Curriculum Vitae. prof. dr Harm J. J. Jonker tel: (home), (work) web:

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1 November 2009 Curriculum Vitae prof. dr Harm J. J. Jonker tel: (home), (work) web: Personal details Date of birth July 23, 1963 Nationality Dutch Family status Married, three children Employment record and Education 2009-now: 2006-now: Antoni van Leeuwenhoek professor Affiliate scientist National Center for Atmospheric Research (CO, US) Leader Research Group Clouds, Climate and Air Quality, & Head of the Virtual Reality Laboratory Department of Multi-Scale Physics, Delft University of Technology : Associate professor, Department of Multi-Scale Physics, Delft University of Technology atmospheric boundary layers and clouds : Assistant professor, Section for Thermal and Fluids Sciences, Department of Multi-Scale Physics, Delft University of Technology turbulent heat- and mass-transfer in engineering flows, turbulence in atmospheric boundary layers, combustion : Postdoc, Royal Netherlands Meteorological Institute (KNMI) cloud topped atmospheric boundary layers : Postdoc, Institute for Marine and Atmospheric Research (IMAU), Utrecht University dry convective atmospheric boundary layers : Postdoc, Royal Netherlands Meteorological Institute (KNMI) wavelet analysis of satellite images : Research associate, Faculty of Physics and Astronomy, Utrecht University Physics Education : PhD, Faculty of Physics and Astronomy, Utrecht University statistical physics of brain inspired neuronal networks : Experimental Physics, Utrecht University (cum laude)

2 Organization, Committees, Panel member board member Delft Research Initiative Environment (new university wide activity) management team, dept. of Multi-Scale Physics, TU-Delft. head of the Virtual Reality Laboratory, TU Delft Boundary Layers and Turbulence Committee, American Meteorological Society, January exam committee BSc Applied Physics, TU Delft organizer (with dr J. Vila) Research school on the role of Atmospheric Boundary Layer processes in atmospheric chemistry, Castelldefels (Spain), November 2006 chairman and convenor special session Geophysics and Meteorology - Atmospheric Physics and Climate Change, Physica 2006, Leiden. Panel member recent contributions of nonlinear science in atmospheric research: from paradigm shifts to problem solving American Geophysical Union (AGU), Spring 2001 Meeting, Boston, USA Modelling of turbulent spray combustion, STW user committees, Applied Sciences, TU Delft, Air Film Cooling through Laser Drilled Nozzles, STW user committees, Mechanical Engineering, Eindhoven University, Unified computing methods for compressible and incompressible flows on staggered unstructured grids, STW user committees, Applied Mathematics, TU Delft, Lagrangian methods for simulation of turbulent reacting flows, STW user committees, Applied Sciences, TU Delft, Heat transfer from impinging jet arrays, STW user committees, Applied Sciences, TU Delft, PhD committees Thijs Heus, TU Delft, December 2008 Maarten van Reeuwijk, TU Delft, March 2007 Mohamed Hadziabdic, TU Delft, January 2006 Maria Antonia Jimenez, Universitat de les Illes Balears, Spain, December 2005 Alesandro Dosio, Wageningen University, May 2005 Luuk Thielen, TU Delft, December 2003 Kristof Stawiarsky, TU Delft, March 2003 Roel Neggers, Wageningen University, December 2002 Margreet van Zanten, Utrecht University, 2000

3 Invited lectures for conferences, seminars, workshops, research schools Symposium Climate modeling meets HPC experts, Amsterdam, September 2009 Using. HPC to find the growth-rate law of Atmospheric Boundary Layers Melbourne, Australia, August Second Integrated Land Ecosystem-Atmosphere Study (ileaps) Science Conference. The role of boundary layer clouds in transport and dispersion of trace gases. Paris, France, June Marie-Curie research network MODOBS, Research School on Climate scenarios, downscaling issues (dynamical and statistical) and model evaluation issues (boundary layer focussed). Two tutorial courses on DALES (Dutch Atmospheric Large Eddy Simulation model): clear boundary layer and cumulus topped boundary layer. Toulouse, France, May 2009 International Workshop The Afternoon Transition: boundary layer structure with decaying turbulence, Meteo-France. Laboratory experiments and DNS for the study of planetary boundary layer processes DEISA PRACE Symposium Amsterdam, May 2009 HPC Infrastructures for Petascale Applications PINNACLE: Pinning down the growth-rate law of Atmospheric Convective Boundary Layers Prague, March, CORE-Workshop Simulation and Modelling of Entrainment and Detrainment in Cumulus Clouds Imperial College, London February 2009 Entrainment in the Convective Boundary Layer: Laboratory experiments and numerical simulations University of Reading, dept. of Meteorology, February 2009 Conditional instability of mesoscale structures in convective boundary layers Uppsala, Sweden, January 2009 Clouds & Climate FOM, Veldhoven, January 2009 Multi-Scale Cloud Physics UCLA, Department of Atmospheric Sciences, Los Angeles, USA, January Towards a theory on the formation of mesoscale fluctuations by boundary layer convection National Center for Atmospheric Research, Advanced Study Program, seminar, Boulder (CO) USA, December Towards a theory on the formation of mesoscale fluctuations by boundary layer convection University of Oklahoma, School of Meteorology, USA, Nov 2008, New views on vertical transport by cumulus convection University of Wyoming, Department of Atmospheric Science, USA, Oct 2008, Mesoscale organization by boundary layer convection University of Utrecht, Institute for Marine and Atmospheric Research, Utrecht, July 2008, New views on vertical transport by cumulus convection Summerschool, Atmospheric Boundary Layers: Concepts, Observations, and Numerical Simulations Convective boundary layers June 2008, Les Houches, France Theme of the Year 2008, Geophysical Turbulence Phenomena. Workshop, National Center for Atmospheric Research. Observing the Turbulent Atmosphere: Sampling Strategies, Technology and Applications. Laboratory Experiments of the Convective Boundary Layer May 28-31, 2008, Boulder, USA Workshop, Netherlands Meteorological Institute, High Resolution NWP Modelling in the Netherlands, Visualization of Cumulus Clouds in a Virtual Environment, January 21, 2008, de Bilt, The Netherlands National symposium on Weather Phenomena. Clouds, Delft University, Nov 2007

