The candidate has a strong academic background in mathematics and environmental science, with a focus on fluid mechanics, heat and mass transfer, and mathematical modeling of complex physical systems. Their training has developed a solid foundation in the governing principles of fluid dynamics, including the Navier–Stokes equations, transport phenomena, and numerical methods for solving partial differential equations.
They have prior experience with computational modeling of coupled physical processes, including fluid flow and scalar transport, using numerical simulation tools such as MATLAB, OpenFoam, and COMSOL Multiphysics. This experience has provided familiarity with setting up boundary value problems, interpreting numerical solutions, and analyzing multiphysics interactions in engineered and natural systems.
The candidate has developed strong analytical and computational skills, with particular interest in applying mathematical and numerical approaches to environmental and geophysical fluid dynamics problems. This includes an emerging focus on high-resolution modeling of complex natural systems and the interpretation of physical processes governing transport, mixing, and energy exchange.

Their current doctoral research at AIMs@JCU focuses on applying computational fluid dynamics and biogeochemical modeling to coral reef environments, using high-resolution three-dimensional reef geometries derived from EcoRRAP photogrammetry datasets. This work builds on their background in engineering science and extends it into marine and coastal environmental systems, with a strong emphasis on reef-scale hydrodynamics, nutrient transport, and ecosystem modeling.
The candidate’s background positions them well to undertake advanced numerical modeling of coral reef systems and contribute to improved predictive understanding of reef hydrodynamics and biogeochemical processes.

Improved Local-Scale Hydrodynamic and Biogeochemical Modelling of Coral Reefs on the Great Barrier Reef

2026 to 2029

Project Description

This project aims to improve the representation of coral reef structures in local-scale hydrodynamic and biogeochemical models by incorporating realistic three-dimensional reef geometries derived from EcoRRAP photogrammetry datasets. Current reef modeling frameworks, including components of eReefs and RECOM, typically represent coral reefs as simplified or flat surfaces, which limits their ability to resolve key physical and biogeochemical processes such as near-bed flow dynamics, turbulence generation, and nutrient and sediment transport.

The project will develop and apply high-resolution computational fluid dynamics (CFD) models to simulate water flow and scalar transport over realistic 3D coral reef structures. Using the incompressible Navier–Stokes equations coupled with advection–diffusion equations, the study will investigate how reef morphological complexity influences hydrodynamic behavior and exchange processes at ecologically relevant scales.

A central aim is to quantify the relationship between measurable reef morphology and key physical processes, including flow resistance, turbulence production, and transport efficiency. These relationships will be used to develop reduced-order parameterizations that allow fine-scale reef structural effects to be incorporated into larger-scale ecosystem models without resolving full 3D geometry.

The project will also process EcoRRAP photogrammetry datasets into simulation-ready computational meshes and perform a series of numerical experiments to analyze flow structure, shear stress distribution, boundary layer dynamics, and nutrient and sediment transport pathways across different reef morphologies.

Overall, the project seeks to improve predictive understanding of how coral reef structure controls hydrodynamic and biogeochemical processes and to provide new modeling tools and parameterizations that support reef-scale and regional-scale ecosystem modeling, restoration planning, and management of the Great Barrier Reef under changing environmental conditions.

Project Importance

This project is important because it addresses a fundamental limitation in current coral reef modeling: the simplified representation of reef structures in hydrodynamic and biogeochemical models. Existing large-scale frameworks such as eReefs and RECOM typically treat coral reefs as flat or highly parameterized surfaces, which restricts their ability to resolve key physical processes that occur at fine spatial scales, including turbulence generation, boundary layer dynamics, and nutrient and sediment transport.

By incorporating realistic three-dimensional reef geometries derived from EcoRRAP photogrammetry datasets, this research will significantly improve understanding of how reef structural complexity influences local flow behavior and transport processes. This is critical for accurately representing reef-scale hydrodynamics and biogeochemistry, which underpin coral growth, ecosystem productivity, and resilience to environmental stress.

The project will also contribute to the development of reduced-order parameterizations that translate complex reef morphology into practical modeling tools for use in larger-scale ecosystem models. This will help bridge the gap between high-resolution physical processes and regional-scale reef management and forecasting systems.

