Martini 3 application for the design of bistable nanomachines

TL;DR

This paper develops a coarse-grained Martini model to study the long-time behavior of nanoscale bistable nanomachines, building on previous all-atom molecular dynamics insights into foldamers resembling classical bistable systems.

Contribution

It introduces a new Martini-based coarse-grained modeling approach for nanoscale bistable machines, enabling long-term behavior analysis.

Findings

Identification of foldamers with bistable behavior

Development of a Martini coarse-grained model

Potential for long-time nanoscale machine simulations

Abstract

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