We construct a moduli space of stable pairs over a smooth projective variety, parametrizing morphisms from a fixed coherent sheaf to a varying sheaf of fixed topological type, subject to a stability condition. This generalizes the notion used by Pandharipande and Thomas, following Le Potier, where the fixed sheaf is the structure sheaf of the variety. We then describe the relevant deformation and obstruction theories. We also show the existence of the virtual fundamental class in special cases.

Structures and functions of proteins play various essential roles in biological processes. The functions of newly discovered proteins can be predicted by comparing their structures with that of known functional proteins. Many approaches have been proposed for measuring the protein structure similarity, such as the template-modeling (TM)-score method, GRaphlet (GR)-Align method as well as the commonly used root-mean-square deviation (RMSD) measures. However, the alignment comparisons between the similarity of protein structure cost much time on large dataset, and the accuracy still have room to improve. In this study, we introduce a new three-dimensional (3D) Yau–Hausdorff distance between any two 3D objects. The (3D) Yau–Hausdorff distance can be used in particular to measure the similarity/dissimilarity of two proteins of any size and does not need aligning and super- imposing two structures. We apply structural similarity to study function similarity and perform phylogenetic analysis on several datasets. The results show that (3D) Yau–Hausdorff distance could serve as a more precise and effective method to discover biological relationships between proteins than other methods on structure comparison.

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Convex bodies with identical John and LYZ ellipsoids are characterized. This solves an important problem from convex geometry posed by G. Zhang. As applications, several sharp affine isoperimetric inequalities are established.