Identifying representative sequences of protein families using submodular optimization.

Identifying representative sequences for groups of functionally similar proteins and enzymes poses significant computational challenges. In this study, we applied submodular optimization, a method effective in data summarization, to select representative sequences for thioesterase enzyme families. We introduced and validated two algorithms, Greedy and Bidirectional Greedy, using curated protein sequence data from the ThYme (Thioester-active enzYmes) database.

Predicting Magnetic Barriers in Lanthanide Complexes with Electrostatic Potential Charges.

Single-molecule magnets (SMMs) with slow relaxation of magnetization and blocking temperatures above that of liquid nitrogen are essential for practical applications in high-density data storage devices and quantum computers. A rapid and accurate prediction of the effective magnetic relaxation barrier () is needed to accelerate the discovery of high-performance SMMs. Using density functional theory and multireference calculations, we explored correlations between , partial atomic charges, and the anisotropic barrier for a series of sandwich-type lanthanide complexes containing cyclooctatetraene, substituted cyclopentadiene, phospholyl, boratabenzene, or borane ligands.

exhibits necrotrophic behavior when causing soft rot in ripe fruit.

is known for causing soft rot in fruit and vegetables during postharvest. Although it has traditionally been considered a saprophyte, it appears to behave more like a necrotrophic pathogen. In this study, we propose that invades host tissues by actively killing host cells and overcoming the host defense mechanisms, as opposed to growing saprophytically on decaying plant matter.

Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution.

-average sampling of structures from molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures.

De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee.

Geisha coffee is recognized for its unique aromas and flavors and, accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha.