Publications by authors named "Pedro Gonnet"

Background: Dynamic mathematical models in the form of systems of ordinary differential equations (ODEs) play an important role in systems biology. For any sufficiently complex model, the speed and accuracy of solving the ODEs by numerical integration is critical. This applies especially to systems identification problems where the parameter sensitivities must be integrated alongside the system variables.

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Verlet lists, which are commonly used in many particle-based simulations, are not suited for modern, shared-memory parallel multicore architectures. In this article, we introduce pairwise Verlet lists: local Verlet lists containing only interacting particle pairs between a pair of neighboring computational cells. We show that these pairwise Verlet lists are more efficient and scale much better than the traditional global Verlet list, both on a single processor as well as on multiple shared-memory cores.

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The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA.

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Cell lists are ubiquitous in molecular dynamics simulations--be it for the direct computation of short-range inter-atomic potentials, the short-range direct part of a long-range interaction or for the periodic construction of Verlet lists. The conventional approach to computing pairwise interactions using cell lists leads to a large number of unnecessary interparticle distance calculations. In this paper, an algorithm is presented which reduces the number of spurious distance calculations by first sorting the particles along the cell pair axis and then only interacting two particles if their distance along the axis is smaller than the cutoff distance of the interaction.

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We conduct molecular dynamics simulations to study the effect of the curvature induced static dipole moment of small open-ended single-walled carbon nanotubes (CNTs) immersed in water. This dipole moment generates a nonuniform electric field, changing the energy landscape in the CNT and altering the water conduction process. The CNT remains practically filled with water at all times, whereas intermittent filling is observed when the dipole term is not included.

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A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each other and to ensure a stable definition of a consistent set of lipoproteins.

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Motivation: Motif detection is an important component of the classification and annotation of protein sequences. A method for aligning motifs with an amino acid sequence is introduced. The motifs can be described by the secondary (i.

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