Joke Blom
contact information
Currently I am working within the CWI
Life Sciences group on
and participating in the NISB,
the Netherlands Institute for Systems Biology.
Professional interests
 Scientific Computing
 multiscale processes
 PDEs/RDMEs
time integration, integrals, adaptive grid methods, delay equations,
deterministic/continuum vs. stochastic/particlebased approach, ...
 applied probability theory / queuing theory
renewal, numerics
Projects:
 CWI: Coarsegrained stochastic methods for network motifs in cell biology
collaboration with
Michel Mandjes(UvA/KdV) and
Frank Bruggeman(NISB)
Halldóra Þórsdóttir, PhD, Nov 2011  Feb 2016,
and until Oct 2011 Ton Hellings.
 NWO CLS 20042008: 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
 NWO Wiskunde Toegepast 20042008: 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

uncertainty quantification
Project:
 EUFP7 BioPreDyn: From Data to Models. New Bioinformatics Methods and Tools for DataDriven, Predictive Dynamic Modelling in Biotechnological Applications
Aldemar Torres Valderrama, postdoc, Apr 2012  Sep 2014
Maria Navarro, postdoc, Aug 2012  Dec 2014

parameter estimation (global/local search), parameter identifiability, parameter reduction, model discrimination, experimental design
Projects:
 NWO CLS 20042008: 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 2007May 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

Refined large deviations asymptotics for Markovmodulated infiniteserver systems
Joke Blom, Koen de Turck, Michel Mandjes
European Journal of Operational Research 259:10361044 (2017).
arXiv:1608.04250 [math.PR].

Functional central limit theorems for Markovmodulated infiniteserver systems
Joke Blom, Koen de Turck, Michel Mandjes
Mathematical Methods of Operations Research 83:351372 (2016).
arXiv:1601.02791 [math.PR].

A functional central limit theorem for a Markovmodulated infiniteserver queue
D. Anderson, J. Blom, M. Mandjes, H. Thorsdottir, K. de Turck
Methodology and Computing in Applied Probability18.1, pp 153168 (2016).
CWI Report
LS1303,
arXiv:1309.3962.

A global sensitivity analysis approach for morphogenesis models
Sonja E.M. Boas, Maria I. Navarro Jimenez, Roeland M.H. Merks, and Joke G. Blom
BMC Systems Biology, 9:85 (2015)
arXiv:1507.08504 [qbio.CB] (2015)

Stochastic collocation for correlated inputs
Maria Navarro, Jeroen Witteveen, and Joke Blom
UNCECOMP 2015, Eds. M. Papadrakakis, V. Papadopoulos, G. Stefanou, Crete, Greece (2015)

Analysis of Markovmodulated infiniteserver queues in the centrallimit regime
J. Blom, K. de Turck, M. Mandjes
Probability in the Engineering and Informational Sciences,
29:3, pp 433  459 (2015)
Revised version of
arXiv:1402.5290, (February 2014).

Uncertainty propagation in nerve impulses through the action potential mechanism
A. Torres Valderrama, J. Witteveen, M. Navarro, J. Blom
Journal of Mathematical Neuroscience, 5:3 (2015)

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experimentbased mathematical model
Katja N. Rybakova, Aleksandra Tomaszewska, Simon van Mourik, Joke Blom, Hans V. Westerhoff, Carsten Carlberg, Frank J. Bruggeman
Nucleic Acids Research 43 (1):153161 (2015)
doi: 10.1093/nar/gku1272.
First published online: December 3, 2014

Tail asymptotics of a Markovmodulated infiniteserver queue
J. Blom, K. de Turck, O. Kella, M. Mandjes
Queueing Systems, 78.4, pp 337357 (2014)
Revised version of CWI Report
LS1307.

Markovmodulated infiniteserver queues with general service times
Joke Blom, Offer Kella, Michel Mandjes, and Halldóra Þórsdóttir
Queueing Systems, 76.4, pp 403424 (2014)
Revised version of CWI Report
LS1305
Old stuff
Projects I have worked on previously:

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:
Adaptivegrid methods for timedependent 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 (timedependent) PDEs in 1D and 2D:
(terminated 1992).

Adaptive Moving Grid Solver for systems of (timedependent) PDEs in 1D:
(terminated 1992).

Volterra Integral Equations of the second kind.
(terminated 1986).
Software
 Global Sensitivity Analysis using Polynomial Chaos Expansion.
Published in article
"A global sensitivity analysis approach for morphogenesis models",
BMC Systems Biology, 9:85 (2015).
 Adaptive Grid Solvers for systems of (timedependent) PDEs:
 in 2D:
VLUGR2 (Vectorized Local Uniform Grid Refinement).
Published as
"Algorithm 758: VLUGR2: A Vectorizable Adaptive Grid Solver for PDEs in 2D",
ACM Trans. Math. Softw., Vol. 22, pp. 302328 (1996).
(also in NAG library: D03RAF, D03RBF)
 in 3D:
VLUGR3.
Published as
"Algorithm 759: VLUGR3: A Vectorizable Adaptive Grid Solver for PDEs in 3D.
II. Code Description",
ACM Trans. Math. Softw., Vol. 22, pp. 329347 (1996).
 Adaptive Moving Grid Solver for systems of (timedependent) PDEs in 1D:
MOVGRD.
Published as
"Algorithm 731: A MovingGrid Interface for Systems of OneDimensional TimeDependent Partial Differential Equations",
ACM Trans. Math. Softw., Vol. 20, No. 2, (1994), pp. 194214.
 Collocation Methods for Nonlinear Volterra Integral Equations of the
Second Kind:
COLVI2.
Published as
"Algorithm 689, Discretized collocation and iterated collocation for nonlinear
Volterra integral equations of the second kind",
ACM Trans. Math. Softw., V17, #2, pp. 167177 (1991).
Mandatory CWI disclaimer
En toch wordt Feyenoord kampioen ...
Joke Blom
(gollum@cwi.nl)
Last modified 10/14/2012