Although atoms and molecules are quantum mechanical objects, their movement can often be well simulated using classical physics, with empirical potential energy functions to describe the forces exerted on each atom by its neighbors. Such molecular dynamics calculations have long been performed on proteins containing thousands of atoms (see Physics Today, December 2013, page 13), and now, thanks to powerful supercomputers and specially designed algorithms to exploit their many processors, researchers can model even larger systems, including whole viruses. Using the K computer at RIKEN in Japan, researchers led by Nagoya University’s Susumu Okazaki have turned their attention to the capsid, or shell, of the poliovirus.1 

Shown in the figure, the capsid comprises 240 protein molecules arranged in an icosahedrally symmetric structure. Normally, the capsid is packed with the virus’s genetic material, but natural virus samples also include some capsids that are filled with nothing but...

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