study that adopt desired conformations with both high affinity and high specificity. Our recent work focuses on partition function calculations for nucleic acid secondary structure as a conceptual approach to robust design. The talk will emphasize the strong interplay between physical modeling, design problem formulation, sequence selection algorithms and design objectives.