Related papers: Biological Processes as Exploratory Dynamics
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
Motivated by various recent experimental findings, we propose a dynamical model of intermittently self-propelled particles: active particles that recurrently switch between two modes of motion, namely an active run-state and a turn state,…
We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate…
Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been…
Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical…
This paper presents a high-level conceptual framework to help orient the discussion and implementation of open-endedness in evolutionary systems. Drawing upon earlier work by Banzhaf et al., three different kinds of open-endedness are…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the…
The self-organization of microbial ecosystems involves a large variety of mechanisms, ranging from biochemical signaling to population dynamics. Among these, the role of motility regulation has been little studied, despite the importance of…
Biological systems are influenced by fluid mechanics at nearly all spatiotemporal scales. This broad relevance of fluid mechanics to biology has been increasingly appreciated by engineers and biologists alike, leading to continued expansion…
Stochastic biochemical and transport processes have various final outcomes, and they can be viewed as dynamic systems with multiple exits. Many current theoretical studies, however, typically consider only a single time scale for each…
Active matter systems comprise self-propelled particles that move on a substrate while leaving chemical trails that influence other particles through chemotaxis (e.g., slime-depositing bacteria). Orientational chemotaxis manifests as a…
Considering deterministic classical lattice systems with continuous variables, we show that, if the initial conditions are sampled according to a probability distribution in which the dynamical variables are statistically independent, the…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The idea is advanced that self-organization in complex systems can be treated as decision making (as it is performed by humans) and, vice versa, decision making is nothing but a kind of self-organization in the decision maker nervous…