4 Workshop, Wageningen University, On the relevance of surface and boundary layer processes for the exchanges of reactive- and greenhouse gases. Dynamics and reactivity in cloudy boundary layers 9-12 October, 2007, Wageningen, The Netherlands National Center for Atmospheric Research, Boulder, Colorado, June 2007 The importance of cloud edge for transport by shallow cumulus clouds. Workshop, Universitat Politecnica de Catalunya, Intermittency in the stable boundary layer Barcelona, March 2007, The Netherlands Workshop, Netherlands Meteorological Institute, Stochastic modelling of unresolved motions in atmosphere and ocean models. Spectral energy transfer: LES modeling results Amersfoort, March 2007, The Netherlands Research school, the role of Atmospheric Boundary Layer processes in Atmospheric Chemistry, Clouds in the atmospheric boundary layer, Castelldefels (Spain), November 2006 Nonlinear Dynamics of Natural Systems Workshop: Mathematics and Earth Science, Nov 2006, Groningen Challenges in modelling Cumulus cloud physics Workshop Leiden Lorentz Center: Environmental Dispersion Processes. Sep 2006 The dispersion characteristics in convective and cloud-topped atmospheric boundary layers Arizona State University (Phoenix), USA, Aug 2006 Laboratory experiments on entrainment in convective boundary layers National Center for Atmospheric Research, Boulder, Colorado, August 2006 The formation of mesoscale fluctuations by boundary layer convection Kronig-lecture Physics of Film: the Day after Tomorrow, April 2006 Delft University ECMWF Workshop on The representation of subgrid processes using stochastic-dynamic models, UK, June Spectral transfer of TKE and scalar variance in the meso- and micro-scale range: direction of the average flow and the significance of backscatter. International Conference on Micromixing in Turbulent Flows with Chemical Reaction (ICMM- 2004), May 14-17, 2004, Moscow, Russia Diffusion of chemical reacting species in a convective atmospheric boundary layer Climate Conference, Utrecht, August, 2001 Mesoscale perturbations by boundary layer convection. American Geophysical Union (AGU), Spring 2001 Meeting, Boston, USA Anomalous scaling of cumulus cloud boundaries. the Conference on Air Pollution Modeling and Simulation 2001 (APMS2001) April 9-13, 2001, Paris. Characteristic length-scales of chemical species in a convective boundary layer. Working visits and visitors dr W. Grabowski, National Center for Atmospheric Research, short visit scientist section Clouds, Climate and Air Quality, October 2009 dr W. Angevine, CIRES/NOAA, short visit scientist section Clouds, Climate and Air Quality, October 2009 prof. E. Fedorovich, University of Oklahoma, short visit Clouds, Climate and Air Quality, June 2009 dr W. Grabowski, National Center for Atmospheric Research, short visit scientist section Clouds, Climate and Air Quality, May 2009

5 H. Jonker, visiting scientist, National Center for Atmospheric Research, Boulder, Colorado, August January 2009 H. Jonker, short visit Department of Atmospheric Science, UCLA January 2009 dr P. Sullivan, short visit scientist section Clouds, Climate and Air Quality, December 2008 prof P. Austin, short visit scientist section Clouds, Climate and Air Quality, December 2008 H. Jonker, short visit University of Oklahoma, November 2008 prof. C. Bretherton, University of Washington, short visit Clouds, Climate and Air Quality, June 2008 S. Alfieri, Naples, Italy, visiting scientist section Clouds, Climate and Air Quality, April - June 2008 dr W. Grabowski, National Center for Atmospheric Research, visiting scientist section Clouds, Climate and Air Quality, November 2007 dr M.A. Jimenez, Universitat de les Illes Balears, Spain, visiting scientist section Clouds, Climate and Air Quality, Nov July 2009 M. Khalil, Nansen Environmental and Remote Sensing Center (NERSC), Norway, visiting scientist section Clouds, Climate and Air Quality Nov, 2007, prof. E. Fedorovich, University of Oklahoma, short visit Clouds, Climate and Air Quality, November 2007 H. Jonker, visiting scientist, National Center for Atmospheric Research, Boulder, Colorado, June 2007 dr. J. Hierro, Spain, visiting scientist section Clouds, Climate and Air Quality, Jan-April 2007 prof. L. Kantha, Univ. of Colorado at Boulder, USA, visiting scientist section Clouds, Climate and Air Quality, Oct 2006 H. Jonker, visiting scientist, National Center for Atmospheric Research, Boulder, Colorado, June-August 2006 H. Jonker, visiting scientist, Universitat de les Illes Balears, Spain, December 2005 M.A. Jimenez, Universitat de les Illes Balears, Spain, visiting scientist section Clouds, Climate and Air Quality, Sept-Nov 2005 M.A. Jimenez, Universitat de les Illes Balears, Spain, visiting scientist section Clouds, Climate and Air Quality, May-June 2005 H. Jonker, visiting scientist, Universitat de les Illes Balears, Spain, July 2004 H. Jonker, visiting scientist, Universitat Politecnica de Catalunya, Barcelona, May H. Jonker, visiting scientist, Department of Theoretical Physics, Oxford University, Outreach, Dutch popular media Reuters, Interview, April 2009 (yielded countless items on internet sites and newspapers (China Daily, Vancouver Sun, the Times, Tapei Times, etc) Determing the Growth-Rate Law of the Atmospheric Boundary Layer: One step closer to ensuring the accuracy of weather models DEISA-Newsletter, Vol. 4, 2009 TELEAC, Radio-5, kettingvraag, April 2009

