Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries

Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries

Chemical reactions inside cells are generally considered to happen within fixed-size compartments. However, cells and their compartments are highly dynamic. Thus, such stringent geometrical assumptions may not reflect biophysical reality, and can highly bias conclusions from simulation studies. In this work, we present an intuitive algorithm for particle-based diffusion in and on moving boundar...

DIFFUSION AND REACTION WITHIN A SHAPED NICKEL PEROVSKITE CATALYST

  Abstract : In this study, we prepared a LaNi0.3Al0.7O3 perovskite catalyst using a sol-gel related method (with prop ionic acid as a solvent) for use in the methane dry reforming reaction to produce synthesis gas. We defined the catalyst structure on the basis of X-ray diffraction analysis and measurements of the specific surface area and particle size distribution. The mixed oxide structure ...

STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python

We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did...

Stochastic Simulation of Reaction-Diffusion Systems

Stochastic Simulation of Reaction-Diffusion Systems

Reactiondiffusion systems are mathematical models that describe how the concentration of one or more substances distributed in space changes under the influence of local chemical reactions in which the substances are converted into each other, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear par...