Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the structural correlations in atomistic simulations, the general use of bottom-up CG methods is limited because of the nontransferable nature of these CG models under different thermodynamic conditions. Because bottom-up CG potentials usually correspond to configuration-dependent free energies of the system, recent studies have focused on adjusting enthalpic or entropic contributions to account for issues with transferability. However, these approaches can require a manual adjustment of the CG interaction a priori and are usually limited to constant volume ensembles. To overcome these limitations, we construct temperature and phase transferable CG models under constant pressure by developing the ultra-coarse-graining (UCG) methodology in the mean-field limit. In the mean-field ansatz, an embedded semi-global order parameter recapitulates global changes to the system by automatically adjusting the effective CG interactions, thus bridging free energy decompositions with UCG theory. The method presented is designed to faithfully capture structural correlations under different thermodynamic conditions, using a single UCG model. Specifically, we test the applicability of the developed theory in three distinct cases: (1) different temperatures at constant pressure in liquids, (2) different temperatures across thermodynamic phases, and (3) liquid/vapor interfaces. We demonstrate that the systematic construction of both temperature and phase transferable bottom-up CG models is possible using this generalized UCG theory. Based on our findings, this approach significantly extends the transferability and applicability of the bottom-up CG theory and method.
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http://dx.doi.org/10.1021/acs.jctc.0c00832 | DOI Listing |
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School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China.
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Nat Commun
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NYU-ECNU Institute of Physics, NYU Shanghai, Shanghai, China.
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Nanoscale Biophotonics Laboratory, University of Galway, University Road, Galway H91 TK33 Ireland. Electronic address:
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College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China. Electronic address:
Tartary buckwheat (Fagopyrum tataricum), a functional grain known for its medicinal and nutritional properties, has garnered significant attention due to its high flavonoid content and unique health benefits. Heat stress during the flowering stage can lead to sterility in Tartary buckwheat, resulting in reduced yields. This study investigates the effects of a treatment (30/27 °C for 7 days) on flower development, fertility, stress physiology, and gene expression in Tartary buckwheat, while also validating the efficacy of hormone treatments in alleviating the negative effects of heat stress.
View Article and Find Full Text PDFNat Commun
January 2025
Center for Advanced Radiation Sources, University of Chicago, Chicago, IL, USA.
Phase transitions in the mantle control its internal dynamics and structure. The post-spinel transition marks the upper-lower mantle boundary, where ringwoodite dissociates into bridgmanite plus ferropericlase, and its Clapeyron slope regulates mantle flow across it. This interaction has previously been assumed to have no lateral spatial variations, based on the assumption of a linear post-spinel boundary in pressure and temperature.
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