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.

Wave dynamics in topological materials has been widely studied recently. A striking feature is the existence of robust and chiral wave propagations that have potential applications in many fields. A common way to realize such wave patterns is to utilize Dirac points which carry topological indices and is supported by the symmetries of the media. In this work, we investigate these phenomena in photonic media. Starting with Maxwell's equations with a honeycomb material weight as well as the nonlinear Kerr effect, we first prove the existence of Dirac points in the dispersion surfaces of transverse electric and magnetic Maxwell operators under very general assumptions of the material weight. Our assumptions on the material weight are almost the minimal requirements to ensure the existence of Dirac points in a general hexagonal photonic crystal. We then derive the associated wave packet dynamics in the scenario where the honeycomb structure is weakly modulated. It turns out the reduced envelope equation is generally a two-dimensional nonlinear Dirac equation with a spatially varying mass. By studying the reduced envelope equation with a domain-wall-like mass term, we realize the subtle wave motions which are chiral and immune to local defects. The underlying mechanism is the existence of topologically protected linear line modes, also referred to as edge states. However, we show that these robust linear modes do not survive with nonlinearity. We demonstrate the existence of nonlinear line modes, which can propagate in the nonlinear media based on high-accuracy numerical computations. Moreover, we also report a new type of nonlinear modes which are localized in both directions.

Mathematical analysis on electromagnetic waves in photonic graphene, a photonic topological material which has a honeycomb structure, is one of the most important current research topics. By modulating the honeycomb structure, numerous topological phenomena have been observed recently. The electromagnetic waves in such a media are generally described by the 2-dimensional wave equation. It has been shown that the corresponding elliptic operator with a honeycomb material weight has Dirac points in its dispersion surfaces. In this paper, we study the time evolution of the wave packets spectrally concentrated at such Dirac points in a modulated honeycomb material weight. We prove that such wave packet dynamics is governed by the Dirac equation with a varying mass in a large but finite time. Our analysis provides mathematical insights to those topological phenomena in photonic graphene.

Consider electromagnetic waves in two-dimensional honeycomb structured media. The properties of transverse electric (TE) polarized waves are determined by the spectral properties of the elliptic operator L^A=-\nabla_x·A(x) \nabla_x, where A(x) is Λ_h− periodic (Λ_h denotes the equilateral triangular lattice), and such that with respect to some origin of coordinates, A(x) is PC− invariant (A(x)=\overline{A(-x)}) and 120° rotationally invariant (A(R*x)=R*A(x)R, where R is a 120° rotation in the plane). We first obtain results on the existence, stability and instability of Dirac points, conical intersections between two adjacent Floquet-Bloch dispersion surfaces. We then show that the introduction through small and slow variations of a domain wall across a line-defect gives rise to the bifurcation from Dirac points of highly robust (topologically protected) edge states. These are time-harmonic solutions of Maxwell's equations which are propagating parallel to the line-defect and spatially localized transverse to it. The transverse localization and strong robustness to perturbation of these edge states is rooted in the protected zero mode of a one-dimensional effective Dirac operator with spatially varying mass term. These results imply the existence of uni-directional propagating edge states for two classes of time-reversal invariant media in which C symmetry is broken: magneto-optic media and bi-anisotropic media. Our analysis applies and extends the tools previously developed in the context of honeycomb Schrödinger operators.

Photonic graphene, a photonic crystal with honeycomb structures, has been intensively studied in both theoretical and applied fields. Similar to graphene which admits Dirac Fermions and topological edge states, photonic graphene supports novel and subtle propagating modes (edge modes) of electromagnetic waves. These modes have wide applications in many optical systems. In this paper, we propose a novel gradient recovery method based on Bloch theory for the computation of topological edge modes in the honeycomb structure. Compared to standard finite element methods, this method provides higher order accuracy with the help of gradient recovery technique. This high order accuracy is highly desired for constructing the propagating electromagnetic modes in applications. We analyze the accuracy and prove the superconvergence of this method. Numerical examples are presented to show the efficiency by computing the edge mode for the P-symmetry and C-symmetry breaking cases in honeycomb structures.