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Validating Structural Predictions of Conjugated Macromolecules in Espaloma-Enabled Reproducible Workflows.
Int J Mol Sci
January 2025
Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA.
We incorporated Espaloma forcefield parameterization into MoSDeF tools for performing molecular dynamics simulations of organic molecules with HOOMD-Blue. We compared equilibrium morphologies predicted for perylene and poly-3-hexylthiophene (P3HT) with the ESP-UA forcefield in the present work against prior work using the OPLS-UA forcefield. We found that, after resolving the chemical ambiguities in molecular topologies, ESP-UA is similar to GAFF.
View Article and Find Full Text PDFLow-Cost Preparation of Wafer-Scale Au(111) Single Crystals for the Epitaxy of Two-Dimensional Layered Materials.
ACS Nano
January 2025
School of Materials Science and Engineering, Peking University, Beijing 100871, People's Republic of China.
Single-crystal Au(111), renowned for its chemically inert surface, long-range "herringbone" reconstruction, and high electrical conductivity, has long served as an exemplary template in diverse fields, , crystal epitaxy, electronics, and electrocatalysis. However, commercial Au(111) products are high-priced and limited to centimeter sizes, largely restricting their broad applications. Herein, a low-cost, high-reproducible method is developed to produce 4 in.
View Article and Find Full Text PDFInstabilities, thermal fluctuations, defects and dislocations in the crystal-R-R rotator phase transitions of -alkanes.
Soft Matter
January 2025
Department of Physics, Government College of Engineering and Textile Technology, 12 William Carey Road, Serampore, Hooghly-712201, India.
The theoretical study of instabilities, thermal fluctuations, and topological defects in the crystal-rotator-I-rotator-II (X-R-R) phase transitions of -alkanes has been conducted. First, we examine the nature of the R-R phase transition in nanoconfined alkanes. We propose that under confined conditions, the presence of quenched random orientational disorder makes the R phase unstable.
View Article and Find Full Text PDFDeciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization.
RSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
View Article and Find Full Text PDFTriply Ordered 6H Halide Perovskites: A Family of Triangular Lattice Antiferromagnets.
Inorg Chem
January 2025
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.
Three new hexagonal perovskites with CsMMRhCl (M = Na, Ag; M = Mn, Fe) stoichiometry have been synthesized from solution precipitation reactions. These air-stable compounds crystallize as triply cation-ordered variants of the 6H perovskite structure. This structure contains octahedra that share a common face to form MRhCl dimers that are arranged on a two-dimensional triangular network.
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