6 Spelcomputer verricht serieus rekenwerk, Delta, February 2009 Lastpak in een ring van dalende lucht, Delta, December 2008 Mooiweerwolken belangrijk in klimaatmodellen, Technisch weekblad, December 2008, (http://www.technischweekblad.nl/) Probus, Bilthoven, April 2008, invited lecture De rol van wolken in het klimaat Dutch national radio, interview on the importance of clouds for the global climate, Oct 2007 Groei van een atmosferische grenslaag in een laboratoriumopstelling, NPT Procestechnologie, February 2007, (http://www.npt.nl) Dutch national radio, interview on atmospheric boundary layers Jan 2007 National symposium on Weather Phenomena. Clouds, Delft University, Nov 2007 Interview Delft-Outlook: Climate change clouds remain the misty factor, 2007 (3) Interview Delta (38), december 2006, Atmosfeer in een bak water Kronig-lecture Physics of Film: the Day after Tomorrow, April 2006 Delft University NVOX, (Tijdschrift voor natuurwetenschap op school) January 2006, Bevriest New York in n dag? Een kritische fysische kijk op de rampenfilm The day after tomorrow. De Physicus (VvTP), february 2006, Orkanen, cyclonen en typhonen Delta (38), february 2006, Hoorbril getest in watertunnel Delta (34), november 2005, Hollywoodverzinsel of werkelijkheid. AD/Haagsche Courant, 10 november 2005, Film overdrijft maar ijstijd is niet ondenkbaar. Delta (28), september 2005, Virtual reality lab: mes snijdt aan twee kanten. Splendid Science: a voyage of discovery 2004 (Applied Sciences, TU Delft, 2005): The earth s atmosphere in a water tank. World Year of Physics 2005: Physics and Phantasy, TU Delft. (lecture about the Physics in the Day After Tomorrow) World Year of Physics 2005: co-organiser part of the Techniektoernooi Magazine van het Informaticaonderzoek Platform Nederland, Jaargang 1, nr 2, september 2004: In gesprek met... Delft Integraal : Een scheve draai in een recht rooster. Symmetriebreking in de bakoven. Delta, juni 2003, Scientific visualization in virtual reality. Telegraaf, wetenschapsbijlage december 2002: Stapelwolken in kaart gebracht. Volkskrant, wetenschapsbijlage augustus 2000: Het weer krijgt wolken. Intermediair, februari 1997, Wiskundige microscoop ontdekt verstekeling. Kijk, oktober 1994, Je gelooft je ogen niet.

7 Recently granted projects High Resolution Regional Climate Modeling of Convection and Precipitation over the Netherlands, Kennis voor Klimaat, 1PhD, (icw prof. A.P. Siebesma) Droplet-turbulence dynamics under heterogeneous conditions, FOM-program Droplets & Turbulence, 1PhD, (icw dr L. Portela, prof. dr R Mudde) H. Jonker and A.P. Siebesma 2008, Large Eddy Simulation of Deep Convective Clouds Multi- Scale Physics, 1 PhD E. van Meijgaard, A.P. Siebesma, and H. Jonker, 2008, Construction and application of an MSG/SEVIRI simulator to improve the interpretation of climate model-to-satellite comparisons. NWO/SRON, 1 postdoc H. Jonker, M. van Reeuwijk and P. Sullivan, 2008, PINNACLE: Pinning down the growth-rate law of Atmospheric Convective Boundary Layers 1,935,000 CPU-core-h (250 keuro), sponsor: Distributed European Infrastructure for Supercompting, 2008 H. Jonker 2007, Integration of ICT in Physics education. 1kE, grassroot proposal, TU-Delft. J. Vila and H. Jonker 2006, Research school, the role of Atmospheric Boundary Layer processes in Atmospheric Chemistry. 20kE, European Science Foundation H. Jonker et al. 2005, A laboratory experiment to study the effect of turbulence on droplet growth and size distributions in clouds. NWO/ALW Climate Variability Program, 1 PhD Cuxart et al. and H. Jonker 2005, TRANSCLA-2005 C. Kleijn and H. Jonker, 2004 Miniaturization of chemical reactors for sustainable processes, Delft University, Delft Center for Sustainable Industrial Processes, 1 PhD. H. Jonker, B.J. Boersma, D. Roekaerts, and F. Nieuwstadt, 2003 Simulation of a realistic industrial burner, Delft Center for Computational Science and Engineering, Delft University, 1 PhD. H. Jonker and F. Post, 2003 Visualization of Cumulus Clouds in Virtual Reality, NWO/EW open competition, 2 PhDs K. Hanjalic and H. Jonker, 2002, Hybrid simulation methods for high Reynolds number wallbounded flows and conjugate heat transfer, FOM, 1PhD Various visiting grants (see working visits) Supercomputer time, sponsor NWO/NCF: 400,000hr (equivalent to 52 keuro), July ,000hr (equivalent to 98 keuro), July ,000hr (equivalent to 93 keuro), March ,000hr (equivalent to 64 keuro), March ,000hr (equivalent to 33 keuro), March 2001 Valorization Consultant for Innovatie Platform Luchtkwaliteit, 2009 (sound barrier impact on air quality) Consultant for TNO/FEL 2005 (disturbance of infrared imaging by atmospheric turbulence) Consultant for Organon, 2004 (confidential) X-stream, software developed and maintained together with TNO/TPD DALES, Dutch Atmospheric Large Eddy Simulation code, developed and maintained together with KNMI, Wageningen University and Utrecht University.

