The directed three-dimensional self-assembly of microstructures and nanostructures through the selective hybridization of DNA is the focus of great interest toward the fabrication of new materials. Single-stranded DNA is covalently attached to polystyrene latex microspheres. Single-stranded DNA can function as a sequence-selective Velcro by only bonding to another strand of DNA that has a complementary sequence. The attachment of the DNA increases the charge stabilization of the microspheres and allows controllable aggregation of microspheres by hybridization of complementary DNA sequences. In a mixture of microspheres derivatized with different sequences of DNA, microspheres with complementary DNA form aggregates, while microspheres with noncomplementary sequences remain suspended. The process is reversible by heating, with a characteristic "aggregate dissociation temperature" that is predictably dependent on salt concentration, and the evolution of aggregate dissociation with temperature is observed with optical microscopy.

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A more accurate, stable, finite-difference time-domain (FDTD) algorithm is developed for simulating Maxwell's equations with isotropic or anisotropic dielectric materials. This algorithm is in many cases more accurate than previous algorithms (G. R. Werner et. al., 2007;A. F. Oskooi et. al., 2009), and it remedies a defect that causes instability with high dielectric contrast (usually for 10) with either isotropic or anisotropic dielectrics. Ultimately this algorithm has first-order error (in the grid cell size) when the dielectric boundaries are sharp, due to field discontinuities at the dielectric interface. Accurate treatment of the discontinuities, in the limit of infinite wavelength, leads to an asymmetric, unstable update (C. A. Bauer et. al., 2011), but the symmetrized version of the latter is stable and more accurate than other FDTD methods. The convergence of field values supports the hypothesis that global first-order error can be achieved by second-order error in bulk material with zero-order error on the surface. This latter point is extremely important for any applications measuring surface fields.

Optimization of a truncated, dielectric photonic crystal cavity leads to configurations that are far from truncated crystal cavities, and which have significantly better radiation confinement. Starting from a two-dimensional truncated photonic crystal cavity with optimal Q-factor, moving the rods from the lattice positions can increase the Q-factor by orders of magnitude, e.g., from 130 to 11 000 for a cavity constructed from 18 rods. In the process, parity symmetry breaking occurs. Achieving the same Q-factor with a regular lattice requires 60 rods. Therefore, using optimized irregular structures for photonic cavities can greatly reduce material requirements and device size.