Related papers: Biological Processes as Exploratory Dynamics
Biological tissues have been observed to display emergent fluid-like properties, owing to physical interactions between cells. However, it remains unclear in general how these fluid-like properties affect tissue structure and function.…
This paper is to show that most discrete models used for population dynamics in ecology are inherently pathological that their predications cannot be independently verified by experiments because they violate a fundamental principle of…
We study the dynamics of a non-minimally coupled scalar field cosmology with a potential function. We use the framework of dynamical systems theory to investigate all evolutional paths admissible for all initial conditions. Additionally, we…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…
We analyze the fate of dynamical systems that consist of two kind of processes. The first type is supposed to perform a certain function by processing information at a required high accuracy, which is, however, limited to less than 100…
Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
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…
A computational revolution unleashed the power of artificial neural networks. At the heart of that revolution is automatic differentiation, which calculates the derivative of a performance measure relative to a large number of parameters.…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Traditionally, Probability theory was dealing with limit theorems where 'limit" means that time tends to infinity. Questions about finite time dynamics (evolution) were always considered as, although important for practical applications,…
We numerically examine the dynamics of a probe particle driven at a constant force through an assembly of particles with competing long-range repulsion and short-range attraction that forms a bubble or stripe state. In the bubble regime, we…
We develop a dynamical systems approach to prioritizing and selecting multiple recurring tasks with the aim of conferring a degree of deliberative goal selection to a mobile robot confronted with competing objectives. We take navigation as…
When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current…
We present a geometric framework to study the growth-division dynamics of cells and protocells, and demonstrate that self-reproduction emerges only when a system's growth dynamics and division strategy are mutually compatible. Using several…
An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Yet often neglected, dynamical interdependencies between concomitant contagion processes can alter their intrinsic equilibria and bifurcations. A particular case of interest for disease control is the emergence of explosive transitions in…