Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses

Many viruses, such as SARS-CoV-2 or Influenza, possess spike-decorated envelopes. Depending on the virus type, a large variability is present in spikes number, morphology and reactivity, which remains generally unexplained. Since viruses' transmissibility depend on features beyond their genetic sequence, new tools are required to discern the effects of spikes functionality, interaction, and morphology. Here, we postulate the relevance of hydrodynamic interactions in the viral infectivity of enveloped viruses and propose micro-rheological characterization as a platform for viruses differentiation. To understand how the spikes affect virion mobility and infectivity, we investigate the diffusivity of spike-decorate structures using mesoscopic-hydrodynamic simulations. Furthermore, we explored the interplay between affinity and passive viral transport. Our results revealed that the diffusional mechanism of SARS-CoV-2 is strongly influenced by the size and distribution of its spikes. We propose and validate a universal mechanism to explain the link between optimal virion structure and maximal infectivity for many virus families.

Thermally Fluctuating, Semiflexible Sheets in Simple Shear Flow

We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy...

Hydrodynamic interactions and extreme particle clustering in turbulence

Expanding recent observations by Hammond & Meng (J. Fluid Mech., vol. 921, 2021, A16), we present a range of detailed experimental data of the radial distribution function (r.d.f.) of inertial particles in isotropic turbulence for different Stokes number, $St$ , showing that the r.d.f. grows explosively with decreasing separation r, exhibiting $r^{-6}$ scaling as the collision radius is approached, regardless of $St$ or particle radius $a$ . To understand such explosive clustering, we correct a number of errors in the theory by Yavuz et al. (Phys. Rev. Lett., vol. 120, 2018, 244504) based on hydrodynamic interactions between pairs of small, weakly inertial particles. A comparison between the corrected theory and the experiment shows that the theory by Yavuz et al. underpredicts the r.d.f. by orders of magnitude. To explain this discrepancy, we explore several alternative mechanisms for this discrepancy that were not included in the theory and show that none of them are likely the explanation. This suggests new, yet-to-be-identified physical mechanisms are at play, requiring further investigation and new theories.

AN EXPERIMENTAL STUDY OF SHIP MOTIONS DURING REPLENISHMENT AT SEA OPERATIONS BETWEEN A SUPPLY VESSEL AND A LANDING HELICOPTER DOCK

Hydrodynamic interactions during Replenishment at Sea (RAS) operations can lead to large ship motions and make it difficult for vessels to maintain station during the operation. A research program has been established which aims to validate numerical seakeeping tools to enable the development of enhanced operator guidance for RAS. This paper presents analysis of the first phase of scale model experiments and focuses on the influence that both the lateral and longitudinal separations between two vessels have on the interactions during RAS. The experiments are conducted in regular head seas on a Landing Helicopter Dock (LHD) and a Supply Vessel (SV) in intermediate water depth. The SV is shorter than the LHD by approximately 17%, but due to its larger block coefficient, it displaces almost 16% more than the LHD. Generally, the motions of the SV were larger than the LHD. It was found that hydrodynamic interactions can lead to large SV roll motions in head seas. Directions for future work are provided.

Simulations of dynamically cross-linked actin networks: Morphology, rheology, and hydrodynamic interactions

Cross-linked actin networks are the primary component of the cell cytoskeleton and have been the subject of numerous experimental and modeling studies. While these studies have demonstrated that the networks are viscoelastic materials, evolving from elastic solids on short timescales to viscous fluids on long ones, questions remain about the duration of each asymptotic regime, the role of the surrounding fluid, and the behavior of the networks on intermediate timescales. Here we perform detailed simulations of passively cross-linked non-Brownian actin networks to quantify the principal timescales involved in the elastoviscous behavior, study the role of nonlocal hydrodynamic interactions, and parameterize continuum models from discrete stochastic simulations. To do this, we extend our recent computational framework for semiflexible filament suspensions, which is based on nonlocal slender body theory, to actin networks with dynamic cross linkers and finite filament lifetime. We introduce a model where the cross linkers are elastic springs with sticky ends stochastically binding to and unbinding from the elastic filaments, which randomly turn over at a characteristic rate. We show that, depending on the parameters, the network evolves to a steady state morphology that is either an isotropic actin mesh or a mesh with embedded actin bundles. For different degrees of bundling, we numerically apply small-amplitude oscillatory shear deformation to extract three timescales from networks of hundreds of filaments and cross linkers. We analyze the dependence of these timescales, which range from the order of hundredths of a second to the actin turnover time of several seconds, on the dynamic nature of the links, solvent viscosity, and filament bending stiffness. We show that the network is mostly elastic on the short time scale, with the elasticity coming mainly from the cross links, and viscous on the long time scale, with the effective viscosity originating primarily from stretching and breaking of the cross links. We show that the influence of nonlocal hydrodynamic interactions depends on the network morphology: for homogeneous meshworks, nonlocal hydrodynamics gives only a small correction to the viscous behavior, but for bundled networks it both hinders the formation of bundles and significantly lowers the resistance to shear once bundles are formed. We use our results to construct three-timescale generalized Maxwell models of the networks.

Interactions in Active Colloids

The past two decades have seen a remarkable progress in the development of synthetic colloidal agents which are capable of creating directed motion in an unbiased environment at the microscale. These self-propelling particles are often praised for their enormous potential to self-organize into dynamic nonequilibrium structures such as living clusters, synchronized superrotor structures or self-propelling molecules featuring a complexity which is rarely found outside of the living world. However, the precise mechanisms underlying the formation and dynamics of many of these structures are still barely understood, which is likely to hinge on the gaps in our understanding of how active colloids interact. In particular, besides showing comparatively short-ranged interactions which are well known from passive colloids (Van der Waals, electrostatic etc.), active colloids show novel hydrodynamic interactions as well as phoretic and substrate-mediated “osmotic” cross-interactions which hinge on the action of the phoretic field gradients which are induced by the colloids on other colloids in the system. The present article discusses the complexity and the intriguing properties of these interactions which in general are long-ranged, non-instantaneous, nonpairwise and non-reciprocal and which may serve as key ingredients for the design of future nonequilibrium colloidal materials. Besides providing a brief overview on the state of the art of our understanding of these interactions a key aim of this review is to emphasize open key questions and corresponding open challenges.

Effects of Gap Resonance on the Hydrodynamics and Dynamics of a Multi-Module Floating System with Narrow Gaps

Multi-module floating system has attracted much attention in recent years as ocean space utilization becomes more demanding. This type of structural system has potential applications in the design and construction of floating piers, floating airports and Mobile Offshore Bases (MOBs) generally consists of multiple modules with narrow gaps in which hydrodynamic interactions play a non-neglected role. This study considers a numerical model consisting of several rectangular modules to study the hydrodynamics and dynamics of the multi-module floating system subjected to the waves. Based on ANSYS-AQWA, both frequency-domain and time-domain simulations are performed to analyze the complex multi-body hydrodynamic interactions by introducing artificial damping on the gap surfaces. Parametric studies are carried out to investigate the effects of the gap width, shielding effects of the multi-body system, artificial damping ratio on the gap surface, and the dependency of the hydrodynamic interaction effect on wave headings is clarified. Based on the results, it is found that the numerical analysis based on the potential flow theory with artificial damping introduced can produce accurate results for the normal wave period range. In addition, the effects of artificial damping on the dynamics and connector loads are investigated by using a simplified RMFC model. For the case of adding an artificial damping ratio of 0.2, the relative heave and pitch motions are found to be reduced by 33% and 50%, respectively. In addition, the maximum cable and fender forces are found to be reduced by 50%, compared with the case without viscosity correction.