Computational study of phage adsorption dynamics on cell membranes

Abstract

The motivation of this work originated from the interest in understanding viral adsorption phenomena from a physical perspective, particularly in systems involving anisotropic particles such as bacteriophages. When suspended in a fluid, bacteriophages interact with bacterial surfaces through a combination of hydrodynamic effects, steric constraints, and anisotropic surface affinities. Therefore, their adsorption and alignment on cellular membranes are governed not only by biochemical interactions but also by fluid-mediated transport and orientation processes. To capture these features, we developed a coarse-grained model composed of anisotropic dimers embedded in a dissipative fluid. The dimers represent elongated viral particles, where anisotropy is introduced through interaction asymmetry between the two components. Bacterial surfaces were represented by granular walls, which allow control of physical characteristics such as roughness and affinity distribution. The construction of the model is intentionally general: although motivated by phage–bacteria interactions, it can be tuned to reproduce other physical systems that share similar geometric constraints, adsorption mechanisms, or anisotropic interactions. Dissipative Particle Dynamics (DPD) was selected as the simulation method due to its ability to simultaneously reproduce hydrodynamic behavior, excluded-volume interactions, and mesoscale thermal fluctuations. Within this framework, we performed systematic studies on the effects of wall morphology, surface affinity, hydrophobicity on dimer adsorption and an analysis of the orientational behavior of the dimers was conducted, revealing how hydrodynamic conditions and heterogeneous surface affinities influence the system.