My research group is engaged in understanding how macromolecules, both biological and synthetic, assume their sizes and shapes, organize into assemblies, and move around in crowded environments. We employ a combination of theoretical, computational, and experimental techniques to uncover the underlying mechanisms of macromolecular phenomena in Physical Biology and Polymer Physics. The major issues that are under active investigation are the following:
The transport of isolated polymer chains through a narrow channel is one of the central fundamental processes in Life. This phenomenon is also of great significance in the separation science. We use statistical mechanics, Langevin Dynamics simulations, Poisson-Nernst-Planck formalism, and electrophysiology experiments to understand the translocation of individual chains through alpha-hemolysin and synthetic pores. Strategies to sequence DNA and to enhance polymer separations are being developed.
2. Virus Assembly
In an effort to identify the general principles behind virus assembly, we investigate the complexation between the capsid proteins and the viral genomes by a combination of Self-Consistent-Field Theory and Brownian Dynamics simulations. We investigate both the ss-RNA viruses and ds-DNA bacteriophages. In addition to the modeling the folded structure of the genome, we model the kinetics of virus assembly.
The wrapping kinetics of a guest macromolecule or a colloidal object by a flexible membrane is investigated theoretically. The competition between attraction between the host and membrane, and the membrane elasticity leads to a nucleation barrier. The kinetics of wrapping/unwrapping is investigated with the formalism of nucleation and growth.
4. Vision Physics
We investigate experimentally the interaction among the various macromolecules (including crystallins, proteoglycans, and collagen) that constitute the major optical components of an eye. The primary objective is to identify the macromolecular mechanisms behind clumping of proteins in crystalline lens in efforts to reverse/remove the onset of cataract and presbyopia.
5. Polyelectrolyte Gel Physics
The gel dynamics is followed by a combination of impedence, light scattering, and rheological measurements to investigate the coupling of counterion dynamics and network elasticity. New theory is developed to understand the volume phase transitions of charged gels, and phase transitions in polyelectrolyte solutions.
Phase behaviors of polyelectrolytes in polar solvents and those of hydrophobic and hydrophilic polymers in ionic liquids are being developed theoretically.
Exquisite crystal structures of minerals are made in Nature where the specific polypeptide chains are able to control the directionality of the crystals. Our objective is to evaluate the relation between the templating polypeptide sequences and the crystal growth kinetics. Our Molecular Dynamics and Monte Carlo simulations are specifically aimed at understanding zinc oxide and silica in the presence of polypeptides of prescribed sequences.
One of the long-standing challenges in the field of polymers is to figure out how long interpenetrating and entangled polymer chains organize into crystals upon cooling. We use a combination of simulations and theory to understand the principles behind spontaneous selection of crystal thicknesses and the crystallization kinetics.