Related papers: Scaling and optimal synergy: Two principles determ…
In this paper, we derive an effective macroscale description suitable to describe the growth of biological tissue within a porous tissue-engineering scaffold. As in our recent work (Holden \textit{et al.} "A multiphase multiscale model for…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
The simultaneous growth of multiple microbial species is a problem of fundamental ecological interest. In media containing more than one growth-limiting substrate, multiple species can coexist. The question then arises: Can single-species…
Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To…
Optimal experimental design for parameter precision attempts to maximize the information content in experimental data for a most effective identification of parametric model. With the recent developments in miniaturization and…
Cell growth in size is a complex process coordinated by intrinsic and environmental signals. In a recent work [Tzur et al., Science, 2009, 325:167-171], size distributions in an exponentially growing population of mammalian cells were used…
Understanding biological phenomena requires a systemic approach that incorporates different mechanisms acting on different spatial and temporal scales, since in organisms the workings of all components, such as organelles, cells, and organs…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
To explore the coupling between a growing population of microorganisms such as E. coli and a nonuniform nutrient distribution, we formulate a minimalistic model. It consists of active Brownian particles that divide and grow at a…
Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses…
I consider how cell shape and environmental geometry affect the rate of nutrient capture and the consequent maximum growth rate of a cell, focusing on rod-like species like \textit{E.\ coli}. Simple modeling immediately implies that it is…
The growth and scaling of organs is a fundamental aspect of animal development. However, how organs grow to the right size and shape required by physiological demands, remains largely unknown. Here, we provide a framework combining theory…
First, we briefly describe the general growth mechanism, which governs the growth of living organisms, and its mathematical representation, the growth equation. Using the growth equation, we compute growth curve for S. cerevisiae and show…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
We incorporate the generic hierarchical architecture of foodwebs into a "{\it unified}" model that describes both "micro" and "macro" evolutions within a single theoretical framework. This model describes the "micro" -evolution in detail by…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…