Related papers: Biological Processes as Exploratory Dynamics
A method is presented that, when used in conjunction with single molecule experimental techniques, allows for the extraction of rates and mechanical properties of a biomolecule undergoing transitions between mechanically distinct states.…
A dynamical systems scenario for developmental cell biology is proposed, based on numerical studies of a system with interacting units with internal dynamics and reproduction. Diversification, formation of discrete and recursive types, and…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
Biological function of living matter is fulfilled by complex motions of biological and soft matter. Unlike general motion is deterministic described by Newton's laws, these motions are mostly random and uncertain for the position in…
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 a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
The macroscopic behaviour of active matter arises from nonequilibrium microscopic processes. In soft materials, active stresses typically drive macroscopic shape changes, which in turn alter the geometry constraining the microscopic…
We introduce a model of the growth of a single microorganism in a self-cycling fermentor in which an arbitrary number of resources are limiting, and impulses are triggered when the concentration of one specific substrate reaches a…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Cell movement, for example during embryogenesis or tumor metastasis, is a complex dynamical process resulting from an intricate interplay of multiple components of the cellular migration machinery. At first sight, the paths of migrating…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
The long-term behaviour of dynamic systems can be classified in two different regimes, regular or chaotic, depending on the values of the control parameters, which are kept constant during the time evolution. Starting from slightly…
The mitotic spindle is an important intermediate structure in eukaryotic cell division, in which each of a pair of duplicated chromosomes is attached through microtubules to centrosomal bodies located close to the two poles of the dividing…
Reaction systems are discrete dynamical systems inspired by bio-chemical processes, whose dynamical behaviour is expressed by set-theoretic operations on finite sets. Reaction systems thus provide a description of bio-chemical phenomena…