Localization for Anchoritic Sensor Networks

We introduce a class of anchoritic sensor networks, where communications between sensor nodes is undesirable or infeasible, e.g., due to harsh environment, energy constraints, or security considerations

Unsolved Problems in Virtual Knot Theory and Combinatorial Knot Theory

This paper is a concise introduction to virtual knot theory, coupled with a list of research problems in this field.Comment: 65 pages, 24 figures. arXiv admin note: text overlap with arXiv:math/040542

Simplified Distributed Programming with Micro Objects

Developing large-scale distributed applications can be a daunting task. object-based environments have attempted to alleviate problems by providing distributed objects that look like local objects. We advocate that this approach has actually only made matters worse, as the developer needs to be aware of many intricate internal details in order to adequately handle partial failures. The result is an increase of application complexity. We present an alternative in which distribution transparency is lessened in favor of clearer semantics. In particular, we argue that a developer should always be offered the unambiguous semantics of local objects, and that distribution comes from copying those objects to where they are needed. We claim that it is often sufficient to provide only small, immutable objects, along with facilities to group objects into clusters.Comment: In Proceedings FOCLASA 2010, arXiv:1007.499

Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009