8 Teaching Environmental Physics period: 2000-now subjects: Greenhouse effect, Physiscs of Climate, Atmospheric Dispersion and Air Quality method: lectures + homework exercises curriculum, credits: MSc Applied Physics, 6ECTS comments: developed from scratch in 2000 nr of students: assessment: homework exercises + written exam Chaotic Processes period: 2004-now subjects: Non-linear differential equations, (strange)attractors, repellors, limit-cycles, bifurcations, Poincare sections, Lyapunov exponents, routes to chaos, fractal geometries. method: integrated form of lectures and computer exercises based on a learning by doing principle curriculum, credits: MSc Applied Physics, 6ECTS comments: developed from scratch in 2004 nr of students: 25 assessment: computer exam Advanced Physical Transport Phenomena period: subjects: Mathematical methods for heat diffusion, separation of variables, Laplace transformation, integral methods. Convection/diffusion problems, natural convection. method: lectures + exercises curriculum, credits: MSc Applied Physics, 6ECTS comments: nr of students 20 assessment: written exam Computational Physics period: subjects: computer programming of physical systems method: lectures + exercises curriculum, credits: BSc Applied Physics, 6ECTS nr of students: 2 groups of 4 assessment: report First year projects since 2001 yearly mentor and supervisor of 1 group-project (8 students per year) Supervision BSc & MSc graduation projects supervisor of 30 projects since 2001 Advanced courses (Summerschools etc) - Atmospheric Boundary Layers: Concepts, Observations, and Numerical Simulations Convective boundary layers June 2008, Les Houches, France - Research school, the role of Atmospheric Boundary Layer processes in Atmospheric Chemistry, Clouds in the atmospheric boundary layer, Castelldefels (Spain), November Post Academic Education (PAO), advanced course on Neuronal Networks, Utrecht, 1993

9 Supervision and co-supervision PhD-students 10. Vacancy, High Resolution Regional Climate Modeling of Convection and Precipitation over the Netherlands, (icw prof. dr Siebesma) 9. Vacancy, Droplet-turbulence dynamics under heterogeneous conditions, (icw dr L. Portela, prof. dr R Mudde) 8. Steef Böing, Large Eddy Simulation of Deep Convection, (icw prof. dr A.P. Siebesma) 7. Tanima Chatterjee, A laboratory experiment to study the effect of turbulence on droplet growth and size distributions in clouds., ongoing (icw dr M Tummers, dr L. Portela, prof. dr R Mudde) 6. Petra Kroon, Flux measurements of CH 4 and N 2 O, ongoing (icw dr A. Hensen, ECN) 5. Steven van der Hoeven, Large Eddy Simulation of a realistic industrial burner, ongoing (icw Prof. dr D. Roekaerts and Prof. dr B.J. Boersma) 4. Thijs Heus, On the edge of a cloud, December 2008 (icw Prof. dr H. van den Akker) 3. Maarten van Reeuwijk, Direct numerical simulation & regularization modeling of turbulent thermal convection, March 2007 (icw Prof. dr K. Hanjalic) 2. Luuk Thielen, Modeling and calculation of flow and heat transfer in multiple impinging jets, December 2003 (icw Prof. dr K. Hanjalic) 1. Roel Neggers, Shallow cumulus convection, December 2002 (icw Prof. dr A.P. Siebesma) Supervision MSc-students (since 2001) 21. Susan Pesman, Descending shell around cumulus clouds, September 2009 (ongoing) 20. Robert van Driel, Atmospheric turbulence at sunset, July 2009 (ongoing) 19. Steef Böing, Intermittent turbulence in stratified flow over a porous canopy, January 2009 (icw dr H. van Dop) 18. Daniel Abrahams, Measuring entrainment in a stratified saline water tank, December Philia Lijdsman, Laboratory experiments on entrainment in the convective boundary layer using a saline convection tank, Oct 2008 (icw dr M.A. Jimenez) 16. Adriaan Schuitmaker, Measurements of turbulent energy spectra in the stable atmospheric boundary layer using Laser Doppler Anemometry, August 2008, (icw dr M Tummers) 15. Remco Verzijlbergh, Turbulent Dispersion in Cloudy Boundary Layers, July 2008 (icw dr T. Heus) 14. Wiet de Ronde, Intermittency in the Stable Boundary Layer: A Study into Land-Atmosphere Interaction during the Nighttime, (icw dr B. van der Wiel, WUR) 13. Jeroen Lebouille, Water tank experiments on entrainment in the Convective Boundary Layer, June, 2007 (icw dr M.A. Jimenez)

