Dr Pedro Gonnet
(email at email@example.com)
Pedro Gonnet is a Lecturer in Computer Science in the School of Engineering and Computing Sciences at Durham University. He recieved a Diploma from the Department of Computer Science at the ETH Zürich in 2003 and later a PhD in Computer Science, under the supervision of Prof. Walter Gander, in 2009.
Following his PhD, he worked as a Post-Doctoral researcher in the group of Prof. Jörg Stelling at the ETH Zürich before moving to Oxford University, to work with Prof. L. N. Trefethen as a member of the Chebfun development team with funding from the Swiss National Science Foundation.
My research, in a nutshell, focuses on new algorithms for scientific computing on massively parallel shared-memory architectures.
In the past few years, we have witnessed an important paradigm shift in computer architecture: Although Moore's Law is still in effect, instead of getting faster, computers are getting more parallel. Most methods and algorithms in the computational sciences, however, were designed for single-processor machines or clusters thereof and do not readily lend themselves for shared-memory multi/many-core parallelization, SIMD-vectorization or GPU computing. In order to exploit this new paradigm, algorithms and methods designed specifically for these new architectures are urgently needed.
- mdcore: A platform-independent, Open-Source library for Molecular Dynamics simulations on shared-memory and GPU architectures.
- odeSD: Second-Derivative ODE Integrator with parameter sensitivity analysis.
- quadcc: Robust, doubly-adaptive quadrature routine using Clenshaw-Curtis rules with an improved error estimate.
- Chebfun: I am a member of the Chebfun Developer Team.
School of Engineering and Computing Sciences
- Innovative Computing Research Group
Department of Computer Science
- Innovative Computing
- Algorithms for Systems Biology
- GPU Computing
- High-Performance Computing
- Hybrid Shared/Distributed-Memory Parallelism
- Numerical Algorithms for Interpolation and Approximation
- Particle-Based Simulations
- Friberg, Markus T., Gonnet, Pedro, Barral, Yves, Schraudolph, Nicol N. & Gonnet, Gaston H. (2006). Measures of codon bias in yeast, the tRNA Pairing Index and possible DNA repair mechanisms. In Algorithms in Bioinformatics. Bucher, P & Moret, BME 4175: 1.
- Gonnet, Pedro (2010), Efficient Algorithms for Molecular Dynamics Simulations on the Cell Broadband Engine Architecture, in Psihoyios, G & Tsitouras, C eds, 1281: NUMERICAL ANALYSIS AND APPLIED MATHEMATICS. Rhodes, Greece, AIP, 1305.
Journal papers: academic
- Gonnet, P. (2013). Pseudo-Verlet lists: a new, compact neighbour list representation. Molecular Simulation 1.
- Gonnet, Pedro (2012). A Review of Error Estimation in Adaptive Quadrature. ACM Computing Surveys 44(4): 1.
- Gonnet, P. (2012). A short note on the fast evaluation of dihedral angle potentials and their derivatives. Journal of Computational Physics 231(7): 2691.
- Gonnet, P., Dimopoulos, S., Widmer, L. & Stelling, J. (2012). A Specialized ODE Integrator for Efficient Computation of Parameter Sensitivities. BMC Systems Biology 6: 46.
- Pachón, R., Gonnet, P. & van Deun, J. (2012). Fast and Stable Rational Interpolation in Roots of Unity and Chebyshev Points. SIAM Journal on Numerical Analysis 50(3): 1713-1734.
- Gonnet, Pedro (2012). Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism. Journal of Computational Chemistry 33(1): 76-81.
- Gonnet, Pedro, Güttel, Stefan & Trefethen, Lloyd N (2012). Robust Padé approximation via SVD. SIAM Review 55(1): 101-117.
- Webb, Marcus, Trefethen, Lloyd N. & Gonnet, Pedro (2012). Stability of Barycentric Interpolation Formulas for Extrapolation. SIAM Journal on Scientific Computing 34(6): A3009-A3015.
- Gonnet, P., Pachón, R. & Trefethen, L.N. (2011). Robust Rational Interpolation and Least-Squares. Electronic Transactions on Numerical Analysis 38: 146-167.
- Cannarrozzi, Gina, Schraudolph, Nicol N., Faty, Mahamadou, von Rohr, Peter, Friberg, Markus T., Roth, Alexander C., Gonnet, Pedro, Gonnet, Gaston & Barral, Yves (2010). A Role for Codon Order in Translation Dynamics. Cell 141(2): 355-367.
- Gonnet, Pedro (2010). Increasing the Reliability of Adaptive Quadrature Using Explicit Interpolants. ACM Transactions on Mathematical Software 37(3): 26.
- Gonnet, P. (2010). Using piecewise polynomials for faster potential function evaluation. Journal of Computational Physics 229(2): 313.
- Gonnet, P., Walther, J.H. & Koumoutsakos, P. (2009). theta-SHAKE: An extension to SHAKE for the explicit treatment of angular constraints. Computer Physics Communications 180(3): 360.
- Gonnet, Pedro (2007). P-SHAKE: A quadratically convergent SHAKE in O(n(2). Journal of Computational Physics 220(2): 740.
- Gonnet, Pedro (2006). A simple algorithm to accelerate the computation of non-bonded interactions in cell-based molecular dynamics simulations. Journal of Computational Chemistry 28(2): 570.
- Zimmerli, Urs, Gonnet, Pedro, Walther, Jens & Koumoutsakos, Petros (2005). Curvature induced L-defects in water conduction in carbon nanotubes. Nano Letters 5(6): 1017.
- Gonnet, P., Rudd, KE. & Lisacek, F. (2004). Fine-tuning the prediction of sequences cleaved by signal peptidase II: A curated set of proven and predicted lipoproteins of Escherichia coli K-12. PROTEOMICS 4(6): 1597.
- Lisacek, F, Chichester, C, Gonnet, P, Jaillet, O, Kappus, S, Nikitin, F, Roland, P, Rossier, G, Truong, L & Appel, R (2004). Shaping biological knowledge: applications in proteomics. Comparative and Functional Genomics 5(2): 190.
- Jaffe, Richard L., Gonnet, Pedro, Werder, Thomas, Walther, Jens H. & Koumoutsakos, Petros (2004). Water-carbon interactions - 2: Calibration of potentials using contact angle data for different interaction models. Molecular Simulation 30(4): 205.
- Walther, JH., Werder, T., Jaffe, RL., Gonnet, P., Bergdorf, M., Zimmerli, U. & Koumoutsakos, P. (2004). Water-carbon interactions III: The influence of surface and fluid impurities. Physical Chemistry Chemical Physics 6(8): 1988.
- Gonnet, P. & Lisacek, F. (2002). Probabilistic alignment of motifs with sequences. Bioinformatics 18(8): 1091.