arXiv subjects

Geyao Gu

Publications and source records attributed to Geyao Gu.

3 recordsLinked to original sources

arXiv2026

It Takes Two to Make a Thing Go Right: Boosting Current in Coupled Motors

Catalysis-driven synthetic molecular motors operate in a loose mechanochemical coupling regime, one in which a decomposition of a fuel molecule does not reliably produce a forward step. In that regime, stochastic backward steps can significantly degrade the motor's current, prompting us to ask whether mechanically coupling multiple such motors can boost their averaged current. By simulating rotaxane-based motors with two classes of models--particle-based nonequilibrium molecular dynamics and jump-diffusion models--we show that current boosts are physically achievable. Our observed boosts, which amplify current by single-digit factors, emerge when coupling between motors can increase the activity, speeding up the rate of both forward and backward steps. In doing so, the bias for preferring forward steps actually degrades, but the lost bias can be largely recovered by raising the fuel concentration, demonstrating a general design strategy: amplify activity through coupling and restore bias through stronger driving.

cond-mat.stat-mech↗

arXiv2023

Sterically Driven Current Reversal in a Model Molecular Motor

Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical behavior to reverse directions. Inspired by autonomous synthetic catenane motors, we study the molecular dynamics of a minimal motor model, consisting of a shuttling ring that moves along a track containing interspersed binding sites and catalytic sites. The binding sites attract the shuttling ring while the catalytic sites speed up a reaction between molecular species, which can be thought of as fuel and waste. When that fuel and waste are held in a nonequilibrium steady-state concentration, the free energy from the reaction drives directed motion of the shuttling ring along the track. Using this model and nonequilibrium molecular dynamics, we show that the shuttling ring's direction can be reversed by simply adjusting the spacing between binding and catalytic sites on the track. We present a steric mechanism behind the current reversal, supported by kinetic measurements from the simulations. These results demonstrate how molecular simulation can guide future development of artificial molecular motors.

cond-mat.stat-mech↗

arXiv2023

Limits on the Precision of Catenane Molecular Motors: Insights from Thermodynamics and Molecular Dynamics Simulations

Thermodynamic uncertainty relations (TURs) relate precision to the dissipation rate, yet the inequalities can be far from saturation. Indeed, in catenane molecular motor simulations, we record precision far below the TUR limit. We further show that this inefficiency can be anticipated by four physical parameters: the thermodynamic driving force, fuel decomposition rate, coupling between fuel decomposition and motor motion, and rate of undriven motor motion. The physical insights might assist in designing molecular motors in the future.

cond-mat.stat-mech↗