Arnab Bhattacharyya is a computer scientist with a long-standing interest in biology. The goal of this visit was for us to explore potential areas of collaboration. During this visit, along with three PhD
students at the Simons Centre (Anjali Jaiman, Amit Singh, Kabir Husain), we made significant progress on a fundamental biological problem: the question of how cells encode the creation of specific branched sugar polymers called glycans which decorate the surface of every living cell. Glycans mediate physical interactions between cells, provide a layer of protection against pathogens, and underlie self-recognition in the immune system. Using ideas from algorithmic self-assembly, we outlined a set of specific local rules of enzyme-based polymer extension (analogous to the colouring rules which underlie the systems of “Wang tiles” proposed by Hao Wang). These rules are able to explain the bulk of existing biochemical data on glycan structure, and also seem to be able to explain the heterogeneity observed in real cells. We are now trying to test out these theories in collaboration with experimental groups, at NCBS as well as at the Centre for Genomic Regulation in Barcelona (Vivek Malhotra). We are also exploring the problem of distributed error correction in biological networks, though this discussion is at a very early stage.