Agent-based modeling of swarm dynamics of motile photokinetic organisms

This dataset contains results from an agent-based modeling framework that simulates the dynamics of motile organisms from the individual to the swarm scale. The model incorporates three organism-level mechanisms: photokinesis, gyrotaxis, and Brownian motion. Their interplay gives rise to a rich range of population-level patterns. The emergent dynamics are regulated by spatiotemporal variations in light and are characterized by two key dimensionless parameters: the Péclet number, Pe, which quantifies the relative importance of directed motion to rotational diffusion, and the vertical swimming asymmetry ratio, W, which measures the bias in vertical motility. The dataset includes two types of files: Simulation output generated using the mathematical framework reported in:Morales, J., Munoz, P., Noto, D., Ulloa, H. N., & Guzmán-Lastra, F. (2025). Emergent collective dynamics from motile photokinetic organisms. arXiv preprint arXiv:2506.19081. Python scripts used to visualize and analyze the results, including: Fig2.py for single-organism dynamics, Fig3.py for swarm-scale dynamics, and Fig4.py for statistical analysis. This repository is intended to support reproducibility and facilitate reuse of the simulation results and visualization tools.