Agent-Based Life Cycle Assessment enables joint economic-environmental analysis of policy to support agricultural biomass for biofuels

Production of agricultural biofuels is expected to rise due to increasing climate change mitigation ambitions. Policy interventions promoting targeted bioenergy solutions can be motivated by the large environmental externalities present in agricultural systems and the local context of biomass production co-benefits. Introducing energy crops in crop rotations in arable land with depleted Soil Organic Carbon (SOC) levels offers the potential to increase SOC stocks and future crop yields as a step towards more sustainable agricultural systems. However, the environmental performance of a policy incentive for energy crops with SOC co-benefits is less evident when considering its land-use effects within and outside of the target agricultural system. We study the potential impacts of a change in agricultural policy on regional agricultural structure and production, and the environment with an Agent-Based Life Cycle Assessment approach. We simulate a policy payment that would achieve adoption of grass leys in crop rotations corresponding to 25 % of the highly productive land in an intensive farming region of southern Sweden. Although enhancing soil health in SOC-depleted farming regions is a desirable environmental objective, its significance is limited within the life-cycle performance of the payment. Instead, crop-displacement impacts and the grass potential as biofuel feedstock are the main drivers. The active utilisation of grasses for biofuel purposes is key in reaching a positive environmental evaluation of the policy instrument. Our environmental evaluation is likely generalisable to other regions with similar technological levels and farming intensity, while our analysis on structural shifts is specific to the policy instrument and agricultural production system under study. Overall, our work provides a method to contrast regional effects and global environmental impacts of policy instruments supporting agricultural biomass for biofuels prior to implementation. This contributes to the environmental assessment of land-based biofuels at a time when their sustainability is highly debated.

The impact of environmental taxation on the structure and performance of industrial symbiosis networks: An agent-based simulation study

How to use appropriate policy measures to intervene industrial symbiosis is valuable in theory but still lacks exploration. This paper discusses the effect of environmental taxation on industrial symbiosis networks. Firstly, the formation mechanism of industrial symbiotic network is analysed with the idea of agent-based modelling. Then, a simulation model was built to simulate the emergence process of industrial symbiosis networks. On this basis, the influence of environmental taxation on the structure and performance of the industrial symbiosis networks is explored. The results show that when the intensity of environmental tax is low, the industrial symbiotic network has the structural characteristics of random network. With the increase of environmental tax intensity, the cyclic ordering of network structure is gradually enhanced. The collection of environmental tax will not only reduce pollution, but also reduce the economic output of the network and reduce enterprise income to a greater extent. Finally, some relevant suggestions for the government to formulate environmental tax policy are provided based on the results.

(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.

Mapping secondary data gaps for social simulation modelling: A case study of Syrian asylum migration to Europe

Simulation models of social processes may require data that are not readily available, have low accuracy, are incomplete or biased. The paper presents a formal process for collating, assessing, selecting, and using secondary data as part of creating, validating, and documenting an agent-based simulation model of a complex social process, in this case, asylum migration to Europe. The process starts by creating an inventory of data sources, and the associated metadata, followed by assessing different aspects of data quality according to pre-defined criteria. As a result, based on the typology of available data, we are able to produce a thematic map of the area under study, and assess the uncertainty of key data sources, at least qualitatively. We illustrate the process by looking at the data on Syrian migration to Europe in 2011-21. In parallel, successive stages of the development of a simulation model allow for identifying key types of information which are needed as input into empirically grounded modelling analysis. Juxtaposing the available evidence and model requirements allows for identifying knowledge gaps that need filling, preferably by collecting additional primary data, or, failing that, by carrying out a sensitivity analysis for the assumptions made. By doing so, we offer a way of formalising the data collection process in the context of model-building endeavours, while allowing the modelling to be predominantly question-driven rather than purely data-driven. The paper concludes with recommendations with respect to data and evidence, both for modellers, as well as model users in practice-oriented applications.

Human Stem Cells for Ophthalmology: Recent Advances in Diagnostic Image Analysis and Computational Modelling

Purpose of Review

To explore the advances and future research directions in image analysis and computational modelling of human stem cells (hSCs) for ophthalmological applications.

Recent Findings

hSCs hold great potential in ocular regenerative medicine due to their application in cell-based therapies and in disease modelling and drug discovery using state-of-the-art 2D and 3D organoid models. However, a deeper characterisation of their complex, multi-scale properties is required to optimise their translation to clinical practice. Image analysis combined with computational modelling is a powerful tool to explore mechanisms of hSC behaviour and aid clinical diagnosis and therapy.

Summary

Many computational models draw on a variety of techniques, often blending continuum and discrete approaches, and have been used to describe cell differentiation and self-organisation. Machine learning tools are having a significant impact in model development and improving image classification processes for clinical diagnosis and treatment and will be the focus of much future research.

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.

A synthetic population of Sweden: datasets of agents, households, and activity-travel patterns

A synthetic population is a simplified microscopic representation of an actual population. Statistically representative at the population level, it provides valuable inputs to simulation models (especially agent-based models) in research areas such as transportation, land use, economics, and epidemiology. This article describes the datasets from the Synthetic Sweden Mobility (SySMo) model using the state-of-art methodology, including machine learning (ML), iterative proportional fitting (IPF), and probabilistic sampling. The model provides a synthetic replica of over 10 million Swedish individuals (i.e., agents), their household characteristics, and activity-travel plans. This paper briefly explains the methodology for the three datasets: Person, Households, and Activity-travel patterns. Each agent contains socio-demographic attributes, such as age, gender, civil status, residential zone, personal income, car ownership, employment, etc. Each agent also has a household and corresponding attributes such as household size, number of children ≤ 6 years old, etc. These characteristics are the basis for the agents' daily activity-travel schedule, including type of activity, start-end time, duration, sequence, the location of each activity, and the travel mode between activities.

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.

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.

Enhancing resilience in construction against infectious diseases using stochastic multi-agent approach

To recover from the adverse impacts of COVID-19 on construction and to avoid further losses to the industry in future pandemics, the resilience of construction industry needs to be enhanced against infectious diseases. Currently, there is a gap for modelling frameworks to simulate the spread of infectious diseases in construction projects at micro-level and to test interventions' effectiveness for data-informed decision-making. Here, this gap is addressed by developing a simulation framework using stochastic agent-based modelling, which enables construction researchers and practitioners to simulate and limit the spread of infectious diseases in construction projects. This is specifically important, since the results of a building project case-study reveals that, in comparison to the general population, infectious diseases may spread faster among construction workers and fatalities can be significantly higher. The proposed framework motivates future research on micro-level modelling of infectious diseases and efforts for intervening the spread of diseases in construction projects.

