Charged Polymers: From DNA to Polyampholytes

Abstract: Three main themes are outlined in this thesis: Polyelectrolytes/DNA : In a living cell, DNA molecules have a compact conformation in order to fit in, while in a test tube they will take on an expanded cylindrical shape, due to the negative phosphate groups along the DNA molecule. With the help of computer simulations it has been shown that like-charged monomers of a poly- electrolyte can attract each other if the counterions are taken into account. This is due to ion-ion correlations, which become important at high electrostatic coupling. These findings are confirmed by fluorescence microscopy. Polyampholytes : Polyampholytes are polymers with both negative and positive charges and they have the ability to adsorb to charged surfaces, modifying the surface properties. With the help of computer simulations it is possible to explain how and why poly- ampholytes adsorb to charged surfaces and how they can affect forces between other charged macroions. The behavior of a polyampholyte is very dependent on the chain topology. Computational Steering and visualization of molecular simulations : GISMOS is a project aimed at providing an intuitive and powerful program suite for visualizing and controlling molecular simulations. The basic idea is to be able to use existing well-tested simulation programs and provide them with a visual interface in which all important aspects of the program can be controlled.