Related papers: Information-Theoretical Measures for Developmental…
Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…
With the help of a mathematical model, the metabolic process of the Krebs cycle is studied. The autocatalytic processes resulting in both the formation of the self-organization in the Krebs cycle and the appearance of a cyclicity of its…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
How to induce differentiated cells into pluripotent cells has elicited researchers' interests for a long time since pluripotent stem cells are able to offer remarkable potential in numerous subfields of biological research. However, the…
$\beta$-cells are biologically essential for humans and other vertebrates. Because their functionality arises from cell-cell interactions, they are also a model system for collective organization among cells. There are currently two…
Most of the grand challenges of humanity today involve complex agent-based systems, such as epidemiology, economics or ecology. However, remains as a pending task the challenge of identifying the general principles underlying their…
As intelligent systems are developed across diverse substrates - from machine learning models and neuromorphic hardware to in vitro neural cultures - understanding what gives a system agency has become increasingly important. Existing…
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…
All cognitive agents are composite beings. Specifically, complex living agents consist of cells, which are themselves competent sub-agents navigating physiological and metabolic spaces. Behavior science, evolutionary developmental biology,…
Here we provide a detailed analysis, along with some extensions and additonal investigations, of a recently proposed self-organised model for the evolution of complex networks. Vertices of the network are characterised by a fitness variable…
In order to keep trace of information and grow up, the infant brain has to resolve the problem about where old information is located and how to index new ones. We propose that the immature prefrontal cortex (PFC) use its primary…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
In this paper it is shown how to map a data manifold into a simpler form by progressively discarding small degrees of freedom. This is the key to self-organising data fusion, where the raw data is embedded in a very high-dimensional space…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
Collective organization in matter plays a significant role in its expressed physical properties. Typically, it is detected via an order parameter, appropriately defined for each given system's observed emergent patterns. Recent developments…
Bayesian design can be used for efficient data collection over time when the process can be described by the solution to an ordinary differential equation (ODE). Typically, Bayesian designs in such settings are obtained by maximising the…
The dissertation extrapolates the theory of self-organization in biological organisms to sociopolitical self-organization, in human social systems. It is stated that the latter is the best way to organize human social systems, given their…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…