Related papers: Aspects of multiscale modelling in a process algeb…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
This paper introduces a new behavioral system model with distinct external and internal signals possibly evolving on different time scales. This allows to capture abstraction processes or signal aggregation in the context of control and…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
As dynamic and control systems become more complex, relying purely on numerical computations for systems analysis and design might become extremely expensive or totally infeasible. Computer algebra can act as an enabler for analysis and…
We present a process algebra aimed at describing interactions that are multiparty, i.e. that may involve more than two processes and that are open, i.e. the number of the processes they involve is not fixed or known a priori. Here we focus…
A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
Biological systems exhibit processes on a wide range of time and length scales. This work demonstrates that models, wherein the interaction between system constituents is captured by algebraic operations, inherently allow for successive…
Due to the intrinsic complexity and nonlinearity of chemical reactions, direct applications of traditional machine learning algorithms may face with many difficulties. In this study, through two concrete examples with biological background,…
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…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Multiscale models provide a unique tool for studying complex processes that study events occurring at different scales across space and time. In the context of biological systems, such models can simulate mechanisms happening at the…
We present and analyse a model for cell signalling processes in biological tissues. The model includes diffusion and nonlinear reactions on the cell surfaces, and both inter- and intracellular signalling. Using techniques from the theory of…
In Model-Based Systems Engineering (MBSE), the Systems Modeling Language (SysML) specification includes a metamodel that defines the language concepts and a user model that defines how the language concepts are represented. In SysML, an…
Web services technology provides a platform on which we can develop distributed services. The interoperability among these services is achieved by various standard protocols. In recent years, several researches suggested that process…
A complex system is made up of many components with many interactions. So the design of systems such as simulation systems, cooperative systems or assistance systems includes a very accurate modelling of interactional and communicational…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…