Professional interests

• Scientific Computing
  • multiscale processes
    • PDEs/RDMEs
      time integration, integrals, adaptive grid methods, delay equations,
      deterministic/continuum vs. stochastic/particle-based approach, ...
    • applied probability theory / queuing theory
      renewal, numerics
    Projects:
    • NWO Wiskunde Toegepast 2004-2008: Mesoscale simulation paradigms in the Silicon Cell
      collaboration with Jaap Kaandorp (UvA/SCS)
      Yousaf Habib PhD, Apr 2004 - Jul 2005
      Luca Ferracina PD, Nov 2005 - Oct 2007
    • NWO CLS 2004-2008: Mathematics and Computation for the System Biology of Cells
      collaboration with Mark Peletier (TUe/CASA), Jaap Kaandorp (UvA/SCS), Jan van Schuppen (CWI/MAS, VU/FEW), and Hans Westerhoff (VU/FALW, MCISB/Manchester)
      Maciej Dobrzyński, PhD, Aug 2004 - Jan 2009
      PhD 2011: Molecules in Motion: a theoretical study of noise in gene expression and cell signaling
    • CWI: Coarse-grained stochastic methods for network motifs in cell biology
      collaboration with Michel Mandjes(UvA/KdV) and Frank Bruggeman(NISB)
      Halldóra Þórsdóttir, PhD, Nov 2011 - Oct 2014,
      and until Oct 2011 Ton Hellings.
  • optimal experimental designHalldóra Þórsdóttir
    parameter estimation (global/local search), parameter identifiability, parameter reduction, model discrimination, experimental design
    Projects:
    • NWO CLS 2004-2008: Mathematics and Computation for the System Biology of Cells
      collaboration with Jaap Kaandorp (UvA/SCS)
      Maksat Ashyraliyev, PhD, Sep 2004 - Aug 2008
      PhD Oct 2009: Modelling, Simulation, and Inferring Regulatory Networks
    • Jan Stolze, MSc TUD, Sep 2007-May 2008
      MSc May 2008: Parameter Identification in System Biology
• Computational Biology
  systems biology of cells, modelling bodyplan formation, continuum modelling of biological membranes, ...
• [old] Fortran 95 / HPF, vectorization and parallelization
  Supercomputers, massively parallel computers, heterogeneous networks

Projects

• Scientific Computing for Systems Biology .

Recent papers

• Markov-modulated infinite-server queues: approximations by time-scaling,
  Ton Hellings, Michel Mandjes and Joke Blom
  CWI Report MAC-1101
• Traffic generated by a semi-Markov additive process,
  Joke Blom and Michel Mandjes
  Probability in the Engineering and Informational Sciences, 25.1 (2011)
  Revised version of CWI Report PNA-E0913
• Gene Circuit Analysis of the Terminal Gap Gene huckebein,
  Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam, Johannes Jaeger
  PLOS Computational Biology, doi/10.1371/journal.pcbi.1000548 (October 2009)
• Systems biology: parameter estimation for biochemical models,
  Maksat Ashyraliyev, Yves Fomekong-Nanfack, Jaap A. Kaandorp, Joke G. Blom
  FEBS Journal, 276:886-902 (2009)
• On Parameter Estimation and Determinability for Drosophila Gap Gene Circuits,
  Maksat Ashyraliyev, Johannes Jaeger and Joke G. Blom
  BMC Systems Biology, 2:83 (2008)
• Modelling genetic regulation of growth and form in a branching sponge,
  Jaap A. Kaandorp, Joke G. Blom, Jozef Verhoef, Max Filatov, M. Postma and Werner E.G. Mueller
  Proceedings of the Royal Society B, 275:1651:2569-2575 (2008)
• On parameter estimation and determinability for the model of pattern formation in Drosophila melanogaster,
  M. Ashyraliyev, J.G. Blom
  CWI Report MAS-E0802
• On the Numerical Solution of Diffusion-Reaction Equations with Singular Source Terms,
  M. Ashyraliyev, J.G. Blom, J.G. Verwer,
  J. Comp. Appl. Math, 216:1:20-38 (2008).
  Extended version of CWI Report MAS-E0512
• Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster,
  Yves Fomekong-Nanfack, Jaap Kaandorp, and Joke Blom
  Bioinformatics, 23:24:3356--3363 (2007).
• Computational methods for diffusion-influenced biochemical reactions,
  Maciej Dobrzyński, Jordi Vidal Rodríguez, Jaap A. Kaandorp, and Joke G. Blom
  Bioinformatics, 23:15:1969--1977 (2007).
• Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli,
  Jordi Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzyński, and Joke G. Blom
  Bioinformatics, 22:15:1895--1901 (2006).

List of publications

Old stuff

• Atmospheric Flow and Transport Problems
  on space discretization and time integration methods for the Shallow Water equations on the sphere (more info). Application: atmospheric hydrodynamics (weather and climate). Joint activity with the GMD. (terminated 2002).
• LOTOS and HPCN.
  Numerical and HPCN aspects of a 3D Air Quality Model. (terminated 2000).
• LUGR: Adaptive-grid methods for time-dependent PDEs in 2D and 3D.
  Numerical simulation of brine flow for predicting the potential transport of radioactive pollutants. (terminated 1994).
• Moving Finite Element method for systems of (time-dependent) PDEs in 1D and 2D: (terminated 1992).
• Adaptive Moving Grid Solver for systems of (time-dependent) PDEs in 1D: (terminated 1992).
• Volterra Integral Equations of the second kind. (terminated 1986).

Software

• Adaptive Grid Solvers for systems of (time-dependent) PDEs:
  • in 2D: VLUGR2 (Vectorized Local Uniform Grid Refinement).
    (also in NAG library: D03RAF, D03RBF)
  • in 3D: VLUGR3.
• Adaptive Moving Grid Solver for systems of (time-dependent) PDEs in 1D: MOVGRD.
• Collocation Methods for Nonlinear Volterra Integral Equations of the Second Kind: COLVI2.