Related papers: Biological Processes as Exploratory Dynamics
A variety of biomolecular systems rely on exploratory dynamics to reach target locations or states within a cell. Without a mechanism to remotely sense and move directly towards a target, the system must sample over many paths, often…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
In spite of the large amount of existing neural models in the literature, there is a lack of a systematic review of the possible effect of choosing different initial conditions on the dynamic evolution of neural systems. In this short…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
We present a simple physical model that recapitulates several features of biological evolution, while being based only on thermally-driven attachment and detachment of elementary building blocks. Through its dynamics, this model samples a…
We propose an alternative to the prevailing two origin of life narratives, one based on a replicator first hypothesis, and one based on a metabolism first hypothesis. Both hypotheses have known difficulties: All known evolvable molecular…
Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…
Natural selection favors the more successful individuals. This is the elementary premise that pervades common models of evolution. Under extreme conditions, however, the process may no longer be probabilistic. Those that meet certain…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on…
Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Biochemical processes typically involve huge numbers of individual reversible steps, each with its own dynamical rate constants. For example, kinetic proofreading processes rely upon numerous sequential reactions in order to guarantee the…
Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…