Connecting dynamics to structural data from diverse experimental sources, molecular
dynamics simulations permit the exploration of biological phenomena in unparalleled detail …

We review approaches aimed at deciphering the physical mechanisms responsible for viral
structure and assembly. We discuss the basic principles of condensed matter physics …

Highlights•Review of the most recent studies in Mechanical Virology, using AFM nano-
indentation.•Mechanics of structural capsid changes during maturation.•Uncoating …

The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

In theoretical modeling of a physical system, a crucial step consists of the identification of
those degrees of freedom that enable a synthetic yet informative representation of it. While in …

Abstract Background Elastic network models (ENMs) are based on the simple idea that a
protein can be described as a set of particles connected by springs, which can then be used …

Recent studies have shown that single-stranded (ss) viral RNAs fold into more compact
structures than random RNA sequences with similar chemical composition and identical …

Elastic network models, simple structure-based representations of biomolecules where
atoms interact via short-range harmonic potentials, provide great insight into a molecule's …

Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for
characterizing functionally oriented structural changes via a parsimonious set of degrees of …

We present a new coarse-grained Cα-based protein model with a nonradial multibody
pseudo-improper-dihedral potential that is transferable, time-independent, and suitable for …