Research

This project primarily aims at deciphering the molecular details of the insulin dimer dissociation process. This represents a general process of immense biological and physiological importance. The project has three goals: (i) Understanding the roe of protein internal friction and associated solvent dynamics, (ii) microscopic details of the initial stages of dissociation, and (iii) calculating the rate of this process based on the theories of chemical kinetics.

Nanoconfined water is known to exhibit several anomalies that are different from those in the bulk phase. We aim to unearth the microscopic origin of such anomalous physicochemical properties under nanoconfinement by employing time-dependent statistical mechanics and computer simulations. We study anisotropic dielectric response, solvation dynamics, reaction acceleration, hydrophobic force law, diffusion, and phase transition under aqueous nanoconfinement. In addition, we investigate the effect of liquid-surface interaction, shape, and size of the nano-enclosures.

Water has an extremely complicated phase diagram with more than 18 known crystalline phases, multiple amorphous phases and different liquid states with characteristic densities and structures. Our primary aim to understand the origin of these phases and their mutual transitions. We study the properties of the phases of water over a wide range of pressure and temperature.

Binary mixtures constitue an important class of systems that play significant roles in biology, chemistry, and several other scientific and industrial fields. These systems often show anomalous properties, particularly at low solute concentrations, for example, water-DMSO at ~15 %, water-ethanol at ~10-12% compositions. We study the nature and molecular origins of these anomalies in binary mixtures.

Aqueous binary mixtures are of paramount importance both as a solvent in the chemical industry and also as a medium of reactions in laboratory. Water-ethanol mixture is known to display a range of startling composition-dependent anomalies. We study the rotational and translational dynamics, re-entrant type behavior and also explore the hydrodynamic predictions and mode-coupling theory approach of diatomics which exhibit remarkable sensitivity to the composition of the mixture. We also aim to explore the diffusion dynamics and composition dependence of ions in binary mixtures.

Our primary goal is to develop a generalized approach for the calculation of reaction rates in a rugged free energy landscapes. We are currently studying the dissociation of insulin dimer in aqueous solution. We obtain the 2D free energy surface using parallel tempering metadynamics simulation. Additionally, we investigate the role of water in the dissociation process.

We model the dynamics of an epidemic and its effects on the population and herd immunity. Currently, we are studying the effect of distributions of susceptibility and infectivity and long range migration on the spatio-temporal evolution of an epidemic and the oigin of multiple infection waves. We develop master equations including all these factors and solve them using Kinetic Monte Carlo Cellular Automata simulations and propagation technique.

The interface between Ice Ih and liquid water is much sharper than that for Lennard-Jones crystal-melt interface. We investigate the origin of this sharpness and study the interfacial fluctuations. We probe the interfacial properties using structural, dynamical and thermodynamical order parameters.

Entropy provides the measure of phase space and diffusion is related to the rate of transition between different regions. We explore the relationship between these seemingly unrelated properties in deterministic two-dimensional Hamiltonian model systems. We investiagte the appearance of crossover in the diffusion-entropy relation when the bottleneck in the phase space becomes narrow.

Förster resonance energy transfer plays a unique role as “Spectroscopic Ruler” because the rate exhibits a strong separation distance (R) dependence. In an earlier study, we showed that optically dark states, in spite of having a large transition rate between the donor and acceptor, are neglected in the Förster expression, which gives the rate as an overlap integral between the donor fluorescence and acceptor absorption spectra. We have started to develop a fully consistent kinetic description of this process, where we study the interplay between relaxation in the donor and acceptor vibronic manifold and the effects of optically dark states contributing to the observed energy transfer rate.

We focus on the coupled water-solute dynamics of small linear molecules like carbon monoxide, nitric oxide and cyanide ion. We also investigate the translation-rotation coupling in the jump motion driven diffusion of these molecules.

Some of the issues that we investigate are the mechanism of protein-water coupling, protein and DNA solvation dynamics, effect of solvent on the structure and dynamics of biomolecules, solvent mediated protein dissociation, stability of biomolecular assemblies like insulin hexamer and dimer, dynamical and thermodynamical properties of hydration layers.

Small molecules, for example, metformin, curcumin, lycopene, and several steroids exhibit extraordinarily diverse biological activities and possess life-saving medicinal properties. However, the physical chemistry of these important small molecules at a molecular level remain largely unexplored. We aim to develop sustainable force-fields for these small molecules (with the help of experimental collaborations) in order to study the structure, dynamics and interaction with biomolecules such as DNA or lipid bilayers.