Publications
Gehrels, E. W.; Chakrabortty, B*.; Perrin, M.-E.; Merkel, M.; Lecuit, T. Curvature Gradient Drives Polarized Tissue Flow in the Drosophila Embryo. Proc. Natl. Acad. Sci. U. S. A. 2023, 120 (6), e2214205120.
We show, with experiments and modeling, that the onset of polarized tissue flow in early Drosophila morphogenesis is orchestrated by a coupling of apical actomyosin contractility to tissue curvature. Particularly, the onset of polarized flow is driven by a mismatch between the position of apical myosin activation and peak curvature at the posterior pole. Our work demonstrates how genetic and geometric information inherited from the mother interact to create polarized flow during embryo morphogenesis.
Chakrabortty, B.; Willemsen, V.; de Zeeuw, T.; Liao, C.-Y.; Weijers, D.; Mulder, B.; Scheres, B. A Plausible Microtubule-Based Mechanism for Cell Division Orientation in Plant Embryogenesis. Curr. Biol. 2018, 28 (19), 3031-3043.e2.
We show that a computational model for dynamic selforganization of cortical microtubules on experimentally extracted cell shapes provides a plausible molecular mechanism for division plane orientation in the first four divisions of early-stage Arabidopsis thaliana embryos, in WT as well as two developmental mutants, bodenlos, and clasp. We simulate microtubules on actual cell surface shapes, from which we derive rules for proper array orientation, which generate early embryonic division plane orientations and potentially offer a framework for understanding patterned cell divisions in plant morphogenesis.
Chakrabortty, B.; Blilou, I.; Scheres, B.; Mulder, B. M. A Computational Framework for Cortical Microtubule Dynamics in Realistically Shaped Plant Cells. PLOS Comput. Biol. 2018, 14 (2), e1005959.
Plant morphogenesis depends on the directional growth and the subsequent oriented division of cells, where both these processes are controlled by the orientation of the cortical microtubule array. We describe a framework for simulating microtubule dynamics on cell surfaces (cortex) obtained from microscopic images. We apply our framework to the highly non-trivial geometry of leaf pavement cells of Arabidopsis thaliana, Nicotiana benthamiana, and Hedera helix. Our simulations revealed strong constraints of cell geometry on the orientation of division planes.
Cao, Y. X.; Chakrabortty, B.; Barker, G. C.; Mehta, A.; Wang, Y. J. Bridges in Three-Dimensional Granular Packings: Experiments and Simulations. Europhys. Lett. 2013, 102 (2), 24004.
We present a combined experimental and computational study of bridge structures in three-dimensional dry granular packings. Small bridges are predominantly linear and have an exponential size distribution, while larger bridges follow a power-law size distribution. Our experiments, which use X-ray tomography, are in good agreement with the simulations for the distribution of sizes, end-to-end lengths, base extensions, and orientations of predominantly linear bridges. Our study revealed that packing fraction is an important determinant of the bridge structure.
Chakrabortty, B.; Mehta, A. A Two-Species Model of a Two-Dimensional Sandpile Surface: A Case of Asymptotic Roughening. Granul. Matter 2012, 14 (4), 523–529.
We present and analyze a model of an evolving sandpile surface where the dynamics of mobile grains and immobile clusters are coupled. Our coupling models the situation where the sandpile is flat on average so that there is no bias due to gravity. We find anomalous scaling: the expected logarithmic smoothing at short length and time scales give way to roughening in the asymptotic limit, where novel and nontrivial exponents are found.