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The emergence of cognition requires a framework that bridges evolutionary principles with neurocomputational mechanisms. This paper introduces the novel "thoughtseed" framework, proposing that cognition arises from the dynamic interaction…
We consider a system of interacting Fisher-Wright diffusions with seed-bank. Individuals carry type one of two types, live in colonies, and are subject to resampling and migration as long as they are active. Each colony has a structured…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
Spatial systems with heterogeneities are ubiquitous in nature, from precipitation, temperature and soil gradients controlling vegetation growth to morphogen gradients controlling gene expression in embryos. Such systems, generally described…
Networks describing the interaction of the elements that constitute a complex system grow and develop via a number of different mechanisms, such as the addition and deletion of nodes, the addition and deletion of edges, as well as the…
Growth in confined spaces can drive cellular populations through a jamming transition from a fluid-like state to a solid-like state. Experiments have found that jammed budding yeast populations can build up extreme compressive pressures…
Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real world systems. Using random matrix analysis of a weighted…
Hierarchy is one of the most conspicuous features of numerous natural, technological and social systems. The underlying structures are typically complex and their most relevant organizational principle is the ordering of the ties among the…
Clusters appear in nature in a diversity of contexts, involving distances as long as the cosmological ones, and down to atoms and molecules and the very small nuclear size. They also appear in several other scenarios, in particular in…
Real complex systems are not rigidly structured; no clear rules or blueprints exist for their construction. Yet, amidst their apparent randomness, complex structural properties universally emerge. We propose that an important class of…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
The discipline of `theoretical biology' has been developing from its inception several decades ago almost in parallel with the advances in biology, so much so that the latter is often considered to be almost exclusively an empirical…
Instances of critical-like characteristics in living systems at each organizational level as well as the spontaneous emergence of computation (Langton), indicate the relevance of self-organized criticality (SOC). But extrapolating complex…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
In complex systems, we often observe complex global behavior emerge from a collection of agents interacting with each other in their environment, with each individual agent acting only on locally available information, without knowing the…
Sequential activation of neurons is a common feature of network activity during a variety of behaviors, including working memory and decision making. Previous network models for sequences and memory emphasized specialized architectures in…
Self-organization is the autonomous assembly of a network of interacting components into a stable, organized pattern. This article shows that the process of self-assembly can be encoded in terms of evolutionary entropy, a statistical…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
We experience a major paradigm change in mobile networks. The infrastructure of cellular networks becomes mobile as it is densified by using mobile and nomadic small cells to increase coverage and capacity. Furthermore, the innovative…