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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.

This project was sponsored through the Schiff Fellowship program of Brandeis University. This project involved using the power series method to construct a third order nonlinear ordinary differential equation, a Schwarzian equation, for each of the "genus zero" modular functions, described in the Conway-Norton paper. We first use the Borcherd recursion formuli to generate, in each case, a modular function up to whatever degree we desire, and then use the fact that there is a Schwarzian equation, determined by a single rational function we call a Q-value. By similar power series methods, we compute the coefficients of our rational function, and hence have all the necessary data to create a Schwarzian differential equation for each modular function. This equation can, in turn, be used to recover the modular function itself.

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We shall be concerned with the indicator$p$of an analytic functional μ on a complex manifold$U$: $$p(\varphi ) = \overline {\mathop {\lim }\limits_{t \to + \infty } } \frac{l}{t}\log \left| {\mu (e^{t\varphi } )} \right|,$$ where ϕ is an arbitrary analytic function on$U$. More specifically, we shall consider the smallest upper semicontinuous majorant$p$^{$J$}of the restriction of$p$to a subspace £ of the analytic functions. An obvious problem is then to characterize the set of functions$p$^{$J$}which can occur as regularizations of indicators. In the case when$U$=$C$^{$n$}and £ is the space of all linear functions on$C$^{$n$}, this set can be described more easily as the set of functions(0.1) $$\mathop {\lim }\limits_{\theta \to \zeta } \overline {\mathop {\lim }\limits_{t \to + \infty } } \frac{l}{t}\log \left| {u(t\theta )} \right|$$ of$n$complex variables ζ∈$C$^{$n$}where$u$is an entire function of exponential type in$C$^{$n$}. We hall prove that a function in$C$^{$n$}is of the form (0.1) for some entire function$u$of exponential type if and only if it is plurisubharmonic and positively homogeneous of order one (Theorem 3.4). The proof is based on the characterization given by Fujita and Takeuchi of those open subsets of complex projective$n$-space which are Stein manifolds.