77 citations · 158 across the 7 of their papers we have counts for
8 papers
Hierarchical Reaction-Diffusion Master Equation
Stefan Hellander, Andreas Hellander
We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, som…
Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning
Stefan Hellander, Andreas Hellander, Linda Petzold
The reaction-diffusion master equation (RDME) is a model that allows for efficient on-lattice simulation of spatially resolved stochastic chemical kinetics. Compared to off-lattice…
Reaction rates for reaction-diffusion kinetics on unstructured meshes
Stefan Hellander, Linda Petzold
The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distributi…
Reaction rates for a generalized reaction-diffusion master equation
Stefan Hellander, Linda Petzold
It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh…
Reaction rates for mesoscopic reaction-diffusion kinetics
Stefan Hellander, Andreas Hellander, Linda Petzold
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME…
Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
Mark B Flegg, Stefan Hellander, Radek Erban
In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated.…
Single molecule simulations in complex geometries with embedded dynamic one-dimensional structures
Stefan Hellander
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highl…
On the Reaction Diffusion Master Equation in the Microscopic Limit
Stefan Hellander, Andreas Hellander, Linda Petzold
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the…