A polymer molecule in solution can be thought of as a long, slender,
but somewhat stiff string-like object whose motion is driven by the
frictional drag and fluctuating thermal forces exerted by the
surrounding solvent medium. In addition, the motion of any segment of
a polymer chain is propagated to all the other segments through the
solvent. That these hydrodynamic interactions play a crucial role in
determining the dynamical behaviour of polymer molecules has been
known for a long time. However, it is only recently that efficient
algorithms for carrying out simulations of stiff polymer molecules
with hydrodynamic interactions have been developed.
In this Project, we use simulations incorporating these new algorithms
to explore several open problems in polymer physics. For instance, it
is well known that isolated polymer molecules collapse in poor
solvents to form compact structures such as rods, toroids and
spherical globules. What are the kinetics of the formation of such
structures? A second interesting question has biological relevance. It
is suspected that a critical step in the replication of DNA in
eukaryotic cells is the formation of loops. In order to form a loop,
however, the ends of the polymer chain need to meet. What is the
influence of hydrodynamic interactions, and other parameters such as
the local stiffness of the chain backbone, and the quality of the
surrounding solvent on, say, the average time it takes for the chain
to loop back? The interactions of polymer chains with surfaces is
still largely unexplored, and are relevant to the study of polymers
adsorbing onto rigid and flexible surfaces. The rates at which
adsorption takes place in quiescent conditions or in flow are not only
affected by van der Waals and electrostatic interactions between
polymers and surfaces, but are also strongly influenced by the
hydrodynamic interaction between the surface and the polymer.
All these simulations are complex, and the APAC-NF facility is
indispensable in performing such computationally intense simulations.