135,401 research outputs found
A layered framework for pattern-based ontology evolution
The challenge of ontology-driven modelling of information
components is well known in both academia and industry. In this paper, we present a novel approach to deal with customisation and abstraction of ontology-based model evolution. As a result of an empirical study, we identify a layered change operator framework based on the granularity,
domain-specificity and abstraction of changes. The implementation of the operator framework is supported through layered change logs. Layered change logs capture the objective of ontology changes at a higher level of granularity and support a comprehensive understanding of ontology evolution. The layered change logs are formalised using a graph-based approach. We identify the recurrent ontology change patterns from an ontology change log for their reuse. The identified patterns facilitate optimizing and improving the definition of domain-specific change patterns
Towards Understanding the Origin of Genetic Languages
Molecular biology is a nanotechnology that works--it has worked for billions
of years and in an amazing variety of circumstances. At its core is a system
for acquiring, processing and communicating information that is universal, from
viruses and bacteria to human beings. Advances in genetics and experience in
designing computers have taken us to a stage where we can understand the
optimisation principles at the root of this system, from the availability of
basic building blocks to the execution of tasks. The languages of DNA and
proteins are argued to be the optimal solutions to the information processing
tasks they carry out. The analysis also suggests simpler predecessors to these
languages, and provides fascinating clues about their origin. Obviously, a
comprehensive unraveling of the puzzle of life would have a lot to say about
what we may design or convert ourselves into.Comment: (v1) 33 pages, contributed chapter to "Quantum Aspects of Life",
edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some
editin
The Triplet Genetic Code had a Doublet Predecessor
Information theoretic analysis of genetic languages indicates that the
naturally occurring 20 amino acids and the triplet genetic code arose by
duplication of 10 amino acids of class-II and a doublet genetic code having
codons NNY and anticodons . Evidence for this scenario
is presented based on the properties of aminoacyl-tRNA synthetases, amino acids
and nucleotide bases.Comment: 10 pages (v2) Expanded to include additional features, including
likely relation to the operational code of the tRNA-acceptor stem. Version to
be published in Journal of Theoretical Biolog
Mapping Atomic Motions with Electrons: Toward the Quantum Limit to Imaging Chemistry
Recent advances in ultrafast electron and X-ray diffraction have pushed imaging of structural dynamics into the femtosecond time domain, that is, the fundamental time scale of atomic motion. New physics can be reached beyond the scope of traditional diffraction or reciprocal space imaging. By exploiting the high time resolution, it has been possible to directly observe the collapse of nearly innumerable possible nuclear motions to a few key reaction modes that direct chemistry. It is this reduction in dimensionality in the transition state region that makes chemistry a transferable concept, with the same class of reactions being applicable to synthetic strategies to nearly arbitrary levels of complexity. The ability to image the underlying key reaction modes has been achieved with resolution to relative changes in atomic positions to better than 0.01 Å, that is, comparable to thermal motions. We have effectively reached the fundamental space-time limit with respect to the reaction energetics and imaging the acting forces. In the process of ensemble measured structural changes, we have missed the quantum aspects of chemistry. This perspective reviews the current state of the art in imaging chemistry in action and poses the challenge to access quantum information on the dynamics. There is the possibility with the present ultrabright electron and X-ray sources, at least in principle, to do tomographic reconstruction of quantum states in the form of a Wigner function and density matrix for the vibrational, rotational, and electronic degrees of freedom. Accessing this quantum information constitutes the ultimate demand on the spatial and temporal resolution of reciprocal space imaging of chemistry. Given the much shorter wavelength and corresponding intrinsically higher spatial resolution of current electron sources over X-rays, this Perspective will focus on electrons to provide an overview of the challenge on both the theory and the experimental fronts to extract the quantum aspects of molecular dynamics
ISO spectroscopy of gas and dust: from molecular clouds to protoplanetary disks
Observations of interstellar gas-phase and solid-state species in the 2.4-200
micron range obtained with the spectrometers on board the Infrared Space
Observatory are reviewed. Lines and bands due to ices, polycyclic aromatic
hydrocarbons, silicates and gas-phase atoms and molecules (in particular H2,
CO, H2O, OH and CO2) are summarized and their diagnostic capabilities
illustrated. The results are discussed in the context of the physical and
chemical evolution of star-forming regions, including photon-dominated regions,
shocks, protostellar envelopes and disks around young stars.Comment: 56 pages, 17 figures. To appear in Ann. Rev. Astron. Astrophys. 2004.
Higher resolution version posted at
http://www.strw.leidenuniv.nl/~ewine/araa04.pd
Knowledge-Intensive Processes: Characteristics, Requirements and Analysis of Contemporary Approaches
Engineering of knowledge-intensive processes (KiPs) is far from being mastered, since they are genuinely knowledge- and data-centric, and require substantial flexibility, at both design- and run-time. In this work, starting from a scientific literature analysis in the area of KiPs and from three real-world domains and application scenarios, we provide a precise characterization of KiPs. Furthermore, we devise some general requirements related to KiPs management and execution. Such requirements contribute to the definition of an evaluation framework to assess current system support for KiPs. To this end, we present a critical analysis on a number of existing process-oriented approaches by discussing their efficacy against the requirements
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