Related papers: MI-Sim: A MATLAB Package for the Numerical Analysi…
A primary motivation for our research in digital ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
We have generalized our ``unified'' model of evolutionary ecology by taking into account the possible movements of the organisms from one ``patch'' to another within the same eco-system. We model the spatial extension of the eco-system…
In recent years, we have seen an emergence of data-driven approaches in robotics. However, most existing efforts and datasets are either in simulation or focus on a single task in isolation such as grasping, pushing or poking. In order to…
This thesis focuses on the applications of mathematical tools and concepts brought from nonequilibrium statistical physics to the modeling of ecological problems. The first part provides a short introduction where the theoretical concepts…
Bipartite networks are widely used to encode the ecological interactions. Being able to compare the organization of bipartite networks is a first step toward a better understanding of how environmental factors shape community structure and…
The simulation and parameter optimization of coupled ocean circulation and ecosystem models in three space dimensions is one of the most challenging tasks in numerical climate research. Here we present a scientific toolkit that aims at…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
The Global Change Analysis Model (GCAM) simulates complex interactions between the coupled Earth and human systems, providing valuable insights into the co-evolution of land, water, and energy sectors under different future scenarios.…
A common issue when analyzing real-world complex systems is that the interactions between the elements often change over time: this makes it difficult to find optimal models that describe this evolution and that can be estimated from data,…
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose…
This paper focuses on a core task in computational sustainability and statistical ecology: species distribution modeling (SDM). In SDM, the occurrence pattern of a species on a landscape is predicted by environmental features based on…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46…
This essay provides a critical overview of the mathematical kinetic theory of active particles, which is used to model and study collective systems consisting of interacting living entities, such as those involved in behavior and evolution.…
Soil moisture estimation is an important task to enable precision agriculture in creating optimal plans for irrigation, fertilization, and harvest. It is common to utilize statistical and machine learning models to estimate soil moisture…
In ecology it is widely recognised that many landscapes comprise a network of discrete patches of habitat. The species that inhabit the patches interact with each other through a foodweb, the network of feeding interactions. The…
Network motifs can capture basic interaction patterns and inform the functional properties of networks. However, real-world complex systems often have multiple types of relationships, which cannot be represented by a monolayer network. The…
In the SysLab project we develop a software engineering method based on a mathematical foundation. The SysLab system model serves as an abstract mathematical model for information systems and their components. It is used to formalize the…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…