Related papers: The structure of MESSI biological systems
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
The task of modelling and forecasting a dynamical system is one of the oldest problems, and it remains challenging. Broadly, this task has two subtasks - extracting the full dynamical information from a partial observation; and then…
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper, we show the benefits to use parametric time Petri nets in order to analyze precisely the…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
Protein phosphorylation cycles are important mechanisms of the post translational modification of a protein and as such an integral part of intracellular signaling and control. We consider the sequential phosphorylation and…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
Shape-morphing networks of mesoscale filaments are a common hierarchical feature in biology and hold significant potential for a range of technological applications, from micro-muscles to shape-morphing optical devices. Here, we demonstrate…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
The analysis of network dynamics is oftentimes restricted to networks with one-dimensional internal dynamics. Here, we show how symmetry explains the relation between behavior of systems with one-dimensional internal dynamics and with…
The methodology named LIFE (Linear-in-Flux-Expressions) was developed with the purpose of simulating and analyzing large metabolic systems. With LIFE, the number of model parameters is reduced by accounting for correlations among the…
Analysis of mathematical models in ecology and epidemiology often focuses on asymptotic dynamics, such as stable equilibria and periodic orbits. However, many systems exhibit long transient behaviors where certain aspects of the dynamics…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
Transitions between metastable states are commonly observed in the neural system and underlie various cognitive functions such as working memory. In a previous study, we have developed a neural network model with the slow and fast…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
We introduce MoTIF, a mode-structured tensor framework for multi-parametric approximation, super-resolution, and temporal forecasting of high-dimensional unsteady systems. The methodology leverages High-Order Singular Value Decomposition…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
Mitogen-activated protein kinase (MAPK) signaling pathways play an essential role in the transduction of environmental stimuli to the nucleus, thereby regulating a variety of cellular processes, including cell proliferation, differentiation…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…