Related papers: Metabolic scaling from Fibonacci dynamics
Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
We study the qualitative behavior of a model to represent local regulation in a metabolic network. The model is based on the end-product control structure introduced in [A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete et al., BMC Syst…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Diffusion is the macroscopic manifestation of disordered molecular motion. Mathematically, diffusion equations are partial differential equations describing the fluid-like large-scale dynamics of parcels of molecules. Spatially…
The formation of biomolecular condensates inside cells often involve intrinsically disordered proteins (IDPs), and several of these IDPs are also capable of forming droplet-like dense assemblies on their own, through liquid-liquid phase…
Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations…
We study a discrete random walk on a one-dimensional finite lattice, where each state has different probabilities to move one step forward, backward, staying for a moment or being absorbed. We obtain expected number of arrivals and expected…
We extend the notions of multipole and subsystem symmetries to more general {\it spatially modulated} symmetries. We uncover two instances with exponential and (quasi)-periodic modulations, and provide simple microscopic models in one, two…
The origin of allometric scaling of metabolic rate is a long-standing question in biology. Several models have been proposed for explaining the origin; however, they have advantages and disadvantages. In particular, previous models only…
Cell movement, for example during embryogenesis or tumor metastasis, is a complex dynamical process resulting from an intricate interplay of multiple components of the cellular migration machinery. At first sight, the paths of migrating…
We study the large population limit of the Moran process, assuming weak-selection, and for different scalings. Depending on the particular choice of scalings, we obtain a continuous model that may highlight the genetic-drift (neutral…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…
Estimating a fractal dimension from a finite stochastic trajectory is a finite-size scaling problem: the apparent box-counting exponent is shaped by an occupancy crossover between the resolved range of scales and the finite number of…
This work builds on an existing model of discrete canonical evolution and applies it to the general case of a linear dynamical system, i.e., a finite-dimensional system with configuration space isomorphic to $ \mathbb{R}^{q} $ and linear…
We analyse how simple local constraints in two dimensions lead a defect to exhibit robust, non-transient, and tunable, subdiffusion. We uncover a rich dynamical phenomenology realised in ice- and dimer-type models. On the microscopic scale…
A general simple theory for the interspecific allometric scaling is developed in the $d+1$-dimensional space ($d$ biological lengths and a physiological time) of metabolic states of organisms. It is assumed that natural selection shaped the…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
An extensive rewiring of cell metabolism supports enhanced proliferation in cancer cells. We propose a systems level approach to describe this phenomenon based on Flux Balance Analysis (FBA). The approach does not explicit a cell biomass…
In this work, a study of epitaxial growth was carried out by means of wavelets formalism. We showed the existence of a dynamic scaling form in wavelet discriminated linear MBE equation where diffusion and noise are the dominant effects. We…