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DY: Fachverband Dynamik und Statistische Physik

DY 43: Poster: Statistical Physics

DY 43.7: Poster

Mittwoch, 11. März 2026, 15:00–18:00, P5

Stochastic Simulation Algorithm for Spatiotemporal Chemical Master Equations — •Fatemeh Tavakkoli, Roya Ebrahimi Viand, Bat-Amalgam Bat-Erdene, Karsten Reuter, and Sebastian Matera — Fritz-Haber-Institut der MPG, Berlin

Spatiotemporal chemical master equations (SCME) have a number of applications ranging from biochemistry to sociodynamics, and have gained interest in mathematical physics. Describing high-dimensional Markov jump processes, SCMEs are typically not solvable, neither analytically nor numerically, but need to be addressed by stochastic simulation using kinetic Monte Carlo methods. We present a software framework for this purpose based on the Berlin Extended Stochastic Simulation Software (BeESSS). A simple to use Python frontend allows to define an SCME model and the software generates efficient backend C++ code (controllable by the Python frontend). The sparse nature of BeESSS allows to exploit the local nature of SCMEs where space is decomposed into compartments and only neighboring compartments interact. We demonstrate the tool on Lottka-Volterra-type predator-prey models and use it to evaluate the time complexity and memory limitations of our simulation approach.

Keywords: kinetic Monte Carlo; Stochastic Simulation Algorithm; Reaction-Diffusion Equations