Aisling Daly

• Doctor of Engineering
• PostDoc Position at Ghent University

Cellular automata (CAs) and convolutional neural networks (CNNs) are closely related due to the local nature of information processing. The connection between these topics is beneficial to both related fields, for conceptual as well as practical reasons. Our contribution solidifies this connection in the case of non-uniform CAs (nuCAs), simulating...

The emergent dynamics in spacetime diagrams of cellular automata (CAs) is often organised by means of a number of behavioural classes. Whilst classification of elementary CAs is feasible and well-studied, non-elementary CAs are generally too diverse and numerous to exhaustively classify manually. In this chapter we treat the spacetime diagram as a...

Higher-order interactions (HOIs) have the potential to greatly increase our understanding of ecological interaction networks beyond what is possible with established models that usually consider only pairwise interactions between organisms. While equilibrium values of such HOI-based models have been studied, the dynamics of these models and the sta...

Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ec...

The negative diversity‐invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader‐resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and func...

Raw data of the experiments described in the paper with title "Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex"

Cellular automata (CAs) are fully-discrete dynamical models that have received much attention due to the fact that their relatively simple setup can nonetheless express highly complex phenomena. Despite the model's theoretical maturity and abundant computational power, the current lack of a complete survey on the 'taxonomy' of various families of C...

Copepods are aquatic invertebrates with a key role at the basis of marine food webs due to their high biomass as well as their elevated fatty acid (FA) content. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are two FA abundant in copepods which have a well demonstrated role in growth and reproduction in marine organisms. While the majo...

Individual biology influences environment‐dependent population dynamics through life history. Population models that consider individual physiology are therefore popular for modelling dynamics under various environments. In recent years, a quantitative framework integrating metabolic theory (dynamic energy budget theory) into individual‐based model...

Copepods are marine invertebrates with a key role at the basis of marine food webs due to their high biomass as well as their elevated fatty acid (FA) content, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), two FA which have a well demonstrated role in growth and reproduction in marine organisms. Temperature is a key drive...

In order to describe the sensitivity of a cellular automaton (CA) to a small change in its initial configuration, one can attempt to extend the notion of Lyapunov exponents as defined for continuous dynamical systems to a CA. So far, such attempts have been limited to a CA with two states. This poses a significant limitation on their applicability,...

Agent-based models (ABMs) are an increasingly popular choice for simulating large systems of interacting components, and have been applied across a wide variety of natural and environmental systems. However, ABMs can be incredibly disparate and often opaque in their formulation, implementation, and analysis. This can impede critical assessment and...

Inspired by the theory of continuous dynamical systems, Lyapunov exponents have been previously defined in the framework of cellular automata (CAs) in order to quantify a CA’s sensitive dependence on initial conditions, i.e. a CA’s sensitivity to a perturbation of an initial configuration. However, the application of these Lyapunov exponents is cur...

Dietary diversity is an established public health principle, and its measurement is essential for studies of diet quality and food security. However, conventional between food group scores fail to capture the nutritional variability and ecosystem services delivered by dietary richness and dissimilarity within food groups, or the relative distributi...

Classification is one of the most important problems in the theory of CA. For instance, assessing how CA design choices impact the generated dynamics requires an overview of the types of dynamics that can occur. Nevertheless, an overview and critical comparison that includes works from the last five years is currently lacking. This paper provides s...

The extinction of ecosystems and the mechanisms that support or limit species coexistence have long been studied by scientists. It has been shown that competition and cyclic dominance among species promote species coexistence, such as in the classic Rock-Paper-Scissors (RPS) game. However, individuals’ mobility and the underlying topology that defi...

Cryptic species are morphologically identical but genetically distinct, and are prominent across numerous phyla. The coexistence of such closely related species on local scales would seem to run counter to traditional coexistence and competition theory; it has been hypothesized as a consequence of differences in their resource use or tolerances to...

Individual-based modelling is an increasingly popular framework for modelling biological systems. Many of these models represent space as a lattice, thus imposing unrealistic limitations on the movement of the modelled individuals. We adapt an existing model of three competing species by using a lattice-free approach, thereby improving the realism...

Many disciplines rely on testing combinations of compounds, materials, proteins, or bacterial species to drive scientific discovery. It is time-consuming and expensive to determine experimentally, via trial-and-error or random selection approaches, which of the many possible combinations will lead to desirable outcomes. Hence there is a pressing ne...

Theoretical and experimental research studies have shown that ecosystems governed by non-transitive competition networks tend to maintain high levels of biodiversity. The theoretical body of work, however, has mainly focused on competition networks in which the outcomes of competition events are predetermined and hence deterministic, and where all...

Diversity is a concept central to ecology, and its measurement is essential for any study of ecosystem health. But summarizing this complex and multidimensional concept in a single measure is problematic. Dozens of mathematical indices have been proposed for this purpose, but these can provide contradictory results leading to misleading or incorrec...

Using experimental data obtained from in vitro bioaugmentation studies of a sand filter community of 13 bacterial species, we develop an individual-based model representing the in silico counterpart of this synthetic microbial community. We assess the inter-species interactions, first by identifying strain identity effects in the data then by synth...

Microbial communities are critical for the proper functioning of each and every ecosystem on Earth. The ability to understand the structure and functioning of these complex communities is crucial to manage and protect natural communities, as well as to rationally design engineered microbial communities for important applications ranging from medica...

Biodiversity is a key factor underpinning the stability and productivity of microbial ecosystems. However, the mechanisms that give rise to and maintain biodiversity in microbial communities are not yet fully understood. The individual-based model (IBM) developed by Reichenbach et al. [1] has been used extensively in literature to investigate biodi...

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorpor...

The critical role that biodiversity plays in ecosystem functioning has motivated many studies of the mechanisms that sustain biodiversity, a notable example being cyclic competition.We extend existing models of communities with cyclic competition by incorporating variable community evenness and resource dependence in demographic processes, two feat...

Initial community evenness has been shown to be a key factor in preserving the functional stability of an ecosystem, but has not been accounted for in previous modelling studies. We formulate a model that allows the initial evenness of the community to be varied in order to investigate the consequent impact on system diversity. We consider a commun...

One of the most important aims in ecology is to identify and comprehend the mechanisms that sustain biodiversity - often critically important for the viability of ecosystems. Many theoretical models have shown that species in competition can coexist – and thus maintain the system’s biodiversity - if ecological processes such as competition and mobi...