Manipulation of the Bitcoin market: an agent-based study

Fraudulent actions of a trader or a group of traders can cause substantial disturbance to the market, both directly influencing the price of an asset or indirectly by misinforming other market participants. Such behavior can be a source of systemic risk and increasing distrust for the market participants, consequences that call for viable countermeasures. Building on the foundations provided by the extant literature, this study aims to design an agent-based market model capable of reproducing the behavior of the Bitcoin market during the time of an alleged Bitcoin price manipulation that occurred between 2017 and early 2018. The model includes the mechanisms of a limit order book market and several agents associated with different trading strategies, including a fraudulent agent, initialized from empirical data and who performs market manipulation. The model is validated with respect to the Bitcoin price as well as the amount of Bitcoins obtained by the fraudulent agent and the traded volume. Simulation results provide a satisfactory fit to historical data. Several price dips and volume anomalies are explained by the actions of the fraudulent trader, completing the known body of evidence extracted from blockchain activity. The model suggests that the presence of the fraudulent agent was essential to obtain Bitcoin price development in the given time period; without this agent, it would have been very unlikely that the price had reached the heights as it did in late 2017. The insights gained from the model, especially the connection between liquidity and manipulation efficiency, unfold a discussion on how to prevent illicit behavior.

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.

Cost-benefit analysis of demolition waste management via agent-based modelling: A case study in Shenzhen

The economic instrument is an effective approach to encourage demolition contractors to conduct low-impact waste management. It is essential for project managers and decision-makers to better understand the cost-benefit of demolition waste (DW) management, to promote development of an effective waste management plan. This study explores the interactive dynamics and adaptive nature between stakeholders, where the cost-benefit of DW management is analysed through the agent-based modelling approach. Shenzhen, a leading city in China in the management of DW, was selected as the study area. It was revealed that if the traditional demolition method is adopted as the primary choice, the net benefit of demolition of buildings in the study case will reach -131.4 billion yuan, i.e. the cost will surpass the revenue. If the selective demolition method is widely used by demolition contractors, simulation results indicate that the net benefit will reach 33.3 billion yuan, an increase of 125.34%, compared to the situation in which the traditional demolition method is widely implemented. Based on the simulation, an optimal management framework for DW management stakeholders was constructed. The research results can provide a decision-making basis for the government and relevant departments to formulate DW management measures.

Quantifying the health effects of exposure to non-exhaust road emissions using agent-based modelling (ABM)

This paper provides an agent-based model, entitled TRAPSim, to examine the exposure to non-exhaust emissions (NEEs) and the consequent health effects of driver and pedestrians groups in Seoul. To make the model reproducible and replicable, TRAPSim uses the ODD protocol to demonstrate the details of the agents and parameters, as well as provide the codes alongside the descriptions to avoid possible ambiguity. The model's main parameters are thoroughly tested through sensitivity experiments and are calibrated with the city's air pollution monitoring networks. This paper also provides the instructions to the model, possible artefacts, and the configurations to submit the model on the HPC cluster.•An ODD protocol is used to document the agent-based model TRAPSim.•Sensitivity experiments and calibration are explained.•The step-by-step codes and annotations are attached in the protocol and HPC sections.

Effectiveness and cost-effectiveness of RSV infant and maternal immunization programs: A case study of Nunavik, Canada

BACKGROUND

Despite passive immunization with palivizumab to select high-risk children under two years of age, the health and economic burden of respiratory syncytial virus (RSV) remains substantial. We evaluated the effectiveness and cost-effectiveness of immunization programs with new generations of RSV prophylactics, including long-acting monoclonal antibodies (LAMA) and maternal vaccines, in terms of reducing hospitalizations in Nunavik, a Canadian Arctic region.

METHODS

We developed an agent-based model of RSV transmission and parameterized it with the demographics and burden of RSV in Nunavik, Québec. We compared various immunization strategies, taking into account the costs associated with program delivery and calculating the incremental cost-effectiveness ratio (ICER) using quality-adjusted life-years (QALYs) gained as a measure of effectiveness. Scenario analyses included immunization with palivizumab and LAMA for infants under one year of age, and maternal vaccination in mild, moderate, and severe RSV seasons. Data were analysed from November 1, 2019 to May 1, 2021.

FINDINGS

We found that a Nunavik pilot program with palivizumab which included healthy full-term infants aged 0-2 months in addition to those considered high-risk for complicated RSV disease is not cost-effective, compared to offering palivizumab only to preterm/chronically ill infants under 1 year of age. Using LAMA as prophylaxis produces ICER values of CAD $39,414/QALY (95% Credible Interval [CrI]: $39,314-$40,017) in a mild season (moderately cost-effective) and CAD $5,255/QALY (95% CrI: $5,222-$5,307) in a moderate season (highly cost-effective). LAMA was a dominant (cost-saving with negative incremental costs and positive incremental effects) strategy in a severe RSV season. Maternal vaccination combined with immunization of preterm/chronically ill infants 3-11 months was also a dominant (cost-saving) strategy in all seasons.

INTERPRETATION

The switch from palivizumab in RSV immunization programs to new prophylactics would lead to significant savings, with LAMA being an effective strategy without compromising benefits in terms of reducing hospitalizations.

