Analyzing Linear Communication Networks using the Ribosome Flow Model

The Ribosome Flow Model (RFM) describes the unidirectional movement of interacting particles along a one-dimensional chain of sites. As a site becomes fuller, the effective entry rate into this site decreases. The RFM has been used to model and analyze mRNA translation, a biological process in which ribosomes (the particles) move along the mRNA molecule (the chain), and decode the genetic information into proteins. Here we propose the RFM as an analytical framework for modeling and analyzing linear communication networks. In this context, the moving particles are data-packets, the chain of sites is a one dimensional set of ordered buffers, and the decreasing entry rate to a fuller buffer represents a kind of decentralized backpressure flow control. For an RFM with homogeneous link capacities, we provide closed-form expressions for important network metrics including the throughput and end-to-end delay. We use these results to analyze the hop length and the transmission probability (in a contention access mode) that minimize the end-to-end delay in a multihop linear network, and provide closed-form expressions for the optimal parameter values

Simulating bacterial transcription and translation in a stochastic pi-calculus

International audienceStochastic simulation of genetic networks based on models in the stochastic pi-calculus is a promising recent approach. This paper contributes an extensible model of the central mechanisms of gene ex- pression i.e. transcription and translation, at the prototypical instance of bacteria. We reach extensibility through object-oriented abstractions, that are expressible in a stochastic π-calculus with pattern guarded inputs. We illustrate our generic model by simulating the effect of translational bursting in bacterial gene expression

A functional central limit theorem for a Markov-modulated infinite-server queue

The production of molecules in a chemical reaction network is modelled as a Poisson process with a Markov-modulated arrival rate and an exponential decay rate. We analyze the distributional properties of $M$, the number of molecules, under specific time-scaling; the background process is sped up by $N^{\alpha}$, the arrival rates are scaled by $N$, for $N$ large. A functional central limit theorem is derived for $M$, which after centering and scaling, converges to an Ornstein-Uhlenbeck process. A dichotomy depending on $\alpha$ is observed. For $\alpha\leq1$ the parameters of the limiting process contain the deviation matrix associated with the background process.Comment: 4 figure

Fundamentals of molecular information and communication science

© 1963-2012 IEEE. Molecular communication (MC) is the most promising communication paradigm for nanonetwork realization since it is a natural phenomenon observed among living entities with nanoscale components. Since MC significantly differs from classical communication systems, it mandates reinvestigation of information and communication theoretical fundamentals. The closest examples of MC architectures are present inside our own body. Therefore, in this paper, we investigate the existing literature on intrabody nanonetworks and different MC paradigms to establish and introduce the fundamentals of molecular information and communication science. We highlight future research directions and open issues that need to be addressed for revealing the fundamental limits of this science. Although the scope of this development encompasses wide range of applications, we particularly emphasize its significance for life sciences by introducing potential diagnosis and treatment techniques for diseases caused by dysfunction of intrabody nanonetworks

Self-Evaluation Applied Mathematics 2003-2008 University of Twente

This report contains the self-study for the research assessment of the Department of Applied Mathematics (AM) of the Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) at the University of Twente (UT). The report provides the information for the Research Assessment Committee for Applied Mathematics, dealing with mathematical sciences at the three universities of technology in the Netherlands. It describes the state of affairs pertaining to the period 1 January 2003 to 31 December 2008

Controlled Information Transfer Through An In Vivo Nervous System.

The nervous system holds a central position among the major in-body networks. It comprises of cells known as neurons that are responsible to carry messages between different parts of the body and make decisions based on those messages. In this work, further to the extensive theoretical studies, we demonstrate the first controlled information transfer through an in vivo nervous system by modulating digital data from macro-scale devices onto the nervous system of common earthworms and conducting successful transmissions. The results and analysis of our experiments provide a method to model networks of neurons, calculate the channel propagation delay, create their simulation models, indicate optimum parameters such as frequency, amplitude and modulation schemes for such networks, and identify average nerve spikes per input pulse as the nervous information coding scheme. Future studies on neuron characterization and artificial neurons may benefit from the results of our work

A framework for energy based performability models for wireless sensor networks

A novel idea of alternating node operations between Active and Sleep modes in Wireless Sensor Network (WSN) has successfully been used to save node power consumption. The idea which started off as a simple implementation of a timer in most protocols has been improved over the years to dynamically change with traffic conditions and the nature of application area. Recently, use of a second low power radio transceiver to triggered Active/Sleep modes has also been made. Active/Sleep operation modes have also been used to separately model and evaluate performance and availability of WSNs. The advancement in technology and continuous improvements of the existing protocols and application implementation demands continue to pose great challenges to the existing performance and availability models. In this study the need for integrating performance and availability studies of WSNs in the presence of both channel and node failures and repairs is investigated. A framework that outlines and characterizes key models required for integration of performance and availability of WSN is in turn outlined. Possible solution techniques for such models are also highlighted. Finally it is shown that the resulting models may be used to comparatively evaluate energy consumption of the existing motes and WSNs as well as deriving required performance measures