Identifying how organisms respond to environmental stressors remains of central importance as human impacts continue to shift the environmental conditions for countless species. Some mammals are able to mitigate these environmental stressors at the cellular level, but the mechanisms by which cells are able to do this and how these strategies vary among species is not well understood. At the cellular level, it is difficult to identify the temporal dynamics of the system through empirical data because fine-grained time course samples are both incomplete and limited by available resources. To help identify the mechanisms by which animal cells mitigate extreme environmental conditions, we propose an agent-based model to capture the dynamics of the system. In the model, agents are regulatory elements and genes, and are able to impact the behaviors of each other. Rather than imposing rules for these interactions among agents, we will begin with randomized sets of rules and calibrate the model based on empirical data of cellular responses to stress. We will apply a common-garden framework to cultured cells from 16 mammalian species, which will yield genomic data and measures of cell morphology and physiology when exposed to different levels of temperature, glucose, and oxygen. These species include humans, dolphins, bats, and camels, among others, which vary in how they respond to environmental stressors, offering a comparative approach for identifying mechanistic rules whereby cells achieve robustness to environmental stressors. For calibration of the model, we will iteratively select for rules that best lead to the emergent outcomes observed in the cellular assays. Our model is generalized for any species, any cell type, and any environmental stressor, offering many applications of the model beyond our study. This study will increase our understanding of how organisms mitigate environmental stressors at the cellular level such that we can better address how organisms are impacted by and respond to extreme environmental conditions.

While the world’s total urban population continues to grow, not all cities are witnessing such growth, some are actually shrinking. This shrinkage causes several problems to emerge including population loss, economic depression, vacant properties and the contraction of housing markets. Such problems challenge efforts to make cities sustainable. While there is a growing body of work on study shrinking cities, few explore such a phenomenon from the bottom up using dynamic computational models. To overcome this issue this paper presents an spatially explicit agent-based model stylized on the Detroit Tri-county area, an area witnessing shrinkage. Specifically, the model demonstrates how through the buying and selling of houses can lead to urban shrinkage from the bottom up. The model results indicate that along with the lower level housing transactions being captured, the aggregated level market conditions relating to urban shrinkage are also captured (i.e., the contraction of housing markets). As such, the paper demonstrates the potential of simulation to explore urban shrinkage and potentially offers a means to test polices to achieve urban sustainability.

More frequently protests are accompanied by an opposing group performing a counter protest. This phenomenon can increase tension such that police must try to keep the two groups separated. However, what is the best strategy for police? This paper uses a simple agent-based model to determine the best strategy for keeping the two groups separated. The ‘thin blue line’ varies in density (number of police), width and the keenness of police to approach protesters. Three different groups of protesters are modelled to mimic peaceful, average and volatile protests. In most cases, a few police forming a single-file ‘thin blue line’ separating the groups is very effective. However, when the protests are more volatile, it is more effective to have many police occupying a wide ‘thin blue line’, and police being keen to approach protesters. To the authors knowledge, this is the first paper to model protests and counter-protests.

This is the R code of the mathematical model that includes the decision making formulations for artificial agents. Plus, the code for graphical output is also added to the original code.

This model is to simulate and compare the admission effects of 3 school matching mechanisms, serial dictatorship, Boston mechanism, and Chinese Parallel, under different settings of information released.

We explore how dynamic processes related to socioeconomic inequality operate to sort students into, and create stratification among, colleges.

We present the Integrated Urban Complexity model (IUCm 1.0) that computes “climate-smart urban forms”, which are able to cut emissions related to energy consumption from urban mobility in half. Furthermore, we show the complex features that go beyond the normal debates about urban sprawl vs. compactness. Our results show how to reinforce fractal hierarchies and population density clusters within climate risk constraints to significantly decrease the energy consumption of urban mobility. The new model that we present aims to produce new advice about how cities can combat climate change. From a technical angle, this model is a geographical automaton, conceptually interfacing between cellular automata and spatial explicit optimisation to achieve normative sustainability goals related to low energy. See a complete user guide at https://iucm.readthedocs.io/en/latest/ .

This model describes and analyses the outcomes of the confrontation of interests, some conflicting, some common, about the management of a small river in SW France

The Nice Musical Chairs (NMC) model represent the competition for space between groups of stakeholders of farming and herding activities in the arid Afro-Eurasia.

We develop an agent-based model for collective behavior of routine medical check-ups, and specifically dental visits, in a social network.