Individual-based modelling of cyanobacteria blooms: Physical and physiological processes

Lakes and reservoirs throughout the world are increasingly adversely affected by cyanobacterial harmful algal blooms (CyanoHABs). The development and spatiotemporal distributions of blooms are governed by complex physical mixing and transport processes that interact with physiological processes affecting the growth and loss of bloom-forming species. Individual-based models (IBMs) can provide a valuable tool for exploring and integrating some of these processes. Here we contend that the advantages of IBMs have not been fully exploited. The main reasons for the lack of progress in mainstreaming IBMs in numerical modelling are their complexity and high computational demand. In this review, we identify gaps and challenges in the use of IBMs for modelling CyanoHABs and provide an overview of the processes that should be considered for simulating the spatial and temporal distributions of cyanobacteria. Notably, important processes affecting cyanobacteria distributions, in particular their vertical passive movement, have not been considered in many existing lake ecosystem models. We identify the following research gaps that should be addressed in future studies that use IBMs: 1) effects of vertical movement and physiological processes relevant to cyanobacteria growth and accumulations, 2) effects and feedbacks of CyanoHABs on their environment; 3) inter and intra-specific competition of cyanobacteria species for nutrients and light; 4) use of high resolved temporal-spatial data for calibration and verification targets for IBMs; and 5) climate change impacts on the frequency, intensity and duration of CyanoHABs. IBMs are well adapted to incorporate these processes and should be considered as the next generation of models for simulating CyanoHABs.

Commentary on Robinson et al. (2021): Evaluating theories of change for public health policies using computer model discovery methods

Recent developments in computer modelling—known as model discovery—could help to confirm the mechanisms underpinning Robinson and colleagues’ important early findings for the effectiveness of minimum unit pricing, and to test the complete theory of change underpinning this crucial evaluation.

Sustainable and resilient strategies for touristic cities against COVID-19: An agent-based approach

Touristic cities will suffer from COVID-19 emergency because of its economic impact on their communities. The first emergency phases involved a wide closure of such areas to support "social distancing" measures (i.e. travels limitation; lockdown of (over)crowd-prone activities). In the "second phase", individual's risk-mitigation strategies (facial masks) could be properly linked to "social distancing" to ensure re-opening touristic cities to visitors. Simulation tools could support the effectiveness evaluation of risk-mitigation measures to look for an economic and social optimum for activities restarting. This work modifies an existing Agent-Based Model to estimate the virus spreading in touristic areas, including tourists and residents' behaviours, movement and virus effects on them according to a probabilistic approach. Consolidated proximity-based and exposure-time-based contagion spreading rules are included according to international health organizations and previous calibration through experimental data. Effects of tourists' capacity (as "social distancing"-based measure) and other strategies (i.e. facial mask implementation) are evaluated depending on virus-related conditions (i.e. initial infector percentages). An idealized scenario representing a significant case study has been analysed to demonstrate the tool capabilities and compare the effectiveness of those solutions. Results show that "social distancing" seems to be more effective at the highest infectors' rates, although represents an extreme measure with important economic effects. This measure loses its full effectiveness (on the community) as the infectors' rate decreases and individuals' protection measures become predominant (facial masks). The model could be integrated to consider other recurring issues on tourist-related fruition and schedule of urban spaces and facilities (e.g. cultural/leisure buildings).

Investigating the practical viability of walk-sharing in improving pedestrian safety

Walk-sharing is a cost-effective and proactive approach that promises to improve pedestrian safety and has been shown to be technically (theoretically) viable. Yet, the practical viability of walk-sharing is largely dependent on community acceptance, which has not, until now, been explored. Gaining useful insights on the community's spatio-temporal and social preferences in regard to walk-sharing will ensure the establishment of practical viability of walk-sharing in a real-world urban scenario. We aim to derive practical viability using defined performance metrics (waiting time, detour distance, walk-alone distance and matching rate) and by investigating the effectiveness of walk-sharing in terms of its major objective of improving pedestrian safety and safety perception. We make use of the results from a web-based survey on the public perception on our proposed walk-sharing scheme. Findings are fed into an existing agent-based walk-sharing model to investigate the performance of walk-sharing and deduce its practical viability in urban scenarios.

Real-time predictions of seabird distribution improve oil spill risk assessments

Current knowledge of the distribution of sensitive seabirds is inadequate to safeguard seabird populations from impacts of oil spills in the Arctic. This gap is mainly driven by the fact that statistical models applied to survey data are coarse-scale and static with limited documentation of the distributional dynamics and patchiness of seabirds relevant to risk assessments related to oil spills. This paper describes a dynamic modelling framework solution for prediction of fine-scale densities and movements of seabirds in close-to-real time using fully integrated 3-D hydrodynamic models, dynamic habitat suitability models and agent-based models. The modelling framework has been developed and validated for the swimming migration of Brünnich's Guillemot Uria lomvia in the Barents Sea. The results document that the distributional dynamics of Brünnich's Guillemot and other seabird species to a large degree can be simulated with in-situ state variables and patterns reflecting the physical meteorology and oceanography and habitat suitability.

Step-by-step comparison of ordinary differential equation and agent-based approaches to pharmacokinetic-pharmacodynamic models

Mathematical models in oncology aid in the design of drugs and understanding of their mechanisms of action by simulation of drug biodistribution, drug effects, and interaction between tumor and healthy cells. The traditional approach in pharmacometrics is to develop and validate ordinary differential equation models to quantify trends at the population level. In this approach, time‐course of biological measurements is modeled continuously, assuming a homogenous population. Another approach, agent‐based models, focuses on the behavior and fate of biological entities at the individual level, which subsequently could be summarized to reflect the population level. Heterogeneous cell populations and discrete events are simulated, and spatial distribution can be incorporated. In this tutorial, an agent‐based model is presented and compared to an ordinary differential equation model for a tumor efficacy model inhibiting the pERK pathway. We highlight strengths, weaknesses, and opportunities of each approach.

Language policy and planning: a discussion on the complexity of language matters and the role of computational methods

In this paper I argue in favour of the adoption of an interdisciplinary approach based on computational methods for the development of language policies. As a consequence of large-scale phenomena such as globalization, economic and political integration and the progress in information and communication technologies, social systems have become increasingly interconnected. Language-related systems are no exception. Besides, language matters are never just language matters. Their causes and consequences are to be found in many seemingly unrelated fields. Therefore, we can no longer overlook the numerous variables involved in the unfolding of linguistic and sociolinguistic phenomena if we wish to develop effective language policy measures. A genuinely interdisciplinary approach is key to address language matters (as well as many other public policy matters). In this regard, the tools of complexity theory, such as computational methods based on computer simulations, have proved useful in other fields of public policy.

