The large-scale collective behavior of biological systems can be characterized by macroscopic transport, which arises from the nonequilibrium microscopic interactions between individual constituents. A prominent example is the formation of dynamic aggregates by motile eukaryotic cells or bacteria mediated by active contractile forces. In this work we develop the two-dimensional fluctuating hydrodynamics theory based on the microscopic dynamics of a model system of aggregation by Neisseria gonorrhoeae bacteria. The derivation of two macroscopic transport coefficients of bulk diffusivity and conductivity which determine the hydrodynamic current of cells is the central result of this work. By showing how transport coefficients depend on cell density and microscopic parameters of the system, we predict transport slowdown during the colony formation process. This study provides valuable analytical tools for quantifying hydrodynamic transport in experimental systems involving cellular aggregation occurring due to intermittent contractile dipole forces.

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• Cell aggregation
• Clustering
• Macroscopic fluctuation theory
• Living matter & active matter
• Hydrodynamics
• Monte Carlo methods