Forschungszentrum Informationstechnik GmbH GMD

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  • Publication
    Folding stabilizes the evolution of catalysts
    ( 2004)
    Altmeyer, S.
    ;
    Füchslin, R.M.
    ;
    McCaskill, J.S.
    Sequence folding is known to determine the spatial structure and catalytic function of proteins and nucleic acids. We show here that folding also plays a key role in enhancing the evolutionary stability of the intermolecular recognition necessary for the prevalent mode of catalytic action in replication, namely, in trans, one molecule catalyzing the replication of another copy, rather than itself. This points to a novel aspect of why molecular life is structured as it is, in the context of life as it Could be: folding allows limited, structurally localized recognition to be strongly sensitive to global sequence changes, facilitating the evolution of cooperative interactions. RNA secondary structure folding, for example is shown to be able to stabilize the evolution of prolonged functional sequences, using only a part of this length extension for intermolecular recognition, beyond the limits of the (cooperative) error threshold. Such folding could facilitate the evolution of polymerases in spatially heterogeneous systems. This facilitation is, in fact, vital because physical limitations prevent complete sequence-dependent discrimination for any significant-size biopolymer substrate. The influence of partial sequence recognition between biopolymer catalysts and complex Substrates is investigated within a stochastic, spatially resolved evolutionary model of trans catalysis. We use an analytically tractable nonlinear master equation formulation called PRESS (McCaskill et at., Biol. Chem. 382: 1343-1363), which makes use of an extrapolation of the spatial dynamics clown from infinite dimensional space, and compare the results with Monte Carlo Simulations.
  • Publication
  • Publication
    Numerical methods for the three-dimensional two-body problem in the action-at-a-distance electrodynamics
    ( 2001)
    Nikitin, I.N.
    ;
    Luca, J. de
    We develop two numerical methods to solve the differential equations with deviating arguments for the motion of two charges in the action-at-a-distance electrodynamics. Our first method uses Sturmer's extrapolation formula and assumes that a step of integration can be taken as a step of light ladder, which limits its use to shallow energies. The second method is an improvement of pre-existing iterative schemes, designed for stronger convergence and can be used at high-energies.
  • Publication
    Optimal mutation rate using Bayesian priors for estimation of distribution algorithms
    ( 2001)
    Mahnig, T.
    ;
    Mühlenbein, H.
    UMDA(the univariate marginal distribution algorithm) was derived by analyzing the mathematical principles behind recombination. Mutation, however, was not considered. The same is true for the FDA (factorized distribution algorithm), an extension of the UMDA which can cover dependencies between variables. In this paper mutation is introduced into these algorithms by a technique called Bayesian prior. We derive theoretically an estimate how to choose the Bayesian prior. The recommended Bayesian prior turns out to be a good choice in a number of experiments. These experiments also indicate that mutation increases in many cases the performance of the algorithms and decreases the dependence on a good choice of the population size.
  • Publication
    Forget the past to win the future
    ( 2001)
    Tsichritzis, D.
  • Publication
    GMD-Schriften. Januar-Dezember 2001
    (GMD Forschungszentrum Informationstechnik, 2001)
  • Publication
    GMD-Schriften. Januar-Dezember 2000
    (GMD Forschungszentrum Informationstechnik, 2001)
  • Publication
    What terms does your metadata use? Application profiles as machine-understandable narratives
    ( 2001)
    Baker, T.
    ;
    Dekkers, M.
    ;
    Heery, R.
    ;
    Patel, M.
    ;
    Salokhe, G.
    The SCHEMAS Registry aims at providing a selected and annotated overview of metadata vocabularies and their use in application environments. Based on harvested metadata in RDF (Resource Description Framework), the registry allows users to explore links between "namespace schemas", which declare standard definitions of metadata terms, and "application profiles" ? RDF statements about the use or adaptation of namespace terms for particular domains, services, or projects. Where instance metadata does not follow standard namespaces or explicit data models, this style allows implementors to assert an explicit mapping to standard terms. Registering profiles can help harmonize metadata usage in particular domains and, in the longer term, could provide a machine-processable basis for automating crosswalks and conversions.
  • Publication
    Der Plankalkül
    (GMD, 2001)
    Zuse, K.