Situating agent-based modelling in population health research

Today's most troublesome population health challenges are often driven by social and environmental determinants, which are difficult to model using traditional epidemiological methods. We agree with those who have argued for the wider adoption of agent-based modelling (ABM) in taking on these challenges. However, while ABM has been used occasionally in population health, we argue that for ABM to be most effective in the field it should be used as a means for answering questions normally inaccessible to the traditional epidemiological toolkit. In an effort to clearly illustrate the utility of ABM for population health research, and to clear up persistent misunderstandings regarding the method's conceptual underpinnings, we offer a detailed presentation of the core concepts of complex systems theory, and summarise why simulations are essential to the study of complex systems. We then examine the current state of the art in ABM for population health, and propose they are well-suited for the study of the 'wicked' problems in population health, and could make significant contributions to theory and intervention development in these areas.

Elementary effects analysis of factors controlling COVID-19 infections in computational simulation reveals the importance of social distancing and mask usage

COVID-19 was declared a pandemic by the World Health Organisation (WHO) on March 11th, 2020. With half of the world's countries in lockdown as of April due to this pandemic, monitoring and understanding the spread of the virus and infection rates and how these factors relate to behavioural and societal parameters is crucial for developing control strategies. This paper aims to investigate the effectiveness of masks, social distancing, lockdown and self-isolation for reducing the spread of SARS-CoV-2 infections. Our findings from an agent-based simulation modelling showed that whilst requiring a lockdown is widely believed to be the most efficient method to quickly reduce infection numbers, the practice of social distancing and the usage of surgical masks can potentially be more effective than requiring a lockdown. Our multivariate analysis of simulation results using the Morris Elementary Effects Method suggests that if a sufficient proportion of the population uses surgical masks and follows social distancing regulations, then SARS-CoV-2 infections can be controlled without requiring a lockdown.

Supporting non-target arthropods in agroecosystems: Modelling effects of insecticides and landscape structure on carabids in agricultural landscapes

Intensification of agricultural practices is one of the most important drivers of the dramatic decline of arthropod species. We do not know, however, the relative contribution to decline of different anthropogenic stressors that are part of this process. We used high-resolution dynamic landscape models and advanced spatially-explicit population modelling to estimate the relative importance of insecticide use and landscape structure for population dynamics of a widespread carabid beetle Bembidion lampros. The effects of in-crop mitigation measures through the application of insecticides with reduced lethality, and off-crop mitigation measures by increasing abundance of grassy field margins, were evaluated for the beetle along the gradient of landscape heterogeneity. Reducing the insecticide-driven lethality (from 90 to 10%) had larger positive impacts on beetle density and occupancy than increasing the abundance of field margins in a landscape. The effects of increasing field margins depended on their width and overall abundance in the landscape, but only field margins 4 m wide, applied to at least 40% of fields, resulted in an increase in beetle population density comparable to the scenario with the smallest reduction of insecticide-driven lethality we considered. Our findings suggest the importance of field margins rather as a supporting not stand-alone mitigation measure, as they generally improved effects of reduction of insecticide-driven lethality. Therefore, adding sufficiently broad off-field habitats should help to maintain viable beetle populations in agricultural landscapes even with moderate use of insecticides. In general, the less persistent the insecticides are in the environment, the larger positive impacts of applied mitigation measures on beetle populations were found. We also showed that the effectiveness of applied mitigation measures strongly depends on landscape and farmland heterogeneity. Thus, to achieve the same management or mitigation target in different landscapes might require different strategies.

UTLDR: an agent-based framework for modeling infectious diseases and public interventions

Due to the SARS-CoV-2 pandemic, epidemic modeling is now experiencing a constantly growing interest from researchers of heterogeneous study fields. Indeed, due to such an increased attention, several software libraries and scientific tools have been developed to ease the access to epidemic modeling. However, only a handful of such resources were designed with the aim of providing a simple proxy for the study of the potential effects of public interventions (e.g., lockdown, testing, contact tracing). In this work, we introduce UTLDR, a framework that, overcoming such limitations, allows to generate "what if" epidemic scenarios incorporating several public interventions (and their combinations). UTLDR is designed to be easy to use and capable to leverage information provided by stratified populations of agents (e.g., age, gender, geographical allocation, and mobility patterns…). Moreover, the proposed framework is generic and not tailored for a specific epidemic phenomena: it aims to provide a qualitative support to understanding the effects of restrictions, rather than produce forecasts/explanation of specific data-driven phenomena.

A spatiotemporal dataset for integrated assessment and modelling of crop-livestock integration with the MAELIA simulation platform

The general purpose of the primary and secondary data available in this article is to support an integrated assessment of scenarios of crop-livestock integration at the territorial level i.e. of exchanges between arable and livestock farms. The data is a result of a research collaboration between the scientist from INRAE, agricultural advisers from Chamber of Agriculture of Pays de la Loire (CRAPL) and a collective of five arable and two livestock farmers located in the district of Pays de Pouzauges (Vendée department, western France). All participants formed part of the DiverIMPACTS project (https://www.diverimpacts.net/) that aims to achieve the full potential of diversification of cropping systems for improved productivity, delivery of ecosystem services and resource-efficient and sustainable value chains in Europe. The first dataset corresponds to the inputs of MAELIA (http://maelia-platform.inra.fr/), a spatial agent-based simulation platform that was used to support an iterative design and assessment of scenarios to redesign cropping systems. The second dataset corresponds to the outputs of MAELIA simulations and the associated indicators at the farm, group and territory level. The data comprise multiple shape and csv files characterizing the edaphic-climatic heterogeneity of the territory and cropping systems, farmers’ crop management rules (IF-THEN rules) and general information about the farms (e.g. crops, agricultural equipment, average crop yields). Data is reported for the baseline situation and three exchange scenarios containing different innovative cropping systems co-designed by scientists, agricultural advisers and the farmers. The data presented here can be found in the Portail Data INRA repository (https://doi.org/10.15454/3ZTCF5) and were used in the research article “Fostering local crop-livestock integration via legume exchanges using an innovative integrated assessment and modelling approach: MAELIA” [1].

