The conventional formula for relating CD2 average order parameters
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http://dx.doi.org/10.1016/S0006-3495(99)77403-5 | DOI Listing |
Mol Biol Evol
January 2025
Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH).
A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Biology, Stanford University, Stanford, CA 94305.
Models of conformity and anticonformity have typically focused on cultural traits with unordered variants, such as baby names, strategies (cooperate/defect), or the presence/absence of an innovation. There have been fewer studies of conformity to cultural traits with ordered variants, such as level of cooperation (low, medium, high) or proportion of time spent on a task (0% to 100%). In these studies of ordered cultural traits, conformity is defined as a preference for the mean trait value in a population even if no members of the population have variants near this mean; e.
View Article and Find Full Text PDFSimulating large molecular systems over long timescales requires force fields that are both accurate and efficient. In recent years, E(3) equivariant neural networks have lifted the tension between computational efficiency and accuracy of force fields, but they are still several orders of magnitude more expensive than established molecular mechanics (MM) force fields. Here, we propose Grappa, a machine learning framework to predict MM parameters from the molecular graph, employing a graph attentional neural network and a transformer with symmetry-preserving positional encoding.
View Article and Find Full Text PDFJ Acoust Soc Am
January 2025
Department of Physics, Naval Postgraduate School, 833 Dyer Road, Monterey, California 93943-5216, USA.
The shear wave speed is often small compared to the compressional wave speed in the top part of the seabed, where acoustic normal modes penetrate. In sediments with weak but finite shear rigidity, the strongest conversion from compressional to shear waves occurs at interfaces within the sediment. Shear wave generation at such interfaces and interference within sediment layers lead to first-order perturbations in the normal mode phase speed and contributions to sound attenuation, which vary rapidly with frequency.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
College of Physics and Electronic Engineering, Nanyang Normal University, Nanyang 473061, Henan, People's Republic of China.
Silicon germanium alloy materials have promising potential applications in the optoelectronic and photovoltaic industries due to their good electronic properties. However, due to the inherent brittleness of semiconductor materials, they are prone to rupturing under harsh working environments, such as high stress or high temperature. Here, we conducted a systematic search for silicon germanium alloy structures using a random sampling strategy, in combination with group theory and graph theory (RG), and 12 stable SiGe structures in 2-8 stacking orders were predicted.
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