Matthew Adams

Matthew Adams
Queensland University of Technology | QUT · School of Mathematical Sciences

BAppSc, BAppSc(Hons), PhD

About

56
Publications
10,485
Reads
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798
Citations
Introduction
I am an applied mathematical modeller of environmental and biological systems, with a strong interest in using these models to inform decision-making. My work aims to bridge the gaps between modellers and decision-makers, by showing how mathematics can be used to gain substantial insights into how environmental systems function as well as inform their management.
Additional affiliations
January 2020 - present
Queensland University of Technology
Position
  • Lecturer
September 2017 - January 2020
The University of Queensland
Position
  • Research Associate
March 2013 - September 2017
The University of Queensland
Position
  • Fellow

Publications

Publications (56)
Article
Feedbacks between seagrass and the local environmental conditions may hinder attempts to restore seagrass by inducing alternative stable states. A one-dimensional physical-biological model was used to identify the conditions under which a feedback between seagrass, sediment and light can yield alternative stable states of seagrass presence and abse...
Article
Full-text available
Well-intentioned environmental management can backfire, causing unforeseen damage. To avoid this, managers and ecologists seek accurate predictions of the ecosystem-wide impacts of interventions , given small and imprecise datasets, which is an incredibly difficult task. We generated and analysed thousands of ecosystem population time series to inv...
Article
Full-text available
Seagrass ecosystems are increasingly subjected to multiple interacting stressors, making the consequent trajectories difficult to predict. Here, we present a new process-based model of seagrass decline in response to cumulative light and temperature stress. The model is calibrated to laboratory datasets for Great Barrier Reef seagrasses using Bayes...
Preprint
It can be difficult to identify ways to reduce the complexity of large models whilst maintaining predictive power, particularly where there are hidden parameter interdependencies. Here, we demonstrate that the analysis of model sloppiness can be a new invaluable tool for strategically simplifying complex models. Such an analysis identifies paramete...
Article
This work introduces a comprehensive approach to assess the sensitivity of model outputs to changes in parameter values, constrained by the combination of prior beliefs and data. This approach identifies stiff parameter combinations strongly affecting the quality of the model-data fit while simultaneously revealing which of these key parameter comb...
Article
Data-hungry, complex ecosystem models are often used to predict the consequences of threatened species management, including perverse outcomes. Unfortunately, this approach is impractical in the many systems that have insufficient data to parameterize ecosystem interactions or reliably calibrate or validate such models. We devised a different appro...
Article
Full-text available
Compositional data, which is data consisting of fractions or probabilities, is common in many fields including ecology, economics, physical science and political science. If these data would otherwise be normally distributed, their spread can be conveniently represented by a multivariate normal distribution truncated to the non-negative space under...
Preprint
Full-text available
The ensemble Kalman filter (EnKF) is a Monte Carlo approximation of the Kalman filter for high dimensional linear Gaussian state space models. EnKF methods have also been developed for parameter inference of static Bayesian models with a Gaussian likelihood, in a way that is analogous to likelihood tempering sequential Monte Carlo (SMC). These meth...
Article
Full-text available
The global carbon sequestration and avoided emissions potentially achieved via blue carbon is high (∼3% of annual global greenhouse gas emissions); however, it is limited by multidisciplinary and interacting uncertainties spanning the social, governance, financial, and technological dimensions. We compiled a transdisciplinary team of experts to elu...
Preprint
Compositional data, which is data consisting of fractions or probabilities, is common in many fields including ecology, economics, physical science and political science. If these data would otherwise be normally distributed, their spread can be conveniently represented by a multivariate normal distribution truncated to the non-negative space under...
Preprint
This work introduces a Bayesian approach to assess the sensitivity of model outputs to changes in parameter values, constrained by the combination of prior beliefs and data. This novel approach identifies stiff parameter combinations that strongly affect the quality of the model-data fit while simultaneously revealing which of these key parameter c...
Conference Paper
Full-text available
All models are imperfect, so it is important to consider uncertainty in their predictions. When calibrating models to measured data, uncertainty in the model can be simultaneously estimated, although there are multiple methods available for doing this. In this study, we applied ensemble smoothers and Bayesian inference to calibrate a model of nitro...
Technical Report
Full-text available
This project synthesizes and refines the carbonate budget produced for the Great Barrier Reef (GBR) in Wolfe et al. (2019). Here, we present robust methodological advances to facilitate the calculation of carbonate budgets for the GBR, including: 1. The first method to quantify carbonate budgets using percent-cover data, alleviating the requirement...