A formalism for modelling traction forces and cell shape evolution during cell migration in various biomedical processes

The phenomenological model for cell shape deformation and cell migration Chen (BMM 17:1429–1450, 2018), Vermolen and Gefen (BMM 12:301–323, 2012), is extended with the incorporation of cell traction forces and the evolution of cell equilibrium shapes as a result of cell differentiation. Plastic deformations of the extracellular matrix are modelled using morphoelasticity theory. The resulting partial differential differential equations are solved by the use of the finite element method. The paper treats various biological scenarios that entail cell migration and cell shape evolution. The experimental observations in Mak et al. (LC 13:340–348, 2013), where transmigration of cancer cells through narrow apertures is studied, are reproduced using a Monte Carlo framework.

Agent-based modelling of complex factors impacting malaria prevalence

Background

Increasingly complex models have been developed to characterize the transmission dynamics of malaria. The multiplicity of malaria transmission factors calls for a realistic modelling approach that incorporates various complex factors such as the effect of control measures, behavioural impacts of the parasites to the vector, or socio-economic variables. Indeed, the crucial impact of household size in eliminating malaria has been emphasized in previous studies. However, increasing complexity also increases the difficulty of calibrating model parameters. Moreover, despite the availability of much field data, a common pitfall in malaria transmission modelling is to obtain data that could be directly used for model calibration.

Methods

In this work, an approach that provides a way to combine in situ field data with the parameters of malaria transmission models is presented. This is achieved by agent-based stochastic simulations, initially calibrated with hut-level experimental data. The simulation results provide synthetic data for regression analysis that enable the calibration of key parameters of classical models, such as biting rates and vector mortality. In lieu of developing complex dynamical models, the approach is demonstrated using most classical malaria models, but with the model parameters calibrated to account for such complex factors. The performance of the approach is tested against a wide range of field data for Entomological Inoculation Rate (EIR) values.

Results

The overall transmission characteristics can be estimated by including various features that impact EIR and malaria incidence, for instance by reducing the mosquito–human contact rates and increasing the mortality through control measures or socio-economic factors.

Conclusion

Complex phenomena such as the impact of the coverage of the population with long-lasting insecticidal nets (LLINs), changes in behaviour of the infected vector and the impact of socio-economic factors can be included in continuous level modelling. Though the present work should be interpreted as a proof of concept, based on one set of field data only, certain interesting conclusions can already be drawn. While the present work focuses on malaria, the computational approach is generic, and can be applied to other cases where suitable in situ data is available.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12936-021-03721-2.

Comparative analysis of continuum angiogenesis models

Although discrete approaches are increasingly employed to model biological phenomena, it remains unclear how complex, population-level behaviours in such frameworks arise from the rules used to represent interactions between individuals. Discrete-to-continuum approaches, which are used to derive systems of coarse-grained equations describing the mean-field dynamics of a microscopic model, can provide insight into such emergent behaviour. Coarse-grained models often contain nonlinear terms that depend on the microscopic rules of the discrete framework, however, and such nonlinearities can make a model difficult to mathematically analyse. By contrast, models developed using phenomenological approaches are typically easier to investigate but have a more obscure connection to the underlying microscopic system. To our knowledge, there has been little work done to compare solutions of phenomenological and coarse-grained models. Here we address this problem in the context of angiogenesis (the creation of new blood vessels from existing vasculature). We compare asymptotic solutions of a classical, phenomenological “snail-trail” model for angiogenesis to solutions of a nonlinear system of partial differential equations (PDEs) derived via a systematic coarse-graining procedure (Pillay et al. in Phys Rev E 95(1):012410, 2017. https://doi.org/10.1103/PhysRevE.95.012410). For distinguished parameter regimes corresponding to chemotaxis-dominated cell movement and low branching rates, both continuum models reduce at leading order to identical PDEs within the domain interior. Numerical and analytical results confirm that pointwise differences between solutions to the two continuum models are small if these conditions hold, and demonstrate how perturbation methods can be used to determine when a phenomenological model provides a good approximation to a more detailed coarse-grained system for the same biological process.

Evaluation of undetected cases during the COVID-19 epidemic in Austria

BACKGROUND

Knowing the number of undetected cases of COVID-19 is important for a better understanding of the spread of the disease. This study analyses the temporal dynamic of detected vs. undetected cases to provide guidance for the interpretation of prevalence studies performed with PCR or antibody tests to estimate the detection rate.

METHODS

We used an agent-based model to evaluate assumptions on the detection probability ranging from 0.1 to 0.9. For each general detection probability, we derived age-dependent detection probabilities and calibrated the model to reproduce the epidemic wave of COVID-19 in Austria from March 2020 to June 2020. We categorized infected individuals into presymptomatic, symptomatic unconfirmed, confirmed and never detected to observe the simulated dynamic of the detected and undetected cases.

RESULTS

The calculation of the age-dependent detection probability ruled values lower than 0.4 as most likely. Furthermore, the proportion of undetected cases depends strongly on the dynamic of the epidemic wave: during the initial upswing, the undetected cases account for a major part of all infected individuals, whereas their share decreases around the peak of the confirmed cases.

CONCLUSIONS

The results of prevalence studies performed to determine the detection rate of COVID-19 patients should always be interpreted with regard to the current dynamic of the epidemic wave. Applying the method proposed in our analysis, the prevalence study performed in Austria in April 2020 could indicate a detection rate of 0.13, instead of the prevalent ratio of 0.29 between detected and estimated undetected cases at that time.

Coasting: Model description, global sensitivity analysis, and scenario discovery

This manuscript provides information for replicating the Coasting agent-based model presented in “Simulating emerging coastal tourism vulnerabilities: an agent-based modelling approach”. The model description follows the Overview, Design Concepts, and Details + Human Decision-making (ODD+D) protocol. Moreover, this paper includes implementation details on global sensitivity analysis and scenario discovery. Finally, we provide supplementary tables and figures for scenario discovery results not included in the main paper.



