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We propose a method for finding metabolic parameters of cells, organs and whole organisms, which is based on the earlier discovered general growth law. Based on the obtained results and analysis of available biological models, we propose a…

We derive general kinetic and hydrodynamic models of chemotactic aggregation that describe certain features of the morphogenesis of biological colonies (like bacteria, amoebae, endothelial cells or social insects). Starting from a…

A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…

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…

Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…

Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…

We investigate the structure and stability of the steady states for a bacterial colony model with density-suppressed motility. We treat the growth rate of bacteria as a bifurcation parameter to explore the local and global structure of the…

Damped-driven systems are ubiquitous in engineering and science. Despite the diversity of physical processes observed in a broad range of applications, the underlying instabilities observed in practice have a universal characterization…

This paper investigates the conditions for the stability and emergence of patterns in a new three-component reaction-diffusion system. The system describes the coexistence and interaction of water reservoirs, vegetation, and bushfire…

A central feature of complex systems is the relevance and entanglement of different levels of description. For instance, the dynamics of ecosystems can be alternatively described in terms of large ecological processes and classes of…

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…

A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…

In this work we consider a mathematical model of the water treatment process and determine the effective characteristics of this model. At the microscopic length scale we describe our model in terms of a lattice random walk in a…

We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…

We develop an unstructured mathematical model describing the growth kinetics of the Trichoderma fungus and the production of enzymes (cellulase) by degradation of a substrate (cellulose) in the rhizosphere. We integrate into this model the…

We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…

Multiple stable states - the coexistence of two or more distinct ecological configurations under identical environmental conditions - have attracted sustained interest in ecology, yet the field still lacks a unified framework connecting…

The landscape of computational modeling in cancer systems biology is diverse, offering a spectrum of models and frameworks, each with its own trade-offs and advantages. Ideally, models are meant to be useful in refining hypotheses, to…

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.…

In an ecological context, panel data arise when time series measurements are made on a collection of ecological processes. Each process may correspond to a spatial location for field data, or to an experimental ecosystem in a designed…