An Unstructured Mesh Convergent Reaction-Diffusion Master Equation for Reversible Reactions

The convergent reaction-diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction-diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction-diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle-particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model.Comment: 35 pages, 9 figures. Accepted, J. Comp. Phys. (2018

A convergent string method: Existence and approximation for the Hamiltonian boundary-value problem

This article studies the existence of long-time solutions to the Hamiltonian boundary value problem, and their consistent numerical approximation. Such a boundary value problem is, for example, common in Molecular Dynamics, where one aims at finding a dynamic trajectory that joins a given initial state with a final one, with the evolution being governed by classical (Hamiltonian) dynamics. The setting considered here is sufficiently general so that long time transition trajectories connecting two configurations can be included, provided the total energy $E$ is chosen suitably. In particular, the formulation presented here can be used to detect transition paths between two stable basins and thus to prove the existence of long-time trajectories. The starting point is the formulation of the equation of motion of classical mechanics in the framework of Jacobi's principle; a curve shortening procedure inspired by Birkhoff's method is then developed to find geodesic solutions. This approach can be viewed as a string method

High order direct Arbitrary-Lagrangian-Eulerian schemes on moving Voronoi meshes with topology changes

We present a new family of very high order accurate direct Arbitrary-Lagrangian-Eulerian (ALE) Finite Volume (FV) and Discontinuous Galerkin (DG) schemes for the solution of nonlinear hyperbolic PDE systems on moving 2D Voronoi meshes that are regenerated at each time step and which explicitly allow topology changes in time. The Voronoi tessellations are obtained from a set of generator points that move with the local fluid velocity. We employ an AREPO-type approach, which rapidly rebuilds a new high quality mesh rearranging the element shapes and neighbors in order to guarantee a robust mesh evolution even for vortex flows and very long simulation times. The old and new Voronoi elements associated to the same generator are connected to construct closed space--time control volumes, whose bottom and top faces may be polygons with a different number of sides. We also incorporate degenerate space--time sliver elements, needed to fill the space--time holes that arise because of topology changes. The final ALE FV-DG scheme is obtained by a redesign of the fully discrete direct ALE schemes of Boscheri and Dumbser, extended here to moving Voronoi meshes and space--time sliver elements. Our new numerical scheme is based on the integration over arbitrary shaped closed space--time control volumes combined with a fully-discrete space--time conservation formulation of the governing PDE system. In this way the discrete solution is conservative and satisfies the GCL by construction. Numerical convergence studies as well as a large set of benchmarks for hydrodynamics and magnetohydrodynamics (MHD) demonstrate the accuracy and robustness of the proposed method. Our numerical results clearly show that the new combination of very high order schemes with regenerated meshes with topology changes lead to substantial improvements compared to direct ALE methods on conforming meshes

The Virtual Element Method with curved edges

In this paper we initiate the investigation of Virtual Elements with curved faces. We consider the case of a fixed curved boundary in two dimensions, as it happens in the approximation of problems posed on a curved domain or with a curved interface. While an approximation of the domain with polygons leads, for degree of accuracy $k \geq 2$, to a sub-optimal rate of convergence, we show (both theoretically and numerically) that the proposed curved VEM lead to an optimal rate of convergence