Related papers: The Core & Periphery Hypothesis: A Conceptual Basi…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored…
Systems that exhibit complex behaviours are often found in a particular dynamical condition, poised between order and disorder. This observation is at the core of the so-called criticality hypothesis, which states that systems in a…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
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…
The concept of complexity appears in virtually all areas of knowledge. Its intuitive meaning shares similarities across fields, but disagreements between its details hinders a general definition, leading to a plethora of proposed…
The classical PCP theorem is arguably the most important achievement of classical complexity theory in the past quarter century. In recent years, researchers in quantum computational complexity have tried to identify approaches and develop…
Core-periphery structure is a common property of complex networks, which is a composition of tightly connected groups of core vertices and sparsely connected periphery vertices. This structure frequently emerges in traffic systems, biology,…
Although random cell complexes occur throughout the physical sciences, there does not appear to be a standard way to quantify their statistical similarities and differences. The various proposals in the literature are usually motivated by…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Many real-world networks are theorized to have core-periphery structure consisting of a densely-connected core and a loosely-connected periphery. While this phenomenon has been extensively studied in a range of scientific disciplines, it…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
Cellular development follows a stochastic yet rule-governed trajectory, though the underlying principles remain elusive. Here, we propose that cellular development follows paths of least action, aligning with foundational physical laws that…
Core-periphery (CP) structure is an important meso-scale network property where nodes group into a small, densely interconnected {core} and a sparse {periphery} whose members primarily connect to the core rather than to each other. While…
Finding general principles underlying brain function has been appealing to scientists. Indeed, in some branches of science like physics and chemistry (and to some degree biology) a general theory often can capture the essence of a wide…
The standard assumptions that underlie many conceptual and quantitative frameworks do not hold for many complex physical, biological, and social systems. Complex systems science clarifies when and why such assumptions fail and provides…
Criticality is hypothesized as a physical mechanism underlying efficient transitions between cortical states and remarkable information processing capacities in the brain. While considerable evidence generally supports this hypothesis,…
Ordered polarity alignment of a cell population plays a vital role in biology, such as in hair follicle alignment and asymmetric cell division. Here, we propose a theoretical framework for the understanding of generic dynamical properties…