Related papers: Progress towards quantitative design principles of…
Swarming or collective motion of living entities is one of the most common and spectacular manifestations of living systems having been extensively studied in recent years. A number of general principles have been established. The…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…
Can we quantify the change of complexity throughout evolutionary processes? We attempt to address this question through an empirical approach. In very general terms, we simulate two simple organisms on a computer that compete over limited…
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification…
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Communication of information in complex systems can be considered as major driver of systems evolution. What matters is not the communicated information by itself but rather the meaning that is supplied to the information. However…
Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at…
Improvements in technique in conjunction with an evolution of the theoretical and conceptual approach to neuronal networks provide a new perspective on living neurons in culture. Organization and connectivity are being measured…
A varying number of particles is one of the most relevant characteristics of systems of interest in nature and technology, ranging from the exchange of energy and matter with the surrounding environment to the change of particle number…
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…
This paper is a first step to chase the ambitious objective of developing a mathmatical theory of living systems. The contents refer modeling large systems of interacting living entities with the aim of describing their collective behaviors…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
How multicellular life forms evolved out from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations has shown that selection for…
In multicellular organisms, several cell states coexist. For determining each cell type, cell-cell interactions are often essential, in addition to intracellular gene expression dynamics. Based on dynamical systems theory, we propose a…
The study of networks plays a crucial role in investigating the structure, dynamics, and function of a wide variety of complex systems in myriad disciplines. Despite the success of traditional network analysis, standard networks provide a…