Computing macroscopic reaction rates in reaction-diffusion systems using Monte Carlo simulations
| dc.contributor.author | Swailem, Mohamed | en |
| dc.contributor.author | Täuber, Uwe C. | en |
| dc.date.accessioned | 2024-11-18T14:50:29Z | en |
| dc.date.available | 2024-11-18T14:50:29Z | en |
| dc.date.issued | 2024-07-17 | en |
| dc.description.abstract | Stochastic reaction-diffusion models are employed to represent many complex physical, biological, societal, and ecological systems. The macroscopic reaction rates describing the large-scale, longtime kinetics in such systems are effective, scale-dependent renormalized parameters that need to be either measured experimentally or computed by means of a microscopic model. In a Monte Carlo simulation of stochastic reaction-diffusion systems, microscopic probabilities for specific events to happen serve as the input control parameters. To match the results of any computer simulation to observations or experiments carried out on the macroscale, a mapping is required between the microscopic probabilities that define the Monte Carlo algorithm and the macroscopic reaction rates that are experimentally measured. Finding the functional dependence of emergent macroscopic rates on the microscopic probabilities (subject to specific rules of interaction) is a very difficult problem, and there is currently no systematic, accurate analytical way to achieve this goal. Therefore, we introduce a straightforward numerical method of using lattice Monte Carlo simulations to evaluate the macroscopic reaction rates by directly obtaining the count statistics of how many events occur per simulation time step. Our technique is first tested on well-understood fundamental examples, namely restricted birth processes, diffusion-limited two-particle coagulation, and two-species pair annihilation kinetics. Next we utilize the thus gained experience to investigate how the microscopic algorithmic probabilities become coarse-grained into effective macroscopic rates in more complex model systems such as the Lotka–Volterra model for predator-prey competition and coexistence, as well as the rock-paper-scissors or cyclic Lotka–Volterra model as well as its May–Leonard variant that capture population dynamics with cyclic dominance motifs. Thereby we achieve a more thorough and deeper understanding of coarse-graining in spatially extended stochastic reaction-diffusion systems and the nontrivial relationships between the associated microscopic and macroscopic model parameters, with a focus on ecological systems. The proposed technique should generally provide a useful means to better fit Monte Carlo simulation results to experimental or observational data. | en |
| dc.description.version | Accepted version | en |
| dc.format.mimetype | application/pdf | en |
| dc.identifier | 014124 (Article number) | en |
| dc.identifier.doi | https://doi.org/10.1103/PhysRevE.110.014124 | en |
| dc.identifier.orcid | Tauber, Uwe [0000-0001-7854-2254] | en |
| dc.identifier.uri | https://hdl.handle.net/10919/123625 | en |
| dc.identifier.volume | 110 | en |
| dc.language.iso | en | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.title | Computing macroscopic reaction rates in reaction-diffusion systems using Monte Carlo simulations | en |
| dc.title.serial | Physical Review E | en |
| dc.type | Article - Refereed | en |
| dc.type.dcmitype | Text | en |
| dc.type.other | Article | en |
| dcterms.dateAccepted | 2024-06-21 | en |
| pubs.organisational-group | Virginia Tech | en |
| pubs.organisational-group | Virginia Tech/Science | en |
| pubs.organisational-group | Virginia Tech/Science/Physics | en |
| pubs.organisational-group | Virginia Tech/Faculty of Health Sciences | en |
| pubs.organisational-group | Virginia Tech/All T&R Faculty | en |
| pubs.organisational-group | Virginia Tech/Science/COS T&R Faculty | en |