Martini 3 application for the design of bistable nanomachines

TL;DR

This work addresses long-timescale bistable molecular machines by deploying Martini3 coarse-grained MD to update PNIPA parameters and to validate bistable dynamics of oligo-PF-5 in THF. The approach combines partitioning-free-energy–driven PNIPA parameterization, Divide and Conquer mapping for oligo-PF-5, and NVT simulations with pulling experiments to reveal force-induced bistability and stochastic resonance, including $R_e$ states near $0.4$ nm and $0.75$ nm and a critical force $F_c$ around $70$ pN. It also demonstrates temperature-dependent CG representations for PNIPA, with below LCST and above LCST mappings chosen to reproduce coil/globule behavior, supported by radius-of-gyration analyses. Collectively, the results validate Martini3 as a capable, scalable tool for modeling bistable nanosystems in both hydrophilic and hydrophobic solvents, enabling exploration of large, coupled molecular machines and their dynamic responses.

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.

Figures (5)

• Figure 1: Chemical structure of (a) cis-pyridine-furan monomer unit (b) poly(N-isopropylacrylamide) monomer unit.
• Figure 2: Mapping scheme of (a) cis-pyridine-furan monomer unit (b) poly(N-isopropylacrylamide) monomer unit.
• Figure 3: (a) Coarse-grained model of the oligo-PF-$5$ system with a pulling force. The squeezed and the stress–strain states of the spring are shown on the left and right, respectively. The yellow spheres at the lower end of the spring indicate the fixation of the pyridine ring by rigid harmonic force. The pulling force, $F$, is applied to the top end of the spring. (b) The state diagram shows a linear elasticity of oligo-PF-$5$ spring up to $F\approx 70pN$ and bistability of the spring in the region from $F\approx70- 120pN$; (c) Spontaneous vibrations of the oligo-PF-$5$ spring at $F\approx 100pN$; (d) Evolution of the probability density for the squeezed and stress–strain states when pulling force surpasses the critical value.
• Figure 4: Stochastic resonance of the oligo-PF-$5$ induced by an oscillating field $E = E_{0} \cos (2 \pi \nu t)=E_{0} \cos (2 \pi t/T)$: (a) The dynamic trajectory at $F = 100pN$, $T = 16.67ns$, and $E_{0} = 0.025V\per nm$; (b) Power spectra of spontaneous vibrations (red curve) and stochastic resonance (black curve); (c) The dependence of the main resonance peak amplitude on the period $T$ of oscillating field ($E_{0}=0.025V\per nm$); (d) The dependence of the main resonance peak amplitude on $E_{0}$ ($T_{0}=16.67ns$).
• Figure 5: The representation of isotactic PNIPA of $30$ monomer units: the probability distribution of the radius of gyration at (a) $280K$ and $330K$; (b) the radii of gyration vs time for isotactic PNIPA at $280K$ and $330K$ with $N=30$ monomer units; snapshot of PNIPA at (c) $280K$; (d) $330K$.