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

TL;DR

This study uses dissipative particle dynamics to explore how confinement and oscillatory shear modify the rotational diffusion of a minimal virus-inspired, spike-decorated particle. By modeling a rigid sphere bearing dimers as peplomers and simulating it in an explicit DPD solvent between two walls, the authors quantify rotational diffusion $D_r$ across a wide range of Peclet numbers $Pe$ and peplomer counts $N_s$, revealing regime-dependent trends. High-$Pe$ flows enhance the coupling between surface anisotropy and confinement, producing a clear decrease of $D_r$ with increasing $N_s$ that follows a local logarithmic form, while low-$Pe$ regimes show weak or no systematic dependence on $N_s$ due to thermal fluctuations dominating the dynamics. The work highlights how fluid conditions, confinement, and spike distribution jointly shape the orientational dynamics of spike-bearing particles, with implications for understanding virus–host interactions in complex, confined environments.

Abstract

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.

Figures (10)

• Figure 1: Snapshot of the simulation model, which consists of a DPD fluid between two parallel walls, where periodic boundary conditions are applied in the $x-z$ directions, and wall boundary conditions are applied in the $y$ direction. Blue particles represent the fluid, green and purple particles correspond to the top and bottom walls, respectively.
• Figure 2: The virus model is composed of DPD particles, where each virus is represented as a rigid structure with a variable distribution of peplomers on its surface. The number of peplomers $N_{s}$ ranges from 20 to 50 to achieve a homogeneous distribution on the virus surface. The second virus model with $N_{s}=30$ is based on the work of Yu et al.Yu. The case without peplomers ($N_{s}=0$) is also considered to provide a meaningful comparison with the virus containing peplomers.
• Figure 3: Schematic representation of the rigid virus model rotating around the $z$-axis with an angular frequency $\bar{\omega}$.
• Figure 4: Velocity profiles of a confined DPD fluid subjected to oscillatory shear at a constant frequency, $\omega$. The velocity component $v_{x}(y)$ is normalized by the velocity $U_{o}$ (see Eq. (\ref{['upper']}) or Eq. (\ref{['lower']}). Profiles are recorded over a time interval ranging from $0$ to $\sim 5\times 10^{3}$ time steps, corresponding to frames from $t_{0}$ to $t_{74}$, where the subscripts denote frame numbers sampled every $80$ time steps. (a) $Pe = 17.6$: the oscillatory shear flow fully dominates over thermal fluctuations. (b) $Pe = 5.03$: the shear flow remains dominant, although thermal motion introduces noticeable fluctuations. (c) $Pe = 1.26$: thermal motion becomes dominant over the imposed shear, leading to significant profile distortions while a weak shear signature persists. (d) $Pe = 0.754$: thermal fluctuations dominate, effectively suppressing the shear-induced velocity profile.
• Figure 5: Initial configuration of the virus model subjected to oscillatory shear flow between two parallel walls. The red arrows indicate the oscillatory velocities applied to the walls. The wall separation is $2h$, and the virus is placed at the center of the simulation box, without contacting the walls. Fluid beads are rendered at a reduced size to improve the visibility of the virus.