The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes.
The driven self-assembly behaviors of hard nanoplates on soft elastic shells are investigated by using molecular dynamics(MD) simulation method, and the driven self-assembly structures of adsorbed hard nanoplates depend on the shape of hard nanoplates and the bending energy of soft elastic shells. Three main structures for adsorbed hard nanoplates,including the ordered aggregation structures of hard nanoplates for elastic shells with a moderate bending energy, the collapsed structures for elastic shells with a low bending energy, and the disordered aggregation structures for hard shells,are observed. The self-assembly process of adsorbed hard nanoplates is driven by the surface tension of the elastic shell,and the shape of driven self-assembly structures is determined on the basis of the minimization of the second moment of mass distribution. Meanwhile, the deformations of elastic shells can be controlled by the number of adsorbed rods as well as the length of adsorbed rods. This investigation can help us understand the complexity of the driven self-assembly of hard nanoplates on elastic shells.
A nonequilibrium molecular dynamics(NEMD) method is employed to study the dynamics of two identical vesicles with attractive interactions immersed in shear flow. The dynamics behaviors of attractive vesicles depend on the attractive interactions and the shear rates simultaneously. There are four motion types for attractive vesicles in shear flow: a coupled-tumbling(CTB) motion, a coupled-trembling(CTR) motion, a collision/rotation mixture(CRM) motion and a separated-tank-treading(STT) motion, which are determined by the competition between the shear flow and the attractive interactions. Furthermore, the dynamics behavior of an individual vesicle shows three main motion types such as tumbling, trembling and tank-treading motions, and relies mainly on the shear rates. Meanwhile, comparisons with rigid vesicles for the dynamics behaviors are made, and the collision/rotation mixture(M) motion isn't observed for rigid vesicles.
