Eulerian simulation of complex suspensions and biolocomotion in three dimensions

We present a numerical method specifically designed for simulating three-dimensional fluid–structure interaction (FSI) problems based on the reference map technique (RMT). The RMT is a fully Eulerian FSI numerical method that allows fluids and large-deformation elastic solids to be represented on a single fixed computational grid. This eliminates the need for meshing complex geometries typical in other FSI approaches and greatly simplifies the coupling between fluid and solids. We develop a three-dimensional implementation of the RMT, parallelized using the distributed memory paradigm, to simulate incompressible FSI with neo-Hookean solids. As part of our method, we develop a field extrapolation scheme that works efficiently in parallel. Through representative examples, we demonstrate the method’s suitability in investigating many-body and active systems, as well as its accuracy and convergence. The examples include settling of a mixture of heavy and buoyant soft ellipsoids, lid-driven cavity flow containing a soft sphere, and swimmers actuated via active stress.

Size and Structure of Empty and Filled Nanocontainer Based on Peptide Dendrimer with Histidine Spacers at Different pH

Novel peptide dendrimer with Lys-2His repeating units was recently synthesized, studied by NMR (Molecules, 2019, 24, 2481) and tested as a nanocontainer for siRNA delivery (Int. J. Mol. Sci., 2020, 21, 3138). Histidine amino acid residues were inserted in the spacers of this dendrimer. Increase of their charge with a pH decrease turns a surface-charged dendrimer into a volume-charged one and should change all properties. In this paper, the molecular dynamics simulation method was applied to compare the properties of the dendrimer in water with explicit counterions at two different pHs (at normal pH with neutral histidines and at low pH with fully protonated histidines) in a wide interval of temperatures. We obtained that the dendrimer at low pH has essentially larger size and size fluctuations. The electrostatic properties of the dendrimers are different but they are in good agreement with the theoretical soft sphere model and practically do not depend on temperature. We have shown that the effect of pairing of side imidazole groups is much stronger in the dendrimer with neutral histidines than in the dendrimer with protonated histidines. We also demonstrated that the capacity of a nanocontainer based on this dendrimer with protonated histidines is significantly larger than that of a nanocontainer with neutral histidines.

Sound Velocities of Generalized Lennard-Jones (n − 6) Fluids Near Freezing

In a recent paper [S. Khrapak, Molecules 25, 3498 (2020)], the longitudinal and transverse sound velocities of a conventional Lennard–Jones system at the liquid–solid coexistence were calculated. It was shown that the sound velocities remain almost invariant along the liquid–solid coexistence boundary lines and that their magnitudes are comparable with those of repulsive soft-sphere and hard-sphere models at the fluid–solid phase transition. This implies that attraction does not considerably affect the magnitude of the sound velocities at the fluid–solid phase transition. This paper provides further evidence to this by examining the generalized Lennard–Jones (n − 6) fluids with n ranging from 12 to 7 and demonstrating that the steepness of the repulsive term has only a minor effect on the magnitude of the sound velocities. Nevertheless, these minor trends are identified and discussed.

Critical spin periods of sub-km-sized cohesive rubble-pile asteroids: dependencies on material parameters

In this work, we employed a soft-sphere discrete element method with a cohesion implementation to model the dynamical process of sub-km-sized cohesive rubble piles under continuous spinup. The dependencies of the critical spin periods Tc on several material parameters for oblate rubble piles with different diameters were explored. Our simulations show that the interparticle cohesive force can strengthen the bodies as expected, especially for the smaller ones. The simulated results of Tc were fitted with the continuum theory developed by Holsapple (2007), through which we find the interparticle cohesion is proportional to the best-fit bulk cohesion and the ratio shows no dependency on the density. In addition, we find Tc decreases as the density increases in the compressive regime, while the trend reverses when transitioning to the tensile regime. Besides, though a higher friction angle can strengthen the bodies, its influence on Tc is minimized near the separation between the two regimes. Our numerical findings are generally consistent with the continuum theory, except that the latter predicts that Tc should increase as the friction angle increases in the tensile regime, which is contrary to the numerical results. This remarkable difference reminds us to take caution when applying the continuum theory to critically spinning cohesive rubble piles in the tensile regime, especially when dealing with the effect of the friction angle. Finally, we emphasize that the separation between the regimes can be specified by a characteristic period, which is only a function of density for a given shape.