title: Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic acid Origami Nanoplates.
abstract: Deoxyribonucleic acid (DNA) origami is a method for the bottom-up self-assembly of complex nanostructures for applications, such as biosensing, drug delivery, nanopore technologies, and nanomechanical devices. Effective design of such nanostructures requires a good understanding of their mechanical behavior. While a number of studies have focused on the mechanical properties of DNA origami structures, considering defects arising from molecular self-assembly is largely unexplored. In this paper, we present an automated computational framework to analyze the impact of such defects on the structural integrity of a model DNA origami nanoplate. The proposed computational approach relies on a noniterative conforming to interface-structured adaptive mesh refinement (CISAMR) algorithm, which enables the automated transformation of a binary image of the nanoplate into a high fidelity finite element model. We implement this technique to quantify the impact of defects on the mechanical behavior of the nanoplate by performing multiple simulations taking into account varying numbers and spatial arrangements of missing DNA strands. The analyses are carried out for two types of loading: uniform tensile displacement applied on all the DNA strands and asymmetric tensile displacement applied to strands at diagonal corners of the nanoplate.
authors.affiliation: Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210.
authors.forename: Bowen
authors.initials: B
authors.lastname: Liang
authors.affiliation: Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210.
authors.forename: Anand
authors.initials: A
authors.lastname: Nagarajan
authors.affiliation: Department of Engineering, Otterbein University, Westerville, OH 43081.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Hudoba
authors.affiliation: Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Alvarez
authors.affiliation: Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210.
authors.forename: Carlos E
authors.initials: CE
authors.lastname: Castro
authors.affiliation: Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210;Department of Materials Science and Engineering, The Ohio State University, Columbus, OH 43210 e-mail: soghrati.1@osu.edu.
authors.forename: Soheil
authors.initials: S
authors.lastname: Soghrati
mesh_terms: D001331:Automation; D004247:DNA / Q000737:chemistry*; D008422:Materials Testing; D055595:Mechanical Phenomena; D049329:Nanostructures; D013718:Tensile Strength
chemical_list: D004247:DNA