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The process of self-assembly of biomolecules underlies the formation of macromolecular assemblies, biomolecular materials and protein folding, and thereby is critical in many disciplines and related applications. This process typically spans numerous spatiotemporal scales and hence, is well suited for scientific interrogation via coarse-grained (CG) models used in conjunction with a suitable computational approach. This perspective provides a discussion on different coarse-graining approaches which have been used to develop CG models that resolve the process of self-assembly of biomolecules. 

Abstract Previous research has shown a consistent discrepancy in the reported structure of alkaline earth aluminosilicate glasses using molecular dynamics (MD) simulations versus nuclear magnetic resonance (NMR) experiments. Past MD results have consistently shown less than 5% five‐coordinated Al units (Al^[5]) in peraluminous glass compositions, but with high fractions of triple‐bonded oxygens (TBO, i.e., triclusters). Experimental results have shown a high fraction of Al^[5]with no direct evidence for TBO. One of the main criticisms associated with high TBO content found in MD‐generated glass structures is the use of classical interatomic potentials. To investigate this issue, we analyze the formation of both TBO and Al^[5]using three independently developed potentials with varying silica content and [Al₂O₃]/[MgO] ratios for the magnesium aluminosilicate (MAS) system. We specifically choose compositions with high ratios of alumina to magnesium oxide as this region is not as commonly explored. Results indicate that Al^[5]charge compensates the Al network in metaluminous compositions (compositions with more Mg than Al) while both TBO and Al^[5]are prevalent in peraluminous ranges (high Al content compositions) to charge balance Al units. From the literature, NMR experiments report MAS glasses with varying Al^[5]fractions and show significant differences for the same reported compositions. When comparing MD results from this work, the fraction of calculated Al^[5]is within the experimental variation found in the literature. This indicates that classical potentials can accurately capture alumina environments and that both Al^[5]and TBO can coexist in relatively high fractions. From the consistency in our results, we conclude that TBOs are inherent to the aluminosilicate glass system and are not simulation artifacts. 

Abstract Germanate glasses are of particular interest for their excellent optical properties as well as their abnormal structural changes that appear with the addition of modifiers, giving rise to the so‐calledgermanate anomaly. This anomaly refers to the nonmonotonic compositional scaling of properties exhibited by alkali germanate glasses and has been studied with various spectroscopy techniques. However, it has been difficult to understand its atomic scale origin, especially since the germanium nucleus is not easily observed by nuclear magnetic resonance. To gain insights into the mechanisms of the germanate anomaly, we have constructed a structural model using statistical mechanics and topological constraint theory to provide an accurate prediction of alkali germanate glass properties. The temperature onsets for the rigid bond constraints are deduced from in situ Brillouin light scattering, and the number of constraints is shown to be accurately calculable using statistical methods. The alkali germanate model accurately captures the effect of the germanate anomaly on glass transition temperature, liquid fragility, and Young's modulus. We also reveal that compositional variations in the glass transition temperature and Young's modulus are governed by the O–Ge–O angular constraints, whereas the variations in fragility are governed by the Ge–O radial constraints.