10 12. Eric Woittiez, How turbulence influences droplet coalescence in convective clouds, April 2007 (icw dr L. Portela) 11. Gertjan van Dijk, The implementation of a Lagrangian Particle Dispersion Model in Large Eddy Simualtions of the Atmospheric Boundary Layer, March 2007 (icw dr T. Heus) 10. Paul de Brabander, Manipulation of a droplet of ferrofluid, April 2006 (icw prof. dr R Mudde) 9. Petra Kroon, Measuring the turbulent energy spectrum in the atmosphere using Laser Doppler Anemometry, June 2005 (icw dr M Tummers) 8. Esther Hagen, Experiments on entrainment in a convective boundary layer using a saline water tank, May 2005 (icw dr M.A. Jimenez) 7. Ralph van Doorn, The efficiency and feasibility of energy conversion using a thermosyphon in a transverse magnetic field, September Michiel van Noord, Analysis of the technical and sustainable potential of the PITCH hybrid solar collector (a model for a PV-integrated evacuated tubular collector with heat pipe), August 2004 (icw dr. H. Zondag, ECN) 5. Marleen van Aartrijk, Experiments and simulations on combined natural and thermomagnetic convection in magnetic fluids, March Thijs Heus, Laboratory experiments on the convective boundary layer, January Saskia Hekker, Temperature measurements in Rayleigh-Benard convection using suspended liquid crystals, April 2003 (icw dr M Tummers) 2. Jos Verdoold, A laboratory experiment of the convective boundary layer: formation of large scale fluctuations, April Stefaan Rodts, Shallow cumulus dynamics: observations and parameterization, 2001 (icw dr P. Duynkerke) Supervision BSc-students (since 2004) 9. Sinta de Wildt Turbulent dispersion in stratocumulus-topped boundary layers, ongoing 8. Frans van Hoogstraten, Direct simulation of Laser Doppler Anemometry, (icw dr M Tummers), April Aljen Uitbeijerse Adding colour to the dripping faucet, March Jerome Schalkwijk LES study on the flux imbalance in the Convective Boundary Layer, June Freek Pols Mass-flux distribution of Cumulus clouds from aircraft observations, December 2007 (icw dr T. Heus) 4. Philia Lijdsman, A conceptual analysis of the solar chimney, September Maarten Sanders, Descending Shell around a Cumulus Cloud Simulation, August 2007

11 2. Remco Verzijlbergh Shallow Cumulus clouds: a study of relations between sub-cloud length scales, cloud size distributions and entrainment profiles, February 2006 (icw dr T. Heus) 1. Bas Reintjes, Shallow cumulus clouds: a parameter study of the development and stability of cumulus clouds in the Atmospheric Boundary Layer, September 2005 (icw dr T. Heus) Prizes and honors for students under my supervision Thijs Heus, nominated by the Nederlandse Vereniging van Beroepsmeteorologen for the Young Scientist Award of the European Meteorological Society (best PhD thesis). Eric Woittiez, best student graduation report in Physical Technology (1500 euro), December 2008 Thijs Heus, best oral student presentation at the 17th Boundary Layers and Turbulence conference, American Meteorological Society, San Diego, USA, June 2006 ($200+books) Esther Hagen, best student graduation report in Physical Technology (1500 euro), December, 2006 Wiet de Ronde, MSc Applied Physics TU Delft, graduated cum laude 2008 Eric Woittiez, MSc Applied Physics TU Delft, graduated cum laude 2007 Marleen van Aartrijk, MSc Applied Physics TU Delft, graduated cum laude, 2004 Saskia Hekker, MSc Applied Physics TU Delft, graduated cum laude, 2003 Stefaan Rodts, MSc Applied Physics TU Delft, graduated cum laude, 2001

12 Publications Books Analysis and Modelling of Physical Transport Phenomena K. Hanjalic, S. Kenjeres, M. Tummers, H.J.J. Jonker, 2007, VSSD, Delft in progress: Harm J.J. Jonker and Maarten van Reeuwijk. A Course in Nonlinear and Chaotic Systems using Maple (tentative title), draft manuscript ready. Journal papers in press / under review 4. P.S. Kroon, A. Schuitmaker, H.J.J. Jonker, M.J. Tummers, A. Hensen, F.C. Bosveld An evaluation by laser Doppler anemometry of the correction algorithm based on Kaimal co-spectra for high frequency losses of EC flux measurements of CH 4 and N 2 O. Agricultural and Forest Meteorology, 2009, in press (available online October 2009) 3. P.S. Kroon, A. Hensen, H.J.J. Jonker, H.G. Ouwersloot, A.T. Vermeulen, F.C. Bosveld Overview of uncertainties in EC flux measurements of CH 4 and N 2 O Agricultural and Forest Meteorology, 2009, in press (available online October 2009) 2. P.S. Kroon, A.P. Schrier-Uijl, A. Hensen, E.M. Veenendaal and H.J.J. Jonker Annual balances of CH4 and N2O from a managed fen meadow using eddy covariance flux measurements European Journal of Soil Science, 2009, under review 1. B.J.H. van de Wiel, A.F. Moene, H.J.J. Jonker. Local similarity profiles from direct numerical simulation. Journal of the Atmospheric Sciences, 2009, under review Journal papers 37. Maarten van Reeuwijk, Harm J.J. Jonker, and Kemo Hanjalić Leray-α simulations of wall-bounded turbulent flows Int. J. Heat Fluid Flow, 30(6) Eric J P Woittiez, Harm J J Jonker, Luis M Portela On the combined effects of turbulence and gravity on droplet collision in convective clouds: a numerical study. Journal of the Atmospheric Sciences, 66, Thijs Heus, Harm J. J. Jonker, Harry E. A. van den Akker, Eric J. Grifith, Michal Koutek and Frits H. Post A statistical approach to the life cycle analysis of cumulus clouds selected in a virtual reality environment. Journal of Geophysical Research, 114, D06208, doi: /2008jd R.A. Verzijlbergh, H.J.J. Jonker, T. Heus and J. Vila Turbulent dispersion in cloudtopped boundary layers. Atmospheric Chemistry and Physics, 9, Thijs Heus, C. Freek J. Pols, Harm J. J. Jonker, Harrie E. A. Van den Akker and Donald H. Lenschow Observational validation of the compensating mass flux through the shell around cumulus clouds. Quarterly Journal of the Royal Meteorological Society, 135,

