108 research outputs found

    Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis

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    The calculation of the 3D structure of a protein molecule is important because it is associated to its biological function. Nuclear Magnetic Resonance (NMR) experiments can provide distance information between atoms that are close enough in a given protein and the problem is how to use these distances to determine the protein structure. Using the chemistry of proteins and supposing all the distances are precise values, it is possible to define an atomic order v1, ⋅⋅⋅, vn, such that the distances related to the pairs are available, and solve the problem iteratively using a combinatorial method, called Branch-and-Prune (BP). However, due to uncertainty in NMR data, the distances associated with pairs may not be precise, which implies that there are many difficulties in applying the BP algorithm to this scenario. The use of standard interval arithmetic can be directly applied to the algorithm, but it is known that it generates overestimations. This paper proposes a new methodology to compute possible conformations on the presence of uncertainties arising from NMR distance measurements using a constraint interval analysis approach. Some numerical examples are presented.415/4164152CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPSem informaçãoSem informaçã

    Sensitivity of selection procedures for priority conservation areas to survey extent, survey intensity and taxonomic knowledge

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    Many procedures exist for identifying sets of sites that collectively represent regional biodiversity. Whereas the mechanics and suitability of these procedures have received considerable attention, little effort has been directed towards assessing and quantifying the effects of varying data inputs on their outcomes. In the present paper, we use sensitivity analysis to evaluate the impacts of varying degrees of (i) survey intensity, (ii) survey extent and (iii) taxonomic diversity on iterative reserve selection procedures. A comprehensive distribution database of the mammalian fauna from the Transvaal region of South Africa is systematically perturbed before implementation of a site selection algorithm. The resulting networks of sites are then compared to quantitatively assess the impact of database variations on algorithm performance. Systematic data deletions result in increased network variability (identity of selected sites), decreased numbers of frequently selected sites, decreased spatial congruence among successive runs and a rapid increase in the number of additional sites required to represent all species present in the region. These effects become particularly evident once data sets are reduced to below 20% of the original data. Consequently, a mixed survey strategy that balances survey effort with survey extent and maximizes taxonomic knowledge is more likely to ensure appropriate planning outcomes

    Generalized interval vector spaces and interval optimization

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    This paper presents a method for endowing the generalized interval space with some different structures, such as vector spaces, order relations and an algebraic calculus. With these concepts we formulate interval optimization problems and relate them to classic multi-objective optimization problems. We also present a version of the Von Neumann's Mini-max Theorem in the interval context. (c) 2015 Elsevier Inc. All rights reserved.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq
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