Article
Saltmarsh is a coastal ecosystem providing crucial ecosystem services, and its continued degradation and fragmentation has drawn increasing attention. However, how to effectively restore the connectivity between fragmented saltmarsh patches remains an open challenge. In this study, we developed a metric and modelling framework that prioritised salt...
Article
Catchment impacts on downstream ecosystems are difficult to quantify, but important for setting management targets. Here we compared 12 years of monitoring data of seagrass area and biomass in Cleveland Bay, northeast Australia, with discharge and associated sediment loads from nearby rivers. Seagrass biomass and area exhibited different trajectori...
Article
Poor water quality and light reduction owing to anthropogenic impacts are the most widespread causes behind marine submerged angiosperm (seagrass) declines, worldwide. Seagrasses could respond to sustained environmental stresses, such as increasing water depth and light reduction, through morphological changes, particularly shoot density and/or bio...
Technical Report
Full-text available
In 2017, the Great Barrier Reef Marine Park Authority (GBRMPA) convened a summit to discuss the resilience of the reef and explore the benefits of taking a resilience-based approach to its management, RBM (Great Barrier Reef Marine Park Authority 2017). Resilience-based management is defined as “using knowledge of current and future drivers influen...
Technical Report
Full-text available
Catchment activities, such as logging, grazing, agriculture and urbanization,generate elevated sediment loads which impact downstream water quality and coastal ecosystems. Quantifying the complex link between catchment sediment sources and downstream ecosystems is challenging but important for the development of reliable land-based ecologically rel...
Article
Full-text available
Since the mid 1990s, Australia's Commonwealth Science Industry and Research Organisation (CSIRO) has developed a biogeochemical (BGC) model for coupling with a hydrodynamic and sediment model for application in estuaries, coastal waters and shelf seas. The suite of coupled models is referred to as the CSIRO Environmental Modelling Suite (EMS) and h...
Article
Full-text available
Implementing management actions to achieve environmental outcomes requires defining and quantifying ecological targets, but this is a complex challenge, and there are few examples of how to quantitatively set them in complex dynamic marine ecosystems. Here we develop a methodology to devise ‘desired state’ for tropical seagrasses in Cleveland Bay,...
Article
Predicting algal population dynamics using models informed by experimental data has been used as a strategy to inform the management and control of harmful cyanobacterial blooms. We selected toxic bloom-forming species Microcystis spp. and Raphidiopsis raciborskii (basionym Cylindrospermopsis raciborskii) for further examination as they dominate in...
Conference Paper
Full-text available
Catchment degradation causing increased sediment flow is one of the key stressors facing Great Barrier Reef (GBR) habitats. Ecologically relevant targets (ERTs) for sediment and nutrient loads have been previously proposed based on seagrass light requirements, the next step is to connect these to ecological response. The overarching goal of the pre...
Article
Full-text available
Tree stems swell and shrink daily, which is thought to reflect changes in the volume of water within stem tissues. We observed these daily patterns using automatic dendrometer bands in a diverse group of mangrove species over five mangrove forests across Australia and New Caledonia. We found that mangrove stems swelled during the day and shrank at...
Article
Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of...
Article
Trace element accumulation is an anthropogenic threat to seagrass ecosystems, which in turn may affect the health of humans who depend on these ecosystems. Trace element accumulation in seagrass meadows may vary temporally due to, e.g., seasonal patterns in sediment discharge from upstream areas. In addition, when several trace elements are present...
Chapter
This chapter describes the distribution of key seagrass species in the estuarine-nearshore coastal (ENC) continuum of the south-east region of Australia. We explore the potential influences of hydrodynamics (e.g. tidal currents, wave energy), estuary entrance dynamics (recruitment) and water quality, in addition to light, as primary stressors on se...
Chapter
Seagrass habitat is strongly constrained by light availability. Decline in benthic light due to anthropogenic activities (e.g. eutrophication, dredging and catchment modification) is a major threat to seagrass ecosystems, both within Australia and internationally. Even in pristine conditions, light available to seagrasses can be highly variable on...
Article
Full-text available
Seagrasses are globally important coastal habitat‐forming species, yet it is unknown how seagrasses respond to the combined pressures of ocean acidification and warming of sea surface temperature. We exposed three tropical species of seagrass (Cymodocea serrulata, Halodule uninervis, and Zostera muelleri) to increasing temperature (21, 25, 30, and...
Article
Full-text available
