A generalized numerical model for clonal growth in scleractinian coral colonies.

Coral reefs, vital ecosystems supporting diverse marine life, are primarily shaped by the clonal expansion of coral colonies. Although the principles of coral clonal growth, involving polyp division for spatial extension, are well-understood, numerical modelling efforts are notably scarce in the literature. In this article, we present a parsimonious numerical model based on the cloning of polyps, using five key parameters to simulate a range of coral shapes. The model is agent-based, where each polyp represents an individual. The colony's surface expansion is dictated by the growth mode parameter (s), guiding the preferred growth direction. Varying s facilitates the emulation of diverse coral shapes, including massive, branching, cauliflower, columnar and tabular colonies. Additionally, we introduce a novel approach for self-regulatory branching, inspired by the intricate mesh-like canal system and internode regularity observed in Acropora species. Through a comprehensive sensitivity analysis, we demonstrate the robustness of our model, paving the way for future applications that incorporate environmental factors, such as light and water flow. Coral colonies are known for their high plasticity, and understanding how individual polyps interact with each other and their surroundings to create the reef structure has been a longstanding question in the field. This model offers a powerful framework for studying these interactions, enabling a future implementation of environmental factors and the possibility of identifying the key mechanisms influencing coral colonies' morphogenesis.

Commentary on Antosz et al. (2023): The role of macro-micro-macro frameworks and critical realism in agent-based modelling.

Antosz and colleagues' review of the role of theory in agent-based modelling (ABM) makes important recommendations for modelling practitioners. However, macro-micro-macro frameworks are not necessarily as reliant on existing theory as the review suggests. Adopting a critical realist perspective to ABM design would help to deliver the recommendations, within which macro-micro-macro frameworks can play an important enabling role.

Simulation and social network analysis provide insight into the acquisition of tool behaviour in hybrid macaques.

The pathways through which primates acquire skills are a central focus of cultural evolution studies. The roles of social and genetic inheritance processes in skill acquisition are often confounded by environmental factors. Hybrid macaques from Koram Island (Thailand) provide an opportunity to examine the roles of inheritance and social learning to skill acquisition within a single ecological setting. These hybrids are a cross between tool-using Burmese long-tailed (Macaca fascicularis aurea) and non-tool-using common long-tailed macaques (Macaca fascicularis fascicularis). This population provides an opportunity to explore the roles of social learning and inheritance processes while being able to exclude underlying ecological factors. Here, we investigate the roles of social learning and inheritance in tool use prevalence within this population using social network analysis and simulation. Agent-based modelling (ABM) is used to generate expectations for how social/asocial learning and inheritance structure the patterning in a social network. The results of the simulation show that various transmission mechanisms can be differentiated based on associations between individuals in a social network. The results provide an investigative framework for discussing tool use transmission pathways in the Koram social network. By combining ABM, network analysis, and behavioural data from the field we can investigate the roles social learning and inheritance play in tool acquisition of wild primates.

Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae.

This work provides a systematic and comprehensive overview of available resources for the molecular-scale modelling of the translation process through agent-based modelling. The case study is the translation in Saccharomyces cerevisiae, one of the most studied yeasts. The data curation workflow encompassed structural information about the yeast (i.e. the simulation environment), and the proteins, ribonucleic acids and other types of molecules involved in the process (i.e. the agents). Moreover, it covers the main process events, such as diffusion (i.e. motion of molecules in the environment) and collision efficiency (i.e. interaction between molecules). Data previously determined by wet-lab techniques were preferred, resorting to computational predictions/extrapolations only when strictly necessary. The computational modelling of the translation processes is of added industrial interest, since it may bring forward knowledge on how to control such phenomena and enhance the production of proteins of interest in a faster and more efficient manner.

Measuring unequal distribution of pandemic severity across census years, variants of concern and interventions.

BACKGROUND: The COVID-19 pandemic stressed public health systems worldwide due to emergence of several highly transmissible variants of concern. Diverse and complex intervention policies deployed over the last years have shown varied effectiveness in controlling the pandemic. However, a systematic analysis and modelling of the combined effects of different viral lineages and complex intervention policies remains a challenge due to the lack of suitable measures of pandemic inequality and nonlinear effects. METHODS: Using large-scale agent-based modelling and a high-resolution computational simulation matching census-based demographics of Australia, we carried out a systematic comparative analysis of several COVID-19 pandemic scenarios. The scenarios covered two most recent Australian census years (2016 and 2021), three variants of concern (ancestral, Delta and Omicron), and five representative intervention policies. We introduced pandemic Lorenz curves measuring an unequal distribution of the pandemic severity across local areas. We also quantified pandemic biomodality, distinguishing between urban and regional waves, and measured bifurcations in the effectiveness of interventions. RESULTS: We quantified nonlinear effects of population heterogeneity on the pandemic severity, highlighting that (i) the population growth amplifies pandemic peaks, (ii) the changes in population size amplify the peak incidence more than the changes in density, and (iii) the pandemic severity is distributed unequally across local areas. We also examined and delineated the effects of urbanisation on the incidence bimodality, distinguishing between urban and regional pandemic waves. Finally, we quantified and examined the impact of school closures, complemented by partial interventions, and identified the conditions when inclusion of school closures may decisively control the transmission. CONCLUSIONS: Public health response to long-lasting pandemics must be frequently reviewed and adapted to demographic changes. To control recurrent waves, mass-vaccination rollouts need to be complemented by partial NPIs. Healthcare and vaccination resources need to be prioritised towards the localities and regions with high population growth and/or high density.

