Related papers: Simulating and model checking membrane systems usi…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Rewriting is a formalism widely used in computer science and mathematical logic. When using rewriting as a programming or modeling paradigm, the rewrite rules describe the transformations one wants to operate and rewriting strategies are…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Existing procedures for model validation have been deemed inadequate for many engineering systems. The reason of this inadequacy is due to the high degree of complexity of the mechanisms that govern these systems. It is proposed in this…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
In this paper we propose a language for conveniently defining a wide range of execution strategies for real-time rewrite theories, and provide Maude-strategy-implemented versions of most Real-Time Maude analysis methods, albeit with…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Robustness to a wide variety of negative factors and the ability to self-repair is an inherent and natural characteristic of all life forms on earth. As opposed to nature, man-made systems are in most cases not inherently robust and a…
Most research on formal system design has focused on optimizing various measures of efficiency. However, insufficient attention has been given to the design of systems optimizing resilience, the ability of systems to adapt to unexpected…
When designing systems that are complex, dynamic and stochastic in nature, simulation is generally recognised as one of the best design support technologies, and a valuable aid in the strategic and tactical decision making process. A…
We improve the precision of a previous Control Flow Analysis for Brane Calculi, by adding information on the context and introducing causality information on the membranes. This allows us to prove some biological properties on the behaviour…
We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Word embeddings are a popular way to improve downstream performances in contemporary language modeling. However, the underlying geometric structure of the embedding space is not well understood. We present a series of explorations using…
Probabilistic model checking is a technique for formal automated reasoning about software or hardware systems that operate in the context of uncertainty or stochasticity. It builds upon ideas and techniques from a diverse range of fields,…
The starting point of this paper is a system described in form of a UML class diagram where system states are characterized by OCL invariants and system transitions are defined by OCL pre- and postconditions. The aim of our approach is to…