13 32. B.J.H. van de Wiel, A.F. Moene, W.H. De Ronde, H.J.J. Jonker Local Similarity in the Stable Boundary Layer and Mixing-Length Approaches: Consistency of Concepts Boundary- Layer Meteorology Thijs Heus, Gertjan van Dijk, Harm J.J. Jonker, Harry E.A. van den Akker Mixing in Shallow Cumulus Clouds Studied by Lagrangian Particle Tracking. Journal of the Atmospheric Sciences, 65, Harm J.J. Jonker, Thijs Heus and Peter P. Sullivan A refined view of vertical mass transport by cumulus convection. Geophysical Research Letters 35, L07810, doi: /2007gl Maarten van Reeuwijk, Harm J.J. Jonker, and Kemo Hanjalić Wind and boundary layers in Rayleigh-Bénard convection. I: Analysis and modeling. Phys. Rev. E, 77, Maarten van Reeuwijk, Harm J.J. Jonker, and Kemo Hanjalić Wind and boundary layers in Rayleigh-Bénard convection. II: Boundary layer character and scaling Phys. Rev. E, 77, Jos Verdoold, Maarten van Reeuwijk, Mark J. Tummers, Harm J.J. Jonker, and Kemo Hanjalić Spectral analysis of boundary layers in Rayleigh-Bénard convection. Phys. Rev. E, 77, Thijs Heus and Harm J.J. Jonker Subsiding Shells around Shallow Cumulus Clouds. Journal of the Atmospheric Sciences, 65, Jordi Vila-Guerau de Arallano, Harm Jonker, David Pino, Harry M. Ten Brink, Nadine Chaumerliac, Ian Faloona, Stefano Galmarini, Millán Millán, and Jochen Stutz, The role of atmospheric boundary layer processes in atmospheric chemistry. BAMS (DOI: ) 24. P.S. Kroon, A. Hensen, H.J.J. Jonker, M.S. Zahniser, W.H. van t Veen, and A.T. Vermeulen Suitability of quantum cascade laser spectroscopy for CH 4 and N 2 O eddy covariance flux measurements. Biogeosciences, 4, D. Pino, H.J.J. Jonker, J. Vilà-Guerau de Arellano, A. Dosio Role of shear and the inversion strength during sunset turbulence over land: Characteristic length scales. Boundary- Layer Meteorology, 121, 3, , /s M. van Reeuwijk, H.J.J. Jonker, and K. Hanjalic Incompressibility of the Leray-alpha model for wall-bounded flows. Physics of Fluids 18 (1) Art. No M. van Reeuwijk, H.J.J. Jonker, and K. Hanjalic Identication of the wind in Rayleigh- Benard convection. Physics of Fluids 17 (5) Art. No H. van Dop, D. van As, A. van Herwijnen, M. Hibberd and H. Jonker Length scales of scalar diffusion in the convective boundary layer: Laboratory observations. Boundary-Layer Meteorology 116 (1): H.J.J. Jonker and J. Vilà-Guerau de Arellano The influence of chemistry on length scales of reactive species in convective atmospheric boundary layers. Rus. J. Chemical Physics 24 (5): L. Thielen, K. Hanjalić, H. Jonker, R. Manceau Predictions of flow and heat transfer in multiple impinging jets with an elliptic-blending second-moment closure. International Journal of Heat and Mass Transfer, 48(8) pp

14 17. J. Vilà-Guerau de Arellano, B. Gioli, F. Miglietta, H.J.J. Jonker, H.K. Klein Baltink, R.W.A. Hutjes, A.A.M. Holtslag Entrainment process of carbon dioxide in the atmospheric boundary layer. Journal of Geophysical Research 109, D18110, pp H.J.J. Jonker, J. Vilà-Guerau de Arellano and P.G. Duynkerke Characteristic Length Scales of Reactive Species in a Convective Boundary Layer. Journal of the Atmospheric Sciences 61, pp S.R. de Roode, P.G. Duynkerke and H.J.J. Jonker Large Eddy Simulation of atmospheric boundary layers: How large is large enough? Journal of the Atmospheric Sciences, 61, pp S.R. de Roode, H.J.J. Jonker, P.G. Duynkerke and B. Stevens Countergradient fluxes of conserved variables in the clear convective and stratocumulus-topped boundary layer. The role of the entrainment flux. Boundary-Layer Meteorology, 112 pp L. Thielen, H.J.J. Jonker, K. Hanjalić Symmetry breaking of flow and heat transfer in multiple impinging jets. International Journal of Heat and Fluid Flow 24, pp S.M.A. Rodts, P.G. Duynkerke and H.J.J. Jonker Size distributions and dynamical properties of shallow cumulus clouds from aircraft observations and satellite data. Journal of the Atmospheric Sciences 60, pp R.A.J. Neggers, H.J.J. Jonker and A.P. Siebesma Size statistics of cumulus cloud populations in large-eddy simulations. Journal of the Atmospheric Sciences 60, pp R.A.J. Neggers, A.P. Siebesma and H.J.J. Jonker A stochastic parcel model for shallow cumulus convection. Journal of the Atmospheric Sciences 59, pp A. Feijt and H.J.J. Jonker Comparison of scaling parameters from spatial and temporal distributions of cloud properties. Journal of Geophysical Research 105 No. D23 pp A.P. Siebesma and H.J.J. Jonker Anomalous scaling of cumulus cloud boundaries. Phys. Rev. Lett H.J.J. Jonker, P.G. Duynkerke and J.W.M. Cuijpers Mesoscale fluctuations in scalars generated by boundary layer convection. Journal of the Atmospheric Sciences H.J.J. Jonker, A.C.C. Coolen and J.J. Denier van der Gon Autonomous development of decorrelation filters in neural networks with recurrent inhibition. Network: Comput. Neural Syst Ph.W. Koken, H.J.J. Jonker and C.J. Erkelens A model of the human smooth pursuit system based on an unsupervised adaptive controller. IEEE Transactions on Systems, Man and Cybernetics H.J.J. Jonker, A.C.C. Coolen and J.J. Denier van der Gon On the function and development of spatial structure in layered neural networks. J. Phys. A: Math. Gen H.J.J. Jonker and A.C.C. Coolen Learning in neural networks by eliminating frustrated bonds. J. Phys. A: Math. Gen

