Dynamic sharing of a multiple access channel

In this paper we consider the mutual exclusion problem on a multiple access channel. Mutual exclusion is one of the fundamental problems in distributed computing. In the classic version of this problem, n processes perform a concurrent program which occasionally triggers some of them to use shared resources, such as memory, communication channel, device, etc. The goal is to design a distributed algorithm to control entries and exits to/from the shared resource in such a way that in any time there is at most one process accessing it. We consider both the classic and a slightly weaker version of mutual exclusion, called ep-mutual-exclusion, where for each period of a process staying in the critical section the probability that there is some other process in the critical section is at most ep. We show that there are channel settings, where the classic mutual exclusion is not feasible even for randomized algorithms, while ep-mutual-exclusion is. In more relaxed channel settings, we prove an exponential gap between the makespan complexity of the classic mutual exclusion problem and its weaker ep-exclusion version. We also show how to guarantee fairness of mutual exclusion algorithms, i.e., that each process that wants to enter the critical section will eventually succeed

A Protocol for the Atomic Capture of Multiple Molecules at Large Scale

With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative programming models. The chemical programming paradigm, which models applications as chemical solutions where molecules representing digital entities involved in the computation, react together to produce a result, has been recently shown to provide the needed abstractions for autonomic coordination of services. However, the execution of such programs over large scale platforms raises several problems hindering this paradigm to be actually leveraged. Among them, the atomic capture of molecules participating in concur- rent reactions is one of the most significant. In this paper, we propose a protocol for the atomic capture of these molecules distributed and evolving over a large scale platform. As the density of possible reactions is crucial for the liveness and efficiency of such a capture, the protocol proposed is made up of two sub-protocols, each of them aimed at addressing different levels of densities of potential reactions in the solution. While the decision to choose one or the other is local to each node participating in a program's execution, a global coherent behaviour is obtained. Proof of liveness, as well as intensive simulation results showing the efficiency and limited overhead of the protocol are given.Comment: 13th International Conference on Distributed Computing and Networking (2012

Algon: a framework for supporting comparison of distributed algorithm performance

Programmers often need to use distributed algorithms to add non-functional behaviour such as mutual exclusion, deadlock detection and termination, to a distributed application. They find the selection and implementation of these algorithms daunting. Consequently, they have no idea which algorithm will be best for their particular application. To address this difficulty the Algon framework provides a set of pre-coded distributed algorithms for programmers to choose from, and provides a special performance display tool to support choice between algorithms. The performance tool is discussed. The developer of a distributed application will be able to observe the performance of each of the available algorithms according to a set of of widely accepted and easily-understandable performance metrics and compare and contrast the behaviour of the algorithms to support an informed choice. The strength of the Algon framework is that it does not require a working knowledge of algorithmic theory or functionality in order for the developer to use the algorithms

Stochastic theory of protein synthesis and polysome: ribosome profile on a single mRNA transcript

The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the track. Often several ribosomes may translate the same (mRNA) simultaneously. The ribosomes bound simultaneously to a single mRNA transcript are the members of a polyribosome (or, simply, {\it polysome}). Experimentally measured {\it polysome profile} gives the distribution of polysome {\it sizes}. Recently a breakthrough in determining the instantaneous {\it positions} of the ribosomes on a given mRNA track has been achieved and the technique is called {\it ribosome profiling} \cite{ingolia10,guo10}. Motivated by the success of these techniques, we have studied the spatio-temporal organization of ribosomes by extending a theoretical model that we have reported elsewhere \cite{sharma11}. This extended version of our model incorporates not only (i) mechano-chemical cycle of individual ribomes, and (ii) their steric interactions, but also (iii) the effects of (a) kinetic proofreading, (b) translational infidelity, (c) ribosome recycling, and (d) sequence inhomogeneities. The theoretical framework developed here will serve in guiding further experiments and in analyzing the data to gain deep insight into various kinetic processes involved in translation.Comment: Minor revisio