Highlights:

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Model description for simulating emerging environmental vulnerabilities in a coastal tourism context

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Coasting’s design facilitates model adaptations to other coastal tourism destinations

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Implementation details for applying global sensitivity analysis and scenario discovery to vulnerability assessments

Agent-based modelling and parameter sensitivity analysis with a finite-element method for skin contraction

In this paper, we extend the model of wound healing by Boon et al. (J Biomech 49(8):1388–1401, 2016). In addition to explaining the model explicitly regarding every component, namely cells, signalling molecules and tissue bundles, we categorized fibroblasts as regular fibroblasts and myofibroblasts. We do so since it is widely documented that myofibroblasts play a significant role during wound healing and skin contraction and that they are the main phenotype of cells that is responsible for the permanent deformations. Furthermore, we carried out some sensitivity tests of the model by modifying certain parameter values, and we observe that the model shows some consistency with several biological phenomena. Using Monte Carlo simulations, we found that there is a significant strong positive correlation between the final wound area and the minimal wound area. The high correlation between the wound area after 4 days and the final/minimal wound area makes it possible for physicians to predict the most probable time evolution of the wound of the patient. However, the collagen density ratio at the time when the wound area reaches its equilibrium and minimum, cannot indicate the degree of wound contractions, whereas at the 4th day post-wounding, when the collagen is accumulating from null, there is a strong negative correlation between the area and the collagen density ratio. Further, under the circumstances that we modelled, the probability that patients will end up with 5% contraction is about 0.627.

Trust and Social Control: Sources of Cooperation, Performance, and Stability in Informal Value Transfer Systems

We study the functioning of informal value transfer systems through the example of Hawala. By complementing the institutional theory with computational experiments that use the first agent-based model of IVTS, we examine the roles of generalized trust and social control for the emergence, stability, and efficiency of Hawala. We show that both trust and control are necessary, but not sufficient to guarantee its functioning, and that their relationship is time-dependent. The success of Hawala also depends on population size, interaction density, and forgiveness of the agents. Finally, we provide a theoretically grounded operationalization of generalized trust and social control that is applicable to informal exchange systems in general.

An agent-based spatiotemporal integrated approach to simulating in-home water and related energy use behaviour: A test case of Beijing, China

Water and energy consumptions in the residential sector are highly correlated. A better understanding of the correlation would help save both water and energy, for example, through technological innovations, management and policies. Recently, there is an increasing need for a higher spatiotemporal resolution in the analysis and modelling of water-energy demand, as the results would be more useful for policy analysis and infrastructure planning in both water and energy systems. In response, this paper developed an agent-based spatiotemporal integrated approach to simulate the water-energy consumption of each household or person agent in second throughout a whole day, considering the influences of out-of-home activities (e.g., work and shopping) on in-home activities (e.g., bathing, cooking and cleaning). The integrated approach was tested in the capital of China, Beijing. The temporal results suggested that the 24-hour distributions of water and related energy consumptions were quite similar, and the water-energy consumptions were highly correlated (with a Pearson correlation coefficient of 0.89); The spatial results suggested that people living in the central districts and the central areas of the outer districts tended to consume more water and related energy, and also the water-energy correlation varies across space. Such spatially and temporally explicit results are expected to be useful for policy making (e.g., time-of-use tariffs) and infrastructure planning and optimization in both water and energy sectors.

Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: Insights from an agent-based model

Intestinal crypts are responsible for the total cell renewal of the lining of the intestines; this turnover is governed by the interplay between signalling pathways and the cell cycle. The role of Wnt signalling in cell proliferation and differentiation in the intestinal crypt has been extensively studied, with increased signalling found towards the lower regions of the crypt. Recent studies have shown that the Wnt signalling gradient found within the crypt may arise as a result of division-based spreading from a Wnt ‘reservoir’ at the crypt base. The discovery of the Hippo pathway’s involvement in maintaining crypt homeostasis is more recent; a mechanistic understanding of Hippo pathway dynamics, and its possible cross-talk with the Wnt pathway, remains lacking. To explore how the interplay between these pathways may control crypt homeostasis, we extended an ordinary differential equation model of the Wnt signalling pathway to include a phenomenological description of Hippo signalling in single cells, and then coupled it to a cell-based description of cell movement, proliferation and contact inhibition in agent-based simulations. Furthermore, we compared an imposed Wnt gradient with a division-based Wnt gradient model. Our results suggest that Hippo signalling affects the Wnt pathway by reducing the presence of free cytoplasmic β-catenin, causing cell cycle arrest. We also show that a division-based spreading of Wnt can form a Wnt gradient, resulting in proliferative dynamics comparable to imposed-gradient models. Finally, a simulated APC double mutant, with misregulated Wnt and Hippo signalling activity, is predicted to cause monoclonal conversion of the crypt.

Alarm communication networks as a driver of community structure in African savannah herbivores

Social information networks have the potential to shape the spatial structure of ecological communities by promoting the formation of mixed‐species groups. However, what actually drives social affinity between species in the wild will depend on the characteristics of the species available to group. Here we first present an agent‐based model that predicts trait‐related survival benefits from mixed‐species group formation in a multi‐species community and we then test the model predictions in a community‐wide field study of African savannah herbivores using multi‐layered network analysis. We reveal benefits from information transfer about predators as a key determinant of mixed‐species group formation, and that dilution benefits alone are not enough to explain patterns in interspecific sociality. The findings highlight the limitations of classical ecological approaches focusing only on direct trophic interactions when analysing community structure and suggest that declines in species occupying central social network positions, such as key informants, can have significant repercussions throughout communities.

From individual Fuzzy Cognitive Maps to Agent Based Models: Modeling multi-factorial and multi-stakeholder decision-making for water scarcity

Policy making for complex Social-Ecological Systems (SESs) is a multi-factorial and multi-stakeholder decision making process. Therefore, proper policy simulation in a SES should consider both the complex behavior of the system and the multi-stakeholders' interventions into the system, which requires integrated methodological approaches. In this study, we simulate impacts of policy options on a farming community facing water scarcity in Rafsanjan, Iran, using an integrated modeling methodology combining an Agent Based Model (ABM) with Fuzzy Cognitive Mapping (FCM). First, the behavioral rules of farmers and the causal relations among environmental variables are captured with FCMs that are developed with both qualitative and quantitative data, i.e. farmers' knowledge and empirical data from studies. Then, an ABM is developed to model decisions and actions of farmers and simulate their impacts on overall groundwater use and emigration of farmers in this case study. Finally, the impacts of different policy options are simulated and compared with a baseline scenario. The results suggest that a policy of facilitating farmers' participation in management and control of their groundwater use leads to the highest reduction of groundwater use and would help to secure farmers' activities in Rafsanjan. Our approach covers four main aspects that are crucial for policy simulation in SESs: 1) causal relationships, 2) feedback mechanisms, 3) social-spatial heterogeneity and 4) temporal dynamics. This approach is particularly useful for ex-ante policy options analysis.

