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This is supplementary information for arXiv:1204.4896, which also appeared in Physical Biology 9, 026008 (2012). Main text abstract: Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These…
We present a theory of pattern formation in growing domains inspired by biological examples of tissue development. Gradients of signaling molecules regulate growth, while growth changes these graded chemical patterns by dilution and…
We propose a growing network model that consists of two tunable mechanisms: growth by merging modules which are represented as complete graphs and a fitness-driven preferential attachment. Our model exhibits the three prominent statistical…
Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can…
Collective behaviour in biological systems is often accompanied by strong correlations. The question has therefore arisen of whether correlation is amplified by the vicinity to some critical point in the parameters space. Biological…
Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
In the subtropical gyres, phytoplankton rely on eddies for transporting nutrients from depth to the euphotic zone. But, what controls the rate of nutrient supply for new production? We show that vertical nutrient flux depends both on the…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
We have shown elsewhere that the presence of mixed-culture growth of microbial species in fermentation processes can be detected with high accuracy by employing the wavelet transform. This is achieved because the crosses in the different…
In this paper a macroscopic model of tumor cord growth is developed, relying on the mathematical theory of deformable porous media. Tumor is modeled as a saturated mixture of proliferating cells, extracellular fluid and extracellular…
A numerical model for mixotrophic phytoplankton is described in this paper. In contrast with traditional approach where nutrient uptake rates are constrained by a predefined growth rate, this model uses empirical traits to compute nutrient…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
Most real systems are growing. In order to model the evolution of real systems, many growing network models have been proposed to reproduce some specific topology properties. As the structure strongly influences the network function,…
This paper establishes and discusses the consistency and the range of applicability of a simple, but general and predictive analytical formula, enabling to easily assess the maximum volumetric biomass growth rates (the productivities) in…
Parallels between the signal processing tasks and biological neurons lead to an understanding of the principles of self-organized optimization of input signal recognition. In the present paper, we discuss such similarities among biological…
Understanding how stimuli and synaptic connectivity in uence the statistics of spike patterns in neural networks is a central question in computational neuroscience. Maximum Entropy approach has been successfully used to characterize the…
Biclustering algorithms play a central role in the biotechnological and biomedical domains. The knowledge extracted supports the extraction of putative regulatory modules, essential to understanding diseases, aiding therapy research, and…
Survival of living tumor cells underlies many influences such as nutrient saturation, oxygen level, drug concentrations or mechanical forces. Data-supported mathematical modeling can be a powerful tool to get a better understanding of cell…
In this letter a mathematical model to design nano-bio-inspired hierarchical materials is proposed. An optimization procedure is also presented. Simple formulas describing the dependence of strength, fracture toughness and stiffness on the…