Colloids driven by phoresis constitute one of the main avenues for the design of synthetic microswimmers. For these swimmers, the specific form of the phoretic and hydrodynamic interactions dramatically influences their dynamics. Explicit solvent simulations allow the investigation of the different behaviors of dimeric Janus active colloids. The phoretic character is modified from thermophilic to thermophobic, and this, together with the relative size of the beads, strongly influences the resulting solvent velocity fields. Hydrodynamic flows can change from puller-type to pusher-type, although the actual flows significantly differ from these standard flows. Such hydrodynamic interactions combined with phoretic interactions between dimers result in several interesting phenomena in three-dimensional bulk conditions. Thermophilic dimeric swimmers are attracted to each other and form large and stable aggregates. Repulsive phoretic interactions among thermophobic dimeric swimmers hinder such clustering and lead, together with long- and short-ranged attractive hydrodynamic interactions, to short-lived, aligned swarming structures. Graphic Abstract

One of the most important components of a virus is the protein shell or capsid that encloses its genetic material. The main role of the capsid is to protect the viral genome against external aggressions, facilitating its safe and efficient encapsulation and delivery. As a consequence, viral capsids have developed astonishing mechanical properties that are crucial for viral function. These remarkable properties have started to be unveiled in single-virus nanoindentation experiments, and are opening the door to the use of viral-derived artificial nanocages for promising bio- and nano-technological applications. However, the interpretation of nanoindentation experiments is often difficult, requiring the support of theoretical and simulation analysis. Here we present a 'Virtual AFM' (VAFM), a Brownian Dynamics simulation of a coarse-grained model of virus aimed to mimic the standard setup of atomic force microscopy (AFM) nanoindentation experiments. Despite the heavy level of coarse-graining, these simulations provide valuable information which is not accessible in experiments. Rather than focusing on a specific virus, the VAFM will be used to analyze how the mechanical response and breaking of viruses depend on different parameters controlling the effective interactions between capsid's structural units. In particular, we will discuss the influence of adsorption, the tip radius, and the rigidity and shape of the shell on its mechanical response.

A realistic and effective model to simulate phoretic Brownian dynamics swimmers based on the general form of the thermophoretic force is here presented. The collective behavior of self-phoretic dimers is investigated with this model and compared with two simpler versions, allowing the understanding of the subtle interplay of steric interactions, propulsion, and phoretic effects. The phoretic Brownian dynamics method has control parameters which can be tuned to closely map the properties of experiments or simulations with explicit solvent, in particular those performed with multiparticle collision dynamics. The combination of the phoretic Brownian method and multiparticle collision dynamics is a powerful tool to precisely identify the importance of hydrodynamic interactions in systems of self-phoretic swimmers. Graphic Abstract

Self-thermophilic dimers are characterized by a net phoretic attraction which, in combination with hydrodynamic interactions, results into the formation of crystalline-like aggregates. To distinguish the effect of the different contributions...