(95i) Stability of Peptoid Sheets and Tubes with Atomistic Molecular Dynamics Simulations

Authors: 
Wang, S., University of Washington
Alamdari, S., University of Washington
Dollar, O., University of Washington
Pfaendtner, J., University of Washington
Peptoids are n-substituted glycines that have great potential in nanotechnology and medicine due to their ability to assemble into hierarchical morphologies. It has previously been shown that amphiphilic peptoids can spontaneously assembly into both nanotube and sheet morphologies, through slight tuning of the side chain chemistry. However, the mechanism that drives peptoid nanotube formation remains unknown. We hypothesize that sheet formation is a precursor to the tube-configuration, and the mechanism of tube assembly is directly related to the flexibility of the peptoid sheet precursor. The goal of this project is to apply a computational technique known as molecular dynamics (MD) simulations to evaluate the fluctuations of peptoid sheets, probing these mechanisms of assembly. To accomplish this, first, we built a python package peptoid_tools which automates the construction of peptoid sheets with varying size and chemistry. Then we use Gromacs, an MD engine, to extract system dynamics. Lastly, we analyze the dynamics and calculate the bending modulus, providing a direct correlation between sheet flexibility and side-chain chemistry.