gcyu@connect.hku.hk or tqyhe@jnu.edu.cn.

Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

One of the key problems in studying alloy nanoparticle catalysis is their surface morphology and segregation behavior. We have developed an accurate embedded atom method ͑EAM͒ potential and employed it in the simulation of PdAu metal alloy nanoparticles. The potential was parameterized based on an extensive set of density-functional-theory ͑DFT͒ calculations of metal clusters in addition to bulk-alloy properties. The EAM potential accurately reproduces DFT energies of both bulk PdAu alloys and small nanoparticles. We utilized the developed EAM potential in a Monte Carlo simulation of PdAu nanoparticles ranging from 55-atom ͑ϳ1 nm͒ to 5083-atom particles ͑ϳ4.5 nm͒. The effects of different factors ͑particle size, temperature, and composition ratios͒ on the segregation behavior of PdAu alloy are examined. Our simulation results quantitatively reveal the extent of surface segregation and a strong dependence of surface morphology on the nanoparticle size.

Oxygen dissociation is one of the most critical steps in the CO oxidation reaction on transition metal surfaces. It has been shown both experimentally and theoretically that oxygen dissociation on clean platinum (Pt) surface proceeds via a precursor-mediated reaction path, with negligible activation barrier. On the other hand, the oxygen dissociation pathway under diesel engine operating conditions, where the metal surface is packed with CO molecules, is understood less clearly. In this paper, we report density functional theory calculations for O 2 dissociation on Pt(111) in the presence of varying CO coverage. Classical Monte Carlo simulations have been used to get an estimate of coadsorbed CO and O 2 configurations. Oxygen molecular precursor states binding energies were found to shift up in energy with increasing CO coverage, with transition state energies and final product energies following the same trend. The dissociated product state becomes endothermic beyond a critical CO coverage of 0.44 monolayer, where oxygen dissociation is no longer energetically favored on Pt(111). The origin of the change in activation barrier can be attributed to the limited space available for oxygen dissociation and the lateral repulsion from neighboring CO molecules. A linear correlation exists between the oxygen dissociation barrier and the molecular precursor binding energy. These findings give useful insight into the CO oxidation mechanism under realistic diesel engine operating conditions.