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  1. Biology exploits biomacromolecular phase separation to form condensates, known as membraneless organelles. Despite significant advancements in deciphering sequence determinants for phase separation, modulating these features in vivo remains challenging. A promising approach inspired by biology is to use post-translational modifications (PTMs)—to modulate the amino acid physicochemistry instead of altering protein sequences—to control the formation and characteristics of condensates. However, despite the identification of more than 300 types of PTMs, the detailed understanding of how they influence the formation and material properties of protein condensates remains incomplete. In this study, we investigated how modification with myristoyl lipid alters the formation and characteristics of the resilin-like polypeptide (RLP) condensates, a prototypical disordered protein with upper critical solution temperature (UCST) phase behaviour. Using turbidimetry, dynamic light scattering, confocal and electron microscopy, we demonstrated that lipidation—in synergy with the sequence of the lipidation site—significantly influences RLPs' thermodynamic propensity for phase separation and their condensate properties. Molecular simulations suggested these effects result from an expanded hydrophobic region created by the interaction between the lipid and lipidation site rather than changes in peptide rigidity. These findings emphasize the role of “sequence context” in modifying the properties of PTMs, suggesting that variations in lipidation sequences could be strategically used to fine-tune the effect of these motifs. Our study advances understanding of lipidation's impact on UCST phase behaviour, relevant to proteins critical in biological processes and diseases, and opens avenues for designing lipidated resilins for biomedical applications like heat-mediated drug elution. 
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    Free, publicly-accessible full text available May 15, 2025
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  3. Free, publicly-accessible full text available September 13, 2024
  4. Titanium and Fe isotopic compositions of lavas from a calc-alkaline differentiation suite and corresponding mineral separates from the Rindjani Volcano, Indonesia show that Fe and Ti isotopic fractionations between minerals and melts are lower than those recorded in other suites at all stages of differentiation. The limited isotopic fractionation for Ti is likely due to low-Ti magnetite and clinopyroxene being the dominant carriers of Ti in Rindjani lavas, as these minerals are thought to have limited equilibrium Ti isotopic fractionation relative to silicate magmas. Other magmatic differentiation suites controlled by removal of Ti-rich magnetite and characterized by a lesser role of clinopyroxene have larger Ti isotopic fractionations. This effect is an indirect consequence of the elevated Fe3+/Fe2+ ratio of calc-alkaline magmas such as Rindjani, which promotes Fe3+ incorporation into magnetite at the expense of Fe2+-Ti4+ pairs, such that increased oxygen fugacity will subdue Ti isotopic fractionation in global magmatic series. Similarly, we find negligible Fe isotopic fractionation in Rindjani bulk rocks and mineral separates, unlike previous studies. This is also likely due to the oxidized nature of the Rindjani differentiation suite, which leads to similar Fe3+/Fe2+ ratios in melt and minerals and decreases overall mineral-melt Fe fractionation factors. Paired Ti and Fe isotopic analyses may therefore represent a powerful tool to assess oxygen fugacity during differentiation, independent from Fe 3+ determinations of erupted samples. 
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    Free, publicly-accessible full text available August 1, 2024
  5. Abstract

    In this article, we investigate the creep mechanism of clay at the nanoscale. We conduct the molecular dynamics (MD) modeling of clay samples consisting of hexagonal particles under compression and shear. The MD simulations include oedometer creep, shear creep, direct shear tests, and stress relaxation. The numerical results show that the nanoscale creep mechanism of clay is related to particle rotation, translation, and stacking under different loading conditions. The clay sample under creep shows two types of particle arrangements, that is, the shifted face‐to‐face configuration and the face‐to‐edge configuration. The orientation angle of clay particles is computed to track the rotation of individual particles due to creep. The fabric variation of the clay under creep is characterized by the dihedral angle between the basal particle plane and the x‐y plane and the order parameter. It is found that the factors affecting the microstructure variation of the clay aggregate include stress levels, loading rates, and particle sizes. In the nanoscale shear creep test, the creep process comprises three stages, that is, primary, secondary, and tertiary. The microstructure change during creep depends on the initial alignment of clay particles. The clay creep under a more significant stress level results in a more considerable order parameter and a more orientated clay structure.

     
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  6. Free, publicly-accessible full text available August 1, 2024
  7. Bardanis, M. (Ed.)
    This paper characterizes nanoscale soil-water retention mechanism of unsaturated clay through molecular dynamics simulation. Series of molecular dynamics simulations of clay at low degrees of saturation were conducted. Soil water was represented by a point cloud through the centre-of-massmethod. Water-air interface area was measured numerically by the alpha shape method. Spatial variation of water number density is characterized and used to determine the adsorbed water layer. The soil-water retention mechanism at the nanoscale was analysed by distinguishing adsorptive pressure and capillary pressure at different mass water contents and considering apparent interface area (water-air interface area per unit water volume). 
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