1
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      Probing the network topology in network-forming materials: The case of water

      ,
      AIP Advances

      Read this article at

      ScienceOpenPublisher
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Rings statistic has been widely used to investigate the network topology in numerically simulated network-forming materials in order to rationalize their physical and mechanical properties. However, different topologies arise depending on how rings are counted, leading to incomplete or even contrasting physical interpretations. Solving this critical ambiguity is of primary importance for the correct assessment of material properties. Here, we show how such differences emerge in water, a complex network-forming material endowed with polyamorphism and a directional network of hydrogen bonds whose topology is correlated with the anomalous behavior of water. We probe the network in the liquid state at several thermodynamic points under equilibrium conditions, as well as during the out-of-equilibrium first-order-like low density to high density amorphous transformation. We study three schemes for counting rings and show that each of them provides complementary insightful information about the network, suggesting that a single counting scheme may not be sufficient to properly describe network topologies and to assess material properties. Our results provide a molecular description of the rings in supercooled water and of the amorphous-to-amorphous transformation kinetics, hence shedding light on the complex nature of water. Nonetheless, our results expose how delicate the proper choice of method for counting rings is, an issue with important consequences for rationalizing the properties of network-forming materials at large.

          Related collections

          Most cited references99

          • Record: found
          • Abstract: found
          • Article: not found

          GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

          Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. GROMACS is an open source and free software available from http://www.gromacs.org. Supplementary data are available at Bioinformatics online.
            Bookmark
            • Record: found
            • Abstract: not found
            • Article: not found

            THE ATOMIC ARRANGEMENT IN GLASS

              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Packing structures and transitions in liquids and solids.

              Classification of potential energy minima-mechanically stable molecular packings-offers a unifying principle for understanding condensed phase properties. This approach permits identification of an inherent structure in liquids that is normally obscured by thermal motions. Melting and freezing occur through characteristic sequences of molecular packings, and a defect-softening phenomenon underlies the fact that they are thermodynamically first order. The topological distribution of feasible transitions between contiguous potential minima explains glass transitions and associated relaxation behavior.
                Bookmark

                Author and article information

                Contributors
                (View ORCID Profile)
                Journal
                AIP Advances
                2158-3226
                May 01 2020
                May 2020
                May 01 2020
                May 04 2020
                May 2020
                : 10
                : 5
                Article
                10.1063/5.0005332
                e0d52172-5f56-4d20-abc1-d5f5b173ad38
                © 2020
                History

                Comments

                Comment on this article