In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy model is discussed in great detail. Mathematically, unlike the previous persistent entropy or topological entropy, a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our multiscale persistent entropy can be used in conformation entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of a multiscale rigidity function built from bond and/or dihedral angle distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. It is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the mediate range. Moreover, our method can be successfully used in protein classification. For a test database with around nine hundred proteins, a clear separation between all-alpha and all-beta proteins can be achieved, using only the dihedral and pseudo-bond angle information. Finally, a special protein structure index (PSI) is proposed, for the first time, to describe the "regularity" of protein structures. Essentially, PSI can be used to describe the "regularity" information in any systems.
Homology theory relative to classes of objects other than those of projective or injective objects in abelian categories has been widely studied in the last years, giving a special relevance to Gorenstein homological algebra.
We prove the existence of Gorenstein flat precovers in any locally finitely presented Grothendieck category in which the class of flat objects is closed under extensions, the existence of Gorenstein injective preenvelopes in any locally noetherian Grothendieck category in which the class of all Gorenstein injective objects is closed under direct products, and the existence of special Gorenstein injective preenvelopes in locally noetherian Grothendieck categories with a generator lying in the left orthogonal class to that of Gorenstein injective objects.
We study cluster categories arising from marked surfaces (with punctures and nonempty boundaries). By constructing skewed-gentle algebras, we show that there is a bijection between tagged curves and string objects. Applications include interpreting
dimensions of Ext1 as intersection numbers of tagged curves and Auslander-Reiten translation as tagged rotation. An important consequence is that the cluster(-tilting) exchange graphs of such cluster categories are connected.
We study derived categories arising from quivers with potential associated to a decorated marked surface S_Delta, in the sense taken in a paper by Qiu. We prove two conjectures from Qiu’s paper in which, under a bijection between certain objects in these categories and certain arcs in S, the dimensions of morphisms between these objects equal the intersection numbers between the corresponding arcs.
We prove that any “finite-type” component of a stability space of a triangulated category is contractible. The motivating example of such a component is the stability space of the Calabi–Yau–N category D(Gamma_N Q) associated to an ADE Dynkin quiver. In addition to showing that this is contractible we prove that the braid group Br(Q) acts freely upon it by spherical twists, in particular that the spherical twist group Br(Gamma_N Q) is isomorphic to Br(Q). This generalises the result of Brav–Thomas for the N=2 case. Other classes of triangulated categories with finite-type components in their stability spaces include locally finite triangulated categories with finite-rank Grothendieck group and discrete derived categories of finite global dimension.