Computational DNA Nanotechnology Research Assistant

Duke University – Dr. Gaurav Arya's Lab

Duke University – Dr. Gaurav Arya's Lab | Summer 2026

Conducted computational research in DNA nanotechnology, focusing on the design, simulation, and structural analysis of DNA origami nanostructures. Designed DNA origami architectures in caDNAno, generated coarse-grained molecular models, and performed molecular dynamics simulations using oxDNA on Duke's high-performance computing cluster (DCC). Analysed simulation trajectories using oxDNA Analysis Tools (OAT) and developed a custom Python-based analysis toolkit to quantify structural stability through metrics including radius of gyration, centre of mass, energy profiles, and principal dimensions. Investigated DNA origami conformational behaviour and validated simulation outputs through computational analysis and visualization in oxView. Additionally, studied brush-functionalized DNA origami and the computational methods used to model and validate programmable polymer-functionalized nanostructures.

Skills & Tools: Python, Molecular Dynamics, oxDNA, oxDNA Analysis Tools (OAT), caDNAno, High-Performance Computing (Linux/Slurm), NumPy, Matplotlib, Scientific Computing, DNA Nanotechnology, Computational Modelling.