Related papers: Exploratory Adaptation in Large Random Networks
Living systems adapt to various environmental conditions by changing their internal states. Inspired by gene expression and epigenetic modification dynamics, we herein propose a generic mechanism for adaptation by combining fast oscillatory…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
Animals excel at adapting their intentions, attention, and actions to the environment, making them remarkably efficient at interacting with a rich, unpredictable and ever-changing external world, a property that intelligent machines…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Artificial life aims to understand the fundamental principles of biological life by creating computational models that exhibit life-like properties. Although artificial life systems show promise for simulating biological evolution,…
Adaptive (or co-evolutionary) network dynamics, i.e., when changes of the network/graph topology are coupled with changes in the node/vertex dynamics, can give rise to rich and complex dynamical behavior. Even though adaptivity can improve…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
Characterization of pluripotent states, in which cells can both self-renew and differentiate, and the irreversible loss of pluripotency are important research areas in developmental biology. In particular, an understanding of these…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary timescales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
The emergence of complex networks from evolutionary games is studied occurring when agents are allowed to switch interaction partners. For this purpose a coevolutionary iterated Prisoner's Dilemma game is defined on a random network with…
Networks exhibiting "accelerating" growth have total link numbers growing faster than linearly with network size and can exhibit transitions from stationary to nonstationary statistics and from random to scale-free to regular statistics at…
Drug resistance and metastasis - the major complications in cancer - both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be…
The design space of networked embedded systems is very large, posing challenges to the optimisation of such platforms when it comes to support applications with real-time guarantees. Recent research has shown that a number of inter-related…
Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…