Ejection dynamics of polymeric chains from viral capsids: effect of solvent quality.
We present simulations investigating the effects of solvent quality on the dynamics of flexible (RNA-like) and semiflexible (DNA-like) polymers ejecting from spherical viral capsids. We find that the mean ejection time increases and the ejection time distributions are broadened as the solvent quality decreases. Our results thus suggest that DNA ejection may be very efficiently controlled by tuning the salt concentration in the environment, in agreement with recent experimental findings. We also observe random pauses in the ejection. These become extremely long for semiflexible polymers at lower solvent quality, and we interpret this as a signature of a low driving force for ejection. We find that, for most polymers, ejection is an all-or-nothing process at the solvent conditions we investigated: polymers normally completely eject once the process is initiated.
Ali
I
I
Department of Physics, College of Science, Sultan Qaboos University, Al-Khod, Oman.
Marenduzzo
D
D
Yeomans
J M
JM
D002213:Capsid / Q000737:chemistry* / Q000502:physiology; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry* / Q000502:physiology; D008954:Models, Biological; D008956:Models, Chemical; D011108:Polymers / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry* / Q000502:physiology; D012997:Solvents / Q000737:chemistry*; D014775:Virus Activation; D016662:Virus Integration / Q000502:physiology
D004279:DNA, Viral; D011108:Polymers; D012367:RNA, Viral; D012997:Solvents