Related papers: Static Analysis for Biological Systems (BioAmbient…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
We present a general model allowing static analysis based on abstract interpretation for systems of communicating processes. Our technique, inspired by Regular Model Checking, represents set of program states as lattice automata and…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…
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,…
In this paper, we define B-smooth discontinuous dynamical systems which can be used as models of various processes in mechanics, electronics, biology and medicine. We find sufficient conditions to guarantee the existence of such systems.…
Networks effectively capture interactions among components of complex systems, and have thus become a mainstay in many scientific disciplines. Growing evidence, especially from biology, suggest that networks undergo changes over time, and…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
[Context & Motivation] Adaptive systems are an important research area. The dominant reason for adaptivity in systems are changes in the environment. Thus, it is an important question how to model the environment and how to determine the…
The topic of statistical inference for dynamical systems has been studied extensively across several fields. In this survey we focus on the problem of parameter estimation for non-linear dynamical systems. Our objective is to place results…
The climate system is a forced, dissipative, nonlinear, complex and heterogeneous system that is out of thermodynamic equilibrium. The system exhibits natural variability on many scales of motion, in time as well as space, and it is subject…
Context-Aware systems are becoming useful components in autonomic and monitoring applications and the assessment of their properties is an important step towards reliable implementation, especially in safety-critical applications. In this…
Recent measurements of durations of non-equilibrium processes provide valuable information on microscopic mechanisms and energetics. Comprehensive theory for corresponding experiments so far is well developed for single-particle systems…
In this paper we present recent results on parametric analysis of biological models. The underlying method is based on the algorithms for computing trajectory sets of hybrid systems with polynomial dynamics. The method is then applied to…
Impulsive systems are a very flexible class of systems that can be used to represent switched and sampled-data systems. We propose to extend here the previously obtained results on deterministic impulsive systems to the stochastic setting.…
This article presents a theoretical summary of the source code static analysis, its definition, uses and applications, how static analysis is performed, their intermediate representation formats, models and most common analysis techniques,…
Information flow analysis has largely ignored the setting where the analyst has neither control over nor a complete model of the analyzed system. We formalize such limited information flow analyses and study an instance of it: detecting the…
Static analysis (aka offline analysis) of a model of an IP network is useful for understanding, debugging, and verifying packet flow properties of the network. There have been static analysis approaches proposed in the literature for…
Context-dependent nature of biological phenomena are well documented in every branch of biology. While there have been few previous attempts to (implicitly) model various facets of biological context-dependence, a formal and general…