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.

The Episim framework builds upon the established transportation simulation MATSim and is capable of tracking agents’ movements within a network and thus computing infection chains. Several characteristics of the virus and the environment can be parametred, whilst the infection dynamics is computed based upon a compartment model. The spread of the virus can be mitigated by restricting the agents’ activity in certain places.

We present an agent-based model that maps out and simulates the processes by which individuals within ecological restoration organizations communicate and collectively make restoration decisions.

This model extends the original Artifical Anasazi (AA) model to include individual agents, who vary in age and sex, and are aggregated into households. This allows more realistic simulations of population dynamics within the Long House Valley of Arizona from AD 800 to 1350 than are possible in the original model. The parts of this model that are directly derived from the AA model are based on Janssen’s 1999 Netlogo implementation of the model; the code for all extensions and adaptations in the model described here (the Artificial Long House Valley (ALHV) model) have been written by the authors. The AA model included only ideal and homogeneous “individuals” who do not participate in the population processes (e.g., birth and death)–these processes were assumed to act on entire households only. The ALHV model incorporates actual individual agents and all demographic processes affect these individuals. Individuals are aggregated into households that participate in annual agricultural and demographic cycles. Thus, the ALHV model is a combination of individual processes (birth and death) and household-level processes (e.g., finding suitable agriculture plots).

As is the case for the AA model, the ALHV model makes use of detailed archaeological and paleoenvironmental data from the Long House Valley and the adjacent areas in Arizona. It also uses the same methods as the original model (from Janssen’s Netlogo implementation) to estimate annual maize productivity of various agricultural zones within the valley. These estimates are used to determine suitable locations for households and farms during each year of the simulation.

This model is an extension of the Artificial Long House Valley (ALHV) model developed by the authors (Swedlund et al. 2016; Warren and Sattenspiel 2020). The ALHV model simulates the population dynamics of individuals within the Long House Valley of Arizona from AD 800 to 1350. Individuals are aggregated into households that participate in annual agricultural and demographic cycles. The present version of the model incorporates features of the ALHV model including realistic age-specific fertility and mortality and, in addition, it adds the Black Mesa environment and population, as well as additional methods to allow migration between the two regions.

As is the case for previous versions of the ALHV model as well as the Artificial Anasazi (AA) model from which the ALHV model was derived (Axtell et al. 2002; Janssen 2009), this version makes use of detailed archaeological and paleoenvironmental data from the Long House Valley and the adjacent areas in Arizona. It also uses the same methods as the original AA model to estimate annual maize productivity of various agricultural zones within the Long House Valley. A new environment and associated methods have been developed for Black Mesa. Productivity estimates from both regions are used to determine suitable locations for households and farms during each year of the simulation.

CoDMER v. 2.0 was parameterized with ethnographic data from organizations dealing with prescribed fire and seeding native plants, to advance theory on how collective decisions emerge in ecological restoration.

AMIRIS is the Agent-based Market model for the Investigation of Renewable and Integrated energy Systems.

It is an agent-based simulation of electricity markets and their actors.
AMIRIS enables researches to analyse and evaluate energy policy instruments and their impact on the actors involved in the simulation context.
Different prototypical agents on the electricity market interact with each other, each employing complex decision strategies.
AMIRIS allows to calculate the impact of policy instruments on economic performance of power plant operators and marketers.
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