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Adv Chem Phys 2014;155:1-68

Department of Physics, Brandeis University, Waltham, MA, 02454.

I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. Read More

Adv Chem Phys 2013 ;153:311-372

Adv Chem Phys 2012 Jan;150:255-326

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health(NIH), 5635 Fishers Lane, Room T900, Bethesda, MD 20892-9314.

This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. Read More