Birth: November 29, 1972, Groningen, The Netherlands
Leaf Development ModelingIn collaboration with the Leaf Development Group we are developing cell-centered modeling approaches to leaf growth. We focus on the interplay between patterned cell division, growth factor channeling through the vasculature, and whole leaf growth. Our modeling efforts aim to reconcile known molecular mechanisms of auxin transport with microscopic observations of leaf growth and venation patterning. We start from the hypothesis that PIN1 (an auxin transporter) localizes near the neighboring cells with the highest auxin concentration, producing auxin accumulation points as in previous models (Jonsson et al., 2006; Smith et al., 2006; Barbier de Reuille et al., 2006). Our aim is to reproduce recently published PIN1 expression patterns and PIN1 cellular localizations in the leaf (Scarpella et al., 2006).
Lateral root initiationLateral roots originate from cells in the root basal meristem, a proliferating tissue region just above the root tip, forming a regular branching pattern with evenly spaced lateral roots. The crucial signal for initiating the lateral root is most likely the phytohormone auxin. Auxin levels oscillate at a period of around 15 hours, precisely coinciding with the rhythm by which new lateral roots appear. In collaboration with the Root Development group, we are building computational models of the root basal meristem. We aim at unraveling the mechanisms behind these oscillating auxin flows, which may be driven by a dynamics interaction between auxin and the production and cellular localization of its transporter proteins, including PIN, AUX and LAX. For this project we currently have a PhD position available. Please see here.
Lignin BiosynthesisWood consists for 20% of lignin, a polymer formed in angiosperms from primarily the two monolignols coniferyl (G-subunit) and sinapyl alcohol (S-subunit) that bind non-enzymatically form a huge variety of lignin molecules. In collaboration with the Bioenergy group led by Wout Boerjan, we are building a bottom-up model with the aim of predicting lignin structure from low-level chemical kinetic factors, including subunit coupling probabilities and monolignol synthesis rates. We will use the model to explain the mechanism behind a range of controlling factors, indentified in experimental work, including a) the ratio of coniferyl vs. sinapyl monolignols, b) the monolignol supply rate, and c) the abundancy of alternative monolignols present in lignin biosynthesis mutants and transgenics. Lignin composition, structure and its interaction with hemicellulose are important factors limiting the quality of lignocellulosic plant material as fodder, conversion to bioethanol or conversion to paper. Eventually the model will suggest new targets for controlled, improved lignin biosynthesis.
Previous research interestsMy previous research interests are also related to biological morphogenesis, including coral growth simulation, modeling vasculogenesis and angiogenesis, and biological image analysis. See my personal webpage for details.
Papers(21) Merks, R.M.H., Van de Peer, Y., Inzé, D., Beemster, G.T.S. (2007) Canalization without flux sensors: a traveling-wave hypothesis. Trends Plant Science 12(9):384-90.
(20) Cickovski, T., Aras, K., Swat, M., Merks, R.M.H., Glimm, T., Hentschel, G., Alber, M., Glazier, J.A., Newman, S.A., Izaguirre, J. (2007) From Genes To Organisms Via The Cell: A Problem-Solving Environment For Multicellular Development. Comput. Sci. Eng. 9(4):50-60.
(19) Savill, N. J., Merks, R.M.H. (2007) The Cellular Potts Model in Biomedicine. In: Katarzyna A. Rejniak, Alexander Anderson and Mark Chaplain (eds). Single Cell Based Models in Biology and Medicine Birkhaüser-Verlag, Basel, Boston and Berlin. series Mathematics and Biosciences in Interaction. Chapter (ii).3. pp. 137-150.
(18) Balter, A., Merks, R.M.H., Popławski, N., Swat, M., Glazier, J.A. (2007) The Glazier?Graner?Hogeweg Model: Extensions, future directions, and opportunities for further study. Chapter (ii).4. ibid, pp. 151-168.
