Spatiotemporal intermittency and localized dynamic fluctuations upon approaching the glass transition.

We introduce a robust approach for characterizing spatially and temporally heterogeneous behavior within a system based on the evolution of dynamic fluctuations averaged over different space lengths and timescales. We apply it to investigate the dynamics in two canonical systems as the glass transition is approached: simulated Lennard-Jones liquids and experimental dense colloidal suspensions. In both cases the onset of glassiness is marked by spatially localized dynamic fluctuations originating in regions of correlated mobile particles. By removing the trivial system size dependence we show that the spatial heterogeneity of the dynamics extends to large length scales containing tens to hundreds of particles, corresponding to the timescale of maximally non-Gaussian dynamics.

Structure and dynamics of high- and low-density water molecules in the liquid and supercooled regimes.

By combining the local structure index with potential energy minimisations we study the local environment of the water molecules for a couple of water models, TIP5P-Ew and SPC/E, in order to characterise low- and high-density "species". Both models show a similar behaviour within the supercooled regime, with two clearly distinguishable populations of unstructured and structured molecules, the fraction of the latter increasing with supercooling. Additionally, for TIP5P-Ew, we find that the structured component vanishes quickly at the normal liquid regime (above the melting temperature). Thus, while SPC/E provides a fraction of structured molecules similar to that found in X-ray experiments, we show that TIP5P-Ew underestimates such value. Moreover, unlike SPC/E, we demonstrate that TIP5P-Ew does not follow the linear dependence of the logarithm of the structured fraction with inverse temperature, as predicted by the two-order parameter model. Finally, we link structure to dynamics by showing that there exists a strong correlation between structural fluctuation and dynamics in the supercooled state with spatial correlations in both static and dynamic quantities.

Hydrophilic behavior of graphene and graphene-based materials.

Graphene and the graphene-based materials like graphite, carbon nanotubes, and fullerenes are not only usually regarded as hydrophobic but also have been widely employed as paradigms for the investigation of the behavior of water under nonpolar confinement, a question of major concern for fields ranging from biology to materials design. However, some experimental and theoretical insights seem to contradict, at least partially, such a picture. In this work, we will provide firm evidence for a neat hydrophilic nature of graphene surfaces. Our molecular dynamics studies will demonstrate that parallel graphene sheets present a strong tendency to remain fully hydrated for moderately long times (even when the equilibrium state is indeed the collapse of the plates), and thus, they are less prone to self-assembly than model hydrophobic surfaces we shall employ as control which readily undergo a hydrophobic collapse. Potential of mean force calculations will indeed make evident that the solvent exerts a repulsive contribution on the self-assembly of graphene surfaces. Moreover, we shall also quantify graphene hydrophilicity by means of the calculation of water density at two pressures and water density fluctuations. This latter study has never been performed on graphene and represents a means both to confirm and to quantify its neat hydrophilic behavior. We shall also make evident the relevance of the mildly attractive water-carbon interactions, since their artificial weakening will be shown to revert from typically hydrophilic to typically hydrophobic behavior.

Protein packing defects "heat up" interfacial water.

Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

Wrapping effects within a proposed function-rescue strategy for the Y220C oncogenic mutation of protein p53.

Soluble proteins must protect their structural integrity from water attack by wrapping interactions which imply the clustering of nonpolar residues around the backbone hydrogen bonds. Thus, poorly wrapped hydrogen bonds constitute defects which have been identified as promoters of protein associations since they favor the removal of hydrating molecules. More specifically, a recent study of our group has shown that wrapping interactions allow the successful identification of protein binding hot spots. Additionally, we have also shown that drugs disruptive of protein-protein interfaces tend to mimic the wrapping behavior of the protein they replace. Within this context, in this work we study wrapping three body interactions related to the oncogenic Y220C mutation of the tumor suppressor protein p53. Our computational results rationalize the oncogenic nature of the Y220C mutation, explain the binding of a drug-like molecule already designed to restore the function of p53 and provide clues to help improve this function-rescue strategy and to apply in other drug design or re-engineering techniques.