Modeling Polymer Structures and Dynamics

 

Polymers, which many people think refer only to plastic, are actually a large group of natural and man-made materials. They have many uses in industry and as consumer products. Some of these include the super-absorbant polymers used in disposable diapers, the heat-stable materials used for non-stick cookware, and the fiber spandex, used for stretchy clothing like athletic wear and foundation garments. The research group of Associate Professor Kevin Dorfman (Chemical Engineering and Materials Science) is using MSI for research into the structures and dynamics of polymers, especially DNA. On the engineering side, understanding the dynamics of DNA has many important applications in genomics. On the scientific side, DNA is a model system for investigating the basic physical properties of semiflexible polymers. The Dorfman group is using several computer-simulation techniques, including Metropolis and chain growth Monte Carlo methods.

Professor Dorfman and graduate student Douglas Tree, along with their colleague Yanwei Wang (Soochow University, China), recently published research in Physical Review Letters concerning DNA confinement in nanochannels. DNA confinement is becoming an important tool for genomics research. It also provides researchers a platform for testing theories concerning confined wormlike polymers. The classical theories for polymer chains in confinement only work in cases where the nanochannels are very small or very large compared to the polymer. The Dorfman group has investigated an intermediate case between the two models. In the graphic above, the Odijk theory applies to DNA in small channels and the Flory-de Gennes theory works for large channels. The newly proposed regime of behavior, called the “Gauss-de Gennes” regime by the researchers, works for the intermediate channel sizes that have been typically used in genomic devices. The researchers propose that this regime applies to the general class of semiflexible polymers, which includes DNA as a special case.

The article can be read on the American Physical Society website: “Extension of DNA in a Nanochannel as a Rod-to-Coil Transition,” DR Tree, Y Wang, DK Dorfman, Physical Review Letters, 110:208103, DOI:10.1103/PhysRevLett.110.208103 (2013).

Image description: Illustration of the analogy between free solution and confined configurations of a wormlike chain. The classical theories renormalize the chain into a series of subchains, where these subchains are either rodlike (Odijk) or excluded-volume blobs (de Gennes). (For clarity, the authors refer to the classic de Gennes regime as the “Flory-de Gennes” regime.) The middle drawing illustrates a universal Gauss-de Gennes regime in confinement that is an intermediate step between the two classical ones. © 2013 American Physical Society

Posted on September 11, 2013.

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