In order to realize their promise for advancing molecular scale technology, nanoparticles must be arranged into spatial patterns that dictate specific routes for the transport of charge or excitations. Polymers such as DNA, whose sequences define free energy minima with specific intermolecular relationships, are broadly recognized as potential tools for constructing complex scaffolds with nanometer detail [like the one depicted in (a)]. Methods for designing appropriate sequences, however, require further development to ensure that desired supermolecular structures are both unique and kinetically accessible. While considerable progress has been made in addressing one-dimensional (i.e., sequence alignment) aspects of this problem, the full problem of efficiently assembling higher order nucleic acid structures involves the three-dimensional geometries and topologies of many strands and their progression in time. Professor Geissler and graduate student David Moler use computer simulations of a coarse grained molecular model (b) to identify dynamical bottlenecks impeding assembly of specific sequences. Importance sampling in sequence space is performed to eliminate these bottlenecks. Exploring the relevant range of configurations for multiple DNA strands requires new Monte Carlo methods, such as the "accordion move" shown in (c), to surmount energetic and topolocial barriers. The principles of sequence design and nanoparticle assembly developed through this work will be tested in the laboratory of Professor Paul Alivisatos.