Pedro Gonnet

Learn More
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. The effect is(More)
The aim of the present study was to assess the stimulating effects of bright light (BL) on subjective and objective alertness. Eight subjects were exposed to either bright light or dim light (DL) during a 24-h constant routine (0900-0900). Bright light failed to modify either the 24-h course or the level of body temperature. Compared to DL, BL delayed the(More)
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(More)
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(More)
Protein translation is a rapid and accurate process, which has been optimized by evolution. Recently, it has been shown that tRNA reusage influences translation speed. We present the tRNA Pairing Index (TPI), a novel index to measure the degree of tRNA reusage in any gene. We describe two variants of the index, how to combine various such indices to a(More)
A new method for interpolation by rational functions of prescribed numerator and denominator degrees is presented. When the interpolation nodes are roots of unity or Chebyshev points, the algorithm is particularly simple and relies on discrete Fourier transform matrices, which results in a fast implementation using the Fast Fourier Transform. The method is(More)
The most critical component of any adaptive numerical quadrature routine is the estimation of the integration error. Since the publication of the first algorithms in the 1960s, many error estimation schemes have been presented, evaluated, and discussed. This article presents a review of existing error estimation techniques and discusses their differences(More)
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(More)