Technologies used in PHISHES

To learn more: Daisy – University of Copenhagen

Daisy is an agro-environmental mechanistic system model able to simulate and integrate processes in soil (vadose zone), plants, and the lower atmosphere. It captures the detailed dynamics of water, heat, Carbon, and Nitrogen within the soil-plant-atmosphere continuum at the field scale as a function of weather and agricultural management. This includes simulations of crop growth, as well as additions, transformation, fate and storage of C and N, including leaching and gaseous losses such as carbon dioxide CO₂, nitrogen N2 and nitrous oxide N₂O as well as other chemicals (pesticides, PFAS and natural toxins) in one or two dimensions (1D or 2D).

Daisy can be used to examine the impact of changes in agricultural management, with reference to conservation and precision agriculture, as well as climate changes on both agricultural production, soil quality and environmental loads, such as leaching of nitrate and pesticides to groundwater and surface waters. 

To learn more: PC-PROGRESS – HYDRUS 

The Hydrus software suite has become standard tools for addressing many soil, agricultural, environmental, and hydrological problems requiring the evaluation of various subsurface physical, chemical, and biological processes. Hydrus is a standalone software designed for simulating water, heat, and solute movement in 1D, 2D, or 3D variably saturated porous media. An advanced formalism of the Richards equation dealing with (constant or time-varying) boundary conditions and non-uniformity of the simulated domain is solved. conditions. These conditions can be prescribed as either pressure head or flux boundaries, as well as boundaries controlled by atmospheric conditions. During the simulation, soil surface boundary conditions may shift from prescribed flux to prescribed head-type conditions (and vice versa), accounting for infiltration, ponding, surface runoff or actual soil evaporation processes. Moreover, a special boundary condition simulating plant water uptake as a sink term with an explicit distribution of the root zone along the soil profile can be applied to the water flow equation. Hydrus software also incorporates hysteresis, assuming that scanning curves are scaled from the main drying curve and wetting curves from the main wetting curve. The code further implements a scaling procedure to approximate variability in the hydraulic properties along a soil profile using a set of linear scaling transformations. To simulate fate and transport of contaminant as well as several soil functions related to carbon and nutrient cycles or organic matter dynamics, a specific add-on of the Hydrus software suite can be used, called HPx, coupling Hydrus with PHREEQC geochemical code. Due to the flexibility of the PHREEQC code, a broad range of low-temperature (bio)-geochemical reactions can be simulated. HPx has been used to simulate the fate and transport of a broad range of contaminant in soils, including nitrogen, phosphorus, pesticides, metals and metalloids as well as emerging contaminants. A recent development of Hydrus has been also conducted for modifying Richards and advection-dispersion-reaction equations to simulate PFAS mobility in soils.

To learn more: MODFLOW 6 – USGS Modular Hydrological Models

For nearly four decades, MODFLOW has been a trusted tool among academics, private consultants, and government scientists for its accuracy, reliability, and efficiency in simulating groundwater flow. MODFLOW 6 is an object-oriented program and framework designed to support multiple models and model types within a single simulation. The “6” represents the sixth major version of MODFLOW released by the USGS, following previous versions from 1984, 1988, 1996, 2000, and 2005. MODFLOW 6 enables the inclusion of multiple models in a simulation, which can operate independently, exchange information, or be tightly coupled at the matrix level through a shared numerical solution. Information transfer between models is managed through exchange objects, enabling independent model development and use. This flexible framework supports diverse modeling approaches, such as coupling a regional-scale groundwater model with multiple local-scale models or integrating a surface-water flow model with multiple groundwater flow models.  

In the PHISHES project, conceptual models of current and future pathways involving surface water, groundwater, and the unsaturated zone in the soil will be analyzed using numerical models.  Since MODFLOW 6 has already been used for the saturated zone in the case study of Rotterdam, solute transport in this zone will be applied. However, particular attention is needed for the interaction between storage in the infiltration facility and the unsaturated zone.

To learn more: MIKE SHE | Integrated Hydrological Modelling Software

MIKE SHE is integrated catchment hydrological modelling software designed to simulate surface water and groundwater interactions in complex systems. Developed by leading experts in the field, MIKE SHE is widely used by hydrologists, engineers, and researchers to evaluate water resources, predict flooding events, and optimise water management strategies. It incorporates advanced algorithms to simulate rainfall-runoff processes, groundwater flow, soil moisture dynamics, and surface water routing. By integrating these components, MIKE SHE enables users to assess the impact of various factors like land use changes, climate variability, and water management interventions on water resources and ecosystems.

To learn more: MIKE ECO Lab | Ecological Modelling Software

MIKE ECO Lab is a versatile software tool that facilitates ecological modelling and environmental impact assessments across aquatic ecosystems. Tailored for simulating and analysing the intricate dynamics of marine, freshwater, and estuarine environments, it empowers users to model diverse ecological processes like nutrient cycling, primary production, and plankton dynamics. Leveraging advanced algorithms, MIKE ECO Lab accurately simulates the behaviour and distribution of organisms and chemical compounds in ecological systems and biogeochemical systems.

MIKE ECO Lab can be used for a wide range of applications including environmental impact assessments, ecosystem management, water quality modelling, and fisheries management. Its user-friendly interface and powerful modelling capabilities, enables scientists, environmental consultants, and decision-makers to assess the impact of human activities, climate change, and pollution on aquatic ecosystems, and to develop sustainable management strategies.

To learn more: Ecotoxmodels

TKTD (Toxico-Kinetics-Toxico-Dynamics) models are implemented in the open-source software OpenModel. The Toxico-Kinetics (TK) translates external exposure concentration into internal concentration within the organism, while Toxico-Dynamics (TD) describes the development of toxic effects over time.  

By separating the TK and TD parts, it becomes possible to estimate the rates at which compounds of interest are taken up and eliminated (TK part) and then relate the internal concentrations to the development of the observed adverse effects (TD part). Toxico-Kinetics-Toxico-Dynamics (TKTD) simulations are used to assess ecotoxicity effects across multiple endpoints, such as those for pesticides and organic pollutants in organisms at field scale and catchment scale.