Related papers: Static Analysis for Biological Systems (BioAmbient…
Kinematical and dynamical properties of chaotic systems are reviewed and a few applications are described.
We discuss the problems of modeling, control, and decision support in complex dynamic systems from a general system theoretic point of view. The main characteristics of complex systems and of system approach to complex system study are…
Explaining why the species lives at a particular location is important for understanding ecological systems and conserving biodiversity. However, existing ecological workflows are fragmented and often inaccessible to non-specialists. We…
Documenting the context in which data are collected is an integral part of the scientific research lifecycle. In field-based research, contextual information provides a detailed description of scientific practices and thus enables data…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
To illustrate the power of the biophysical approach in solving important problems in life science, I present here one of our current research projects as an example. We have developed special biophotonic techniques to study the dynamic…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
The paper considers some class of dynamical systems that called density systems. For such systems the derivative of quadratic function depends on so-called density function. The density function is used to set the properties of phase space,…
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…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
We review some recent methods of subgrid-scale parameterization used in the context of climate modeling. These methods are developed to take into account (subgrid) processes playing an important role in the correct representation of the…
Static analysis by abstract interpretation is generally designed to be "sound", that is, it should not claim to establish properties that do not hold-in other words, not provide "false negatives" about possible bugs. A rarer requirement is…
Designing a static analysis is generally a substantial undertaking, requiring significant expertise in both program analysis and the domain of the program analysis, and significant development resources. As a result, most program analyses…
The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are…
There has been much research on network flows over time due to their important role in real world applications. This has led to many results, but the more challenging continuous time model still lacks some of the key concepts and techniques…
Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity" we use an information theory approach to formulate general measures of systems complexity. We examine the properties of…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
Dynamics is central to living systems. In the last two decades, experiments have revealed that the dynamics in diverse biological systems - from intracellular cytoplasm to cellular and organismal aggregates - are remarkably similar to that…
We study a two-state quantum system with a non linearity intended to describe interactions with a complex environment, arising through a non local coupling term. We study the stability of particular solutions, obtained as constrained…
This paper investigates the mathematical modeling and the stability of multi-lane traffic in the microscopic scale, studying a model based on two interaction terms. To do this we propose simple lane changing conditions and we study the…