We are working with DNA nano-structures that fold from a single strand of DNA. We have recently started a new project where we use a new method to create libaries of DNA structures that display aptamers in diverse 2D and 3D patterns. We apply these structure libraries to multimeric protein and viral targets and perform selection experiments where we retain the patterns that bind strongly to the targets. We then use nanopore sequencing to recover identity of the strong binders at a relatively large scale, (10k-100k). The goal of this computational project is to understand the shape of the structures that bind strongly compared to the crude population. We will perform 2D structure prediction locally and then hope to use cluster resources to understand the 3D shape using the coarse grained molecular dynamics software package oxDNA.