Lubricants can affect quasicrystalline coating surfaces by modifying the commensurability of the interfaces. We report results of the first computer simulation studies of physically adsorbed hydrocarbons on a quasicrystalline surface: methane, propane, and benzene on decagonal Al-Ni-Co. The grand canonical Monte Carlo method is employed, using novel embedded-atom method potentials generated from ab initio calculations, and standard hydrocarbon interactions. The resulting adsorption isotherms and calculated structures show the films' evolution from submonolayer to condensation. We discover the presence and absence of the fivefold to sixfold topological transition, for benzene and methane, respectively, in agreement with a previously formulated phenomenological rule based on adsorbate-substrate size mismatch.
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http://dx.doi.org/10.1103/PhysRevLett.102.055501 | DOI Listing |
We introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all 110,667 possible 2D dual graphs for vertex numbers ranging from 2 to 9. Among them, only 0.
View Article and Find Full Text PDFHeliyon
January 2025
College of Since and Art, Department of Mathematics, King Khalid University, Mahayil, Saudi Arabia.
New developments in the field of chemical graph theory have made it easier to comprehend how chemical structures relate to the graphs that underlie them on a more profound level using the ideas of classical graph theory. Chemical graphs can be effectively probed with the help of quantitative structure-property relationship (QSPR) analysis. In order to statistically correlate physical attributes.
View Article and Find Full Text PDFProtein Sci
February 2025
Department of Physics, University of Washington, Seattle, Washington, USA.
Proteins' flexibility is a feature in communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene expression. When binding with the disordered parts of a protein, calcium ions must balance their charge states with the shape of calcium-binding proteins and their versatile pool of partners depending on the circumstances they transmit. Accurately determining the ionic charges of those ions is essential for understanding their role in such processes.
View Article and Find Full Text PDFEBioMedicine
January 2025
Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, New Cornerstone Science Foundation, Beijing, 100084, China. Electronic address:
Background: The widespread and evolution of RNA viruses, such as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the importance of fast identification of virus subtypes, particularly in non-laboratory settings. Rapid and inexpensive at-home testing of viral nucleic acids with single-base resolution remains a challenge.
Methods: Topologically constrained DNA ring is engineered as substrates for the trans-cleavage of Cas13a to yield an accelerated post isothermal amplification.
J Mol Model
January 2025
PG & Research Department of Mathematics, Sanatana Dharma College, Kerala University, Alappuzha, Kerala, 688003, India.
Holey nanographene, an allotrope of carbon arranged in two dimensions, has gained remarkable attention as a nanomaterial with several potential uses in numerous industries, such as electronics, energy storage, healthcare, and environmental cleanup, because of its high carrier mobility, flexibility, transparency, high surface area, conductivity, and chemical stability. The fundamental holey nanographene is assembled in a linear form to create the holey nanographene chain (HNC) that is being discussed. To fully utilize it in various applications, it is essential to comprehend the basic ideas guiding its behavior at the nanoscale; for that, we find various topological indices for this holey nanographene chain using the cut method.
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