Visitors

The purpose of this visit was two-fold: (i) to teach a course during the Monsoon school, (ii) to continue collaborative work with Sandeep Krishna on Bayesian inference in biological processes. Manoj has demonstrated the link between chemical networks and Bayesian posterior calculations of models consisting of combinations of Poisson processes. In collaboration with Sandeep Krishna, he's now looking at the application of these ideas to bacterial quorum sensing systems and bacteriophage decision networks.

Abhishek and Debasish, both soft matter physicist visited the Simons Centre from 7th June to 8th July, 2015. Right at the start, they introduced their research interest to the wider NCBS fraternity, in back-to-back talks on "Soft and Active Matter" (Debasish Chaudhuri) and  "Dynamics of Biopolymers" (Abhishek Chaudhuri). Though they primarily interacted with Madan Rao and Vijay Krishnamurthy (ICTS-TIFR, Bangalore), they also had many intense discussions with Mukund Thattai, Sandeep Krishna, Sanjay Sane and others, and Amit Singh, Debsankar Banerjee and other PhD students. These discussions included topics such as, (i) influence of mechanical stresses at the cell surface on gene expression, (ii) transmission of information encoding the spatial organization of chromosomes across generations, (iii) role of multiplicative noise in active hydrodynamics, (iv) pattern formation in confined termites under shaking, (v) chiral symmetry breaking in active hydrodynamics, (vi) role of active mechano-chemical processes in the processing and transfer of information and distributed computing. 

With Madan Rao and Vijay Krishnamurthy, they worked on how spatially varying mechanical signals could propagate from the cell surface to the nucleus by treating the cytoplasm as an active elastomer with turnover of components (an appropriate description at  short time scales). The idea is that this description will naturally give rise to force-chains, which might explain the sensitivity to changes in mechanical signal applied at the cell surface. This work is still under progress and they will continue their collaboration on this and the many other ideas that came up during this visit. 

The purpose of this visit was to further a collaboration between the groups of Mogens Jensen (a previous Simons visitor), Sanjay Sane (NCBS) and Sandeep Krishna. The project involves the experimental study, in Sanjay Sane's lab, of coupled oscillators involved in insect flight and theoretical modelling of such coupled oscillators by Mathias, supervised by Mogens Jensen and Sandeep Krishna. The insect wing and the haltere are the two oscillators that are mechanically coupled through the insect body. In normal flies, the coupling causes the two structures to synchronize and oscillate out of phase. Theoretical analysis of coupled oscillators predicts the presence of finite windows of synchronization, called Arnold tongues, as the frequency of one of the oscillators is varied. And this is indeed observed by Tanvi Deora, Sanjay Sane's student, when she increases the frequency of the wing by clipping portions off. The project has two aims: (i) to use mathematical models to understand the nature of nonlinearities in the insect oscillators and their couplings, (ii) to discover new physics in coupled oscillators because the biological system works in a parameter regime which is not at all well understood, where Arnold tongues start overlapping.

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.