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Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Dynamic recrystallization is one of the main phenomena responsible for microstructure evolutions during hot forming. Consequently, getting a better understanding of DRX mechanisms and being able to predict them is crucial. This paper…
Cyanobacteria are an integral part of the Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2 . Growth and metabolism of cyanobacteria are inherently tied to the diurnal…
This work presents a framework for modeling three-dimensional scaffold-mediated bone regeneration and the associated optimization problem. By incorporating microstructure into the model through periodic homogenization, we capture the…
The global population increase leads to a high food demand, and to reach this target products such as pesticides are needed to protect the crops. Research is focusing on the development of new products that can be less harmful to the…
Soil is a complex, dynamic material, with physical properties that depend on its biological content. We propose a cellular automaton model for self-organizing soil structure, where soil aggregates and serves as food for microbial species.…
We investigate the evolution of tumor growth relying on a nonlinear model of partial differential equations which incorporates mechanical laws for tissue compression combined with rules for nutrients availability and drug application.…
Cellular nutrient consumption is influenced by both the nutrient uptake kinetics of an individual cell and the cells' spatial arrangement. Large cell clusters or colonies have inhibited growth at the cluster's center due to the shielding of…
We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient reservoir (the blood), aimed at characterizing the role of…
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…
Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these…
Information theory has explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Some scholars have proposed that information should…
Modeling of growth (or decay) curves arises in many fields such as microbiology, epidemiology, marketing, and econometrics. Parametric forms like Logistic and Gompertz are often used for modeling such monotonic patterns. While useful for…
Tumor growth beyond a critical size relies on the development of a functional vascular network, which ensures adequate oxygen and nutrient supply. In this work, we present a modeling framework based on an optimization-based 3D-1D coupling…
In this paper, we establish a reaction-diffusion-advection partial differential equation model to describe the growth of algae depending on both nutrients and inorganic carbon in a poorly mixed water column. Nutrients from the water bottom…
Starting from a particle model we derive a macroscopic aggregation-diffusion equation for the evolution of slime mold under the assumption of propagation of chaos in the large particle limit. We analyze properties of the macroscopic model…
Optimal growth of structures governed by spatially stochastic dynamics arises in many scientific settings, for example in processes such as solution-based crystallization and the formation of microbial biofilms on patterned substrates or…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…