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 …

Biopolymers in vivo are typically subject to spatial restraints, either as a result of molecular
crowding in the cellular medium or of direct spatial confinement. DNA in living organisms …

Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems,
from mixtures of polymers and DNA filaments packed in vivo to interlocked line defects in …

We used molecular dynamics simulations to investigate the statics and dynamics of poly [n]
catenanes for different bending rigidities of the constituent rings. We show that stiffer rings …

The mechanism by which type-2A topoisomerases transport one DNA duplex through a
transient double-strand break produced in another exhibits fascinating traits. One of them is …

The folding of a protein towards its native state is a rather complicated process. However,
there is empirical evidence that the folding time correlates with the contact order, a simple …

The three dimensional organization of genomes remains mostly unknown due to their high
degree of condensation. Biophysical studies predict that condensation promotes the …

" Knot theory is a fascinating mathematical subject, with multiple links to theoretical physics.
This enyclopedia is filled with valuable information on a rich and fascinating subject."–Ed …

In this work we present a computational study of the kinetoplast genome, modelled as a
large number of semiflexible unknotted loops, which are allowed to link with each other. As …

We study random knots and links in R^ 3 R 3 using the Petaluma model, which is based on
the petal projections developed in 2. In this model we obtain a formula for the limiting …