Nonequilibrium Dynamics of Macromolecules

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The project is designed to explore the nonequilibrium kinetics of conformational transitions in macromolecules. Particular emphasis will be laid on the role of solvent viscosity in the kinetics of the collapse transition of a polymer upon changing the solvent condition from good to poor. We will employ a coarse-grained explicit solvent framework for Molecular Dynamics (MD) simulations using the Lowe-Andersen (LA) thermostat that allows easy tuning of the solvent viscosity and preserves hydrodynamic interactions. To a great extent, this mimics the situation a real polymer experiences in a solution. The nonequilibrium kinetics of the collapse transition will be probed in terms of various scaling laws for the relaxation time, growth of the relevant time-dependent length scale characterizing the local ordering, and aging properties. We will first consider the case of flexible homopolymers followed by a study of semiflexible homopolymers. Motivated by the hydrophobic (H) and hydrophilic (P) classification of amino acid residues of proteins, in the next step we will study HP-heteropolymers for selected sequences. Preliminary results for flexible homopolymers suggest that depending on the solvent viscosity one observes prolonged periods of intermediate sausage-like structures along with the usual pearl-necklace-like local ordering. For semiflexible homopolymers and flexible HP-heteropolymers too, we expect to encounter such novel phenomena. We will design analysis tools for extracting quantitative information relying on our experience with coarsening kinetics of spin and particle systems, and on our expertise in identifying different shape factors (asphericity, prolateness, cylindricity, etc.) of equilibrium polymer conformations. We will compare the results obtained for these three different classes of polymers to identify the presence of any universality in the kinetics. Taking a step ahead, in the final part of the project we will perform MD simulations of a chemically realistic polymer, viz., polyalanine which shows a coil-helix transition. We will use an all-atom description of polyalanine and initially a coarse-grained solvent setup using the LA thermostat. Next we shall use specifically water as a solvent using an all-atom description (TIP3P). In combination with the preceding results, this part will lead to a comprehensive understanding of the kinetics of various conformational transitions of macromolecules. At the same time, this will also make our results amenable to experimental verification.