The existence of current species can be attributed to a dynamic interplay between evolutionary forces and the maintenance of genetic information [...].
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10531423 | PMC |
http://dx.doi.org/10.3390/genes14091747 | DOI Listing |
The growing body of experimental and computational studies suggested that the cross-neutralization antibody activity against Omicron variants may be driven by balance and tradeoff of multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with the epitope residues remain scarcely characterized. In this study, we performed molecular dynamics simulations, ensemble-based deep mutational scanning of SARS-CoV-2 spike residues and binding free energy computations for two distinct groups of broadly neutralizing antibodies : E1 group (BD55-3152, BD55-3546 and BD5-5840) and F3 group (BD55-3372, BD55-4637 and BD55-5514).
View Article and Find Full Text PDFConnections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence.
View Article and Find Full Text PDFSci Rep
January 2025
College of Civil Engineering and Architecture, Dalian university, Dalian, 116622, China.
It is significant to study the stability of surrounding rock in soft rock tunnels to ensure construction safety and improve efficiency. Through triaxial shear tests on soft rock at various confining pressures, we observed the failure characteristics transitioning from strain softening to strain hardening as confining pressure increases. An improved Hoek-Brown strength criterion has been proposed to characterize the critical confining pressure effect of soft rock, with tensile strength in the tensile zone aligning with experimental results, showing an error of less than 5%.
View Article and Find Full Text PDFNat Commun
January 2025
i-lab, Vacuum Interconnected Nanotech Workstation (Nano-X), Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China.
Transition-metal carbides have been advocated as the promising alternatives to noble-metal platinum-based catalysts in electrocatalytic hydrogen evolution reaction over half a century. However, the effectiveness of transition-metal carbides catalyzing hydrogen evolution in high-pH electrolyte is severely compromised due to the lowered proton activity and intractable alkaline-leaching issue of transition-metal centers. Herein, on the basis of validation of molybdenum-carbide model-catalyst system by taking advantage of surface science techniques, MoC micro-size spheres terminated by Al doped MoO layer exhibit a notable performance of alkaline hydrogen evolution with a near-zero onset-potential, a low overpotential (40 mV) at a typical current density of 10 mA/cm, and a small Tafel slope (45 mV/dec), as well as a long-term stability for continuous hydrogen production over 200 h.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Earth and Planetary Sciences, Yale University, New Haven 06511.
The origin of complex life and the evolution of terrestrial ecosystems are fundamental aspects of the natural history on Earth. Here, we present evidence for a protracted stabilization of the Earth's ozone layer. The destruction of atmospheric ozone today is inherently linked to the cycling of marine and atmospheric iodine.
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