15 2. H.J.J. Jonker and A.C.C. Coolen Unsupervised dynamic learning in layered neural networks. J. Phys. A: Math. Gen A.C.C. Coolen, H.J.J. Jonker and Th. W. Ruijgrok Size of the domains of attraction in the Hopfield model. Phys. Rev. A Book chapters 2. H.J.J. Jonker and J. Vilà-Guerau de Arellano Diffusion of chemically reacting species in a convective atmospheric boundary layer. Micromixing in turbulent reactive flows eds. S. Frolov, V. Frost, D. Roekaerts Torus Press (Moscow, Russia; ISBN ) p J.J. Denier van der Gon, A.C.C. Coolen, C.J. Erkelens and H.J.J. Jonker Selforganizing neural mechanisms possibly responsible for muscle coordination. Multiple Muscle Systems: Biomechanics and Movement Organization, J.M. Winters and S.L-Y. Woo (eds) (Springer-Verlag, New York) Conference proceedings 32. Wiet H. De Ronde, H.J.J. Jonker and B.J.H. Van de Wiel, and A.F. Moene. A Numerical and Analytical Study of Intermittency in the Stable Boundary Layer. Proc. of the 18th Symp. on Boundary Layers and Turbulence, June 2008, Stockholm, Sweden 31. Remco A. Verzijlbergh, H.J.J. Jonker and T. Heus. Dispersion in Cloudy Boundary Layers. Proc. of the 18th Symp. on Boundary Layers and Turbulence, June 2008, Stockholm, Sweden 30. Thijs Heus, G. Van Dijk, H. J. J. Jonker, and H. E. A. Van den Akker. Mixing in shallow cumulus clouds studied by Lagrangian particle tracking. Proc. of the 18th Symp. on Boundary Layers and Turbulence, June 2008, Stockholm, Sweden 29. Thijs Heus, F. Pols, H.J.J. Jonker, H.E.A. van den Akker, and D.H. Lenschow. Analysis of the downward transport in RICO observations. Proc. of the 18th Symp. on Boundary Layers and Turbulence, June 2008, Stockholm, Sweden 28. M. van Reeuwijk, H.J.J. Jonker, K. Hanjalic. Boundary Layer Scaling in Rayleigh-Benard Convection, Proc. 5th European Thermal Sciences Conference, May 18-22, E.J. Griffith, M. Koutek, F.H. Post, T. Heus, H.J.J. Jonker, 2007, Quantitative data analysis in virtual environments through reprocessing. In FW Jansen, GEO Pierre, CJ Veenman & JWJ Heijnsdijk (Eds.), 13th annual conference of the advanced school for computing and imaging (pp ). Delft: ASCI Technische Universiteit Delft. 26. S. van der Hoeven, B.J. Boersma, H.J.J. Jonker, D.J.E.M. Roekaerts, Development of a large eddy simulation code for turbulent non-premixed jet flames. In DJEM Roekaerts, BJ Boersma, K Claramunt & Coelho (Eds.), 2nd Eccomas Thematic Conference on Computational Combustion (pp. 1-9). Delft: TU Delft.

