45 research outputs found
Floating Patches of HCN at the Surface of Their Aqueous Solutions - Can They Make "HCN World" Plausible?
The liquid/vapor interface of the aqueous solutions of HCN of different concentrations has been investigated using molecular dynamics simulation and intrinsic surface analysis. Although HCN is fully miscible with water, strong interfacial adsorption of HCN is observed at the surface of its aqueous solutions, and, at the liquid surface, the HCN molecules tend to be located even at the outer edge of the surface layer. It turns out that in dilute systems the HCN concentration can be about an order of magnitude larger in the surface layer than in the bulk liquid phase. Furthermore, HCN molecules show a strong lateral self-association behavior at the liquid surface, forming thus floating HCN patches at the surface of their aqueous solutions. Moreover, HCN molecules are staying, on average, an order of magnitude longer at the liquid surface than water molecules, and this behavior is more pronounced at smaller HCN concentrations. Because of this enhanced dynamical stability, the floating HCN patches can provide excellent spots for polymerization of HCN, which can be the key step in the prebiotic synthesis of partially water-soluble adenine. All of these findings make the hypothesis of "HCN world" more plausible
Plate tectonics of virus shell assembly and reorganization in phage φ8, a distant relative of mammalian reoviruses
The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity
The phase diagram of water at high pressures as obtained by computer simulations of the TIP4P/2005 model: the appearance of a plastic crystal phase
In this work the high pressure region of the phase diagram of water has been
studied by computer simulation by using the TIP4P/2005 model of water. Free
energy calculations were performed for ices VII and VIII and for the fluid
phase to determine the melting curve of these ices. In addition molecular
dynamics simulations were performed at high temperatures (440K) observing the
spontaneous freezing of the liquid into a solid phase at pressures of about
80000 bar. The analysis of the structure obtained lead to the conclusion that a
plastic crystal phase was formed. In the plastic crystal phase the oxygen atoms
were arranged forming a body center cubic structure, as in ice VII, but the
water molecules were able to rotate almost freely. Free energy calculations
were performed for this new phase, and it was found that for TIP4P/2005 this
plastic crystal phase is thermodynamically stable with respect to ices VII and
VIII for temperatures higher than about 400K, although the precise value
depends on the pressure. By using Gibbs Duhem simulations, all coexistence
lines were determined, and the phase diagram of the TIP4P/2005 model was
obtained, including ices VIII and VII and the new plastic crystal phase. The
TIP4P/2005 model is able to describe qualitatively the phase diagram of water.
It would be of interest to study if such a plastic crystal phase does indeed
exist for real water. The nearly spherical shape of water makes possible the
formation of a plastic crystal phase at high temperatures. The formation of a
plastic crystal phase at high temperatures (with a bcc arrangements of oxygen
atoms) is fast from a kinetic point of view occurring in about 2ns. This is in
contrast to the nucleation of ice Ih which requires simulations of the order of
hundreds of ns