To derive the hidden dynamics from observed data is one of the fundamental but also challenging problems in many different fields. In this study, we propose a new type of interpretable network called the ordinary differential equation network (ODENet), in which the numerical integration of explicit ordinary differential equations (ODEs) are embedded into the machine learning scheme to build a general framework for revealing the hidden dynamics buried in massive time-series data efficiently and reliably. ODENet takes full advantage of both machine learning algorithms and ODE modeling. On one hand, the embedding of ODEs makes the framework more interpretable benefiting from the mature theories of ODEs. On the other hand, the schemes of machine learning enable data handling, paralleling, and optimization to be easily and efficiently implemented. From classical Lotka-Volterra equations to chaotic Lorenz equations, the ODENet exhibits its remarkable capability in handling time-series data even in the presence of large noise. We further apply the ODENet to real actin aggregation data, which shows an impressive performance as well. These results demonstrate the superiority of ODENet in dealing with noisy data, data with either non-equal spacing or large sampling time steps over other traditional machine learning algorithms.

In this paper, we propose an unfitted Nitsche's method for computing wave modes in topological materials. The proposed method is based on Nitsche's technique to study the performance-enhanced topological materials which have strongly heterogeneous structures (e.g., the refractive index is piecewise constant with high contrasts). For periodic bulk materials, we use Floquet-Bloch theory and solve an eigenvalue problem on a torus with unfitted meshes. For the materials with a line defect, a sufficiently large domain with zero boundary conditions is used to compute the localized eigenfunctions corresponding to the edge modes. The interfaces are handled by Nitsche's method on an unfitted uniform mesh. We prove the proposed methods converge optimally, and present numerical examples to validate the theoretical results and demonstrate the capability of simulating topological materials.

In this article, we study wave dynamics in the fractional nonlinear Schrödinger equation with a modulated honeycomb potential. This problem arises from recent research interests in the interplay between topological materials and nonlocal governing equations. Both are current focuses in scientific research fields. We first develop the Floquet-Bloch spectral theory of the linear fractional Schrödinger operator with a honeycomb potential. Especially, we prove the existence of conical degenerate points, i.e., Dirac points, at which two dispersion band functions intersect. We then investigate the dynamics of wave packets spectrally localized at a Dirac point and derive the leading effective envelope equation. It turns out the envelope can be described by a nonlinear Dirac equation with a varying mass. With rigorous error estimates, we demonstrate that the asymptotic solution based on the effective envelope equation approximates the true solution well in the weighted-H^s space.

In this paper, we propose an unfitted Nitsche's method to compute the band structures of phononic crystal with impurities of general geometry. The proposed method does not require the background mesh to fit the interfaces of impurities, and thus avoids the expensive cost of generating body-fitted meshes and simplifies the inclusion of interface conditions in the formulation. The quasi-periodic boundary conditions are handled by the Floquet-Bloch transform, which converts the computation of band structures into an eigenvalue problem with periodic boundary conditions. More importantly, we show the well-posedness of the proposed method using a delicate argument based on the trace inequality, and further prove the convergence by the Babuška-Osborn theory. We achieve the optimal convergence rate at the presence of the impurities of general geometry. We confirm the theoretical results by two numerical examples, and show the capability of the proposed methods for computing the band structures without fitting the interfaces of impurities.

Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background, we illustrate how the key ideas of multiscale modeling can help to reduce the computational cost of machine learning a lot, as well as how machine learning algorithms perform model reduction automatically in a time-scale separated system. Our study highlights the necessity and effectiveness of an integration of machine learning algorithms and multiscale modeling during the study of chemical reactions.