Coarse-Grained Molecular Dynamic Simulation of DNA-Linked Nanoparticle Building Blocks on a GPU

Abstract

Synthesis of DNA-linked nanoparticle building blocks (nBLOCKs) with well-defined arrangements of mono-functionalized anisotropic DNA in all three dimensions promises advancement in the programmable self-assembly of anisotropic nanostructures with precisely designed geometry and complex functionality. Designing for the self-assembly of complex functional structures with arbitrary sizes, shapes, and compositions remains challenging. Simulating the molecular dynamics of the self-assembly of nanostructures is a principled approach to designing systems of nBLOCKs. However, as the number of nBLOCKs increases, the time required to simulate the molecular dynamics of these nBLOCKs rapidly escalates. Here, we present a coarse-grained model for the self-assembly of nBLOCKs as an extension of the oxDNA2 model, which we implemented for central processing units (CPUs) and graphical processing units (GPUs). We demonstrated the potential of self-assembling the nanostructures of our previous experimental results and present results which verify the nBLOCK model as well as the CPU/GPU software implementations of this model.