Computational modeling of passive transport of functionalized nanoparticles.

Functionalized nanoparticles (NPs) are complex objects present in a variety of systems ranging from synthetic grafted nanoparticles to viruses. The morphology and number of the decorating groups can vary widely between systems. Thus, the modeling of functionalized NPs typically considers simplified spherical objects as a first-order approximation. At the nanoscale label, complex hydrodynamic interactions are expected to emerge as the morphological features of the particles change, and they can be further amplified when the NPs are confined or near walls. Direct estimation of these variations can be inferred via diffusion coefficients of the NPs. However, the evaluation of the coefficients requires an improved representation of the NPs morphology to reproduce important features hidden by simplified spherical models. Here, we characterize the passive transport of free and confined functionalized nanoparticles using the Rigid Multi-Blob (RMB) method. The main advantage of RMB is its versatility to approximate the mobility of complex structures at the nanoscale with significant accuracy and reduced computational cost. In particular, we investigate the effect of functional groups' distribution, size, and morphology over nanoparticle translational and rotational diffusion. We identify that the presence of functional groups significantly affects the rotational diffusion of the nanoparticles; moreover, the morphology of the groups and number induce characteristic mobility reduction compared to non-functionalized nanoparticles. Confined NPs also evidenced important alterations in their diffusivity, with distinctive signatures in the off-diagonal contributions of the rotational diffusion. These results can be exploited in various applications, including biomedical, polymer nanocomposite fabrication, drug delivery, and imaging.

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 envelopes decorated with surface proteins (a.k.a. spikes). Depending on the virus type, a large variability is present in the surface-proteins number, morphology and reactivity, which remains generally unexplained. Since viruses' transmissibility depends 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 virus differentiation. To understand how the spikes affect virion mobility and infectivity, we investigate the diffusivity of spike-decorated 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.

Metallic microswimmers driven up the wall by gravity.

Experiments on autophoretic bimetallic nanorods propelling within a fuel of hydrogen peroxide show that tail-heavy swimmers preferentially orient upwards and ascend along inclined planes. We show that such gravitaxis is strongly facilitated by interactions with solid boundaries, allowing even ultraheavy microswimmers to climb nearly vertical surfaces. Theory and simulations show that the buoyancy or gravitational torque that tends to align the rods is reinforced by a fore-aft drag asymmetry induced by hydrodynamic interactions with the wall.

Relating Rheotaxis and Hydrodynamic Actuation using Asymmetric Gold-Platinum Phoretic Rods.

We explore the behavior of micron-scale autophoretic Janus (Au/Pt) rods, having various Au/Pt length ratios, swimming near a wall in an imposed background flow. We find that their ability to robustly orient and move upstream, i.e., to rheotax, depends strongly on the Au/Pt ratio, which is easily tunable in synthesis. Numerical simulations of swimming rods actuated by a surface slip show a similar rheotactic tunability when varying the location of the surface slip versus surface drag. The slip location determines whether swimmers are pushers (rear actuated), pullers (front actuated), or in between. Our simulations and modeling show that pullers rheotax most robustly due to their larger tilt angle to the wall, which makes them responsive to flow gradients. Thus, rheotactic response infers the nature of difficult to measure flow fields of an active particle, establishes its dependence on swimmer type, and shows how Janus rods can be tuned for flow responsiveness.

Brownian dynamics without Green's functions.

We develop a Fluctuating Immersed Boundary (FIB) method for performing Brownian dynamics simulations of confined particle suspensions. Unlike traditional methods which employ analytical Green's functions for Stokes flow in the confined geometry, the FIB method uses a fluctuating finite-volume Stokes solver to generate the action of the response functions "on the fly." Importantly, we demonstrate that both the deterministic terms necessary to capture the hydrodynamic interactions among the suspended particles, as well as the stochastic terms necessary to generate the hydrodynamically correlated Brownian motion, can be generated by solving the steady Stokes equations numerically only once per time step. This is accomplished by including a stochastic contribution to the stress tensor in the fluid equations consistent with fluctuating hydrodynamics. We develop novel temporal integrators that account for the multiplicative nature of the noise in the equations of Brownian dynamics and the strong dependence of the mobility on the configuration for confined systems. Notably, we propose a random finite difference approach to approximating the stochastic drift proportional to the divergence of the configuration-dependent mobility matrix. Through comparisons with analytical and existing computational results, we numerically demonstrate the ability of the FIB method to accurately capture both the static (equilibrium) and dynamic properties of interacting particles in flow.

Applications of computational geometry to the molecular simulation of interfaces.

The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose an alternative point of view, making use of concepts taken from the field of computational geometry, where the definition of the "shape" of a set of points is a well-known problem. In particular, we employ the alpha -shape construction which, applied to the positions of the molecules, selects a shape and identifies its boundary points, which we will take to define our interfacial molecules. A single parameter needs to be fixed (the "alpha" of the alpha shape), and several proposals are examined, all leading to very similar choices. Results of this methodology are evaluated against previous proposals, and seen to be reasonable.