Snap-Stabilization in Message-Passing Systems

In this paper, we tackle the open problem of snap-stabilization in message-passing systems. Snap-stabilization is a nice approach to design protocols that withstand transient faults. Compared to the well-known self-stabilizing approach, snap-stabilization guarantees that the effect of faults is contained immediately after faults cease to occur. Our contribution is twofold: we show that (1) snap-stabilization is impossible for a wide class of problems if we consider networks with finite yet unbounded channel capacity; (2) snap-stabilization becomes possible in the same setting if we assume bounded-capacity channels. We propose three snap-stabilizing protocols working in fully-connected networks. Our work opens exciting new research perspectives, as it enables the snap-stabilizing paradigm to be implemented in actual networks

Self-stabilizing minimum-degree spanning tree within one from the optimal degree

International audienceWe propose a self-stabilizing algorithm for constructing a Minimum-Degree Spanning Tree (MDST) in undirected networks. Starting from an arbitrary state, our algorithm is guaranteed to converge to a legitimate state describing a spanning tree whose maximum node degree is at most ∆∗ + 1, where ∆∗ is the minimum possible maximum degree of a spanning tree of the network. To the best of our knowledge our algorithm is the first self stabilizing solution for the construction of a minimum-degree spanning tree in undirected graphs. The algorithm uses only local communications (nodes interact only with the neighbors at one hop distance). Moreover, the algorithm is designed to work in any asynchronous message passing network with reliable FIFO channels. Additionally, we use a fine grained atomicity model (i.e. the send/receive atomicity). The time complexity of our solution is O(mn2 log n) where m is the number of edges and n is the number of nodes. The memory complexity is O(δ log n) in the send-receive atomicity model (δ is the maximal degree of the network)

Synchronization Algorithms on Oriented Chains

We present a space- and time-optimal self-stabilizing algorithm, SSDS, for a given synchronization problem on asynchronous oriented chains. SSDS is uniform and works under the unfair distributed daemon. From SSDS we derive solutions for the local mutual exclusion and distributed sorting. Algorithm SSDS can also be used to obtain optimal space solutions for other problems such as broadcasting, leader election, and mutual exclusion

On the Limits and Practice of Automatically Designing Self-Stabilization

A protocol is said to be self-stabilizing when the distributed system executing it is guaranteed to recover from any fault that does not cause permanent damage. Designing such protocols is hard since they must recover from all possible states, therefore we investigate how feasible it is to synthesize them automatically. We show that synthesizing stabilization on a fixed topology is NP-complete in the number of system states. When a solution is found, we further show that verifying its correctness on a general topology (with any number of processes) is undecidable, even for very simple unidirectional rings. Despite these negative results, we develop an algorithm to synthesize a self-stabilizing protocol given its desired topology, legitimate states, and behavior. By analogy to shadow puppetry, where a puppeteer may design a complex puppet to cast a desired shadow, a protocol may need to be designed in a complex way that does not even resemble its specification. Our shadow/puppet synthesis algorithm addresses this concern and, using a complete backtracking search, has automatically designed 4 new self-stabilizing protocols with minimal process space requirements: 2-state maximal matching on bidirectional rings, 5-state token passing on unidirectional rings, 3-state token passing on bidirectional chains, and 4-state orientation on daisy chains

A novel musculoskeletal joint modelling for orthopaedic applications

This thesis was submitted for the degree of Docter of Philosophy and awarded by Brunel University.The objective of the work carried out in this thesis was to develop analytical and computational tools to model and investigate musculoskeletal human joints. It was recognised that the FEA was used by many researchers in modelling human musculoskeletal motion, loading and stresses. However the continuum mechanics played only a minor role in determining the articular joint motion, and its value was questionable. This is firstly due to the computational cost and secondly due to its impracticality for this application. On the other hand, there isn’t any suitable software for precise articular joint motion analysis to deal with the local joint stresses or non standard joints. The main requirement in orthopaedics field is to develop a modeller software (and its associated theories) to model anatomic joint as it is, without any simplification with respect to joint surface morphology and material properties of surrounding tissues. So that the proposed modeller can be used for evaluating and diagnosing different joint abnormalities but furthermore form the basis for performing implant insertion and analysis of the artificial joints. The work which is presented in this thesis is a new frame work and has been developed for human anatomic joint analysis which describes the joint in terms of its surface geometry and surrounding musculoskeletal tissues. In achieving such a framework several contributions were made to the 6DOF linear and nonlinear joint modelling, the mathematical definition of joint stiffness, tissue path finding and wrapping and the contact with collision analysis. In 6DOF linear joint modelling, the contribution is the development of joint stiffness and damping matrices. This modelling approach is suitable for the linear range of tissue stiffness and damping properties. This is the first of its kind and it gives a firm analytical basis for investigating joints with surrounding tissue and the cartilage. The 6DOF nonlinear joint modelling is a new scheme which is described for modelling the motion of multi bodies joined by non-linear stiffness and contact elements. The proposed method requires no matrix assembly for the stiffness and damping elements or mass elements. The novelty in the nonlinear modelling, relates to the overall algorithmic approach and handling local non-linearity by procedural means. The mathematical definition of joint stiffness is also a new proposal which is based on the mathematical definition of stiffness between two bodies. Based on the joint stiffness matrix properties, number of joint stiffness invariants was obtained analytically such as the centre of stiffness, the principal translational stiffnesses, and the principal rotational stiffnesses. In corresponding to these principal stiffnesses, their principal axes have been also obtained. Altogether, a joint is assessed by six principal axes and six principal stiffnesses and its centre of stiffness. These formulations are new and show that a joint can be described in terms of inherent stiffness properties. It is expected that these will be better in characterising a joint in comparison to laxity based characterisation. The development of tissue path finding and wrapping algorithms are also introduced as new approaches. The musculoskeletal tissue wrapping involves calculating the shortest distance between two points on a meshed surface. A new heuristic algorithm was proposed. The heuristic is based on minimising the accumulative divergence from the straight line between two points on the surface and the direction of travel on the surface (i.e. bone). In contact and collision based development, the novel algorithm has been proposed that detects possible colliding points on the motion trajectory by redefining the distance as a two dimensional measure along the velocity approach vector and perpendicular to this vector. The perpendicular distance determines if there are potentially colliding points, and the distance along the velocity determines how close they are. The closest pair among the potentially colliding points gives the “time to collision”. The algorithm can eliminate the “fly pass” situation where very close points may not collide because of the direction of their relative velocity. All these developed algorithms and modelling theories, have been encompassed in the developed prototype software in order to simulate the anatomic joint articulations through modelling formulations developed. The software platform provides a capability for analysing joints as 6DOF joints based on anatomic joint surfaces. The software is highly interactive and driven by well structured database, designed to be highly flexible for the future developments. Particularly, two case studies are carried out in this thesis in order to generate results relating to all the proposed elements of the study. The results obtained from the case studies show good agreement with previously published results or model based results obtained from Lifemod software, whenever comparison was possible. In some cases the comparison was not possible because there were no equivalent results; the results were supported by other indicators. The modelling based results were also supported by experiments performed in the Brunel Orthopaedic Research and Learning Centre