Submerged macrophytes can have a profound effect on shallow lake ecosystems through their ability to modify the thermal structure and dissolved oxygen levels within the lake. Invasive macrophytes, in particular, can grow rapidly and induce thermal gradients in lakes that may substantially change the ecosystem structure and challenge the survival of...
Article
Cyanobacteria Microcystis aeruginosa and Cylindrospermopsis raciborskii are two harmful species which co-occur and successively dominate in freshwaters globally. Within-species strain variability affects cyanobacterial population responses to environmental conditions, and it is unclear which species/strain would dominate under different environment...
Article
Full-text available
Rising sea water temperature will play a significant role in responses of the world’s seagrass meadows to climate change. In this study, we investigated seasonal and latitudinal variation (spanning more than 1500km) in seagrass productivity, and the optimum temperatures at which maximum photosynthesis and net productivity (for the leaf and the whol...
Article
Full-text available
When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indic...
Article
1. Seagrass habitat is globally threatened from the cumulative impact of human activities on coastal ecosystems. Successful conservation and restoration of seagrass requires knowledge of the environmental factors that limit seagrass presence; however, quantifying the relative importance of these environmental factors is a significant challenge. 2....
Article
Seagrasses worldwide are highly vulnerable to, and at increasing risk from reduced light availability, and robust light thresholds are required for evaluating future impacts of changing light conditions. We tested the morphological response (shoot density and growth) of four Indo-West Pacific seagrass species (Cymodocea serrulata, Halodule uninervi...
Article
A feedback between seagrass presence, suspended sediment and benthic light can induce bistability between two ecosystem states: one where the presence of seagrass reduces suspended sediment concentrations to increase benthic light availability thereby favoring growth, and another where seagrass absence increases turbidity thereby reducing growth. T...
Article
Oxygen flux between aquatic ecosystems and the water column is a measure of ecosystem metabolism. However, the oxygen flux varies during the day in a ''hysteretic'' pattern: there is higher net oxygen production at a given irradiance in the morning than in the afternoon. In this study, we investigated the mechanism responsible for the hysteresis in...
Article
This project investigated the calcium distributions of the skin, and the growth patterns of skin substitutes grown in the laboratory, using mathematical models. The research found that the calcium distribution in the upper layer of the skin is controlled by three different mechanisms, not one as previously thought. The research also suggests that t...
Conference Paper
Full-text available
Seagrasses are rapidly declining worldwide due to anthropogenic impacts on coastal environments. One major contributor to seagrass loss is the degradation of water quality which reduces light availability. In this paper we use a data-driven approach to compare several indicators of light history for their ability to predict seagrass biomass. Data...
Thesis
Full-text available
This project investigated the calcium distributions of the skin, and the growth patterns of skin substitutes grown in the laboratory, using mathematical models. The research found that the calcium distribution in the upper layer of the skin is controlled by three different mechanisms, not one as previously thought. The research also suggests that t...
Article
Full-text available
We propose and mathematically examine a theory of calcium profile formation in unwounded mammalian epidermis based on: changes in keratinocyte proliferation, fluid and calcium exchange with the extracellular fluid during these cells' passage through the epidermal sublayers, and the barrier functions of both the stratum corneum and tight junctions l...
Conference Paper
Full-text available
Techniques are presented for enhancing weak Raman scattering signals for rapid yet accurate substance detection. Novel surfaces that allow signal enhancement quantification are described as are eye-safe methodologies that maximize the stand-off Raman detection range.
Article
The surface enhanced Raman scattering effect has shown immense potential for detecting trace amounts of explosive vapor molecules. To date, efforts to produce a commercially available, reliable SERS sensor have been impeded by an inability to separate the electromagnetic enhancement produced by the metallic nanostructure from other signal enhancing...
Conference Paper
Full-text available
Problems involving the solution of advection-diffusion-reaction equations on domains and subdomains whose growth affects and is affected by these equations, commonly arise in developmental biology. Here, a mathematical framework for these situations, together with methods for obtaining spatio-temporal solutions and steady states of models built fro...
Article
Full-text available
We present a porous medium model of the growth and deterioration of the viable sublayers of an epidermal skin substitute. It consists of five species: cells, intracellular and extracellular calcium, tight junctions, and a hypothesised signal chemical emanating from the stratum corneum. The model is solved numerically in Matlab using a finite differ...

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Projects

Project (1)
Archived project
To predict the harmful algal blooms and mitigate the bad effects of them.