Related papers: Internal Feedback in Biological Control: Architect…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
We developed a strategy to control p53 levels when the p53 concentration falls below a desired threshold . Based on an established p53-MDM2 mathematical model that also incorporates microRNA regulators (p53-MDM2-miRNA), we applied a control…
Communication signals often comprise an array of colors, lines, spots, notes or odors that are arranged in complex patterns, melodies or blends. Receiver perception is assumed to influence preference and thus the evolution of signal design,…
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are…
Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on…
A ubiquitous way that cells share information is by exchanging molecules. Yet, the fundamental ways that this information exchange is influenced by intracellular dynamics remain unclear. Here we use information theory to investigate a…
Plant-soil feedback is recognized as a causal mechanism for the emergence of vegetation patterns of the same species especially when water is not a limiting resource (e.g. humid environments). Nevertheless, in the field, plants rarely grow…
Biologically-inspired methods such as evolutionary algorithms and neural networks are proving useful in the field of information fusion. Artificial Immune Systems (AISs) are a biologically-inspired approach which take inspiration from the…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
In this thesis, we provide new insights into the theory of cascade feedback linearization of control systems. In particular, we present a new explicit class of cascade feedback linearizable control systems, as well as a new obstruction to…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here we propose that inter-molecular frustration…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…
Identifying the mechanism of intercellular feedback regulation is critical for the basic understanding of tissue growth control in organisms. In this paper, we analyze a tissue growth model consisting of a single lineage of two cell types…
A general framework for analyzing the topology of quantum channels of single-particle systems is developed to find a class of genuinely dynamical topological phases that can be realized by means of discrete quantum feedback control. We…
The Gaia hypothesis (Lovelock and Margulis, 1974) proposes that there is a control system operating at global level that regulates climate and chemistry at a habitable state for the biota. Here we provide statistically significant…
A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes,…