Annotation and comparative analysis of fungal genomes: a hitchhiker's guide to genomics

This thesis describes several genome-sequencing projects such as those from the fungi Laccaria bicolor S238N-H82, Glomus intraradices DAOM 197198, Melampsora laricis-populina 98AG31, Puccinia graminis, Pichia pastoris GS115 and Candida bombicola, as well as the one of the haptophyte Emiliania huxleyi CCMP1516. These species are important organisms in many aspects, for instance: L. bicolor and G. intraradices are symbiotic fungi growing associate with trees and present an important ecological niches for promoting tree growth; M. laricis- populina and P. graminis are two devastating fungi threating plants; the tiny yeast P. pastoris is the major protein production platform in the pharmaceutical industry; the biosurfactant production yeast C. bombicola is likely to provide a low ecotoxicity detergent and E. huxleyi places in a unique phylogeny position of chromalveolate and contributes to the global carbon cycle system. The completion of the genome sequence and the subsequent functional studies broaden our understanding of these complex biological systems and promote the species as possible model organisms. However, it is commonly observed that the genome sequencing projects are launched with lots of enthusiasm but often frustratingly difficult to finish. Part of the reason are the ever-increasing expectations regarding quality delivery (both with respect to data and analyses). The Introductory Chapter aims to provide an overview of how best to conduct a genome sequencing project. It explains the importance of understanding the basic biology and genetics of the target organism. It also discusses the latest developments in new (next) generation high throughput sequencing (HTS) technologies, how to handle the data and their applications. The emergence of the new HTS technologies brings the whole biology research into a new frontier. For instance, with the help of the new sequencing technologies, we were able to sequence the genome of our interest, namely Pichia pastoris. This tiny yeast, the analysis of which forms the bulk of this thesis, is an important heterologous production platform because its methanol assimilation properties makes it ideally suitable for large scale industrial production. The unique protein assembly pathway of P. pastoris also attracts much basic research interests. We used the new HTS method to sequence and assemble the GS115 genome into four chromosomes and made it publicly available to the research community (Chapter 2 and Chapter 3). The public release of the GS115 brought broader interests on the comparison of GS115 and its parental strains. By sequencing the parental strain of GS115 with different new sequencing platforms, we identified several point mutations in the coding genes that likely contribute to the higher protein translocation efficiency in GS115. The sequence divergence and copy number variation of rDNA between strains also explains the difference of protein production efficiency (Chapter 4). Before 2008, the Sanger sequencing method was the only technology to obtain high quality complete genomes of eukaryotes. Because of the high cost of the Sanger method, regarding the other genome projects discussed in this thesis, it was necessary to team up with many other partners and to rely on the U.S. Department of Energy Joint Genome Institute (DOE-JGI) and the Broad Institute to generate the genome sequence. The M. larici-populina srain 98AG31 and the Puccinia graminis f. sp. tritici strain CRL 75-36-700-3 are two devastating basidiomycete ‘rusts’ that infect poplar and wheat. Lineage-specific gene family expansions in these two rusts highlight the possible role in their obligate biotrophic life-style. Two large sets of effector-like small-secreted proteins with different pri- mary sequence structures were identified in each organism. The in planta-induced transcriptomic data showed upregulation of these lineage-specific genes and they are likely involved in the establishing of the rust-host interaction. An additional immunolocalization study on M. larici-populina confirmed the accumulation of some candidate effectors in the haustoria and infection hyphae, which is described in Chapter 5

Aeronautical engineering: A continuing bibliography with indexes (supplement 231)

This bibliography lists 469 reports, articles, and other documents introduced into the NASA scientific and technical information system in September, 1988

Efficient Passive Clustering and Gateways selection MANETs

Passive clustering does not employ control packets to collect topological information in ad hoc networks. In our proposal, we avoid making frequent changes in cluster architecture due to repeated election and re-election of cluster heads and gateways. Our primary objective has been to make Passive Clustering more practical by employing optimal number of gateways and reduce the number of rebroadcast packets