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Theoretical Condensed Matter

Numerical Simulation of Active Proteins and of Gene Transcription. Self-Assembly of Viruses Self-Assembly of DNA and the Physics of Chromatin. Electrostatics of DNA and electrical transport along DNA. Adhesion of vesicles and cells.

Our Groups' Previous Work in Studying the Pressure of DNA Viruses - Packing DNA in Bacteriophage

Bacteriophage lambda, shown in the electron micrograph, consists of a protein capsid 30 nm in radius that has a long cylindrical tail. Its genome, double stranded DNA (dsDNA), is protected by the capsid from attack by nuclease enzymes that would break it down into its nucleotides and therefore lose the genetic information needed to replicate the phage. The DNA contains 48.6 kilo-base pairs; if it were fully extended it would be 17 micrometers long. When the phage is replicated in the host cell, an early form of the capsid, the procapsid, is formed and the DNA is driven into it by a molecular motor at one of the procapsid vertices. This is quite feat! Imagine packing a length of string into an object that is only 1/400th its size. To make the job harder, add negative charges to the string and make it stiff. The stiffness of ds DNA is very high; a measure of this stiffness is its persistence length. It is difficult to bend objects on a scale smaller than the persistence length. The persistence length of dsDNA is 50 nm, and to bend it so that it can fit into the capsid is therefore highly costly in energy.
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