Martini 3 application for the design of bistable nanomachines

Abstract

During our previous modeling using all-atom molecular dynamics, we identified several foldamers whose nanoscale behavior resembles that of classic bistable machines, namely, Euler archs and Duffing oscillators. However, the time limitations of the all-atom molecular dynamics prevent us from performing a full-scale investigation of the long-time behavior and prompt us to develop a coarse-grained model. In this paper, we summarize our recent research on developing such models using the most widely available method called Martini.