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

An Evolutionary Algorithm for solving the Two-Dimensional Irregular Shape Packing Problem combined with the Knapsack Problem

This work presents an evolutionary algorithm to solve a joint problem of the Packing Problem and the Knapsack Problem, where the objective is to place items (with shape, value and weight) in a container (defined by its shape and capacity), maximizing the container's value, without intersections

Minimal knotted polygons in cubic lattices

An implementation of BFACF-style algorithms on knotted polygons in the simple cubic, face centered cubic and body centered cubic lattice is used to estimate the statistics and writhe of minimal length knotted polygons in each of the lattices. Data are collected and analysed on minimal length knotted polygons, their entropy, and their lattice curvature and writhe

Shear-induced rigidity of frictional particles: Analysis of emergent order in stress space

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a non-uniform density pattern, which results from either minimizing the energy cost or maximizing the entropy or both. In this work, we focus on a class of systems, where this paradigm is challenged. We show that shear-driven jamming in dry granular materials is a collective process controlled solely by the constraints of mechanical equilibrium. We argue that these constraints lead to a broken translational symmetry in a dual space that encodes the statistics of contact forces and the topology of the contact network. The shear-jamming transition is marked by the appearance of this broken symmetry. We extend our earlier work, by comparing and contrasting real space measures of rheology with those obtained from the dual space. We investigate the structure and behavior of the dual space as the system evolves through the rigidity transition in two different shear protocols. We analyze the robustness of the shear-jamming scenario with respect to protocol and packing fraction, and demonstrate that it is possible to define a protocol-independent order parameter in this dual space, which signals the onset of rigidity.Comment: 14 pages, 17 figure

The Flip Diameter of Rectangulations and Convex Subdivisions

We study the configuration space of rectangulations and convex subdivisions of $n$ points in the plane. It is shown that a sequence of $O(n\log n)$ elementary flip and rotate operations can transform any rectangulation to any other rectangulation on the same set of $n$ points. This bound is the best possible for some point sets, while $\Theta(n)$ operations are sufficient and necessary for others. Some of our bounds generalize to convex subdivisions of $n$ points in the plane.Comment: 17 pages, 12 figures, an extended abstract has been presented at LATIN 201