Ability of epidemiological studies to monitor HPV post-vaccination dynamics: a simulation study.

Genital human papillomavirus (HPV) infections are caused by a broad diversity of genotypes. As available vaccines target a subgroup of these genotypes, monitoring transmission dynamics of nonvaccine genotypes is essential. After reviewing the epidemiological literature on study designs aiming to monitor those dynamics, we evaluated their abilities to detect HPV-prevalence changes following vaccine introduction. We developed an agent-based model to simulate HPV transmission in a heterosexual population under various scenarios of vaccine coverage and genotypic interaction, and reproduced two study designs: post-vs.-prevaccine and vaccinated-vs.-unvaccinated comparisons. We calculated the total sample size required to detect statistically significant prevalence differences at the 5% significance level and 80% power. Although a decrease in vaccine-genotype prevalence was detectable as early as 1 year after vaccine introduction, simulations indicated that the indirect impact on nonvaccine-genotype prevalence (a decrease under synergistic interaction or an increase under competitive interaction) would only be measurable after >10 years whatever the vaccine coverage. Sample sizes required for nonvaccine genotypes were >5 times greater than for vaccine genotypes and tended to be smaller in the post-vs.-prevaccine than in the vaccinated-vs.-unvaccinated design. These results highlight that previously published epidemiological studies were not powerful enough to efficiently detect changes in nonvaccine-genotype prevalence.

Modelling mass drug administration strategies for reducing scabies burden in Monrovia, Liberia.

Scabies is a parasitic infestation with high global burden. Mass drug administrations (MDAs) are recommended for communities with a scabies prevalence of >10%. Quantitative analyses are needed to demonstrate the likely effectiveness of MDA recommendations. In this study, we developed an agent-based model of scabies transmission calibrated to demographic and epidemiological data from Monrovia. We used this model to compare the effectiveness of MDA scenarios for achieving scabies elimination and reducing scabies burden, as measured by time until recrudescence following delivery of an MDA and disability-adjusted-life-years (DALYs) averted. Our model showed that three rounds of MDA delivered at six-month intervals and reaching 80% of the population could reduce prevalence below 2% for three years following the final round, before recrudescence. When MDAs were followed by increased treatment uptake, prevalence was maintained below 2% indefinitely. Increasing the number of and coverage of MDA rounds increased the probability of achieving elimination and the number of DALYs averted. Our results suggest that acute reduction of scabies prevalence by MDA can support a transition to improved treatment access. This study demonstrates how modelling can be used to estimate the expected impact of MDAs by projecting future epidemiological dynamics and health gains under alternative scenarios.

The Effects of Information on the Formation of Migration Routes and the Dynamics of Migration.

Most models of migration simply assume that migrants somehow make their way from their point of origin to their chosen destination. We know, however, that-especially in the case of asylum migration-the migrant journey often is a hazardous, difficult process where migrants make decisions based on limited information and under severe material constraints. Here we investigate the dynamics of the migration journey itself using a spatially explicit, agent-based model. In particular we are interested in the effects of limited information and information exchange. We find that under limited information, migration routes generally become suboptimal, their stochasticity increases, and migrants arrive much less frequently at their preferred destination. Under specific circumstances, self-organised consensus routes emerge that are largely unpredictable. Limited information also strongly reduces the migrants' ability to react to changes in circumstances. We conclude, first, that information and information exchange is likely to have considerable effects on all aspects of migration and should thus be included in future modelling efforts and, second, that there are many questions in theoretical migration research that are likely to profit from the use of agent-based modelling techniques.

Self-Isolation and Testing Behaviour During the COVID-19 Pandemic: An Agent-Based Model.

Since the beginning of the COVID-19 pandemic, various models of virus spread have been proposed. While most of these models focused on the replication of the interaction processes through which the virus is passed on from infected agents to susceptible ones, less effort has been devoted to the process through which agents modify their behaviour as they adapt to the risks posed by the pandemic. Understanding the way agents respond to COVID-19 spread is important, as this behavioural response affects the dynamics of virus spread by modifying interaction patterns. In this article, we present an agent-based model that includes a behavioural module determining agent testing and isolation propensity in order to understand the role of various behavioural parameters in the spread of COVID-19.

