The Physics of DNA in Bacteriophages
Bacteriophages are the 'viruses of bacteria', and they arguably provide the simplest possible biological system to study genome organisation, as most of them (the so-called DNA phages) are packed with double stranded DNA up to almost crystalline densities. Restricting to DNA phages, I will briefly present computer simulation investigations on the physics of DNA packaging and ejection in and out of bacteriophages. I will combine different coarse-grained simulation techniques (Monte-Carlo, kinetic Monte-Carlo and the stochastic rotation dynamic algorithm) to attempt to answer some (old and new) questions, mostly prompted by the increasingly accurate observations coming from experiments. E.g., how is the DNA arranged inside the phage capsid? Can we quantitatively understand the force which a molecular motor needs to exert to pack DNA? Does capsid shape affect packaging and ejection, i.e. is there an optimal shape for e.g. fastest ejection?
This is a weekly series of informal talks given primarily by members of the soft condensed matter and statistical mechanics groups, but is also open to members of other groups and external visitors. The aim of the series is to promote discussion and learning of various topics at a level suitable to the broad background of the group. Everyone is welcome to attend..