Improved representation of reef hydrodynamics and transport processes is essential for predicting how coral reefs respond to environmental pressures such as climate change, ocean warming, nutrient enrichment, and sedimentation. The outcomes of this research will therefore provide valuable insights for reef restoration strategies, conservation planning, and long-term management of the Great Barrier Reef.

In conclusion, the project will advance both fundamental knowledge of coral reef fluid dynamics and applied modeling capability, supporting evidence-based decision-making for reef resilience under changing environmental conditions.

Project Methods

This project will combine high-resolution three-dimensional coral reef datasets with advanced numerical modelling to investigate hydrodynamic and biogeochemical processes over complex reef structures. The study will utilise EcoRRAP photogrammetry-derived digital surface models to generate realistic, simulation-ready computational geometries of coral reef environments.

The processed 3D reef geometries will be converted into computational meshes suitable for numerical simulation. A range of mesh processing techniques will be applied, including geometry cleaning, mesh generation, and refinement to preserve key morphological features that influence flow and transport processes.

Hydrodynamic modelling will be conducted using the incompressible Navier–Stokes equations, solved using the OpenFOAM computational fluid dynamics framework. Appropriate turbulence modelling approaches, including Reynolds-Averaged Navier–Stokes (RANS) and selected Large Eddy Simulation (LES) cases, will be used depending on the required spatial and temporal resolution of the flow features being investigated.

The hydrodynamic simulations will be coupled with advection–diffusion equations to model nutrient and sediment transport processes over reef structures. Boundary conditions will be defined based on reef geometry, open water exchange, and physically realistic inflow and outflow conditions.

Simulation outputs will be analysed to quantify key variables such as velocity fields, pressure distribution, shear stress, turbulence intensity, diffusive boundary layer thickness, and scalar concentration gradients. Relationships between reef morphological descriptors (such as surface roughness, rugosity, and structural complexity) and transport characteristics will be systematically evaluated.

The project will also involve the development of reduced-order parameterisations that link fine-scale reef structure to effective hydrodynamic and transport properties. These parameterisations will be designed for potential integration into larger-scale ecosystem models of the Great Barrier Reef.

Model validation and sensitivity analysis will be conducted using available observational and EcoRRAP-derived datasets to ensure physical realism and robustness of the simulations. The overall workflow will integrate data processing, numerical simulation, and quantitative analysis to produce a consistent framework for studying coral reef hydrodynamics and biogeochemistry.

Project Results

The project aims to improve understanding of how three-dimensional coral reef morphology influences local hydrodynamics and biogeochemical transport processes. It is expected to reveal clear quantitative relationships between reef structural complexity and key physical processes such as flow resistance, turbulence generation, nutrient exchange, and sediment transport.

A key anticipated outcome is the identification of how specific morphological features, including rugosity, surface slope, and structural sheltering, control the formation of flow patterns and mixing zones within reef environments. These results are expected to demonstrate that small-scale reef geometry has a significant and previously under-resolved influence on nutrient delivery and boundary layer processes critical for coral health and ecosystem function.

The project also aims to develop reduced-order parameterizations that translate complex three-dimensional reef structures into effective hydrodynamic and transport properties. These parameterizations are expected to provide a practical bridge between high-resolution reef simulations and large-scale ecosystem models such as eReefs and RECOM.

One of the most significant expected contributions is a validated computational framework that integrates EcoRRAP-derived reef geometries with advanced CFD modeling tools, enabling realistic simulation of flow and transport processes over natural reef structures.

The most exciting outcome anticipated from this research is the ability to move beyond simplified representations of coral reefs and instead quantify how real, highly complex reef geometries actively shape the physical and biogeochemical environment that supports coral ecosystems. This has the potential to significantly improve predictive capability for reef resilience, restoration planning, and management under changing environmental conditions.

Keywords

Algae,
Artificial reef,
Behaviour,
Benthic,
Biochemistry,
Climate change,
Communication / Education,
Controlled Environment,
Coral reefs,
Corals,
Demersal,
Distribution,
Ecology,
Human use,
Interaction,
Management tools,
Mapping,
Marine planning,
Modelling,
Monitoring,
Natural disturbance,
Ocean acidification,
Oceanography,
Physiology,
Pollution,
Porifera (sponges),
Quantitative marine science,
Remote Sensing,
Sediment dwellers,
Temporal change