Respiratory healthcare by design: Computational approaches bringing respiratory precision and personalised medicine closer to bedside

Precision medicine represents a potentially powerful means to alleviate the growing burden of chronic respiratory diseases. To realise its potential, however, we need a systems level understanding of how biological events (signalling pathways, cell-cell interactions, tissue mechanics) integrate across multiple spatial and temporal scales to give rise to pathology. This can be achieved most practically in silico: a paradigm that offers tight control over model parameters and rapid means of testing and generating mechanistic hypotheses. Patient-specific computational models that can enable identification of pathological mechanisms unique to patients' (omics, physiological, and anatomical) profiles and, therefore, personalised drug targets represent a major milestone in precision medicine. Current patient-based models in literature, especially medical devices, cardiac modelling, and respiratory medicine, rely mostly on (partial/ordinary) differential equations and have reached relatively advanced level of maturity. In respiratory medicine, patient-specific simulations mainly include subject scan-based lung mechanics models that can predict pulmonary function, but they treat the (sub)cellular processes as "black-boxes". A recent advance in simulating human airways at a cellular level to make clinical predictions raises the possibility of linking omics and cell level data/models with lung mechanics to understand respiratory pathology at a systems level. This is significant as this approach can be extended to understanding pathologies in other organs as well. Here, I will discuss ways in which computational models have already made contributions to personalised healthcare and how the paradigm can expedite clinical uptake of precision medicine strategies. I will mainly focus on an agent-based, asthmatic virtual patient that predicted the impact of multiple drug pharmacodynamics at the patient level, its potential to develop efficacious precision medicine strategies in respiratory medicine, and the regulatory and ethical challenges accompanying the mainstream application of such models.

Activity-based air pollution exposure assessment: Differences between homemakers and cycling commuters

Long-term air pollution exposure may lead to an increase in incidences and mortality rates of chronic diseases and adversely affect human health. The effects of long-term air pollution exposure have not been comprehensively studied due to the lack of human mobility data collected over a long period. In this study, we develop and apply a personal mobility model to long-term hourly air pollution concentration predictions to quantify personal long-term air pollution exposure for all individuals. We implement our model assuming mobility patterns for commuters and homemakers, and separate between weekdays and weekend. Our results show that NO₂ exposure of commuters are on average slightly higher and vary less spatially as they are exposed to NO₂ at multiple locations.

Flood risk management in Sint Maarten - A coupled agent-based and flood modelling method

Disaster risk reduction is a major concern of small island developing states. Measures to reduce risk should not only be based on the magnitude of physical hazard, but also on the exposure and vulnerability of communities. In this article, we examine flood risk management policies in the Caribbean island of Sint Maarten using coupled agent-based and flood models. The agent-based model is used to model actors' behaviour in relation to urban building development and policies that are designed to reduce flood hazard and communities' vulnerability and exposure. The policies considered in the model are a Beach Policy, a Building and Housing Ordinance, a Flood Zoning policy and hazard mitigation structural measures. The flood model is used to simulate coastal and pluvial floods on the island. Agent behaviour such as building new houses and implementing hazard reduction measures affect the flood model as these actions affect the rainfall-runoff process. The flood maps generated from the updated flood model simulations are then used to assess the impact and update agents' attributes and behaviour. The simulations results show that low-lying areas are populated, which increases the exposure, and the number of vulnerable houses is also high. Hence, out of the four policies, implementing hazard reduction measures is the most important. Reducing the flood hazard by widening existing drainage channels, constructing new ones and building dykes as coastal flood defence would reduce the hazard, hence reducing the number of flooded houses. As it affects all households on the island, the Building and Housing Ordinance is an important policy to reduce vulnerability. In general, the coupled model outputs can be used to inform policy decision making and provide insights to policymakers on the island.

Knowledge transfer in agent-based computational social science

This article addresses knowledge transfer dynamics in agent-based computational social science. The goal of the text is twofold. First, it describes the tensions arising from the convergence of different disciplinary traditions in the emergence of this new area of study and, second, it shows how these tensions are dealt with through the articulation of distinctive practices of knowledge production and transmission. To achieve this goal, three major instances of knowledge transfer dynamics in agent-based computational social science are analysed. The first instance is the emergence of the research field. Relations of knowledge transfer and cross-fertilisation between agent-based computational social science and wider and more established disciplinary areas: complexity science, computational science and social science, are discussed. The second instance is the approach to scientific modelling in the field. It is shown how the practice of agent-based modelling is affected by the conflicting coexistence of shared methodological commitments transferred from both empirical and formal disciplines. Lastly, the third instance pertains internal practices of knowledge production and transmission. Through the discussion of these practices, the tensions arising from converging dissimilar disciplinary traditions in agent-based computational social science are highlighted.

Biomass encounter rates limit the size scaling of feeding interactions

The rate that consumers encounter resources in space necessarily limits the strength of feeding interactions that shape ecosystems. To explore the link between encounters and feeding, we first compiled the largest available dataset of interactions in the marine benthos by extracting data from published studies and generating new data. These data indicate that the size-scaling of feeding interactions varies among consumer groups using different strategies (passive or active) to encounter different resource types (mobile or static), with filter feeders exhibiting the weakest feeding interactions. Next, we used these data to develop an agent-based model of resource biomass encounter rates, underpinned by consumer encounter strategy and resource biomass density. Our model demonstrates that passive strategies for encountering small, dispersed resources limits biomass encounter rates, necessarily limiting the strength of feeding interactions. Our model is based on generalisable assumptions, providing a framework to assess encounter-based drivers of consumption and coexistence across systems.

A multi-model framework for the Arabidopsis life cycle

Linking our understanding of biological processes at different scales is a major conceptual challenge in biology and aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model species Arabidopsis is very widely used to study plant growth processes and has also been tested more recently in ecophysiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from ecophysiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis, FM-lite. By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-model FM-life, which allows us to simulate at the population level in various genotype × environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulating evolution directly in future.

