Visitors

Arnab Bhattacharyya (Indian Institute of Science)
May 2015

Arnab Bhattacharyya is a computer scientist at the Indian Institute of Science. He returned to NCBS for the second year as a long-term visitor, and spent two months at the Simons Centre interacting with the group of Mukund Thattai as well as of other faculty members. Bhattacharyya and Thattai continued their collaborations applying methods of theoretical computer science to various biological problems. In particular, they have applied methods in graph theory to understand sets of “impossible topologies” of vesicular traffic systems, the network of transport which moves material inside eukaryotic cells. They have also started investigating the role of information exchange during sexual reproduction in eukaryotes, with the goal of identifying fundamental limits on the benefits of such exchange.

Mathias Heltberg (Niels Bohr Institute, Copenhagen)
Apr 2015

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 (Indian Institute of Science)
Jun 2014 to Jul 2014

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.

Dr. Garud Iyengar (Columbia University)
Jul 2014

Simons Colloquium and discussions and collaborative work with Madan Rao on (i) Nonequilibrium Statistical Mechanics formalism for information optimisation when the sensors are dynamic; (ii) Information theoretic approach to constraints on Golgi cistern number arising from sequential chemical processing.

Madhavan Mukund (Chennai Mathematical Institute)
Jul 2014

Exploring potential routes of collaboration between CMI and the Simons Centre.

Dave Thirumalai (University of Maryland)
May 2014

Talk and discussions on co-translational protein folding, ideas of control theory applied to cellular homeostasis and ideas of globular proteins as nematic amorphous drops. Simons-NCBS CDF Deepika Janakiraman is scheduled to go to Maryland to work in the Thirumalai group.

Chandra Shekhar Verma (BII, Singapore )
Mar 2014

During this visit, we plan to work on the folding and aggregation of the tumour-suppressor protein p53. In addition, Dr. Varma will teach a workshop in atomistic simulations, and also interact with experimental protein aggregation research efforts across the NCBS campus.

Chandra Verma (Bioinformatics Institute Singapore)
Feb 2014

 

Chandra is an expert on computational protein dynamics. While at NCBS he presented a seminar titled, “Stapled diet: Food for thought,” on the importance of dynamics in the design and development of stapled peptides to target and abrogate protein-protein interactions. He also presented an informal tutorial on techniques for analysing cavity water dynamics in MD simulations. The Gosavi group is interested in using these techniques to understand the propagation or disruption of allosteric networks in proteins (specifically a pair of immune response proteins, IL-33 and IL-1β) through cavity water. The visit also led to several long term joint projects with the Gosavi group on multiscale modelling of the dynamics of proteins involved in cancer, particularly p53 and EGFR. An NCBS student, Shilpa Yadahalli, is on an extended visit to the Verma group to further some of these projects.

Szabolcs Semsey (Niels Bohr Institute)
Feb 2014

During the visit we made significant progress on a project comparing the effects of transcriptional regulation with translation, proteolytic and allosteric regulation. This is based on a synthetic transcription factor constructed in the Semsey lab in Copenhagen, based on the Lac repressor of E. coli, that could be controlled simultaneously by all four types of regulators. Models developed by Sandeep Krishna during this visit enabled us to explore and compare the full range of dynamical capabilities of each regulatory mechanism. A paper on this has been submitted to the Journal of Biological Chemistry. In addition, the visit triggered a new collaboration between with Aswin Seshasayee (NCBS) studying restriction-modification systems (RM-systems) in bacteria, which are thought to be important defense mechanisms against bacteriophage attack. Our preliminary simulations suggest that weak RM-systems are not particularly useful as defenses against phage, but are extremely important for creating phage that can be used by one bacterial strain as a weapon against other competing strains. A manuscript on this work is under preparation.

Ian Dodd (Adelaide University)
Oct 2013

This visit was instrumental in the completion of an existing project, studying protein roadblocking of DNA transcription in bacteria. Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. We have been combining systematic experiments (in Ian Dodd’s laboratory) and mathematical modelling (a collaboration between Kim Sneppen and Sandeep Krishna) to analyse how roadblocking by the lac repressor (LacI) in E. coli cells is affected by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein Mfd, and promoter-roadblock spacing. In this visit we were able to build models of RNAP traffic and LacI roadblocking, and combine them with experiments to make specific predictions that will lead to further experiments. In the spring of 2014 we submitted a manuscript on this work to Nucelic Acids Research where it is currently under second round of reviewing after revisions.

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