Fast and precise inference on diffusivity in interacting particle systems.

Particle systems made up of interacting agents is a popular model used in a vast array of applications, not the least in biology where the agents can represent everything from single cells to animals in a herd. Usually, the particles are assumed to undergo some type of random movements, and a popular way to model this is by using Brownian motion. The magnitude of random motion is often quantified using mean squared displacement, which provides a simple estimate of the diffusion coefficient. However, this method often fails when data is sparse or interactions between agents frequent. In order to address this, we derive a conjugate relationship in the diffusion term for large interacting particle systems undergoing isotropic diffusion, giving us an efficient inference method. The method accurately accounts for emerging effects such as anomalous diffusion stemming from mechanical interactions. We apply our method to an agent-based model with a large number of interacting particles, and the results are contrasted with a naive mean square displacement-based approach. We find a significant improvement in performance when using the higher-order method over the naive approach. This method can be applied to any system where agents undergo Brownian motion and will lead to improved estimates of diffusion coefficients compared to existing methods.

Opinion Dynamics Explain Price Formation in Prediction Markets.

Prediction markets are heralded as powerful forecasting tools, but models that describe them often fail to capture the full complexity of the underlying mechanisms that drive price dynamics. To address this issue, we propose a model in which agents belong to a social network, have an opinion about the probability of a particular event to occur, and bet on the prediction market accordingly. Agents update their opinions about the event by interacting with their neighbours in the network, following the Deffuant model of opinion dynamics. Our results suggest that a simple market model that takes into account opinion formation dynamics is capable of replicating the empirical properties of historical prediction market time series, including volatility clustering and fat-tailed distribution of returns. Interestingly, the best results are obtained when there is the right level of variance in the opinions of agents. Moreover, this paper provides a new way to indirectly validate opinion dynamics models against real data by using historical data obtained from PredictIt, which is an exchange platform whose data have never been used before to validate models of opinion diffusion.

Heterogeneous Retirement Savings Strategy Selection with Reinforcement Learning.

Saving and investment behaviour is crucial for all individuals to guarantee their welfare during work-life and retirement. We introduce a deep reinforcement learning model in which agents learn optimal portfolio allocation and saving strategies suitable for their heterogeneous profiles. The environment is calibrated with occupation- and age-dependent income dynamics. The research focuses on heterogeneous income trajectories dependent on agents' profiles and incorporates the parameterisation of agents' behaviours. The model provides a new flexible methodology to estimate lifetime consumption and investment choices for individuals with heterogeneous profiles.

Emergence of kinship structures and descent systems: multi-level evolutionary simulation and empirical data analysis.

In many indigenous societies, people are categorized into several cultural groups, or clans, within which they believe they share ancestors. Clan attributions provide certain rules for marriage and descent. Such rules between clans constitute kinship structures. Anthropologists have revealed several kinship structures. Here, we propose an agent-based model of indigenous societies to reveal the evolution of kinship structures. In the model, several societies compete. Societies themselves comprise multiple families with parameters for cultural traits and mate preferences. These values determine with whom each family cooperates and competes, and they are transmitted to a new generation with mutation. The growth rate of each family is determined by the number of cooperators and competitors. Through this multi-level evolution, family traits and preferences diverge to form clusters that can be regarded as clans. Subsequently, kinship structures emerge, including dual organization and generalized or restricted exchange, as well as patrilineal, matrilineal and double descent systems. These structures emerge depending on the necessity of cooperation and the strength of mating competition. Their dependence is also estimated analytically. Finally, statistical analysis using the Standard Cross-Cultural Sample, a global ethnographic database, empirically verified the theoretical results. Such collaboration between theoretical and empirical approaches will unveil universal features in anthropology.

Accounting for dimensional differences in stochastic domain invasion with applications to precancerous cell removal.

We consider a specific form of domain invasion that is an abstraction of pancreatic tissue eliminating precancerous mutant cells through juxtacrine signalling. The model is explored discretely, continuously, stochastically and deterministically, highlighting unforeseen nonlinear dependencies on the dimension of the solution domain. Specifically, stochastically simulated populations invade with a dimension dependent wave speed that can be over twice as fast as their deterministic analogues. Although the wave speed can be analytically derived in the cases of small domains, the probabilistic state space grows exponentially and, thus, we use numeric simulation and curve fitting to predict limiting dynamics.

Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions.

The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

An economically realistic asset exchange model.

