Related papers: Von Neumann's growth model: statistical mechanics …
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…
We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. In the asymptotic regime of slow diffusion, that coincides…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
The growth rate of organisms depends both on external conditions and on internal states, such as the expression levels of various genes. We show that to achieve a criterion mean growth rate over an ensemble of conditions, the internal…
A new model for biological growth is introduced that couples the geometry of an organism (or part of the organism) to the flow and deposition of material. The model has three dynamical variables (a) a Riemann metric tensor for the geometry,…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
Dormancy is an essential strategy for microorganisms to cope with environmental stress. However, global ecosystem models typically ignore microbial dormancy, resulting in major model uncertainties. To facilitate the consideration of…
Cell cultures exhibit rich and complex behaviors driven by dynamic metabolic interactions among cells. In this work, we present a model that captures these interactions through a framework inspired by statistical mechanics. Using Monte…
After summarizing basic features of self-organization such as entropy export, feedbacks and nonlinear dynamics, we discuss several examples in biology. The main part of the paper is devoted to a model of active Brownian motion that allows a…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles. However, metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes, but also affected by regulatory…
A macroscopic model of the tumor Gompertzian growth is proposed. The new approach is based on the energetic balance among the different cell activities, described by methods of statistical mechanics and related to the growth inhibitor…
Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed through the kinetics of particular models, which requires…
Within the framework of Von Neumann's expanding model, we study the maximum growth rate r achievable by an autocatalytic reaction network in which reactions involve a finite (fixed or fluctuating) number D of reagents. r is calculated…
Analytic relations that describe crack growth are vital for modeling experiments and building a theoretical understanding of fracture. Upon constructing an idealized model system for the crack and applying the principles of statistical…
In this work maximum entropy distributions in the space of steady states of metabolic networks are defined upon constraining the first and second moment of the growth rate. Inherent bistability of fast and slow phenotypes, akin to a Van-Der…
Biological membranes and vesicles play a central role in living systems, forming dynamic interfaces that regulate cellular organization and function. Classical descriptions of membrane mechanics that are rooted in equilibrium statistical…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…