A two species interacting system motivated by the density functional theory for triblock copolymers contains long range interaction that affects the two species differently. In a two species periodic assembly of discs, the two species appear alternately on a lattice. The minimal two species periodic assembly is the one with the least energy per lattice cell area. There is a parameter $b$ in $[0,1]$ and the type of the lattice associated with the minimal assembly varies depending on $b$. There are several threshold defined by a number $B=0.1867...$ If $b \in [0, B)$, the minimal assembly is associated with a rectangular lattice whose ratio of the longer side and the shorter side is in $[\sqrt{3}, 1)$; if $b \in [B, 1-B]$, the minimal assembly is associated with a square lattice; if $b \in (1-B, 1]$, the minimal assembly is associated with a rhombic lattice with an acute angle in $[\frac{\pi}{3}, \frac{\pi}{2})$. Only when $b=1$, this rhombic lattice is the hexagonal lattice. None of the other values of $b$ yields the hexagonal lattice, a sharp contrast to the situation for one species interacting systems, where the hexagonal lattice is ubiquitously observed.

We show the intersection of a compact almost complex subvariety of dimension 4 and a compact almost complex submanifold of codimension 2 is a J-holomorphic curve. This is a generalization of positivity of intersections for J-holomorphic curves in almost complex 4-manifolds to higher dimensions. As an application, we discuss pseudoholomorphic sections of a complex line bundle. We introduce a method to produce J-holomorphic curves using the differential geometry of almost Hermitian manifolds. When our main result is applied to pseudoholomorphic maps, we prove the singularity subset of a pseudoholomorphic map between almost complex 4-manifolds is J-holomorphic. Building on this, we show degree one pseudoholomorphic maps between almost complex 4-manifolds are actually birational morphisms in pseudoholomorphic category.

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We present a new Matched Interface and Boundary (MIB) regularization method for treating charge singularity in solvated biomolecules whose electrostatics are described by the Poisson–Boltzmann (PB) equation. In a regularization method, by decomposing the potential function into two or three components, the singular component can be analytically represented by the Green’s function, while other components possess a higher regularity. Our new regularization combines the efficiency of two-component schemes with the accuracy of the three-component schemes. Based on this regularization, a new MIB finite difference algorithm is developed for solving both linear and nonlinear PB equations, where the nonlinearity is handled by using the inexact-Newton’s method. Compared with the existing MIB PB solver based on a three-component regularization, the present algorithm is simpler to implement by circumventing the work to solve a boundary value Poisson equation inside the molecular interface and to compute related interface jump conditions numerically. Moreover, the new MIB algorithm becomes computationally less expensive, while maintains the same second order accuracy. This is numerically verified by calculating the electrostatic potential and solvation energy on the Kirkwood sphere on which the analytical solutions are available and on a series of proteins with various sizes.

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.