16 25. H.J.J. Jonker, R.A. Verzijlbergh, Th. Heus, and A.P. Siebesma. The influence of the subcloud moisture field on cloud size distributions and the consequences for entrainment. Proc. of the 17th Symp. on Boundary Layers and Turbulence, June 2006, San Diego, U.S.A. (CDproceedings). 24. Th. Heus and H.J.J. Jonker. Why do descending Shells around Cumulus Clouds exist? Proc. of the 17th Symp. on Boundary Layers and Turbulence, June 2006, San Diego, U.S.A. (CDproceedings). 23. Th. Heus, H.J.J. Jonker, E.J. Griffith, and F.H. Post. Lifecycle analysis of cumulus clouds using a 3D virtual reality environment. Proc. of the 17th Symp. on Boundary Layers and Turbulence, June 2006, San Diego, U.S.A. (CD-proceedings). 22. E.J. Griffith, F.H. Post, M. Koutek, T. Heus, H.J.J. Jonker Feature Tracking in VR for Cumulus Cloud Life-Cycle Studies. Proc. of the 11th Eurographics Workshop on Virtual Environtments (EGVE), Aalborg, Denmark, October, R. Blach and E. Kjems (eds), p M. van Reeuwijk, H.J.J. Jonker, K. Hanjalic Applying the Leray-alpha model to unbounded Rayleigh-Benard convection. Proc. Progress in Turbulence II, Bad Zwischenahn, September 26-28, M. van Reeuwijk, H.J.J. Jonker, K. Hanjalic The role of the wind in unbounded Rayleigh-Benard convection. Proc. 9th UK National Heat Transfer Conference, Manchester, September 5-6, L. Thielen, K. Hanjalić, H.J.J. Jonker, R. Manceau Predictions of flow and heat transfer in multiple-impinging jets with an elliptic-blending second-moment closure. Proceedings of CHT-04, ICHMT International Symposium on Advances in Computational Heat Transfer, Norway, April, 2004, 19 pages. 18. H.J.J. Jonker and R. Toussaint. The disparate cloud size distributions obtained from aircraft and satellite observations. Proc. of the 16th Symp. on Boundary Layers and Turbulence, 2004, Portland (Maine), U.S.A. (CD-proceedings, 4 pages). 17. H.J.J. Jonker, Th. Heus, E. Hagen, and H. van Dop. Laboratory experiments of entrainment in dry convective boundary layers. Proc. of the 16th Symp. on Boundary Layers and Turbulence, 2004, Portland (Maine), U.S.A. (CD-proceedings, 6 pages). 16. J. Vila-Guerau de Arellano, H.J.J. Jonker, B. Gioli, F. Miglietta, H. Klein Baltink, R.W.A. Hutjes, A.A.M. Holtslag. The entrainment process of Carbon Dioxide in the atmospheric boundary layer. Proc. of the 16th Symp. on Boundary Layers and Turbulence, 2004, Portland (Maine), U.S.A. (CD-proceedings, 5 pages). 15. D. Pino, H.J.J. Jonker, J. Vila-Guerau de Arellano, and A. Dosio. Role of the shear and inversion strength during sunset turbulence over land: characteristic length scales. Proc. of the 16th Symp. on Boundary Layers and Turbulence, 2004, Portland (Maine), U.S.A. (CDproceedings, 6 pages). 14. L. Thielen, H.J.J. Jonker, K. Hanjalić Heat transfer in multiple impinging jet arrays. Proceedings of the 12th International Heat Transfer Conference, Grenoble, August 2002, 6 pages.

17 13. L. Thielen, H.J.J. Jonker, K. Hanjalić Numerical simulation of flow and heat transfer in multiple impinging jets. Proceedings of the 5th International Symposium on Engineering Turbulence Modelling and Measurements, Mallorca, September 2002, R.A.J. Neggers, H.J.J. Jonker, and A.P. Siebesma. Size statistics of cumulus cloud populations in large-eddy simulations. Proc. of the 15th Symp. on Boundary Layers and Turbulence, 2002, Wageningen, The Netherlands P.G. Duynkerke, H.J.J. Jonker and S.R. de Roode. LES: How large is large enough? Proc. of the 15th Symp. on Boundary Layers and Turbulence, 2002, Wageningen, The Netherlands S.R. de Roode, P.G. Duynkerke and H.J.J. Jonker. Countergradient fluxes in the clear convective boundary layer. The role of the entrainment flux. Proc. of the 15th Symp. on Boundary Layers and Turbulence, 2002, Wageningen, The Netherlands S.M.A. Rodts, H.J.J. Jonker, and P.G. Duynkerke. Cumulus properties from aircraft and satellite measurements. Proc. of the 15th Symp. on Boundary Layers and Turbulence, 2002, Wageningen, The Netherlands L. Thielen, H. Jonker, R. Manceau, and K. Hanjalić. Turbulence modelling in a single normally impinging jet. In V. Kudriavtsev and S. Kawano, editors, Proc. Fourth Int. Symp. on Computational Technologies for Fluid/Thermal/Chemical Systems with Industrial Applications, Atlanta 2001, volume 424 1, pages ISBN , R.A.J. Neggers, H.J.J. Jonker, and A.P. Siebesma. An evaluation of cloud size distributions using LES. Proc. of the 14th Symp. on Boundary Layers and Turbulence, 2000, Aspen, U.S.A J. Vilà-Guerau de Arellano and H.J.J. Jonker. Characteristic length scales for reactants in a convective boundary layer. Proc. of the 14th Symp. on Boundary Layers and Turbulence, 2000, Aspen, U.S.A R.A.J. Neggers, H.J.J. Jonker, and A.P. Siebesma. A stochastic parcel model for shallow cumulus convection. Proc. of the 14th Symp. on Boundary Layers and Turbulence, 2000, Aspen, U.S.A A.J. Feijt and H.J.J. Jonker. Comparison of cloud parameters from spatial and temporal distributions. Proc. of the Remote Sensing of Cloud Parameters: retrieval and validation, H.J.J. Jonker, P.G. Duynkerke and A.P. Siebesma. Development of mesoscale fluctuations in cloud topped boundary layers. Proc. of the 13th Symp. on Boundary Layers and Turbulence, 1999, Dallas, U.S.A H.J.J. Jonker, P.G. Duynkerke, and J.W.M. Cuijpers. Energy spectra in the mesoscale range: an LES study. Proc. of the 12th Symp. on Boundary Layers and Turbulence, 1997, Vancouver, Canada, H.J.J. Jonker, A.C.C. Coolen and J.J. Denier van der Gon Linear interpolation with binary neurons. Proc. IEE on artificial Neural Networks, (London: IEE) Other publications Information processing and self-organisation in neural networks with inhibitory feedback. H.J.J. Jonker, PhD Thesis, Utrecht University, 1993

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