Related papers: The simple emergence of complex molecular function

Competitive exclusion, a key principle of ecology, can be generalized to understand many other complex systems. Individuals under surviving pressure tend to be different from others, and correlations among them change correspondingly to the…

In these notes we review emergent phenomena in complex systems, emphasizing ways to identify potential underlying universal mechanisms that generates complexity. The discussion is centered around the emergence of collective behavior in…

Understanding the functional architecture of complex systems is crucial to illuminate their inner workings and enable effective methods for their prediction and control. Recent advances have introduced tools to characterise emergent…

A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential…

We develop a formal model of the emergence of self-constructing objects (e.g. heteropolymers with autocatalytic capability) in an open system, which don't contain such objects initially. The objects are constructed from subunits (e.g.…

From genomes and ecosystems to bureaucracies and cities, the growth of complex systems occurs by adding new types of functions and expanding existing ones. We present a simple generative model that generalizes the Yule-Simon process by…

Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…

A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…

Many real-world complex networks arise as a result of a competition between growth and rewiring processes. Usually the initial part of the evolution is dominated by growth while the later one rather by rewiring. The initial growth allows…

The evolution of the biosphere unfolds as a luxuriant generative process of new living forms and functions. Organisms adapt to their environment, exploit novel opportunities that are created in this continuous blooming dynamics. Affordances…

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…

A universal framework is proposed, where all laws are regularities of relations between things or agents. Parts of the world at one or all times are modeled as networks called SYSTEMS with a minimum of axiomatic properties. A notion of…

Emergent behavior that appears at a given level of organization may be characterized as arising from an organizationally lower level in such a way that it transcends a mere increase in the behavioral degree of complexity. It is therefore to…

There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…

Cooperation is a persistent behavioral pattern of entities pooling and sharing resources. Its ubiquity in nature poses a conundrum. Whenever two entities cooperate, one must willingly relinquish something of value to the other. Why is this…

Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…

Although most networks in nature exhibit complex topology the origins of such complexity remains unclear. We introduce a model of a growing network of interacting agents in which each new agent's membership to the network is determined by…

Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…

Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…