Murugappan Muthukumar

Murugappan Muthukumar

Wilmer D. Barrett Professor of Polymer Science and Engineering, University of Massachusetts

Ph.D.: The University of Chicago

Research Interests

Research activities include theory, simulations, and experiments on biological and synthetic polymers. Topics include characterization, thermodynamics, self-assembly, dynamics and kinetics of variety of polymeric systems. Systems under investigation are polyelectrolytes, self-assembling copolymers and crystallizing coplymers. Theoretical procedures are perturbation theory, variational calculation, renormalization group theory, self-consistent field theory, and density functional theory.

We use molecular dynamics, Brownian dynamics, Monte carlo, and time dependent Landau-Ginzburg methods in our modelling efforts. We also use static and dynamic light scattering and small angle neutron scattering technique as experimental tools.

Our work in polyelectrolytes and pattern recognition is inspired by the organization of self-assembled macromolecules and the controlled exhibition of myriads of their functions in the natural environment of biological cells. A typical cartoon of a mammalian cell is presented in figure 1. The actual details can be found in any textbook on biology. A cell is a very crowded environment consisting of several partitions, each with carefully regulated distributions of macromolecules with prescribed sequenses of various monomers. Almost all of these macromolecules are charged and are present in an electrolytic medium with many kinds of small dissociated ions. The cell may be considered to be a crowded `Coulomb soup'. The charged macromolecules (called polyelectrolytes) physically assemble to form various large structures. For example, the microtubules are self-assembled (i.e., `polymerized' via noncovalent physical association) structures of thousands of tubulin monomers (themselves being monomers) using a combination of hydrophobic and electrostatic interactions. Another example is the chromosome which is a super complex between the negatively charged DNA and many proteins carrying a net positive charge. The rich heirarchy of structures in the self-assembly of chromosomes are nicely documented in many textbooks [1,2] on biology. So we only mention here that during the M-phase of the cell cycle, the chromosome is a compact complex (figure 2) of very many loops of chromatin fiber (itself being a complex of DNA and proteins) stitched along the chromosomal axis using the so called anchoring complexes. It is to be noted that the loop length is much longer than the persistence length of the fiber. These compactly arranged loops are distributed into the euchromatin and heterochromatin in the I-phase which is of the longest duration in the cell cycle. After copying of information contained in the chromosome is completed, the loops are faithfully repackaged back in to the M-phase chromosome. It is empirically known that the inner membrane of the nuclear envelope plays a crucial role in the distribution and redistribution of DNA loops via many complexation processes. A proposed mechanism for the distribution of loops and the chromosomal condensation is presented in figure 3.

The transport of biological macromolecules under crowded environments is known to occur very effectively from one specific location to another using many signaling methods. For example, proteins synthesized in the proximity of the endoplasmic reticulum are transported to the Golgi apparatus, where they undergo modifications and sorting and they then get dispatched to their final destinations. Furthermore the transport of macromolecules is carried out through
narrow pores. For example, the m-RNA is transported from the nucleus to the cytoplasm through nuclear pores. This is a necessary step before proteins are
synthesized which in turn get into the nucleus to control the formation of the m-RNA. Therefore it is clear that there is a tremendous amount of cooperativity in various processes involving complexation and transport.