March30

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

May7

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

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

## Reading List

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

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

*Updated: 2017/7/3, CAA*