In this review, we provide an organized summary of the theoretical and computational
results that are available for polymers subject to spatial or topological constraints. Because …

The mechanical properties of DNA play a critical role in many biological functions. For
example, DNA packing in viruses involves confining the viral genome in a volume (the viral …

Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …

This work presents an all-atom molecular dynamics simulation of a complete virus, the
satellite tobacco mosaic virus. Simulations with up to 1 million atoms for over 50 ns …

We report a study of the structural dynamics of viral capsids, simulated on a microsecond
timescale, by employing a coarse-graining molecular dynamics method. The method was …

The conjunction of insights from structural biology, solution biochemistry, genetics, and
single-molecule biophysics has provided a renewed impetus for the construction of …

A string of nucleotides confined within a protein capsid contains all the instructions
necessary to make a functional virus particle, a virion. Although the structure of the protein …

Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline
density and achieve one of the highest levels of DNA condensation found in nature. Despite …

The critical viral components for packaging DNA, recognizing and binding to host cells, and
injecting the condensed DNA into the host are organized at a single vertex of many …

Recent experiments showed that the linear double-stranded DNA in bacteriophage capsids
is both highly knotted and neatly structured. What is the physical basis of this organization …