Research Projects

The advent of advanced techniques provided unprecedented information about the equilibrium properties of polymer in the confined region. For example, protein-folding research has been dominated by the assumption that thermodynamics determines protein structure and function. However, recently accumulated evidence has supported the emerging paradigm of role of anisotropy. Namely, changing the pulling direction, role of handle, confinement imposed by cellular environment of biopolymers greatly influence their properties. Another interest is theoretical understanding of a biopolymer chain in confined environment, which remains quite challenging. Present proposal envisages the role of CNT and its interaction with biopolymers on the biological processes. We shall use the lattice model along with exact enumeration techniques to get free-energy barrier associated involved in biological processes. These studies will be supplemented by Molecular Dynamics of the off-lattice coarse-grain-model of polymer followed by atomistic simulations, if required to gauge the microscopic information about the processes. The knowledge of the molecular mechanism of biological processes e.g. replication and transcription may provide a deeper understanding of DNA sequencing, information about gens transferring between bacteria, transport of RNA across cell membrane, etc, which are still unexplored or less understood territory of biology. In this context, nucleic acid hairpins may serve as a powerful model system for probing the formation of secondary structure during transcription and replication. We shall investigate the kinetics and thermodynamics of the folding transition for individual DNA hairpins of varying stem length, loop length, and sequence.