BRTSim, a general-purpose computational solver for hydrological, biogeochemical, and ecosystem dynamics. This paper introduces the recent release v3.1a of BRTSim (BioReactive Transport Simulator), a general-purpose multiphase and multi-species liquid, gas and heat flow solver for reaction-advection-dispersion processes in porous and non-porous media with application in hydrology and biogeochemistry. Within the philosophy of the BRTSim platform, the user can define (1) arbitrary chemical and biological species; (2) arbitrary chemical and biological reactions; (3) arbitrary equilibrium reactions; and (4) combine solvers for phases and heat flows as well as for specialized biological processes such as bioclogging and chemotaxis. These capabilities complement a suite of processes and process-feedback solvers not currently available in other general-purpose codes. Along with the flexibility to design arbitrarily complex reaction networks, and setup and synchronize solvers through one input text file, BRTSim can communicate with third-party software with ease. Here, four cases study that combine experimental observations and modeling with BRTSim are reported: (i) water table dynamics in a heterogeneous aquifer for variable hydrometeorological conditions; (ii) soil biological clogging by cells and exopolymers; (iii) biotic degradation and isotopic fractionation of nitrate; and (iv) dispersion and biodegradation of atrazine herbicide in agricultural crops.

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