Related papers: The Community Simulator: A Python package for micr…

Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…

The range of applications of traditional optimization methods are limited by the features of the object variables, and of both the objective and the constraint functions. In contrast, population-based algorithms whose optimization…

Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…

We propose an approach of open-ended evolution via the simulation of swarm dynamics. In nature, swarms possess remarkable properties, which allow many organisms, from swarming bacteria to ants and flocking birds, to form higher-order…

We present cogsworth, an open-source Python tool for producing self-consistent population synthesis and galactic dynamics simulations. With cogsworth one can (1) sample a population of binaries and star formation history, (2) perform rapid…

Mixed microbial communities, usually composed of various bacterial and fungal species, are fundamental in a plethora of environments, from soil to human gut and skin. Their evolution is a paradigmatic example of intertwined dynamics, where…

Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing…

Eco-evolutionary game dynamics which characterizes the mutual interactions and the coupled evolutions of strategies and environments has been of growing interests in very recent years. Since such feedback loops widely exist in a range of…

In this paper, we discuss the need for an integrated software stack that unites artificial intelligence (AI) and modeling and simulation (ModSim) tools to advance scientific discovery. The authors advocate for a unified AI/ModSim software…

Experiments in engineering are typically conducted in controlled environments where parameters can be set to any desired value. This assumes that the same applies in a real-world setting -- an assumption that is often incorrect as many…

Evolutionary Game Theory (EGT) simulations are used to model populations undergoing biological and cultural evolution in a range of fields, from biology to economics to linguistics. In this paper we present DyPy, an open source Python…

The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…

The introduction of non-native organisms into complex microbiome communities holds enormous potential to benefit society. However, microbiome engineering faces several challenges including successful establishment of the organism into the…

We consider the problem of efficiently simulating population protocols. In the population model, we are given a distributed system of $n$ agents modeled as identical finite-state machines. In each time step, a pair of agents is selected…

Complex systems such as ecological communities and neuron networks are essential parts of our everyday lives. These systems are composed of units which interact through intricate networks. The ability to predict sudden changes in the…

Evolutionary computation offers a variety of tools to solve complex real-world optimization problems. However, research often focuses on smaller, simplified problems and optimization algorithms that sometimes miss expectations in real-world…

Eco-evolutionary frameworks can explain certain features of communities in which ecological and evolutionary processes occur over comparable timescales. Here, we investigate whether an evolutionary dynamics may interact with the spatial…

The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be…

The prosperity of services and the frequent interaction between services contribute to the formation of the service ecosystem. Service ecosystem is a complex dynamic system with continuous evolution. Service providers voluntarily or…