Synthetic morphogenesis at EMBL Heidelberg


The use of synthetic biology in engineering biological systems has been rapidly expanding. the conference at EMBL Heidelberg from 17-20 March 2019 on “Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture” highlighted this in the context of understanding growth and developmental morphogenesis. It brought together an unusual combination of researchers ranging from:

  • in vitro reconstitution of cytoskeletal networks
  • giant unilammelar vesicles (GUVs) for encapsulating proteins: towards synthetic cells
  • rebuilding gradients of morphogens by engineering cells
  • organoid models of tissue morphogenesis
  • engineering blastulas and developing embryos predictively modify developmental outcomes

The Physical Basis of Biological Pattern Fomation


Here I hope to keep some of the expanding links, some work and some more information on biological pattern formation that is self-organized and based on physical principles- chemical or mechanical.

Simulation from Random Walk with Drif model (Khetan and Athale, 2016, Plos Comp. Biol.)

Watching List

  1. Bird A. (2015) Apoiological: mathematical speculations about bees. Part 1: Honeycomb Geometry
  2. Spherical Spiral and loxodromes from MATHEMATICA on
  3. On J.T. Bonner and Dicytostelium discoideum: A short documentary
  4. Time-lapse movie of the aggregation of Dicytostelium: Thomas Gregor Lab, Princeton

Reading List

  1. Bonner. The Social Amoebae. The Biology of Cellular Slime Moulds.
  2. C. V. Boys. Soap Bubbles and the Forces Which Mould Them. [Book from arvindguptatoys]
  3. P. Ball. (2001) The Self-Made Tapestry. Pattern Formation in Nature. [Amazon]: Available in the IISER P Library
  4. The Math and the Art of M. C. Escher: Part 1: Tesselation by Polygons
  5. Regular tesselations on Wolfram.mathematica
  6. Dudte et al. (2016) Programming curvature using origami tessellations. Nature Materials 15, 583–588. doi:10.1038/nmat4540. Work from L. Mahadevan’s lab
  7. Phyllotaxy, Fibonacci numbers, the golden ratio (Goldener Schnitt) and their mathematics from Ron Knott, Univ. of Surey, UK

    The spirals in the sunflower

Doing List

  1. Logarithmic spirals: r = a*e^(b*theta), where r: radius of the spiral, a, b: scaling constants, theta: angle range 0 to 2*pi.
  2. Mathematica, MATLAB code (source)

Updated: 2017/7/3, CAA