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Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
We investigate global stability and dynamics of large ecological networks by classical methods of the dynamical system theory, including Hamiltonian methods, and averaging. Our analysis exploits the network topological structure, namely,…
Growth mixture models are an important tool for detecting group structure in repeated measures data. Unlike traditional clustering methods, they explicitly model the repeat measurements on observations, and the statistical framework they…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices…
Descriptions of molecular systems usually refer to two distinct theoretical frameworks. On the one hand the quantum pure state, i.e. the wavefunction, of an isolated system which is determined to calculate molecular properties and to…
Ecological processes depend on the flow and balance of essential elements such as carbon (C) and phosphorus (P), and changes in these elements can cause adverse effects to ecosystems. The theory of Ecological Stoichiometry offers a…
We study a model ecosystem by means of dynamical techniques from disordered systems theory. The model describes a set of species subject to competitive interactions through a background of resources, which they feed upon. Additionally…
In this pedagogical study, carried out by adopting standard mathematical methods of nonlinear dynamics, we have presented some simple analytical models to understand terminal behaviour in industrial growth. This issue has also been…
An evolving yeast colony is simulated by means of a cellular automaton that takes care of many important features of the system under study. A complete survey of the properties of the colony is done and a set of scaling relations is found,…
The question what determines the structure of natural food webs has been listed among the nine most important unanswered questions in ecology. It arises naturally from many problems related to ecosystem stability and resilience. The…
Bacterial growth models are commonly used for the prediction of microbial safety and the shelf life of perishable foods. Growth is affected by several environmental factors such as temperature, acidity level and salt concentration. In this…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
The central goal of a dynamical theory of evolution is to abstract the mean evolutionary trajectory in the trait space by considering ecological processes at the level of the individual. In this work, we develop such a theory for a new…
We present a generic threshold model for the co-evolution of the structure of a network and the state of its nodes. We focus on regular directed networks and derive equations for the evolution of the system toward its absorbing state. It is…
We perform stability analysis of a kinetic bacterial chemotaxis model of bacterial self-organization, assuming that bacteria respond sharply to chemical signals. The resulting discontinuous tumbling kernel represents the key challenge for…
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in various contexts. Here we propose a generative model to capture the dynamics of survival analysis,…
Many physical systems can be modeled as large sets of domains "glued" together along boundaries - biological cells meet along cell membranes, soap bubbles meet along thin films, countries meet along geopolitical boundaries, and metallic…
Co-limitation of marine phytoplankton growth by light and nutrient, both of which are essential for phytoplankton, leads to complex dynamic behavior and a wide array of coherent patterns. The building blocks of this array can be considered…