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We present CEMA: Causal Explanations in Multi-Agent systems; a framework for creating causal natural language explanations of an agent's decisions in dynamic sequential multi-agent systems to build more trustworthy autonomous agents. Unlike…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Simulation models often have parameters as input and return outputs to understand the behavior of complex systems. Calibration is the process of estimating the values of the parameters in a simulation model in light of observed data from…
The liquid crystalline model biomembrane system consisting of a stack of interacting membranes is studied by the newly developed Fourier Monte Carlo simulation technique. In comparison to perturbation theory, substantial quantitative…
Periodic control systems used in spacecrafts and automotives are usually period-driven and can be decomposed into different modes with each mode representing a system state observed from outside. Such systems may also involve intensive…
We show theoretically that networks of membrane memcapacitive systems -- capacitors with memory made out of membrane materials -- can be used to perform a complete set of logic gates in a massively parallel way by simply changing the…
Modeling and simulation of complex systems is key to explore systems dynamics. Many scientific approaches were developed to represent dynamic structure systems but most of these approaches are efficient for some kinds of systems and…
Computationally expensive simulators, implementing mathematical models in computer codes, are commonly approximated using statistical emulators. We develop and assess novel emulation methods for systems best modelled via a chain, series or…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
A feature of current membrane systems is the fact that objects and membranes are persistent. However, this is not true in the real world. In fact, cells and intracellular proteins have a well-defined lifetime. Inspired from these biological…
The biologically-inspired swarm paradigm is being used to design self-organizing systems of locally interacting artificial agents. A major difficulty in designing swarms with desired characteristics is understanding the causal relation…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
This paper motivates why Real-Time Maude should be well suited to provide a formal semantics and formal analysis capabilities to modeling languages for embedded systems. One can then use the code generation facilities of the tools for the…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Computational meshes, as a way to partition space, form the basis of much of PDE simulation technology, for instance for the finite element and finite volume discretization methods. In complex simulations, we are often driven to modify an…
Learning modular structures which reflect the dynamics of the environment can lead to better generalization and robustness to changes which only affect a few of the underlying causes. We propose Recurrent Independent Mechanisms (RIMs), a…
Simulation has become the evaluation method of choice for many areas of distributing computing research. However, most existing simulation packages have several limitations on the size and complexity of the system being modeled. Fine…
This paper introduces the concept of Language-Guided World Models (LWMs) -- probabilistic models that can simulate environments by reading texts. Agents equipped with these models provide humans with more extensive and efficient control,…
We propose a novel approach for the formal verification of biological systems based on the use of a modal linear logic. We show how such a logic can be used, with worlds as instants of time, as an unified framework to encode both biological…