We propose measures of localization and cooperativity for the analysis of atomic rearrangements. We show that for both clusters and bulk material cooperative rearrangements usually have significantly lower barriers than uncooperative ones, irrespective of the degree of localization. We also find that previous methods used to sample stationary points are biased towards rearrangements of particular types. Linear interpolation between local minima in double-ended transition state searches tends to produce cooperative rearrangements, while random perturbations of all the coordinates, as sometimes used in single-ended searches, have the opposite effect.
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http://dx.doi.org/10.1063/1.1794653 | DOI Listing |
Commun Phys
January 2025
Accelerator Laboratory, Department of Physics, University of Jyväskylä, Jyväskylä, Finland.
Atomic nuclei serve as prime laboratories for investigations of complex quantum phenomena, where minor nucleon rearrangements cause significant structural changes. Pb is the heaviest known neutron-deficient Pb isotope that can exhibit three distinct shapes: prolate, oblate, and spherical, with nearly degenerate excitation energies. Here we report on the combined results from three state-of-the-art measurements to directly observe these deformations in Pb.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Advanced Analysis Data Center, Korea Institute of Science and Technology, Hwarang-ro 14-5, Seongbuk-gu, Seoul 02792, Republic of Korea.
Riboswitches are RNAs that recognize ligands and regulate gene expression. They are typically located in the untranslated region of bacterial messenger RNA and consist of an aptamer and an expression platform. In this study, we examine the folding pathway of the Vc2 (Vibrio cholerae) riboswitch aptamer domain, which targets the bacterial secondary messenger cyclic-di-GMP.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
December 2024
Key Laboratory of Advanced Ceramics and Machining Technology of Ministry of Education School of Materials Science and Engineering, Tianjin, University, Tianjin, 300072, China.
Single-atom catalysts (SACs) with nonplanar configurations possess unique capabilities for tailoring the oxygen reduction reaction (ORR) catalytic performance compared with the ones with planar configurations, owing to the additional orbital rearrangement arising from the asymmetric coordination atoms. However, the systematic investigation of these nonplanar SACs has long been hindered by the difficulty in screening feasible nonplanar configurations and precisely controlling the coordination structures. Herein, we demonstrate a combined high-throughput screening and experimental verification of nonplanar SACs (ppy-MN) with metal atoms triple-coordinated by pyrrole-N, for highly active and selective 2e ORR electrocatalysis.
View Article and Find Full Text PDFNat Commun
December 2024
PSI Center for Life Sciences, Villigen PSI, Switzerland.
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors in humans. The binding and dissociation of ligands tunes the inherent conformational flexibility of these important drug targets towards distinct functional states. Here we show how to trigger and resolve protein-ligand interaction dynamics within the human adenosine A receptor.
View Article and Find Full Text PDFAdv Mater
December 2024
Department of Chemistry and Bioscience, Aalborg University, Aalborg, DK-9220, Denmark.
β-CaSiO based glass-ceramics are among the most reliable materials for electronic packaging. However, developing a CaSiO glass-ceramic substrate with both high strength (>230 MPa) and low dielectric constant (<5) remains challenging due to its polycrystalline nature. The present work has succeeded in synthesizing single-crystalline β-CaSiO for a high-performance glass-ceramic substrate.
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