Related papers: A Model-Theoretic Approach to Modular Implementati…
Component-based development is challenging in a distributed setting, for starters considering programming a task may involve the assembly of loosely-coupled remote components. In order for the task to be fulfilled, the supporting…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
Complementarity is one of the main features underlying the interactions in biological and biochemical systems. Inspired by those systems we propose a model for the dynamical evolution of a system composed by agents that interact due to…
We propose a formalism to model and reason about multi-agent systems. We allow agents to interact and communicate in different modes so that they can pursue joint tasks; agents may dynamically synchronize, exchange data, adapt their…
Formal modelling provides a toolkit for understanding cultural dynamics, from individual decisions to recurring patterns of change. This chapter explains what models are and why they matter. Using a precise, shared language, they aid…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
The compositional approach is important for reasoning about large and complex systems. In this work, we address synchronous systems with hierarchical structures, which are often used to model cyber-physical systems. We revisit the theory of…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
A key overall goal of biomolecular simulations is the characterization of "mechanism" -- the pathways through configuration space of processes such as conformational transitions and binding. Some amount of heterogeneity is intrinsic to the…
This paper provides a brief introduction to the work that aims to apply the achievements within the area of engineering psychology to the area of formal methods, focusing on the specification phase of a system development process.
Recent advances in human mobility research have revealed consistent pairwise characteristics in movement behavior, yet existing mobility models often overlook the spatial and topological structure of mobility networks. By analyzing millions…
Robotic cell injection is used for automatically delivering substances into a cell and is an integral component of drug development, genetic engineering and many other areas of cell biology. Traditionally, the correctness of functionality…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Component-based design paradigm is of paramount importance due to prolific growth in the complexity of modern-day systems. Since the components are developed primarily by multi-party vendors and often assembled to realize the overall…
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…
Models of physical systems are used to explain and predict experimental results and observations. When students encounter discrepancies between the actual and expected behavior of a system, they revise their models to include the newly…
Ecological systems can be seen as networks of interactions between individual, species, or habitat patches. A key feature of many ecological networks is their organization into modules, which are subsets of elements that are more connected…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
Honest signals and cues have been observed as part of interspecific and intraspecific communication among animals. Recent theories suggest that existing signaling systems have evolved through natural selection imposed by predators. Honest…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…