相关论文: The structure of MESSI biological systems

Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…

We present a theorem that allows to simplify linear stability analysis of periodic and quasiperiodic nonlinear regimes in N-particle mechanical systems (both conservative and dissipative) with different kinds of discrete symmetry. This…

We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…

Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…

In real-world networks the interactions between network elements are inherently time-delayed. These time-delays can not only slow the network but can have a destabilizing effect on the network's dynamics leading to poor performance. The…

We present the epithelial-to-mesenchymal transition (EMT) from two perspectives: experimental/technological and theoretical. We review the state of the current understanding of the regulatory networks that underlie EMT in three…

We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…

Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…

In this paper we establish strong embedding theorems, in the sense of the Komlos-Major-Tusnady framework, for the performance metrics of a general class of transitory queueing models of nonstationary queueing systems. The nonstationary and…

We analyze a class of chemical reaction networks under mass-action kinetics and involving multiple time-scales, whose deterministic and stochastic models display qualitative differences. The networks are inspired by gene-regulatory…

Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…

We provide a short supplement to the paper "MAPK networks and their capacity for multistationarity due to toric steady states" by P\'erez Mill\'an and Turjanski. We show that the capacity for toric steady states in the three networks…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…

Persistence and permanence are properties of dynamical systems that describe the long-term behavior of the solutions, and in particular specify whether positive solutions approach the boundary of the positive orthant. Mass-action systems…

Mitochondrial networks exhibit a variety of complex behaviors, including coordinated cell-wide oscillations of energy states as well as a phase transition (depolarization) in response to oxidative stress. Since functional and structural…

This paper is a preliminary work to address the problem of dynamical systems with parameters varying in time. An idea to predict their behaviour is proposed. These systems are called \emph{transient systems}, and are distinguished from…

Here, we provide an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random…

Most real-world networks evolve over time. Existing literature proposes models for dynamic networks that are either unlabeled or assumed to have a single membership structure. On the other hand, a new family of Mixed Membership Stochastic…

Turing's theory of pattern formation has been used to describe the formation of self-organised periodic patterns in many biological, chemical and physical systems. However, the use of such models is hindered by our inability to predict, in…