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.
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April 2017
Research-Article
Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic Acid Origami Nanoplates
Bowen Liang,
Bowen Liang
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
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Anand Nagarajan,
Anand Nagarajan
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
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Michael W. Hudoba,
Michael W. Hudoba
Department of Engineering,
Otterbein University,
Westerville, OH 43081
Otterbein University,
Westerville, OH 43081
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Ricardo Alvarez,
Ricardo Alvarez
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
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Carlos E. Castro,
Carlos E. Castro
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
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Soheil Soghrati
Soheil Soghrati
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210;
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
Science and Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: soghrati.1@osu.edu
Search for other works by this author on:
Bowen Liang
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Anand Nagarajan
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Michael W. Hudoba
Department of Engineering,
Otterbein University,
Westerville, OH 43081
Otterbein University,
Westerville, OH 43081
Ricardo Alvarez
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Carlos E. Castro
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210
Soheil Soghrati
Department of Mechanical and
Aerospace Engineering,
The Ohio State University,
Columbus, OH 43210;
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
Science and Engineering,
The Ohio State University,
Columbus, OH 43210
e-mail: soghrati.1@osu.edu
1Corresponding author.
Manuscript received October 8, 2016; final manuscript received February 3, 2017; published online March 1, 2017. Assoc. Editor: Jeffrey Ruberti.
J Biomech Eng. Apr 2017, 139(4): 041003 (8 pages)
Published Online: March 1, 2017
Article history
Received:
October 8, 2016
Revised:
February 3, 2017
Citation
Liang, B., Nagarajan, A., Hudoba, M. W., Alvarez, R., Castro, C. E., and Soghrati, S. (March 1, 2017). "Automated Quantification of the Impact of Defects on the Mechanical Behavior of Deoxyribonucleic Acid Origami Nanoplates." ASME. J Biomech Eng. April 2017; 139(4): 041003. https://doi.org/10.1115/1.4036022
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