Related papers: Metabolic rate beyond the 3/4 law
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this…
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…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
Embryogenesis is a multiscale process during which developmental symmetry breaking transitions give rise to complex multicellular organisms. Recent advances in high-resolution live-cell microscopy provide unprecedented insights into the…
We study an optimal control problem arising from a resource allocation problem in cellular metabolism. A minimalistic model that describes the production of enzymatic vs. non-enzymatic biomass components from a single nutrient source is…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities…
In a previous paper we have introduced a phenomenological model of cell metabolism and of the cell cycle to simulate the behavior of large tumor cell populations (Chignola R and Milotti E, Phys. Biol. 2 (2005) 8-22). Here we describe a…
Biroli et al.'s extension of the standard mode-coupling theory to inhomogeneous equilibrium states [Phys. Rev. Lett. 97, 195701 (2006)] allowed them to identify a characteristic length scale that diverges upon approaching the mode-coupling…
This paper is a continuation of a previous work about the study of the survival probability modelizing the molecular predissociation in the Born-Oppenheimer framework. Here we consider the critical case where the reference energy…
Recent concrete proposals suggest it is possible to engineer a two-dimensional bulk phase supporting non-Abelian Fibonacci anyons out of Abelian fractional quantum Hall systems. The low-energy degrees of freedom of such setups can be…
This work presents a new modeling approach to macroscopic, polycrystalline elasto-plasticity starting from first principles and a few well-defined structural assumptions, incorporating the mildly rate-dependent (viscous) nature of plastic…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…
Cell proliferation and cell movement are fundamentally stochastic processes which lead to variability in the growth and spatial structure of cell populations in many biological settings, such as cell invasion, wound healing, and tumour…
We consider a stochastic individual-based model of adaptive dynamics for an asexually reproducing population with mutation, with linear birth and death rates, as well as a density-dependent competition. To depict repeating changes of the…
The mechanical properties of vertebrate bone are largely determined by a process which involves the complex interplay of three different cell types. This process is called {\it bone remodeling}, and occurs asynchronously at multiple sites…
Actin growth is a fundamental biophysical process and it is, at the same time, a prototypical example of diffusion-mediated surface growth. We formulate a coupled chemo-mechanical, one-dimensional growth model encompassing both material…
Standard Spiking Neural Network (SNN) models typically neglect metabolic constraints, treating neurons as energetically unconstrained components. We bridge this gap by implementing a conductance-based leaky integrate-and-fire (gLIF)…