Related papers: Cross-feeding percolation phase transitions of int…
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…
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…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
We study molecular dynamics within populations of diffusively coupled cells under the assumption of fast diffusive exchange. As a technical tool, we propose conditions on boundedness and ultimate boundedness for systems with a singular…
The crossover between dispersion patterns has been frequently observed in various systems. Inspired by the pathway-based kinetic model for E. coli chemotaxis that accounts for the intracellular adaptation process and noise, we propose a…
Multiplex networks describe a large variety of complex systems including infrastructures, transportation networks and biological systems. Most of these networks feature a significant link overlap. It is therefore of particular importance to…
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…
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a…
The ubiquitous existence of microbial communities marks the importance of understanding how species interact within the community to coexist and their spatial organization. We study a two-species mutualistic cross-feeding model through a…
Percolation theory has been widely used to study phase transitions in complex networked systems. It has also successfully explained several macroscopic phenomena across different fields. Yet, the existent theoretical framework for…
We present a novel mathematical model of heterogeneous cell proliferation where the total population consists of a subpopulation of slow-proliferating cells and a subpopulation of fast-proliferating cells. The model incorporates two…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the behaviour of individual populations. This process is driven by the cross-feeding networks that structure these communities,…
The function of a real network depends not only on the reliability of its own components, but is affected also by the simultaneous operation of other real networks coupled with it. Robustness of systems composed of interdependent network…
During the past two decades, percolation has long served as a basic paradigm for network resilience, community formation and so on in complex systems. While the percolation transition is known as one of the most robust continuous…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
In the last two decades, network science has blossomed and influenced various fields, such as statistical physics, computer science, biology and sociology, from the perspective of the heterogeneous interaction patterns of components…
Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic…