Computational Model Library

A minimal genetic algorithm was preliminarily developed to search for the solution of an elementary arithmetic problem. It has been modified to explore the effect of a mutator gene and the consequent entrance into a hypermutation state. The phenomenon is particularly important in some types of tumorigenesis and in a more general way, in cells and tissues submitted to chronic sublethal environmental or genomic stress.
Since a long time, some scholars suppose that organisms speed up their own evolution by varying mutation rate, but evolutionary biologists are not convinced that evolution can select a mechanism promoting more (often harmful) mutations looking forward an environmental challenge.
The model aims to shed light on these controversial points of view and it provides also the features required to check the role of sex and genetic recombination in the mutator genes diffusion.

EMMIT is an end-user developed agent-based simulation of malaria transmission. The simulation’s development is a case study demonstrating an approach for non-technical investigators to easily develop useful simulations of complex public health problems. We focused on malaria transmission, a major global public health problem, and insecticide resistance (IR), a major problem affecting malaria control. Insecticides are used to reduce transmission of malaria caused by the Plasmodium parasite that is spread by the Anopheles mosquito. However, the emergence and spread of IR in a mosquito population can diminish the insecticide’s effectiveness. IR results from mutations that produce behavioral changes or biochemical changes (such as detoxification enhancement, target site alterations) in the mosquito population that provide resistance to the insecticide. Evolutionary selection for the IR traits reduces the effectiveness of an insecticide favoring the resistant mosquito population. It has been suggested that biopesticides, and specifically those that are Late Life Acting (LLA), could address this problem. LLA insecticides exploit Plasmodium’s approximate 10-day extrinsic incubation period in the mosquito vector, a delay that limits malaria transmission to older infected mosquitoes. Since the proposed LLA insecticide delays mosquito death until after the exposed mosquito has a chance to produce several broods of offspring, reducing the selective pressure for resistance, it delays IR development and gives the insecticide longer effectivity. Such insecticides are designed to slow the evolution of IR thus maintaining their effectiveness for malaria control. For the IR problem, EMMIT shows that an LLA insecticide could work as intended, but its operational characteristics are critical, primarily the mean-time-to-death after exposure and the associated standard deviation. We also demonstrate the simulation’s extensibility to other malaria control measures, including larval source control and policies to mitigate the spread of IR. The simulation was developed using NetLogo as a case study of a simple but useful approach to public health research.

This model is designed to address the following research question: How does the amount and topology of intergroup cultural transmission modulate the effect of local group extinction on selectively neutral cultural diversity in a geographically structured population? The experimental design varies group extinction rate, the amount of intergroup cultural transmission, and the topology of intergroup cultural transmission while measuring the effects of local group extinction on long-term cultural change and regional cultural differentiation in a constant-size, spatially structured population. The results show that for most of the intergroup social network topologies tested here, increasing the amount of intergroup cultural transmission (similar to increasing gene flow in a genetic model) erases the negative effect of local group extinction on selectively neutral cultural diversity. The stochastic (i.e., preference attachment) network seems to stand out as an exception.

Studies on the fundamental role of diverse media in the evolution of public opinion can protect us from the spreading brainwashing, extremism, and terrorism. Many fear the information cocoon may result in polarization of the public opinion. The model of opinion dynamics that considers different influences and horizons for every individual, and the simulations are based on a real-world social network.

Co-operative Autonomy

Hani Mohammed Subu Kandaswamy | Published Sat Apr 24 09:38:34 2021

This model presents an autonomous, two-lane driving environment with a single lane-closure that can be toggled. The four driving scenarios - two baseline cases (based on the real-world) and two experimental setups - are as follows:

  • Baseline-1 is where cars are not informed of the lane closure.
  • Baseline-2 is where a Red Zone is marked wherein cars are informed of the lane closure ahead.
  • Strategy-1 is where cars use a co-operative driving strategy - FAS. <sup>[1]</sup>
  • Strategy-2 is a variant of Strategy-1 and uses comfortable deceleration values instead of the vehicle’s limit.

Peer reviewed Evolution of Ecological Communities: Testing Constraint Closure

Steve Peck | Published Sun Dec 6 19:37:54 2020 | Last modified Fri Apr 16 22:17:46 2021

Ecosystems are among the most complex structures studied. They comprise elements that seem both stable and contingent. The stability of these systems depends on interactions among their evolutionary history, including the accidents of organisms moving through the landscape and microhabitats of the earth, and the biotic and abiotic conditions in which they occur. When ecosystems are stable, how is that achieved? Here we look at ecosystem stability through a computer simulation model that suggests that it may depend on what constrains the system and how those constraints are structured. Specifically, if the constraints found in an ecological community form a closed loop, that allows particular kinds of feedback may give structure to the ecosystem processes for a period of time. In this simulation model, we look at how evolutionary forces act in such a way these closed constraint loops may form. This may explain some kinds of ecosystem stability. This work will also be valuable to ecological theorists in understanding general ideas of stability in such systems.

Here we share the raw results of the social experiments of the paper “Gossip and competitive altruism support cooperation in a Public Good Game” by Giardini, Vilone, Sánchez, Antonioni, under review for Philosophical Transactions B. The experiment is thoroughly described there, in the following we summarize the main features of the experimental setup. The authors are available for further clarifications if requested.

Participants were recruited from the LINEEX subjects pool (University of Valencia Experimental Economics lab). 160 participants mean age = 21.7 years; 89 female) took part in this study in return for a flat payment of 5 EUR and the opportunity to earn an additional payment ranging from 8 to 16 EUR (mean total payment = 17.5 EUR). 80 subjects, divided into 5 groups of 16, took part in the competitive treatment while other 80 subjects participated in the non-competitive treatment. Laboratory experiments were conducted at LINEEX on September 16th and 17th, 2015.

This generic agent-based model simulates the evolution of agent’s opinions through their exchange of arguments.
The idea behind this model is to explicitly represent the process of mental deliberation of agents from arguments to an opinion, through the use of Dung’s argumentation framework complemented by a structured description of arguments. An application of the model on the diffusion of vegetarian diets is proposed.

The integrated and spatially-explicit ABM, called DIReC (Demography, Industry and Residential Choice), has been developed for Aberdeen City and the surrounding Aberdeenshire (Ge, Polhill, Craig, & Liu, 2018). The model includes demographic (individual and household) models, housing infrastructure and occupancy, neighbourhood quality and evolution, employment and labour market, business relocation, industrial structure, income distribution and macroeconomic indicators. DIReC includes a detailed spatial housing model, basing preference models on house attributes and multi-dimensional neighbourhood qualities (education, crime, employment etc.).
The dynamic ABM simulates the interactions between individuals, households, the labour market, businesses and services, neighbourhoods and economic structures. It is empirically grounded using multiple data sources, such as income and gender-age distribution across industries, neighbourhood attributes, business locations, and housing transactions. It has been used to study the impact of economic shocks and structural changes, such as the crash of oil price in 2014 (the Aberdeen economy heavily relies on the gas and oil sector) and the city’s transition from resource-based to a green economy (Ge, Polhill, Craig, & Liu, 2018).

Peer reviewed Evolution of Sex

Kristin Crouse | Published Sun Jun 5 08:24:01 2016 | Last modified Mon Feb 15 15:40:39 2021

Evolution of Sex is a NetLogo model that illustrates the advantages and disadvantages of sexual and asexual reproductive strategies. It seeks to demonstrate the answer to the question “Why do we have sex?”

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