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Structures and thermodynamics of water encapsulated by graphene.

ABSTRACT: Understanding phase behaviors of nanoconfined water has driven notable research interests recently. In this work, we examine water encapsulated under a graphene cover that offers an ideal testbed to explore its molecular structures and thermodynamics. We find layered water structures for up to ~1000 trapped water molecules, which is stabilized by the spatial confinement and pressure induced by interfacial adhesion. For monolayer encapsulations, we identify representative two-dimensional crystalline lattices as well as defects therein. Free energy analysis shows that the structural orders with low entropy are compensated by high formation energies due to the pressurized confinement. There exists an order-to-disorder transition for this condensed phase at ~480-490 K, with a sharp reduction in the number of hydrogen bonds and increase in the entropy. Fast diffusion of the encapsulated water demonstrates anomalous temperature dependence, indicating the solid-to-fluid nature of this structural transition. These findings offer fundamental understandings of the encapsulated water that can be used as a pressurized cell with trapped molecular species, and provide guidance for practical applications with its presence, for example, in the design of nanodevices and nanoconfined reactive cells.

SUBMITTER: Jiao S

PROVIDER: S-EPMC5453971 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:MotivationThermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins using expressed sequence tag (EST) data, to the determination of microRNA genes and their targets. Dynamic programming algorithms have been developed to compute the minimum free energy secondary structure and partition function of a given RNA sequence, the minimum free-energy and partition function for the hybridization of two RNA molecules, etc. However, the applicability of dynamic programming methods depends on disallowing certain types of interactions (pseudoknots, zig-zags, etc.), as their inclusion renders structure prediction an nondeterministic polynomial time (NP)-complete problem. Nevertheless, such interactions have been observed in X-ray structures.ResultsA non-Boltzmannian Monte Carlo algorithm was designed by Wang and Landau to estimate the density of states for complex systems, such as the Ising model, that exhibit a phase transition. In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. Our method is shown to be much faster than existent software, such as RNAsubopt. From density of states, we compute the partition function over all secondary structures and over all pseudoknot-free hybridizations. The advantage of the WL method is that by adding a function to evaluate the free energy of arbitrary pseudoknotted structures and of arbitrary hybridizations, we can estimate thermodynamic parameters for situations known to be NP-complete. This extension to pseudoknots will be made in the sequel to this article; in contrast, the current article describes the WL algorithm applied to pseudoknot-free secondary structures and hybridizations.AvailabilityThe WL RNA hybridization web server is under construction at http://bioinformatics.bc.edu/clotelab/.

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Structures and thermodynamics of water encapsulated by graphene.

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