(17) Brodsky, S.V., Merks, R.M.H., Mendelev, N., Goo, C., Chen, J. (2007) Glycated Collagen I Impairs Angiogenesis In Vitro - A Study Using An Innovative Chamber For Cell Research. Diabetes Res. Clin. Pract. 76, 463-7.
(16) Merks, R.M.H., Brodsky, S.V., Goligorsky, M.S., Newman, S.A., Glazier, J.A. (2006) Cell elongation is key to in silico replication of in vitro vasculogenesis and subsequent remodeling. Dev. Biol. 289(1):44-54.
(15) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A., Hogeweg, P. (2006) Problem Solving Environments for Biological Morphogenesis. Comput. Sci. Eng. 8(1), 61-72.
(14) Merks, R.M.H., Glazier, J.A. (2006) Dynamic mechanisms of blood vessel growth. Nonlinearity 19(1):C1-C10.
(13) Kaandorp, J.A., Sloot, P.M.A., Merks, R.M.H., Bak, R.P.M., Maier, C., Vermeij, M.J.A. (2005) Morphogenesis of the branching reef coral Madracis mirabilis. P. Roy. Soc. B. 272(1559):127-33.
(12) Merks, R.M.H., Newman, S.A., Glazier, J.A. (2005) Cell-Oriented Modeling of in vitro Capillary Development. Lect. Notes in Comput. Sci. 3305, 425-434. In Peter M.A. Sloot, et al. editors, From individual to collective behaviour. Sixth international conference on Cellular Automata for Research and Industry.
(11) Merks, R.M.H., Glazier, J.A. (2005) A Cell-Centered Approach to Developmental Biology. Phys. A. 352(1):113-130.
(10) Mezentzev, A., Merks, R.M.H., O'Riordan, E., Chen, J., Goligorsky, M.S., Brodsky, S.V. (2005) Endothelial microparticles affect angiogenesis in vitro: the role of oxidative stress. Am. J. Physiol.-Heart Circul. Physiol. 289(3):H1106-14.
(9) Merks, R.M.H. (2005) Droogzwemmen in het koraalrif. Computersimulaties verklaren koraalgroei (in Dutch). Nederlands Tijdschrift voor Natuurkunde 71 (10), 314-317.
(8) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2004) Polyp Oriented Modelling of Coral Growth. J. Theor. Biol. 228(4):559-76.
(7) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2003) Models of coral growth: Spontaneous branching, compactification and the Laplacian growth assumption. J. Theor. Biol. 224(2):153-66.
(6) Merks, R.M.H. (2003) Branching Growth in Stony Corals: a modelling approach. PhD thesis, University of Amsterdam.
(5) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2003) Diffusion limited growth in laminar flows. Int. J. Mod. Phys. 14:1171-1182.
(4) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2003) A problem solving environment for modelling stony coral morphogenesis. Lect. Notes in Comput. Sci. 639-648.
(3) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2003) Branching and compactification in a model of coral growth: a critical reinvestigation of the effect of hydrodynamics. In V. Capasso, editor. Mathematical Modelling and Computing in Biology and Medicine; 5th ESMTB Conference 2002. pages 539-544, Milano, Italy, MIRIAM.
(2) Merks, R.M.H., Hoekstra, A.G., Sloot, P.M.A. (2002) The moment propagation method for advection-diffusion in the lattice Boltzmann method: validation and Peclet number limits. J. Comput. Phys. 183:563-576.
(1) Merks, R.M.H., Hoekstra, A.G., Kaandorp, J.A., Sloot, P.M.A. (2002) Spontaneous branching in a polyp oriented model of stony coral growth. Lect. Notes in Comput. Sci. 2329, 88-96. In P.M.A. Sloot, C.J. Kenneth Tan, Jack J. Dongarra, and Alfons G. Hoekstra, editors, International Conference on Computational Science (ICCS).
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Bioinformatics & Evolutionary Genomics
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