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The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome…
Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for…
Ecologists and evolutionary biologists are relying on an increasingly sophisticated set of statistical tools to describe complex natural systems. One such tool that has gained increasing traction in the life sciences is structural equation…
Ecosystems are complex systems, currently experiencing several threats associated with global warming, intensive exploitation, and human-driven habitat degradation. Such threats are pushing ecosystems to the brink of collapse. Because of a…
Complex biological processes are usually experimented along time among a collection of individuals. Longitudinal data are then available and the statistical challenge is to better understand the underlying biological mechanisms. The…
This article presents an open-source Python package for simulating micro-thermoelectric generators, based on the work by D. Beretta et al. (Sustainable Energy Fuels, 2017). Featuring a user-friendly graphical user interface and robust…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Urban growth sometimes leads to rigid infrastructure that struggles to adapt to changing demand. This paper introduces a novel approach, aiming to enable cities to evolve and respond more effectively to such dynamic demand. It identifies…
The simulation of the dynamical behavior of pedestrians and crowds in spatial structures is a consolidated research and application context that still presents challenges for researchers in different fields and disciplines. Despite…
Ecologists are interested in understanding and predicting how ecological communities change through time. While it might seem natural to measure this through changes in species' abundances, computational limitations mean transitions between…
Microbes can affect processes from food production to human health. Such microbes are not isolated, but rather interact with each other and establish connections with their living environments. Understanding these interactions is essential…
libEnsemble is a Python-based toolkit for running dynamic ensembles, developed as part of the DOE Exascale Computing Project. The toolkit utilizes a unique generator--simulator--allocator paradigm, where generators produce input for…
Evolutionary computing (EC) has proven to be effective in solving complex optimization and robotics problems. Unfortunately, typical Evolutionary Algorithms (EAs) are constrained by the computational capacity available to researchers. More…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
Dynamics of biological-ecological systems is strongly depending on spatial dimensions. Most of powerful simulators in ecology take into account for system spatiality thus embedding stochastic processes. Due to the difficulty of researching…
Ambient air pollution is a pervasive issue with wide-ranging effects on human health, ecosystem vitality, and economic structures. Utilizing data on ambient air pollution concentrations, researchers can perform comprehensive analyses to…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example,…