Related papers: Chirality modifies the interaction between knots
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
We employ computer simulations and thermodynamic integration to analyse the effects of bending rigidity and slit confinement on the free energy cost of tying knots, $\Delta F_{\rm knotting}$, on polymer chains under tension. A…
Coupling between axial and torsional degrees of freedom often modifies the conformation and expression of natural and synthetic filamentous aggregates. Recent studies on chiral single-walled carbon nanotubes and B-DNA reveal a reversal in…
Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along…
Motivated by the observation of positive Gaussian curvature in kinetoplast DNA networks, we consider the effect of linking chirality in square lattice molecular chainmail networks using Langevin dynamics simulations and constrained gradient…
A coarse-grained computational model is used to investigate how the bending rigidity of a polymer under tension affects the formation of a trefoil knot. Thermodynamic integration techniques are applied to demonstrate that the free-energy…
The elastic properties of the double-stranded DNA handles used in optical tweezers experiments on biomolecules are customarily modeled by an extensible worm-like chain model. Fitting such model to experimental data however is no trivial…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
Chirality is known to play a central role in the properties of many physical systems across a wide range of spatial and temporal scales. Chemical and optical properties of materials are only two of the many examples where transformation…
Circuit topology employs fundamental units of entanglement, known as soft contacts, for constructing knots from the bottom up, utilising circuit topology relations, namely parallel, series, cross, and concerted relations. In this article,…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
The results obtained from molecular dynamics simulations of the friction at an interface between polymer melts and weakly attractive crystalline surfaces are reported. We consider a coarse-grained bead-spring model of linear chains with…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
Chirality, the absence of mirror symmetry, is a fundamental molecular property with far-reaching consequences from chemistry to biology. Yet enantiosensitive optical responses are very weak. Here, we introduce a theoretical framework in…
It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large…
Chirality is a pervasive form of symmetry that is intimately connected to the physical properties of solids, as well as the chemical and biological activity of molecular systems. However, its control with light is challenging, because…
Recent experiments on monolayers of spindle-like cells plated on adhesive stripe-shaped domains have provided a convincing demonstration that certain types of collective phenomena in epithelia are well described by active nematic…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…