Despite their highly idealized nature, certain agent-based models of asset exchange, proposed for the most part by physicists and mathematicians, have been shown to exhibit remarkable agreement with empirical wealth distribution data. While this agre- ement is comforting, there is widespread sentiment that further progress will require a detailed under- standing of the connection between these idealized models and the more realistic microeconomic models of exchange used by economists. In this paper, we examine that connection for a three-parameter asset exchange model, the Affine Wealth Model (AWM), that has demonstrated fraction-of-a-per cent agreement with empirical wealth data. We compare certain properties of this model with those of three great milestones of twentieth century economics, namely (i) Expected Utility Theory, (ii) General Equilibrium Theory and (iii) Prospect Theory. We find that the phenomenology exhibited by the AWM is fundamentally incompatible with Expected Utility Theory and General Equilibrium Theory, but very similar to that exhibited by Prospect Theory. Based on these observations, we argue that AWM transactions are, in a particular sense, an approximation to those described by Prospect Theory, and that Prospect Theory provides the sought-for connection between econophysics and microeconomics, at least for the topic of wealth distribution. This article is part of the theme issue 'Kinetic exchange models of societies and economies'.

A research agenda for the study of social norm change.

Social norms have been investigated across many disciplines for many years, but until recently, studies mainly provided indirect, implicit and correlational support for the role of social norms in driving behaviour. To understand how social norms, and in particular social norm change, can generate a large-scale behavioural change to deal with some of the most pressing challenges of our current societies, such as climate change and vaccine hesitancy, we discuss and review several recent advances in social norm research that enable a more precise underpinning of the role of social norms: how to identify their existence, how to establish their causal effect on behaviour and when norm change may pass tipping points. We advocate future research on social norms to study norm change through a mechanism-based approach that integrates experimental and computational methods in theory-driven, empirically calibrated agent-based models. As such, social norm research may move beyond unequivocal praising of social norms as the missing link between self-interested behaviour and observed cooperation or as the explanation for (the lack of) social tipping. It provides the toolkit to understand explicitly where, when and how social norms can be a solution to solve large-scale problems, but also to recognize their limits. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Modelling herd immunity requirements in Queensland: impact of vaccination effectiveness, hesitancy and variants of SARS-CoV-2.

Long-term control of SARS-CoV-2 outbreaks depends on the widespread coverage of effective vaccines. In Australia, two-dose vaccination coverage of above 90% of the adult population was achieved. However, between August 2020 and August 2021, hesitancy fluctuated dramatically. This raised the question of whether settings with low naturally derived immunity, such as Queensland where less than [Formula: see text] of the population is known to have been infected in 2020, could have achieved herd immunity against 2021's variants of concern. To address this question, we used the agent-based model Covasim. We simulated outbreak scenarios (with the Alpha, Delta and Omicron variants) and assumed ongoing interventions (testing, tracing, isolation and quarantine). We modelled vaccination using two approaches with different levels of realism. Hesitancy was modelled using Australian survey data. We found that with a vaccine effectiveness against infection of 80%, it was possible to control outbreaks of Alpha, but not Delta or Omicron. With 90% effectiveness, Delta outbreaks may have been preventable, but not Omicron outbreaks. We also estimated that a decrease in hesitancy from 20% to 14% reduced the number of infections, hospitalizations and deaths by over 30%. Overall, we demonstrate that while herd immunity may not be attainable, modest reductions in hesitancy and increases in vaccine uptake may greatly improve health outcomes. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Upscaling between an agent-based model (smoothed particle approach) and a continuum-based model for skin contractions.

Skin contraction is an important biophysical process that takes place during and after recovery of deep tissue injury. This process is mainly caused by fibroblasts (skin cells) and myofibroblasts (differentiated fibroblasts which exert larger pulling forces and produce larger amounts of collagen) that both exert pulling forces on the surrounding extracellular matrix (ECM). Modelling is done in multiple scales: agent-based modelling on the microscale and continuum-based modelling on the macroscale. In this manuscript we present some results from our study of the connection between these scales. For the one-dimensional case, we managed to rigorously establish the link between the two modelling approaches for both closed-form solutions and finite-element approximations. For the multi-dimensional case, we computationally evidence the connection between the agent-based and continuum-based modelling approaches.

Demographic models of the reproductive process: Past, interlude, and future.

After 30 years of active development, mechanistic models of the reproductive process nearly stopped attracting scholarly interest in the early 1980s. In the following decades, fertility research continued to thrive, relying on solid descriptive work and detailed analysis of micro-level data. The absence of systematic modelling efforts, however, has also made the field more fragmented, with empirical research, theory building, and forecasting advancing along largely disconnected channels. In this paper we outline some of the drivers of this process, from the popularization of user-friendly statistical software to the limitations of early family building models. We then describe a series of developments in computational modelling and statistical computing that can contribute to the emergence of a new generation of mechanistic models. Finally, we introduce a concrete example of this new kind of model, and show how they can be used to formulate and test theories coherently and make informed projections.