Roughness-Dependent Retention of a Reduced Rabies-Virus Model in a Platinum Nanochannel: A Molecular Dynamics Study

Abstract

Capturing nanoscale biological objects in nanochannels depends strongly on surface geometry and interfacial interactions. However, the spatial and temporal limitations of atomistic simulations prevent the direct representation of a complete rabies virion. In this study, we used molecular dynamics simulations to examine the force-driven retention of a reduced rabies-virus model with a characteristic size of approximately 4 nm in a water-filled platinum nanochannel with non-ideal surface roughness. The simulated construct was developed from reported rabies-virus structural information but did not reproduce the complete morphology, envelope, genomic content, or biological functionality of an intact virion. The atomic interactions were described using DREIDING and Universal Force Field parameters, the TIP3P water model, the embedded atom method for Pt–Pt interactions, and Lennard-Jones and Coulombic terms for interfacial interactions. After 10 ns of canonical equilibration at 300 K, the system underwent a 20 ns force-driven production stage. Roughness sizes of 35, 37, 40, and 43 Å were investigated. Among the four simulated configurations, the 40 Å roughness case produced the largest maximum density (0.187 atom/ų), the lowest maximum velocity (0.006 Å/ps), the largest retained surface-mesh volume (31,118 ų), and the most negative reduced-model–Pt interaction energy (−469.91 kcal/mol). The simulation-defined retained fraction for the reduced construct reached 95% at 20 ns. The weaker responses at 43 Å indicated a nonmonotonic dependence on roughness size within this model and the investigated geometries. These results characterized the force-driven behavior of a specific 4-nm construct under the stated simulation conditions; they did not establish roughness-dependent capture behavior for intact rabies virions or predict experimental device performance.