A 3D Multiscale Model to Explore the Role of EGFR Overexpression in Tumourigenesis

The epidermal growth factor receptor (EGFR) signalling cascade is one of the main pathways that regulate the survival and division of mammalian cells. It is also one of the most altered transduction pathways in cancer. Acquired mutations in the EGFR/ERK pathway can cause the overexpression of EGFR on the surface of the cell, while others downregulate the inactivation of switched on intracellular proteins such as Ras and Raf. This upregulates the activity of ERK and promotes cell division. We develop a 3D multiscale model to explore the role of EGFR overexpression on tumour initiation. In this model, cells are described as individual objects that move, interact, divide, proliferate, and die by apoptosis. We use Brownian Dynamics to describe the extracellular and intracellular regulations of cells as well as the spatial and stochastic effects influencing them. The fate of each cell depends on the number of active transcription factors in the nucleus. We use numerical simulations to investigate the individual and combined effects of mutations on the intracellular regulation of individual cells. Next, we show that the distance between active receptors increase the level of EGFR/ERK signalling. We demonstrate the usefulness of the model by quantifying the impact of mutational alterations in the EGFR/ERK pathway on the growth rate of in silico tumours.

Modelling sea lice control by lumpfish on Atlantic salmon farms: interactions with mate limitation, temperature and treatment rules

Atlantic salmon farming is one of the largest aquaculture sectors in the world. A major impact on farm economics, fish welfare and, potentially, nearby wild salmonid populations, is the sea louse ectoparasite Lepeophtheirus salmonis. Sea louse infestations are most often controlled through application of chemicals, but in most farming regions, sea lice have evolved resistance to the small set of available chemicals. Therefore, alternative treatment methodologies are becoming more widely used. One increasingly common alternative treatment involves the co-culture of farmed salmon with cleaner fish, which prey on sea lice. However, despite their wide use, little is understood about the situations in which cleaner fish are most effective. For example, previous work suggests that a low parasite density results in sea lice finding it difficult to acquire mates, reducing fecundity and population growth. Other work suggests that environmental conditions such as temperature and external sea louse pressure have substantial impact on this mate limitation threshold and may even remove the effect entirely. We used an Agent-Based Model (ABM) to simulate cleaner fish on a salmon farm to explore interactions between sea louse mating behaviour, cleaner fish feeding rate, temperature and external sea louse pressure. We found that sea louse mating has a substantial effect on sea louse infestations under a variety of environmental conditions. Our results suggest that cleaner fish can control sea louse infestations most effectively by maintaining the population below critical density thresholds.

Estimating the impacts of financing support policies towards photovoltaic market in Indonesia: A social-energy-economy-environment model simulation

This study develops a hybrid energy agent-based model that integrates the input-output analysis, environmental factors and socioeconomic characteristics of rural and urban households in Indonesia. We use the model to estimate the effects of four solar energy policy interventions on photovoltaic (PV) investments, government expenditure, economic outputs, CO_2e emissions and the uses of steel, aluminium, concrete and energy. The results of our analysis call for the abolition of the PV donor gift policy, the improvement of production efficiency in the PV industry and the establishment of after-sales services and rural financing institutions. A 100 W peak (Wp) PV under this recommendation would be affordable for 80.6% of rural households that are projected to be without access to electricity in 2029. Net metering is the most effective policy for encouraging urban people to invest in PV in a situation where fossil energy prices are increasing and PV prices are declining. A donor gift policy may induce USD 51.9 new economic outputs for every Wp of PV operating to capacity in 2029, but would require a subsidy of USD 18.6/Wp. The recommended policies do not require subsidies and reduce CO_2eq emissions and the consumption of aluminium, energy, steel and concrete by between 83.1% and 89.7% more than the existing policy. Several policy implications are discussed in response to these findings. As a contribution to energy modelling literature, the model can be used for other developing countries by merely changing its data.

Quantifying the ambient population using hourly population footfall data and an agent-based model of daily mobility

The ambient population, i.e. the demographics and volume of people in a particular location throughout the day, has been studied less than the night-time residential population. Although the spatio-temporal behaviour of some groups, such as commuters, are captured in sources such as population censuses, much less is known about groups such as retired people who have less documented behaviour patterns. This paper uses agent-based modelling to disaggregate some ambient population data to estimate the size and demographics of the constituent populations during the day. This is accomplished by first building a model of commuters to model typical 9-5 workday patterns. The differences between the model outputs and real footfall data (the error) can be an indication of the contributions that other groups make to the overall footfall. The research then iteratively simulates a wider range of demographic groups, maximising the correspondence between the model and data at each stage. An application of this methodology to the town centre of Otley, West Yorkshire, UK, is presented. Ultimately this approach could lead to a better understanding about how town- and city-centres are used by residents and visitors, contributing useful information in a situation where raw data on the populations do not exist.

GEOFIL: A spatially-explicit agent-based modelling framework for predicting the long-term transmission dynamics of lymphatic filariasis in American Samoa

In this study, a spatially-explicit agent-based modelling framework GEOFIL was developed to predict lymphatic filariasis (LF) transmission dynamics in American Samoa. GEOFIL included individual-level information on age, gender, disease status, household location, household members, workplace/school location and colleagues/schoolmates at each time step during the simulation. In American Samoa, annual mass drug administration from 2000 to 2006 successfully reduced LF prevalence dramatically. However, GEOFIL predicted continual increase in microfilaraemia prevalence in the absence of further intervention. Evidence from seroprevalence and transmission assessment surveys conducted from 2010 to 2016 indicated a resurgence of LF in American Samoa, corroborating GEOFIL's predictions. The microfilaraemia and antigenaemia prevalence in 6-7-yo children were much lower than in the overall population. Mosquito biting rates were found to be a critical determinant of infection risk. Transmission hotspots are likely to disappear with lower biting rates. GEOFIL highlights current knowledge gaps, such as data on mosquito abundance, biting rates and within-host parasite dynamics, which are important for improving the accuracy of model predictions.

Developing agent-based models of complex health behaviour

Managing non-communicable diseases requires policy makers to adopt a whole systems perspective that adequately represents the complex causal architecture of human behaviour. Agent-based modelling is a computational method to understand the behaviour of complex systems by simulating the actions of entities within the system, including the way these individuals influence and are influenced by their physical and social environment. The potential benefits of this method have led to several calls for greater use in public health research. We discuss three challenges facing potential modellers: model specification, obtaining required data, and developing good practices. We also present steps to assist researchers to meet these challenges and implement their agent-based model.