Graph theory-based structural analysis on density anomaly of silica glass

Tan, Aik Rui; Urata, Shingo; Yamada, Masatsugu; Gómez‐Bombarelli, Rafael

doi:10.1016/j.commatsci.2023.112190

Cited by 4 publications

(2 citation statements)

References 55 publications

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“…This is helpful because it overcomes weaknesses inherent to analyses of the structure factors and radial distribution functions, which are one-dimensional projections that average over time and molecular orientations. Graph-theoretic approaches have been helpful in analyzing network fluids, for example in studies of hydrogen-bonding networks 95,96,97,98,99,100 and glassy systems 101 . Here, we perform a graph-theoretic analysis of the macromolecular network formed by the N130+rpL5 dense phase in the CG simulations.…”

Section: Graph Theoretic Analyses Of Network Structures Of Condensatesmentioning

confidence: 99%

Biomolecular condensates form spatially inhomogeneous network fluids

Pappu,

Dar,

Cohen

et al. 2023

Preprint

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The functions of biomolecular condensates are thought to be influenced by their material properties, and these are in turn determined by the multiscale structural features within condensates. However, structural characterizations of condensates are challenging, and hence rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and bespoke coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that mimic nucleolar granular components (GCs). We show that facsimiles of GCs are network fluids featuring spatial inhomogeneities across hierarchies of length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights, extracted from a combination of approaches, suggest that condensates formed by multivalent proteins share features with network fluids formed by associative systems such as patchy or hairy colloids.

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Section: Graph Theoretic Analyses Of Network Structures Of Condensatesmentioning

confidence: 99%

Biomolecular condensates form spatially inhomogeneous network fluids

Pappu,

Dar,

Cohen

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The details of the structural variation are clearly critical to the understanding of the materials properties. In the past few decades, the structural origins of such anomalies have been intensively investigated through experiments and simulations [ 7 , 8 , 9 , 10 , 11 , 12 , 13 ]. Despite tremendous efforts, the structural origins of these density anomalies remain elusive.…”

Section: Introductionmentioning

confidence: 99%

The Origin of Anomalous Density Behavior of Silica Glass

Cheng

2023

Materials

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The anomalous density–temperature relationship of vitreous silica with low hydroxyl content is explained by the formation of medium-range ordering structure in the glass transition process. The ordered medium-range structure has the shape of a “nanoflake” and consists of two layers of SiO4 tetrahedra, bonded by O atoms located in the middle of the structure. The nanoflakes interact with their surrounding structures through both covalent chemical bonds and van der Waals bonds. In the formation of the van der Waals bonds, the orientation of SiO4 tetrahedra can change, which results in an increase in distance between the nanoflakes and their surrounding structures. Thus, there is a slight volume enlargement associated with the formation of nanoflakes. Since the nanoflakes’ formation starts at a temperature near 1480 °C, and the population of the nanoflakes grows continuously as temperature decreases until about 950 °C, the bulk volume of silica glass increases in the temperature range from about 1480 °C to 950 °C. Therefore, the density anomaly of silica glass can be explained as a byproduct of forming of medium-range ordering structure in the silica glass transition.

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Biomolecular condensates form spatially inhomogeneous network fluids

Dar,

Cohen,

Mitrea

et al. 2024

Nat Commun

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The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

show abstract

Graph theory-based structural analysis on density anomaly of silica glass

Cited by 4 publications

References 55 publications

Biomolecular condensates form spatially inhomogeneous network fluids

Biomolecular condensates form spatially inhomogeneous network fluids

The Origin of Anomalous Density Behavior of Silica Glass

Biomolecular condensates form spatially inhomogeneous network fluids

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