Related papers: Modeling network dynamics: the lac operon, a case …
Living cells can enhance their fitness by anticipating environmental change. We study how accurately linear signaling networks in cells can predict future signals. We find that maximal predictive power results from a combination of…
We consider a new class of interacting particle systems with a countable number of interacting components. The system represents the time evolution of the membrane potentials of an infinite set of interacting neurons. We prove the existence…
This article provides a taxonomy of current and past network modeling efforts. In all these efforts over the last few years we see a trend towards not only describing the network, but connected devices as well. This is especially current…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
In this chapter, we present a review of latent position models for networks. We review the recent literature in this area and illustrate the basic aspects and properties of this modeling framework. Through several illustrative examples we…
Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the…
A nematic liquid-crystal cell subject to an electric field created by electrodes held at constant potential is modeled as a variable capacitor in an RC circuit. The state of the system is characterized in terms of the director field in the…
Odor-based Molecular Communication (OMC) employs odor molecules to convey information, contributing to the realization of the Internet of Everything (IoE) vision. Despite this, the practical deployment of OMC systems is currently limited by…
We relate structurally dynamic cellular networks, a class of models we developed in fundamental space-time physics, to SDCA, introduced some time ago by Ilachinski and Halpern. We emphasize the crucial property of a non-linear interaction…
A cellular model introduced for the evolution of the fluvial landscape is revisited using extensive numerical and scaling analyses. The basic network shapes and their recurrence especially in the aggregation structure are then addressed.…
The past decade has seen tremendous growth in the field of Complex Social Networks. Several network generation models have been extensively studied to develop an understanding of how real world networks evolve over time. Two important…
Biological organisms are simple at heart: cells, their basic units, perform a variety of behaviors by expressing proteins from DNA-encoded genes. Gene expression though depends on sets of often-convoluted regulatory interactions known as…
We consider a living organism as an observer of the evolution of its environment recording sensory information about the state space X of the environment in real time. Sensory information is sampled and then processed on two levels. On the…
We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model by a low-dimensional system of equations permitting analytical…
This paper is placed at the intersection-point between the study of theoretical computational models aimed at capturing the essence of genetic regulatory networks and the field of Artificial Embryology (or Computational Development). A…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
We construct a cellular automaton (CA) model that describes the movement of a particle in a disordered system. The mathematical properties of the CA model were examined by varying the configuration of grid and determining the number of…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…