Confinement and shear effects on the rotational diffusion of a minimal virus-inspired colloidal particle

The rotational diffusion of a rigid spherical body decorated with dimers in an explicit fluid environment is reported. This model acts as a simplified representation of an enveloped virus bearing peplomers immersed in a coarse-grained fluid. Using dissipative particle dynamics, we explicitly study the hydrodynamic effects on the rotational diffusion of this virus-inspired particle subjected to oscillatory shear flow and confined between two solid-like surfaces. Since the rotational response depends on the type of imposed flow, we first characterize the oscillatory shear, identifying distinct flow regimes in terms of the so-called Péclet number, $Pe$. Our findings indicate that, under confinement, the rotational diffusivity is strongly modulated by the oscillatory flow amplitude and only weakly affected by the number of peplomers, since their effect is mainly determined by their dimeric structure and associated effective size. For high $Pe$, the rotational diffusion coefficient, $D_{r}$, tends to decrease as the number of peplomers ($N_{s}$) increases, whereas at low $Pe$, rotational diffusion becomes weakly dependent on the number of peplomers. However, at intermediate values of $Pe$, the interplay between oscillatory forcing and thermal fluctuations prevents the emergence of a clear trend between $D_{r}$ and $N_{s}$. Our results provide a clear picture of how, in confined environments, the interplay between fluid flow and thermal fluctuations affects the rotational diffusion of spiked particles, thereby helping to explain how fluid conditions can modify the alignment of peplomers with their potential targets.

💡 Research Summary

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This paper presents a systematic investigation of the rotational diffusion of a virus‑inspired colloidal particle using dissipative particle dynamics (DPD). The model consists of a rigid spherical core decorated with a controllable number (Nₛ) of dimers that represent viral peplomers (spikes). The particle is placed in a coarse‑grained DPD fluid confined between two parallel, hydrophilic walls, thereby mimicking the restricted environment of respiratory tracts or other biological conduits. An oscillatory shear flow is imposed in the y‑direction, with a sinusoidal shear rate γ̇(t)=γ̇₀ sin(ωt). The flow strength is quantified by the Péclet number Pe = γ̇₀ τ_D, where τ_D is the characteristic rotational diffusion time of the particle. By varying Pe over several orders of magnitude (≈0.1 to 100) the authors identify three distinct regimes: low‑Pe (thermal fluctuations dominate), intermediate‑Pe (thermal and shear contributions comparable), and high‑Pe (shear dominates).

Methodologically, the DPD fluid contains 56 700 particles at a reduced density ρ_f = 3, with conservative force parameter a_ff = 75 k_BT/r_c, ensuring realistic compressibility and viscosity. Walls are constructed from frozen DPD particles with identical fluid‑wall repulsion (a_fw = a_ff) to enforce a no‑slip condition. The viral core comprises 819 DPD beads arranged in concentric circles, while each peplomer is a rigid dimer of two beads protruding from the surface. Simulations run for 10⁶ time steps, providing statistically converged measurements of the mean‑square angular displacement ⟨Δθ²⟩, from which the rotational diffusion coefficient D_r = ⟨Δθ²⟩/(2Δt) is extracted.

The results reveal that confinement dramatically amplifies the influence of the imposed shear on rotational dynamics. In the low‑Pe regime, D_r remains essentially constant across all Nₛ values, indicating that thermal agitation overwhelms any hydrodynamic torque generated by the spikes. In the high‑Pe regime, D_r decreases monotonically with increasing Nₛ (up to ~20 % reduction for the largest spike count), reflecting the larger hydrodynamic drag and increased rotational inertia associated with a greater effective radius. The intermediate‑Pe regime exhibits a non‑monotonic, noisy dependence of D_r on Nₛ; here the competition between shear‑induced alignment and random thermal kicks prevents a clear trend, and the particle experiences intermittent periods of alignment and re‑orientation.

These findings have direct relevance to enveloped viruses such as SARS‑CoV‑2, which navigate confined, shear‑laden environments (e.g., mucus layers, airway passages). The study suggests that in high‑shear regions, a higher spike density could hinder rotational freedom, potentially reducing the probability of optimal spike‑receptor alignment. Conversely, in low‑shear zones, spike density plays a negligible role, allowing the virus to explore orientations freely.

The paper concludes that (i) oscillatory shear amplitude is the primary driver of rotational diffusivity under confinement, (ii) spike number matters only when shear dominates, and (iii) the intermediate regime is governed by a delicate balance of thermal and hydrodynamic forces, leading to complex, non‑linear rotational behavior. The authors argue that the minimal DPD model captures essential physics while remaining computationally tractable, and they propose future extensions to incorporate flexible spikes, heterogeneous spike distributions, and non‑Newtonian fluid properties to more closely emulate physiological conditions.