Related papers: Static Analysis for Biological Systems (BioAmbient…

We will review some of the theoretical progresses that have been in the study of complex systems in physics and of their applications to biology.

Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent…

Microfluidics, the study of fluids in microscopic channels, has led to important advances in fields as diverse as microelectronics, biotechnology and chemistry. Microfluidic research is primarily based on the use of microfluidic chips,…

The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…

Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…

In this paper, we wish to investigate the dynamics of information transfer in evolutionary dynamics. We use information theoretic tools to track how much information an evolving population has obtained and managed to retain about different…

The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be…

Networks have been studied mainly using statistical methods. Here I collect some dynamical systems tools which are useful to study both the dynamics on networks and their evolution. They include decomposition of differential dynamics,…

In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the…

Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…

In a common experimental setting, the behaviour of a noisy dynamical system is monitored in response to manipulations of one or more control parameters. Here, we introduce a structured model to describe parametric changes in qualitative…

Continuum mechanics (e.g., hydrodynamics, elasticity theory) is based on the assumption that a small set of fields provides a closed description on large space and time scales. Conditions governing the choice for these fields are discussed…

We consider a general class of translation-invariant systems with a specific category of output nonlinearities motivated by biological sensing. We show that no dynamic output feedback can stabilize this class of systems to an isolated…

The aim of this paper is to give an introductory review of the cryoelectron microscopy as a complex data source for the most of the system biology branches, including the most perspective non-local approaches known as "localomics" and…

We present a game of interacting agents which mimics the complex dynamics found in many natural and social systems. These agents modify their strategies periodically, depending on their performances using genetic crossover mechanisms,…

Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…

This paper presents a nonlinear approach to measurements a general framework for dealing with variations of environmental conditions. My method may prove promising to extensions beyond classical physics, economics, and other sciences. I…

Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…

In order to investigate the evolutionary process of many deterministic Dynamical systems with unfixed parameter, a set of dynamical models with parameter changing continuously and the accumulation of this change might be large is introduced…

Changes in environmental or system parameters often drive major biological transitions, including ecosystem collapse, disease outbreaks, and tumor development. Analyzing the stability of steady states in dynamical systems provides critical…