Related papers: Von Neumann's growth model: statistical mechanics …
Cell colonies of bacteria, tumour cells and fungi, under nutrient limited growth conditions, exhibit complex branched growth patterns. In order to investigate this phenomenon we present a simple hybrid cellular automaton model of cell…
This investigation is a part of a research program aiming to characterize the extreme behavior possible in hydrodynamic models by analyzing the maximum growth of certain fundamental quantities. We consider here the rate of growth of the…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Background: The vast computational resources that became available during the past decade enabled the development and simulation of increasingly complex mathematical models of cancer growth. These models typically involve many free…
Modern computation based on the von Neumann architecture is today a mature cutting-edge science. In the Von Neumann architecture, processing and memory units are implemented as separate blocks interchanging data intensively and…
We study the statistical underpinnings of life. We question some common assumptions about the thermodynamics of life and illustrate how, contrary to widespread belief, even in a closed system entropy growth can accompany an increase in…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
Vascular networks play a key role in the development, function, and survival of many organisms, facilitating transport of nutrients and other critical factors within and between systems. The development of these vessel networks has been…
Growing network models can potentially be a useful tool in the development of economic theory. This work introduces an "opportunistic attachment" mechanism where incoming nodes, in deciding where to join a network, consider features of the…
As experiments advance to record from tens of thousands of neurons, statistical physics provides a framework for understanding how collective activity emerges from networks of fine-scale correlations. While modeling these populations is…
We introduce a comprehensive analytical benchmark, relying on Fokker-Planck formalism, to study microbial dynamics in presence of both biotic and abiotic forces. In equilibrium, we observe a balance between the two kinds of forces, leading…
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in…
This work's purpose is to understand the dynamics of some social systems whose properties can be captured by certain iterated function systems. To achieve this intension, we start from the theory of iterated function systems, and then we…
We revisit the modeling of the diauxic growth of a pure microorganism on two distinct sugars which was first described by Monod. Most available models are deterministic and make the assumption that all cells of the microbial ecosystem…
The stochastic exploration of the configuration space and the exploitation of functional states underlie many biological processes. The evolutionary dynamics stands out as a remarkable example. Here, we introduce a novel formalism that…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
A stochastic model for the growth of a virus in a cell population is introduced. The virus has two ways of spreading: either by allowing its host cell to live on and duplicate, or else by multiplying in large numbers within the host cell…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…