Large-scale Simulations of DNA nanostructures and synthetic membranes for protein/DNA integration

Narayana Aluru, University of Texas at Austin

Usage Details

DNA nanostructures have the advantage of being bio-compatible and programmable. The self-assembly features of DNA (due to chemical characteristics of nucleotide types) make DNA structures amenable for drug delivery, cancer therapy and smuggling the material into the cells. In the first part of our proposed project, we plan to explore the programmability features of a DNA origami nanobox by exploring the possibility of anchoring specific proteins/peptides. Since these structures, including the surrounding water, exceed 4,000,000 atoms, we need Blue Waters (BW) to successfully demonstrate the programmability of these nanostructures. In the second part of our project, we will focus on the design of solid-state membranes for transmembrane protein integration. Such designs help to connect the functional membrane proteins (ion channels, transporters, etc.) to electronic device platforms. We plan to use BW to identify next generation materials for the snap self-assembly, and energetically favorable membranes for protein integration. Also, as an extension to our previous efforts on DNA detection using 2D materials, we request more computational time to investigate the transverse quantum tunneling detection of cancerous, mutated DNA bases.