Related papers: Information content and optimization of self-organ…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Self-organizing complex systems typically are comprised of a large number of frequently similar components or events. Through their process, a pattern at the global-level of a system emerges solely from numerous interactions among the…
Bounded agents are limited by intrinsic constraints on their ability to process information that is available in their sensors and memory and choose actions and memory updates. In this dissertation, we model these constraints as…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Living systems self-organize in ways that conventional physical frameworks-based on forces, energies, and continuous fields-cannot fully capture. Processes like gene regulation and cellular decision-making involve rule-based logic and…
Future communication networks are expected to feature autonomic (or self-organizing) mechanisms to ease deployment (self-configuration), tune parameters automatically (self-optimization) and repair the network (self-healing).…
Self-organization is frequently observed in active collectives, from ant rafts to molecular motor assemblies. General principles describing self-organization away from equilibrium have been challenging to identify. We offer a unifying…
In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be…
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…
This thesis details a class of partial orders on the space of probability distributions and the space of density operators which capture the idea of information content. Some links to domain theory and computational linguistics are also…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
In this Chapter, we ask questions (1) What is the right way to measure the quality of information processing in a biological system? and (2) What can real-life organisms do in order to improve their performance in information-processing…
Biological systems often consist of a small number of constituents and are therefore inherently noisy. To function effectively, these systems must employ mechanisms to constrain the accumulation of noise. Such mechanisms have been…
Self-organized criticality has been proposed to be a universal mechanism for the emergence of scale-free dynamics in many complex systems, and possibly in the brain. While such scale-free patterns were identified experimentally in many…
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…
In this work the information loss in deterministic, memoryless systems is investigated by evaluating the conditional entropy of the input random variable given the output random variable. It is shown that for a large class of systems the…
Cyclic cellular automata (CCA) are models of excitable media. Started from random initial conditions, they produce several different kinds of spatial structure, depending on their control parameters. We introduce new tools from information…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…
This paper presents case-study results on the application of information theoretic approach to gate-level evolutionary circuit design. We introduce information measures to provide better estimates of synthesis criteria of digital circuits.…