FURY: Fuzzy unification and resolution based on edit distance

We present a theoretically founded framework for fuzzy unification and resolution based on edit distance over trees. Our framework extends classical unification and resolution conservatively. We prove important properties of the framework and develop the FURY system, which implements the framework efficiently using dynamic programming. We evaluate the framework and system on a large problem in the bioinformatics domain, that of detecting typographical errors in an enzyme name databas

Timetabling in constraint logic programming

In this paper we describe the timetabling problem and its solvability in a Constraint Logic Programming Language. A solution to the problem has been developed and implemented in ECLiPSe, since it deals with finite domains, it has well-defined interfaces between basic building blocks and supports good debugging facilities. The implemented timetable was based on the existing, currently used, timetables at the School of Informatics at out university. It integrates constraints concerning room and period availability

A novel method for comparing topological models of protein structures enhanced with ligand information

This article is available open access through the publisher’s website through the link below. Copyright @ 2008 The Authors.We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model, we consider loops as secondary structure elements (SSEs) as well as helices and strands; in addition we represent ligands as first class objects. Interactions between SSEs and between SSEs and ligands are described by incoming/outgoing arcs and ligand arcs, respectively; and SSEs are annotated with arc interaction direction and type. We are able to abstract away from the ligands themselves, to give a model characterized by a regular grammar rather than the context sensitive grammar of the original TOPS model. Our TOPS+ strings model is sufficiently descriptive to obtain biologically meaningful results and has the advantage of permitting fast string-based structure matching and comparison as well as avoiding issues of Non-deterministic Polynomial time (NP)-completeness associated with graph problems. Our structure comparison method is computationally more efficient in identifying distantly related proteins than BLAST, CLUSTALW, SSAP and TOPS because of the compact and abstract string-based representation of protein structure which records both topological and biochemical information including the functionally important loop regions of the protein structures. The accuracy of our comparison method is comparable with that of TOPS. Also, we have demonstrated that our TOPS+ strings method out-performs the TOPS method for the ligand-dependent protein structures and provides biologically meaningful results. Availability: The TOPS+ strings comparison server is available from http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/topsplus.html.University of Glasgo

Effects of Fermion Flavor on Exciton Condensation in Double Layer Systems

We use fermionic path integral quantum Monte Carlo to study the effects of fermion flavor on the physical properties of dipolar exciton condensates in double layer systems. We find that by including spin in the system weakens the effective interlayer interaction strength, yet this has very little effect on the Kosterlitz-Thouless transition temperature. We further find that, to obtain the correct description of screening, it is necessary to account for correlation in both the interlayer and intralayer interactions. We show that while the excitonic binding cannot completely surpress screening by additional fermion flavors, their screening effectiveness is reduced leading to a much higher transition temperatures than predicted with large-N analysis.Comment: 4 pages, 3 figure

Design of wideband vibration-based electromagnetic generator by means of dual-resonator

This paper describes the design of a wideband electromagnetic energy harvester that utilizes a novel dual-resonator method to improve the operational frequency range of the vibration-based generator. The device consists of two separate resonator systems (coil and magnet), which each comply with their respective resonance frequencies. This is because both resonators are designed in such a way that both magnet and coil components will oscillate at an additive phase angle, and hence create greater relative motion between the two dominating resonance frequencies, which realizes the wideband generator. Each resonator system consists of a distinctive cantilever beam, one attached with four magnets and steel keepers, the other attached with a copper coil and stainless steel holder as the free end mass. Both cantilevers are clamped and fitted to a common base that is subjected to a vibration source. Basic analytical models are derived and a numerical model is implemented in MATLAB-Simulink. Electromagnetic, structural modal and static mechanical analysis for the design of the prototype are completed using ANSYS finite element tools. For a 0.8 m s−2 acceleration, the open-loop voltage obtained from the experiment shows a good correlation with those from the simulation. Peak induced voltage is measured to be 259.5Vrms as compared to 240.9Vrms from the simulator at 21.3 Hz, which implies an error range of 7.7%. The results also indicate that there is a maximum of 58.22% improvement in the induced voltage within the intermediate region which occurs at the intersection point between the output response plots of two single resonator generators