Stochastic self-tuning hybrid algorithm for reaction-diffusion systems
Abstract
Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Dec 27, 2019
- Source ID
- 10.1063/1.5125022
Entities
People
- Daniel M. Tartakovsky
- T. M. Bartol
- Terrence J. Sejnowski
- Á. Ruiz-martínez
Organizations
- Air Force Office of Scientific Research
- Salk Institute for Biological Studies
- Stanford University
- TotalEnergies
- United States Department of Energy
- University of California, San Diego