Related papers: Modularity in biological evolution and evolutionar…
What makes living systems flexible so that they can react quickly and adapt easily to changing environments? This question has not only engaged biologists for decades but is also of great interest to computer scientists and engineers who…
Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…
The growth of world population, limitation of resources, economic problems and environmental issues force engineers to develop increasingly efficient solutions for logistic systems. Pure optimization for efficiency, however, has often led…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Aging is a fundamental aspect of living systems that undergo a progressive deterioration of physiological function with age and an increase of vulnerability to disease and death. Living systems, known as complex systems, require complexity…
Structural modularity is a pervasive feature of biological neural networks, which have been linked to several functional and computational advantages. Yet, the use of modular architectures in artificial neural networks has been relatively…
Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
This paper introduces a method to generate hierarchically modular networks with prescribed node degree list and proposes a metric to measure network modularity based on the notion of edge distance. The generated networks are used as test…
The neural network is a powerful computing framework that has been exploited by biological evolution and by humans for solving diverse problems. Although the computational capabilities of neural networks are determined by their structure,…
Evolutionary computing (EC) is an exciting development in Computer Science. It amounts to building, applying and studying algorithms based on the Darwinian principles of natural selection. In this paper we briefly introduce the main…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
As a result of a hundred million years of evolution, living animals have adapted extremely well to their ecological niche. Such adaptation implies species-specific interactions with their immediate environment by processing sensory cues and…
The ability to absorb mutations while retaining structure and function, or mutational robustness, is a remarkable property of natural proteins. In this Letter, we use a computational model of organismic evolution [Zeldovich et al, PLOS Comp…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative"…
In this article we focus on evolving information systems. First a delimitation of the concept of evolution is provided, resulting in a first attempt to a general theory for such evolutions. The theory makes a distinction between the…
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…