The principles behind the organization of chromatin into a three-dimensional folded structure inside the nucleus remains an important open question. While the specific sequence has a role to play, at large length scales, the assembly is likely dominated by physical interactions. We investigate the role of various chromatin-protein interactions, such as lamin proteins and the SMC proteins in the organization of the nucleus.

• A Lamin Associated Chromatin Model for Chromosome Organization

• The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

• Multivalent binding proteins can drive collapse and reswelling of chromatin in confinement

• Predicting scale-dependent chromatin polymer properties from systematic coarse-graining

• Protein search processes mediated by chromatin topology
  Shuvadip Dutta, Adarshkrishnan R., Ranjith Padinhateeri, Mithun K. Mitra

One of the major areas of research we have been engaged in involves understanding the mechanisms underlying the reprogramming of a fully differentiated cell back to a stem cell state. We attempt to put on a mathematical footing the concept of an "epigenetic landscape" put forward by Waddington, by using dynamical equations that models the underlying gene regulatory networks. In particular, we have been interested in the role of time-delayed feedback loops in this differentiation process.

• Reprogramming, oscillations and transdifferentiation in epigenetic landscapes

• Delayed self-regulation and time-dependent chemical drive leads to novel states in epigenetic landscapes

We are interested in how morphogen gradients form and how cytoplasmic and cortical structures evolve in the early syncitial Drosophila embryo. In particular, we investigate how interactions with cytoplasmic and membrane elements can shape the formation of gradients.

• Cyto-architecture constrains a photoactivation induced tubulin gradient in the syncytial Drosophila embryo

• Pseudocleavage furrows restrict plasma membrane-associated PH domain in syncytial Drosophila embryos

The ability of the cell to maintain the spatial organization of its constituents and modify it in regulated fashion in response to external and internal cues crucially depends on motor driven intracellular transport of cellular cargoes. Cellular cargo is transported by motor proteins - such as kinesins and dynein - walking along cytoskeletal filaments such as Microtubules (MT) and Actin. One of the main aims of our research is to theoretically explore how the property of catch bonding in dynein manifests itself in the emergent collective transport properties within the cell and shapes the mechanical response of cellular constituents.

• Catchbond mediated oscillations in motor-microtubule complexes

• Dynein catch bond as a mediator of codependent bidirectional cellular transport

• Effect of catch bonding on transport of cellular cargo by dynein motors

• Cargo transport by catchbonded motors in optical trapping assays

We are interested in non-equilibrium phase transitions in systems of active rod-like particles, as a model system to understand how activity affects ordering in nematic and polar systems.

• Diffusion dynamics and steady states of systems of hard rods on a square lattice